bioRxiv Channel: Stockholm University https://biorxiv.org This feed contains articles for bioRxiv Channel "Stockholm University" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples ]]> https://biorxiv.org/content/10.1101/2022.09.13.507728v1?rss=1 Mirzazadeh, R. Andrusivova, Z. Larsson, L. Newton, P. Alonso Galicia, L. Abalo, X. M. Avijgan, M. Kvastad, L. Denadai-Souza, A. Stakenborg, N. Firsova, A. B. Shamikh, A. Jurek, A. Schultz, N. Nister, M. Samakovlis, C. Boeckxstaens, G. Lundeberg, J. 2022-09-15 doi:10.1101/2022.09.13.507728 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ Reconstructing the transport cycle in the sugar porter superfamily using coevolution-powered machine learning ]]> https://biorxiv.org/content/10.1101/2022.09.24.509294v1?rss=1 Mitrovic, D. McComas, S. E. Alleva, C. Bonaccorsi, M. Drew, D. Delemotte, L. 2022-09-26 doi:10.1101/2022.09.24.509294 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Gentle and fast all-atom model refinement to cryo-EM densities via Bayes' approach ]]> https://biorxiv.org/content/10.1101/2022.09.30.510249v1?rss=1 Blau, C. Yvonnesdotter, L. Lindahl, E. 2022-09-30 doi:10.1101/2022.09.30.510249 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ aMeta: an accurate and memory-efficient ancient Metagenomic profiling workflow ]]> https://biorxiv.org/content/10.1101/2022.10.03.510579v1?rss=1 Pochon, Z. Bergfeldt, N. Kirdok, E. Vicente, M. Naidoo, T. van der Valk, T. Altinisik, N. E. Krzewinska, M. Dalen, L. Gotherstrom, A. Mirabello, C. Unneberg, P. Oskolkov, N. 2022-10-05 doi:10.1101/2022.10.03.510579 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Structure of mycobacterial respiratory Complex I ]]> https://biorxiv.org/content/10.1101/2022.10.04.510895v1?rss=1 Liang, Y. Plourde, A. Bueler, S. A. Liu, J. Brzezinski, P. Vahidi, S. Rubinstein, J. L. 2022-10-05 doi:10.1101/2022.10.04.510895 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ The heat shock protein LarA activates the Lon protease at the onset of proteotoxic stress. ]]> https://biorxiv.org/content/10.1101/2022.10.10.511565v1?rss=1 Omnus, D. J. Fink, M. J. Kallazhi, A. Xandri Zaragoza, M. Jonas, K. 2022-10-10 doi:10.1101/2022.10.10.511565 Cold Spring Harbor Laboratory Press 2022-10-10 <![CDATA[ High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.) ]]> https://biorxiv.org/content/10.1101/2022.10.10.510802v1?rss=1 Höök, L. Näsvall, K. Vila, R. Wiklund, C. Backström, N. 2022-10-11 doi:10.1101/2022.10.10.510802 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ Effective Molecular Dynamics from Neural-Network Based Structure Prediction Models ]]> https://biorxiv.org/content/10.1101/2022.10.17.512476v1?rss=1 60 s of explicit molecular dynamics simulations of 28 one- and two-domain proteins with varying degree of flexibility. We demonstrate a strong correlation between the statistical prediction scores and the explicit motion derived from extensive atomistic molecular dynamics simulations, and further derive an elastic network model based on the statistical scores of AlphFold2 (AF-ENM), which we benchmark in combination with coarse-grained molecular dynamics simulations. We show that our AF-ENM method reproduces the global protein dynamics with improved accuracy, providing a powerful way to derive effective molecular dynamics using neural-network based structure prediction models. ]]> Jussupow, A. Kaila, V. R. I. 2022-10-18 doi:10.1101/2022.10.17.512476 Cold Spring Harbor Laboratory Press 2022-10-18 <![CDATA[ Genome size variation between pelagic and benthic communities across prokaryotic taxonomy and environmental gradients in the Baltic Sea ]]> https://biorxiv.org/content/10.1101/2022.10.20.512849v1?rss=1 Rodriguez-Gijon, A. Buck, M. Andersson, A. F. Izabel-Shen, D. Nascimento, F. J. A. Garcia, S. L. 2022-10-21 doi:10.1101/2022.10.20.512849 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ "Same same but different"Exploring evolutionary and ecological causes of eye diversification in bumblebees ]]> https://biorxiv.org/content/10.1101/2022.10.25.513654v1?rss=1 Tichit, P. B. T. Bodey, A. J. Rau, C. Baird, E. 2022-10-25 doi:10.1101/2022.10.25.513654 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ Comprehensive interrogation of a Drosophila embryonic patterning network reveals the impact of chromatin state on tissue-specific burst kinetics and RNA Polymerase II promoter-proximal pause release ]]> https://biorxiv.org/content/10.1101/2022.10.25.513691v1?rss=1 Hunt, G. Vaid, R. Pirogov, S. Pfab, A. Ziegenhain, C. Sandberg, R. Reimegard, J. Mannervik, M. 2022-10-25 doi:10.1101/2022.10.25.513691 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ Automated simulation-based membrane-protein refinement into cryo-EM data ]]> https://biorxiv.org/content/10.1101/2022.10.28.514175v1?rss=1 Yvonnesdotter, L. Rovsnik, U. Blau, C. Lycksell, M. Howard, R. J. Lindahl, E. 2022-10-31 doi:10.1101/2022.10.28.514175 Cold Spring Harbor Laboratory Press 2022-10-31 <![CDATA[ Heat stress reveals a fertility debt owing to postcopulatory sexual selection ]]> https://biorxiv.org/content/10.1101/2022.10.31.514482v1?rss=1 Baur, J. Zwoinska, M. Koppik, M. Snook, R. Berger, D. 2022-11-01 doi:10.1101/2022.10.31.514482 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Automated community ecology using deep learning: a case study of planktonic foraminifera ]]> https://biorxiv.org/content/10.1101/2022.10.31.514514v1?rss=1 Hsiang, A. Y. Hull, P. M. 2022-11-01 doi:10.1101/2022.10.31.514514 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Network analysis uncovers associations in the turnover of C1 molecules in a winter lake ]]> https://biorxiv.org/content/10.1101/2022.10.31.514531v1?rss=1 Mondav, R. Martin, G. Peura, S. Garcia, S. L. 2022-11-01 doi:10.1101/2022.10.31.514531 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Dynamic growth re-orientation orchestrates flatness in the Arabidopsis leaf ]]> https://biorxiv.org/content/10.1101/2022.11.01.514736v1?rss=1 Harline, K. Fruleux, A. Lane, B. Mosca, G. Strauss, S. Tavakolian, N. Satterlee, J. W. Li, C.-B. Singh, A. Smith, R. S. Boudaoud, A. S. Roeder, A. H. K. 2022-11-02 doi:10.1101/2022.11.01.514736 Cold Spring Harbor Laboratory Press 2022-11-02 <![CDATA[ The fine-scale recombination rate variation and associations with genomic features in a butterfly ]]> https://biorxiv.org/content/10.1101/2022.11.02.514807v1?rss=1 Palahi i Torres, A. Höök, L. Näsvall, K. Shipilina, D. Wiklund, C. Vila, R. Pruisscher, P. Backström, N. 2022-11-03 doi:10.1101/2022.11.02.514807 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ Nanopore sequencing enables multigenic family reconstruction despite highly frequent PCR-induced recombination ]]> https://biorxiv.org/content/10.1101/2022.11.14.516392v1?rss=1 Namias, A. Sahlin, K. Makoundou, P. Bonnici, I. Sicard, M. Belkhir, K. Weill, M. 2022-11-15 doi:10.1101/2022.11.14.516392 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ Insights into the structure-function relationship of the NorQ/NorD chaperones from Paracoccus denitrificans reveal shared principles of interacting MoxR AAA+/VWA domain proteins ]]> https://biorxiv.org/content/10.1101/2022.11.16.516607v1?rss=1 Kahle, M. Appelgren, S. Elofsson, A. Carroni, M. Aedelroth, P. 2022-11-16 doi:10.1101/2022.11.16.516607 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ The genetic basis of wing spots in Pieris canidia butterflies ]]> https://biorxiv.org/content/10.1101/2022.11.17.516903v1?rss=1 Wee, J. L. Q. Murugesan, S. N. Wheat, C. Monteiro, A. 2022-11-17 doi:10.1101/2022.11.17.516903 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Scavenger receptor endocytosis controls apical membrane morphogenesis in the Drosophila airways ]]> https://biorxiv.org/content/10.1101/2022.12.02.518820v1?rss=1 Pinheiro, A. S. Tsarouhas, V. Senti, K. A. Arefin, B. Samakovlis, C. 2022-12-05 doi:10.1101/2022.12.02.518820 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ Expression of substance P, NPY and their Receptors Is Altered in Major Depression ]]> https://biorxiv.org/content/10.1101/2022.12.14.516867v1?rss=1 in females) and LC (TAC3 and NPY >in females). Elevated expression in DSS was recorded in (i) DLPFC for SP, TAC and TAC3 in females, SP in males, and NPYR1 in both sexes; and (ii) LC for all tachykinin family transcripts in females, SP, TACR1 and TACR3 in males, NPY in both sexes, and NPYR1 in males. CONCLUSIONSThe selective perturbation of neuropeptide systems in MDD patients may assist in the search for novel treatment strategies for subjects afflicted by this grave disorder. ]]> Barde, S. Aguila, J. Zhong, W. Solarz, A. Mei, I. Prud'homme, J. Palkovits, M. Turecki, G. Mulder, J. Uhlen, M. Nagy, C. Mechawar, N. Hedlund, E. Hokfelt, T. 2022-12-15 doi:10.1101/2022.12.14.516867 Cold Spring Harbor Laboratory Press 2022-12-15 <![CDATA[ Evolution of seasonal plasticity in response to climate change differs between life-stages of a butterfly ]]> https://biorxiv.org/content/10.1101/2022.12.16.520735v1?rss=1 Nielsen, M. E. Wiklund, C. Nylin, S. Gotthard, K. 2022-12-19 doi:10.1101/2022.12.16.520735 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM ]]> https://biorxiv.org/content/10.1101/2023.01.06.523006v1?rss=1 Bergh, C. Rovsnik, U. Howard, R. J. Lindahl, E. 2023-01-06 doi:10.1101/2023.01.06.523006 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ Structure and activity of botulinum neurotoxin X ]]> https://biorxiv.org/content/10.1101/2023.01.11.523524v1?rss=1 Martinez-Carranza, M. Skerlova, J. Lee, P.-G. Zhang, J. Burgin, D. Elliott, M. Philippe, J. Donald, S. Hornby, F. Henriksson, L. Masuyer, G. Beard, M. Dong, M. Stenmark, P. 2023-01-11 doi:10.1101/2023.01.11.523524 Cold Spring Harbor Laboratory Press 2023-01-11 <![CDATA[ PRDM16 restricts stem cell proliferation by integrating BMP and Wnt signalling in the developing choroid plexus ]]> https://biorxiv.org/content/10.1101/2023.01.13.523917v1?rss=1 He, L. Wen, J. Dai, Q. 2023-01-13 doi:10.1101/2023.01.13.523917 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ scDual-Seq of Toxoplasma gondii-infected mouse bone marrow-derived dendritic cells reveals host cell heterogeneity and differential infection dynamics ]]> https://biorxiv.org/content/10.1101/2023.01.13.523919v1?rss=1 Hildebrandt, F. Mohammed, M. Dziedziech, A. Bhandage, A. Divne, A.-M. Barrenaes, F. Barragan, A. Henriksson, J. Ankarklev, J. 2023-01-14 doi:10.1101/2023.01.13.523919 Cold Spring Harbor Laboratory Press 2023-01-14 <![CDATA[ Proline catabolism is key to facilitating Candida albicans pathogenicity ]]> https://biorxiv.org/content/10.1101/2023.01.17.524449v1?rss=1 Silao, F. G. S. Jiang, T. Bereczky-Veress, B. Kuehbacher, A. Ryman, K. Uwamohoro, N. Jenull, S. Nogueira, F. Ward, M. Lion, T. Urban, C. F. Rupp, S. Kuchler, K. Chen, C. Peuckert, C. Ljungdahl, P. O. 2023-01-18 doi:10.1101/2023.01.17.524449 Cold Spring Harbor Laboratory Press 2023-01-18 <![CDATA[ Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids ]]> https://biorxiv.org/content/10.1101/2023.01.16.524298v1?rss=1 Haloi, N. Huang, S. Nichols, A. Fine, E. J. Marotta, C. B. Dougherty, D. A. Lindahl, E. Howard, R. J. Mayo, S. L. Lester, H. A. 2023-01-19 doi:10.1101/2023.01.16.524298 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ Latitudinal gradient in avian insectivory: complementary effects of climate, habitat and bird diversity ]]> https://biorxiv.org/content/10.1101/2023.01.19.524212v1?rss=1 SCHILLE, L. VALDES-CORRECHER, E. ARCHAUX, F. BALACENOIU, F. BJOERN, M. C. BOGDZIEWICZ, M. BOIVIN, T. BRANCO, M. DAMESTOY, T. DE GROOT, M. DOBROSAVLJEVIC, J. DUDUMAN, M.-L. DULAURENT, A.-M. GREEN, S. GRUNWALD, J. EOTVOS, C. B. FATICOV, M. FERNANDEZ-CONRADI, P. FLURY, E. FUNOSAS, D. GALMAN, A. GOSSNER, M. M. GRIPENBERG, S. GROSU, L. Hagge, J. HAMPE, A. HARVEY, D. HOUSTON, R. ISENMANN, R. KAVCIC, A. KOZLOV, M. V. LANTA, V. LE TILLY, B. LOPEZ VAAMONDE, C. MALLICK, S. MANTYLA, E. MARELL, A. MILANOVIC, S. MOLNAR, M. MOREIRA, X. MOSER, V. MRAZOVA, A. MUSOLIN, 2023-01-20 doi:10.1101/2023.01.19.524212 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Heterologous expression of genes from a heterocystous cyanobacterial endosymbiont highlights organic carbon exchange with its diatom host ]]> https://biorxiv.org/content/10.1101/2023.01.23.525141v1?rss=1 Nieves-Morion, M. Camargo, S. Bardi, S. Ruiz Perez, M. T. Flores, E. Foster, R. A. 2023-01-23 doi:10.1101/2023.01.23.525141 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ Maternal hormones engage a dormant monomorphic aggression circuit, leading to the introduction of an innate behavior in adulthood in females ]]> https://biorxiv.org/content/10.1101/2023.02.02.526862v1?rss=1 Stagkourakis, S. Williams, P. Spigolon, G. Khanal, S. Ziegler, K. Heikkinen, L. Fisone, G. Broberger, C. 2023-02-03 doi:10.1101/2023.02.02.526862 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Application of nanotags and nanobodies for live cell single-molecule imaging of the Z-ring in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2023.02.19.529144v1?rss=1 Westlund, E. Bergenstrale, A. Pokhrel, A. Skoglund, U. Chan, H. Daley, D. O. Söderström, B. 2023-02-19 doi:10.1101/2023.02.19.529144 Cold Spring Harbor Laboratory Press 2023-02-19 <![CDATA[ Potent GST ketosteroid isomerase activity relevant to ecdysteroidogenesis in the malaria vector Anopheles gambiae ]]> https://biorxiv.org/content/10.1101/2023.03.01.530595v1?rss=1 MANNERVIK, B. Musdal, Y. Ismail, A. Sjödin, B. 2023-03-01 doi:10.1101/2023.03.01.530595 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Structural basis of activation and inhibition of the Ca2+/calmodulin-sensitive adenylyl cyclase 8 ]]> https://biorxiv.org/content/10.1101/2023.03.03.531047v1?rss=1 Khanppnavar, B. Schuster, D. Özel, M. Mehta, V. Leitner, A. Picotti, P. Korkhov, V. M. 2023-03-04 doi:10.1101/2023.03.03.531047 Cold Spring Harbor Laboratory Press 2023-03-04 <![CDATA[ Single cell RNA sequencing in isogenic FUS and TARDBP mutant ALS lines reveals early mitochondrial dysfunction as a common pathway in motor neurons ]]> https://biorxiv.org/content/10.1101/2023.03.16.531876v1?rss=1 Schweingruber, C. Nijssen, J. Mechtersheimer, J. Reber, S. Keuper, M. Mei, I. Aguila Benitez, J. O'Brien, N. Jastroch, M. Ruepp, M.-D. Hedlund, E. 2023-03-16 doi:10.1101/2023.03.16.531876 Cold Spring Harbor Laboratory Press 2023-03-16 <![CDATA[ Conserving genetic diversity during climate change:Niche marginality and discrepant monitoring capacity in Europe ]]> https://biorxiv.org/content/10.1101/2023.03.24.533448v1?rss=1 Pearman, P. B. Broennimann, O. Albayrak, T. Alves, P. C. Bertola, L. D. Biedrzycka, A. Buzan, E. Cubric-Curik, V. Fedorca, A. Godoy, J. A. Hvilsom, C. Klinga, P. Konopinski, M. K. Kopatz, A. Laikre, L. Lopez Fernandez, M. Mergeay, J. Neophytou, C. Palsson, S. Paz-Vinas, I. Posledovich, D. Roleckova, B. Rungis, D. Segelbacher, G. Kavcic Sonnenschein, K. Thurfjell, H. Traeger, S. Vernesi, C. Vila, C. Westergren, M. Zachos, F. E. Guisan, A. Bruford, M. 2023-03-25 doi:10.1101/2023.03.24.533448 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Nascent evolution of recombination rate differences as a consequence of chromosomal rearrangements ]]> https://biorxiv.org/content/10.1101/2023.03.27.534312v1?rss=1 Nasvall, K. Boman, J. Hook, L. Vila, R. Wiklund, C. Backstrom, N. 2023-03-27 doi:10.1101/2023.03.27.534312 Cold Spring Harbor Laboratory Press 2023-03-27 <![CDATA[ The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies ]]> https://biorxiv.org/content/10.1101/2023.03.27.532508v1?rss=1 Willink, B. Tunström, K. Nilen, S. Chikhi, R. Lemane, T. Takahashi, M. Takahashi, Y. Svensson, E. I. Wheat, C. W. 2023-03-29 doi:10.1101/2023.03.27.532508 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton ]]> https://biorxiv.org/content/10.1101/2023.03.29.534285v1?rss=1 Grujcic, V. Saarenpaa, S. Sundh, J. Sennblad, B. Norgren, B. Latz, M. Giacomello, S. Foster, R. A. Andersson, A. F. 2023-03-29 doi:10.1101/2023.03.29.534285 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Characterization of uranyl ion binding to amyloid beta (Aβ) peptides: effects on Aβ structure and aggregation ]]> https://biorxiv.org/content/10.1101/2023.03.29.534802v1?rss=1 Berntsson, E. Vosough, F. Noormagi, A. Padari, K. Asplund, F. Gielnik, M. Paul, S. Jarvet, J. Tougu, V. Roos, P. M. Kozak, M. Graslund, A. Barth, A. Pooga, M. Palumaa, P. Warmlander, S. K. T. S. 2023-04-01 doi:10.1101/2023.03.29.534802 Cold Spring Harbor Laboratory Press 2023-04-01 <![CDATA[ The genetic legacy of the expansion of Bantu-speaking peoples in Africa ]]> https://biorxiv.org/content/10.1101/2023.04.03.535432v1?rss=1 Fortes-Lima, C. A. Burgarella, C. Hammaren, R. Eriksson, A. Vicente, M. Jolly, C. Semo, A. Gunnink, H. Pacchiarotti, S. Mundeke, L. Matonda, I. Muluwa, J. K. Coutros, P. Nyambe, T. S. Cikomola, C. Coetzee, V. de Castro, M. Ebbesen, P. Delanghe, J. Stoneking, M. Barham, L. Lombard, M. Meyer, A. Steyn, M. Malmstrom, H. Rocha, J. Soodyall, H. Pakendorf, B. Bostoen, K. Schlebusch, C. M. 2023-04-05 doi:10.1101/2023.04.03.535432 Cold Spring Harbor Laboratory Press 2023-04-05 <![CDATA[ The exosome degrades chromatin-associated RNAs genome-wide and maintains chromatin homeostasis ]]> https://biorxiv.org/content/10.1101/2023.04.10.536209v1?rss=1 Planells, J. Jordan Pla, A. Jain, S. Guadalupe, J. J. Proux-Wera, E. von Euler, A. Pelechano, V. Visa, N. 2023-04-10 doi:10.1101/2023.04.10.536209 Cold Spring Harbor Laboratory Press 2023-04-10 <![CDATA[ Genome-wide gene birth-death dynamics are associated with diet breadth variation in Lepidoptera ]]> https://biorxiv.org/content/10.1101/2023.04.11.536384v1?rss=1 Dort, H. van der Bijl, W. Wahlberg, N. Nylin, S. Wheat, C. W. 2023-04-12 doi:10.1101/2023.04.11.536384 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ Purifying Selection and Persistent Polymorphism among Nuclei in the Multinucleate Arbuscular Mycorrhizal (AM) Fungi ]]> https://biorxiv.org/content/10.1101/2023.04.18.537338v1?rss=1 Manyara, D. Sanchez-Garcia, M. Thoren, M. H. Montoliu-Nerin, M. Cheng, G. Bever, J. D. Johannesson, H. Rosling, A. 2023-04-20 doi:10.1101/2023.04.18.537338 Cold Spring Harbor Laboratory Press 2023-04-20 <![CDATA[ LDO proteins and Vac8 form a vacuole-lipid droplet contact site required for lipophagy in response to starvation ]]> https://biorxiv.org/content/10.1101/2023.04.21.537797v1?rss=1 Alvarez-Guerra, I. Block, E. Broeskamp, F. Gabrijelcic, S. de Ory, A. Habernig, L. Andreasson, C. Levine, T. Höög, J. L. Büttner, S. 2023-04-21 doi:10.1101/2023.04.21.537797 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ Genetic inactivation of essential HSF1 reveals an isolated transcriptional stress response selectively induced by protein misfolding ]]> https://biorxiv.org/content/10.1101/2023.05.05.539545v1?rss=1 Ciccarelli, M. Masser, A. E. Kaimal, J. M. Planells, J. Andreasson, C. 2023-05-05 doi:10.1101/2023.05.05.539545 Cold Spring Harbor Laboratory Press 2023-05-05 <![CDATA[ Population genomics reveals extensive inbreeding and purging of mutational load in wild Amur tigers ]]> https://biorxiv.org/content/10.1101/2023.05.09.539923v1?rss=1 Lan, T. Li, H. Zhang, L. Shi, M. Liu, B. Cui, L. Dussex, N. Wang, Q. Ma, Y. Liu, D. Kong, W. Wang, J. Lu, H. Zhang, S. Yu, J. Wang, X. Wu, Y. Niu, X. Fan, J. Zhao, Y. Dalen, L. Jiang, G. Liu, H. Xu, Y. 2023-05-10 doi:10.1101/2023.05.09.539923 Cold Spring Harbor Laboratory Press 2023-05-10 <![CDATA[ Spatial connectivity increases ecosystem resilience towards an ongoing regime shift ]]> https://biorxiv.org/content/10.1101/2023.05.12.540484v1?rss=1 7000 fish samplings from the Baltic Sea coast to test this prediction in an ongoing, spatially propagating shift in dominance from predatory fish to an opportunistic mesopredator, with cascading effects throughout the food web. After controlling for the influence of the driver (increasing mesopredator densities), we find that predatory fish habitat connectivity increases resilience towards the shift, but only when densities of fish-eating top predators (seals, cormorants) are low. Resilience also increases with temperature, likely through boosted predatory fish growth and recruitment. These findings confirm theoretical predictions that spatial connectivity and the local environment can act together to shape resilience towards regime shifts. ]]> Olin, A. B. Bergström, U. Bodin, O. Sundblad, G. Eriksson, B. K. Erlandsson, M. Fredriksson, R. Eklöf, J. 2023-05-14 doi:10.1101/2023.05.12.540484 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Timed receptor tyrosine kinase signaling couples the central and a peripheral circadian clock in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.05.14.540706v1?rss=1 Cavieres-Lepe, J. Amini, E. Nässel, D. R. Stanewsky, R. Wegener, C. Ewer, J. 2023-05-14 doi:10.1101/2023.05.14.540706 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Ancient human genomes suggest three ancestral populations for present-day Europeans ]]> https://biorxiv.org/content/10.1101/001552v1?rss=1 Iosif Lazaridis Nick Patterson Alissa Mittnik Gabriel Renaud Swapan Mallick Karola Kirsanow Peter H. Sudmant Joshua G. Schraiber Sergi Castellano Mark Lipson Bonnie Berger Christos Economou Ruth Bollongino Qiaomei Fu Kirsten Bos Susanne Nordenfelt Heng Li Cesare de Filippo Kay Prüfer Susanna Sawyer Cosimo Posth Wolfgang Haak Fredrik Hallgren Elin Fornander Nadin Rohland Dominique Delsate Michael Francken Jean-Michel Guinet Joachim Wahl George Ayodo Hamza A. Babiker Graciela Baillet Elena Balanovska Oleg Balanovsky Ramiro Barrantes Gabriel Bedoya Haim Ben-Ami Judit Bene Fouad Berrada Claudio M. 2013-12-23 doi:10.1101/001552 Cold Spring Harbor Laboratory Press 2013-12-23 <![CDATA[ Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris ]]> https://biorxiv.org/content/10.1101/006783v1?rss=1 Gavin Douglas Gesseca Gos Kim Steige Adriana Salcedo Karl Holm J. Arvid Ågren Khaled Hazzouri Wei Wang Adrian E. Platts Emily B. Josephs Robert J. Williamson Barbara Neuffer Martin Lascoux Tanja Slotte Stephen Wright 2014-07-04 doi:10.1101/006783 Cold Spring Harbor Laboratory Press 2014-07-04 <![CDATA[ On Modeling the Macroecology of Baleen Whale Migration ]]> https://biorxiv.org/content/10.1101/009753v1?rss=1 James Watson Bruna Favetta Charles Stock 2014-09-29 doi:10.1101/009753 Cold Spring Harbor Laboratory Press 2014-09-29 <![CDATA[ Cis-regulatory changes associated with a recent mating system shift and floral adaptation in Capsella ]]> https://biorxiv.org/content/10.1101/017749v1?rss=1 Kim A Steige Johan Reimegård Daniel Koenig Douglas G Scofield Tanja Slotte 2015-04-09 doi:10.1101/017749 Cold Spring Harbor Laboratory Press 2015-04-09 <![CDATA[ THE REGIME SHIFTS DATABASE: A FRAMEWORK FOR ANALYZING REGIME SHIFTS IN SOCIAL-ECOLOGICAL SYSTEMS ]]> https://biorxiv.org/content/10.1101/018473v1?rss=1 Reinette Oonsie Biggs Garry D Peterson Juan Carlos Carlos Rocha 2015-04-23 doi:10.1101/018473 Cold Spring Harbor Laboratory Press 2015-04-23 <![CDATA[ Regime shifts in the Anthropocene: drivers, risks, and resilience ]]> https://biorxiv.org/content/10.1101/018549v1?rss=1 Juan Carlos Carlos Rocha Garry D Peterson Reinette Oonsie Biggs 2015-04-28 doi:10.1101/018549 Cold Spring Harbor Laboratory Press 2015-04-28 <![CDATA[ Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora ]]> https://biorxiv.org/content/10.1101/034025v1?rss=1 Kim A Steige Benjamin Laenen Johan Reimegård Douglas Scofield Tanja Slotte 2015-12-10 doi:10.1101/034025 Cold Spring Harbor Laboratory Press 2015-12-10 <![CDATA[ The role of transposable elements for gene expression in Capsella hybrids and allopolyploids ]]> https://biorxiv.org/content/10.1101/044016v1?rss=1 Kim Steige Johan Reimegård Carolin A Rebernig Claudia Köhler Douglas G Scofield Tanja Slotte 2016-03-16 doi:10.1101/044016 Cold Spring Harbor Laboratory Press 2016-03-16 <![CDATA[ Intrinsic brain connectivity after partial sleep deprivation in young and older adults: results from the Stockholm Sleepy Brain study ]]> https://biorxiv.org/content/10.1101/073494v1?rss=1 Gustav Nilsonne Sandra Tamm Johanna Schwarz Rita Almeida Håkan Fischer Göran Kecklund Mats Lekander Peter Fransson Torbjörn Åkerstedt 2016-09-05 doi:10.1101/073494 Cold Spring Harbor Laboratory Press 2016-09-05 <![CDATA[ Mice deficient of Myc super-enhancer region reveal a differential control mechanism between normal and pathological growth ]]> https://biorxiv.org/content/10.1101/082602v1?rss=1 Dave, K. Sur, I. Yan, J. Zhang, J. Kaasinen, E. Zhong, F. Blaas, L. Li, X. Mansson, R. Taipale, J. 2016-10-24 doi:10.1101/082602 Cold Spring Harbor Laboratory Press 2016-10-24 <![CDATA[ HistMapR: Rapid digitization of historical land-use maps in R ]]> https://biorxiv.org/content/10.1101/109504v1?rss=1 Auffret, A. G. Kimberley, A. Plue, J. Skanes, H. Jakobsson, S. Walden, E. Wennbom, M. Wood, H. Bullock, J. M. Cousins, S. A. O. Gartz, M. Hooftman, D. A. P. Trank, L. 2017-02-17 doi:10.1101/109504 Cold Spring Harbor Laboratory Press 2017-02-17 <![CDATA[ Control of Hox transcription factor concentration and cell-to-cell variability by an auto-regulatory switch ]]> https://biorxiv.org/content/10.1101/115220v1?rss=1 Papadopoulos, D. K. Skouloudaki, K. Engstrom, Y. Terenius, L. Rigler, R. Vukojevic, V. Tomancak, P. 2017-03-14 doi:10.1101/115220 Cold Spring Harbor Laboratory Press 2017-03-14 <![CDATA[ pomp-Astic Inference For Epidemic Models: Simple Vs. Complex ]]> https://biorxiv.org/content/10.1101/125880v1?rss=1 Stocks, T. Britton, T. Hohle, M. 2017-04-13 doi:10.1101/125880 Cold Spring Harbor Laboratory Press 2017-04-13 <![CDATA[ Demography And Mating System Shape The Genome-Wide Impact Of Purifying Selection In Arabis alpina ]]> https://biorxiv.org/content/10.1101/127209v1?rss=1 Laenen, B. Tedder, A. Nowak, M. D. Torang, P. Wunder, J. Wotzel, S. Steige, K. Kourmpetis, Y. Odong, T. Drouzas, A. D. Bink, M. Agren, J. Coupland, G. Slotte, T. 2017-05-04 doi:10.1101/127209 Cold Spring Harbor Laboratory Press 2017-05-04 <![CDATA[ Ophiuroid Phylotranscriptomics Enables Discovery Of Novel Echinoderm Representatives Of Bilaterian Neuropeptide Families And Reconstruction Of Neuropeptide Precursor Evolution Over ~270 Million Years ]]> https://biorxiv.org/content/10.1101/129783v1?rss=1 Zandawala, M. Moghul, I. Yanez Guerra, L. A. Delroisse, J. Abylkassimova, N. Hugall, A. F. O'Hara, T. D. Elphick, M. R. 2017-05-20 doi:10.1101/129783 Cold Spring Harbor Laboratory Press 2017-05-20 <![CDATA[ Cells From The Same Lineage Switch From Reduction To Enhancement Of Size Variability In Arabidopsis Sepals ]]> https://biorxiv.org/content/10.1101/132431v1?rss=1 Tsugawa, S. Hervieux, N. Kierzkowski, D. Routier-Kierzkowska, A.-L. Sapala, A. Hamant, O. Smith, R. S. Roeder, A. H. K. Boudaoud, A. Li, C.-B. 2017-04-30 doi:10.1101/132431 Cold Spring Harbor Laboratory Press 2017-04-30 <![CDATA[ Stable Membrane Topologies Of Small Dual-Topology Membrane Proteins ]]> https://biorxiv.org/content/10.1101/133298v1?rss=1 Fluman, N. Tobiasson, V. von Heijne, G. 2017-05-02 doi:10.1101/133298 Cold Spring Harbor Laboratory Press 2017-05-02 <![CDATA[ Microbial Network, Phylogenetic Diversity And Community Membership In The Active Layer Across A Permafrost Thaw Gradient ]]> https://biorxiv.org/content/10.1101/143578v1?rss=1 Mondav, R. McCalley, C. K. Hodgkins, S. B. Frolking, S. Saleska, S. R. Rich, V. I. Chanton, J. P. Crill, P. M. 2017-05-29 doi:10.1101/143578 Cold Spring Harbor Laboratory Press 2017-05-29 <![CDATA[ Characterization of a set of abdominal neuroendocrine cells that regulate stress physiology using colocalized diuretic peptides in Drosophila ]]> https://biorxiv.org/content/10.1101/164178v1?rss=1 Zandawala, M. Marley, R. Davies, S. A. Nassel, D. R. 2017-07-15 doi:10.1101/164178 Cold Spring Harbor Laboratory Press 2017-07-15 <![CDATA[ Genomics of Mesolithic Scandinavia reveal colonization routes and high-latitude adaptation ]]> https://biorxiv.org/content/10.1101/164400v1?rss=1 Günther, T. Malmström, H. Svensson, E. Omrak, A. Sanchez-Quinto, F. Kılınc, G. M. Krzewinska, M. Eriksson, G. Fraser, M. Edlund, H. Munters, A. R. Coutinho, A. Simoes, L. G. Vicente, M. Sjölander, A. Jansen Sellevold, B. Jorgensen, R. Claes, P. Shriver, M. D. Valdiosera, C. Netea, M. G. Apel, J. Liden, K. Skar, B. Stora, J. Götherström, A. Jakobsson, M. 2017-07-17 doi:10.1101/164400 Cold Spring Harbor Laboratory Press 2017-07-17 <![CDATA[ Sex-biased gene expression resolves sexual conflict through the evolution of sex-specific genetic architecture ]]> https://biorxiv.org/content/10.1101/176990v1?rss=1 Wright, A. E. Fumagalli, M. Cooney, C. R. Bloch, N. I. Vieira, F. G. Buechel, S. D. Kolm, N. Mank, J. E. 2017-08-16 doi:10.1101/176990 Cold Spring Harbor Laboratory Press 2017-08-16 <![CDATA[ Pharmacodynamic Considerations of Collateral Sensitivity in Design of Antibiotic Treatment Regimen ]]> https://biorxiv.org/content/10.1101/189381v1?rss=1 Udekwu, K. I. Weiss, H. 2017-09-20 doi:10.1101/189381 Cold Spring Harbor Laboratory Press 2017-09-20 <![CDATA[ Unique ATP-cone-driven allosteric regulation of ribonucleotide reductase via the radical-generating subunit ]]> https://biorxiv.org/content/10.1101/190033v1?rss=1 Rozman Grinberg, I. Lundin, D. Hasan, M. Crona, M. Jonna, V. R. Loderer, C. Sahlin, M. Markova, N. Borovok, I. Berggren, G. Hofer, A. Logan, D. T. Sjöberg, B.-M. 2017-09-17 doi:10.1101/190033 Cold Spring Harbor Laboratory Press 2017-09-17 <![CDATA[ Compartment and cell type-{-}specific hypoxia responses in the developing Drosophila brain ]]> https://biorxiv.org/content/10.1101/2019.12.12.874404v1?rss=1 Baccino-Calace, M. Prieto, D. Cantera, R. Egger, B. 2019-12-16 doi:10.1101/2019.12.12.874404 Cold Spring Harbor Laboratory Press 2019-12-16 <![CDATA[ Bridging theories for ecosystem stability through structural sensitivity analysis of ecological models in equilibrium ]]> https://biorxiv.org/content/10.1101/2019.12.24.887901v1?rss=1 Kuiper, J. J. Kooi, B. W. Peterson, G. D. Mooij, W. M. 2019-12-27 doi:10.1101/2019.12.24.887901 Cold Spring Harbor Laboratory Press 2019-12-27 <![CDATA[ Mutational analysis of the human Xbp1 translational arrest peptide and construction of arrest-enhanced variants ]]> https://biorxiv.org/content/10.1101/201913v1?rss=1 Schiller, N. Magoulopoulou, A. Cymer, F. Von Heijne, G. 2017-10-11 doi:10.1101/201913 Cold Spring Harbor Laboratory Press 2017-10-11 <![CDATA[ Spring phenology dominates over shade in affecting seedling performance and plant attack during the growing season ]]> https://biorxiv.org/content/10.1101/2020.01.05.895086v1?rss=1 McClory, R. W. van Dijk, L. J. A. Mutz, J. Ehrlen, J. Tack, A. J. M. 2020-01-06 doi:10.1101/2020.01.05.895086 Cold Spring Harbor Laboratory Press 2020-01-06 <![CDATA[ Tissue engineered model of hepatic breast cancer micrometastasis shows host-dependent colonization patterns and drug responses ]]> https://biorxiv.org/content/10.1101/2020.01.08.898163v1?rss=1 Guller, A. E. Rozova, V. S. Kuschnerus, I. Khabir, Z. Nadort, A. Garcia-Bennett, A. E. Liang, L. Qian, Y. Goldys, E. M. Zvyagin, A. V. 2020-01-09 doi:10.1101/2020.01.08.898163 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Convergent Met and voltage-gated Ca2+ channel signaling on Ras-Erk MAPK drives migratory activation of dendritic cells parasitized by Toxoplasma gondii ]]> https://biorxiv.org/content/10.1101/2020.01.08.898197v1?rss=1 Olafsson, E. B. ten Hoeve, A. L. Li Wang, X. Westermark, L. Varas-Godoy, M. Barragan, A. 2020-01-08 doi:10.1101/2020.01.08.898197 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Limited dispersal and an unexpected aggression pattern in a native supercolonial ant ]]> https://biorxiv.org/content/10.1101/2020.01.09.899971v1?rss=1 Hakala, S. M. Ittonen, M. Seppae, P. Helanterae, H. 2020-01-09 doi:10.1101/2020.01.09.899971 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Glutamate dehydrogenase (Gdh2)-dependent alkalization is dispensable for escape from macrophages and virulence of Candida albicans ]]> https://biorxiv.org/content/10.1101/2020.01.20.912592v1?rss=1 Silao, F. G. S. Ryman, K. Jiang, T. Ward, M. Hansmann, N. Liu, N.-N. Chen, C. Ljungdahl, P. O. 2020-01-20 doi:10.1101/2020.01.20.912592 Cold Spring Harbor Laboratory Press 2020-01-20 <![CDATA[ Rapid evolution of coordinated and collective movement in response to artificial selection ]]> https://biorxiv.org/content/10.1101/2020.01.30.926311v1?rss=1 Kotrschal, A. Szorkovszky, A. Herbert Read, J. Bloch, N. Romenskyy, M. Buechel, S. D. Fontrodona, A. Sanchez, L. Zeng, H. LeFoll, A. Braux, G. Pelckmans, K. Mank, J. E. Sumpter, D. J. T. Kolm, N. 2020-01-31 doi:10.1101/2020.01.30.926311 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ Diverse Arctic lake sediment microbiota shape methane emission temperature sensitivity ]]> https://biorxiv.org/content/10.1101/2020.02.08.934661v1?rss=1 Emerson, J. B. Varner, R. K. Wik, M. Parks, D. H. Neumann, R. B. Johnson, J. E. Singleton, C. M. Woodcroft, B. J. Tollerson, R. Owusu-Dommey, A. Binder, M. Freitas, N. L. Crill, P. M. Saleska, S. R. Tyson, G. W. Rich, V. I. 2020-02-10 doi:10.1101/2020.02.08.934661 Cold Spring Harbor Laboratory Press 2020-02-10 <![CDATA[ Altered parasitism of a butterfly assemblage associated with a range-expanding species ]]> https://biorxiv.org/content/10.1101/2020.02.13.947440v1?rss=1 Audusseau, H. Ryrholm, N. Stefanescu, C. Tharel, S. Jansson, C. Champeaux, L. Shaw, M. R. Raper, C. Lewis, O. Janz, N. Schmucki, R. 2020-02-14 doi:10.1101/2020.02.13.947440 Cold Spring Harbor Laboratory Press 2020-02-14 <![CDATA[ Hand-reared wolves show similar, or stronger, attachment toward human caregivers compared to hand-reared dogs ]]> https://biorxiv.org/content/10.1101/2020.02.17.952663v1?rss=1 Hansen Wheat, C. Larsson, L. Temrin, H. 2020-02-19 doi:10.1101/2020.02.17.952663 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ Towards predictive nanotoxicology: from roundabout of molecular events to chronic inflammation prediction ]]> https://biorxiv.org/content/10.1101/2020.02.27.966036v1?rss=1 Majaron, H. Kokot, B. Sebastijanovic, A. Voss, C. Podlipec, R. Zawilska, P. Berthing, T. Ballester, C. Danielsen, P. H. Contini, C. Ivanov, M. Kriselj, A. Cotar, P. Zhou, Q. Ponti, J. Zhernovkov, V. Schneemilch, M. Pusnik, M. Umek, P. Pajk, S. Joubert, O. Schmid, O. Urbancic, I. Irmler, M. Beckers, J. Lobaskin, V. Halappanavar, S. Quirke, N. Lyubartsev, A. Vogel, U. Koklic, T. Stoeger, T. Strancar, J. 2020-02-27 doi:10.1101/2020.02.27.966036 Cold Spring Harbor Laboratory Press 2020-02-27 <![CDATA[ Timing of organ initiation is crucial for robust organ size ]]> https://biorxiv.org/content/10.1101/2020.03.08.982629v1?rss=1 Zhu, M. Chen, W. Mirabet, V. Hong, L. Bovio, S. Strauss, S. Schwarz, E. M. Tsugawa, S. Wang, Z. Smith, R. S. Li, C.-B. Hamant, O. Boudaoud, A. Roeder, A. H. K. 2020-03-10 doi:10.1101/2020.03.08.982629 Cold Spring Harbor Laboratory Press 2020-03-10 <![CDATA[ Prion Protein Folding Mechanism Revealed by Pulling Force Studies ]]> https://biorxiv.org/content/10.1101/2020.03.09.983510v1?rss=1 Kriegler, T. Notari, L. Lang, S. Hessa, T. 2020-03-09 doi:10.1101/2020.03.09.983510 Cold Spring Harbor Laboratory Press 2020-03-09 <![CDATA[ Variation in developmental rates is not linked to environmental unpredictability in annual killifishes ]]> https://biorxiv.org/content/10.1101/2020.03.16.993329v1?rss=1 Rowinski, P. K. Sowersby, W. Näslund, J. Eckerström-Liedholm, S. Gotthard, K. Rogell, B. 2020-03-18 doi:10.1101/2020.03.16.993329 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ Amyloid-β oligomers are captured by the DNAJB6 chaperone: Direct detection of interactions that can prevent primary nucleation ]]> https://biorxiv.org/content/10.1101/2020.03.16.993790v1?rss=1 Österlund, N. Lundqvist, M. Ilag, L. I. Gräslund, A. Emanuelsson, C. 2020-03-18 doi:10.1101/2020.03.16.993790 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ The importance of species interactions in spatially explicit eco-evolutionary community dynamics under climate change ]]> https://biorxiv.org/content/10.1101/2020.03.23.003335v1?rss=1 Akesson, A. Curtsdotter, A. Eklöf, A. Ebenman, B. Norberg, J. Barabas, G. 2020-03-25 doi:10.1101/2020.03.23.003335 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives ]]> https://biorxiv.org/content/10.1101/2020.03.24.005397v1?rss=1 Bohutinska, M. Vlcek, J. Yair, S. Leanen, B. Konecna, V. Fracassetti, M. Slotte, T. Kolar, F. 2020-03-25 doi:10.1101/2020.03.24.005397 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ On the interactions of the receptor-binding domain of SARS-CoV-1 and SARS-CoV-2 spike proteins with monoclonal antibodies and the receptor ACE2 ]]> https://biorxiv.org/content/10.1101/2020.04.05.026377v1?rss=1 Correa Giron, C. Laaksonen, A. Barroso da Silva, F. L. 2020-04-10 doi:10.1101/2020.04.05.026377 Cold Spring Harbor Laboratory Press 2020-04-10 <![CDATA[ Mosquito cellular immunity at single-cell resolution ]]> https://biorxiv.org/content/10.1101/2020.04.08.032508v1?rss=1 Raddi, G. Ferreira, A. B. Efremova, M. Ramirez, J. L. Cantera, R. Teichmann, S. Barillas-Mury, C. Billker, O. 2020-04-09 doi:10.1101/2020.04.08.032508 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ Algal growth at environmentally relevant concentrations of suspended solids: implications for microplastic hazard assessment ]]> https://biorxiv.org/content/10.1101/2020.04.11.036889v1?rss=1 Gorokhova, E. Ek, K. Reichelt, S. 2020-04-13 doi:10.1101/2020.04.11.036889 Cold Spring Harbor Laboratory Press 2020-04-13 <![CDATA[ Temperatures that sterilise males better predict global distributions of species than lethal temperatures ]]> https://biorxiv.org/content/10.1101/2020.04.16.043265v1?rss=1 Parratt, S. R. Walsh, B. Metelmann, S. White, N. Manser, A. Bretman, A. Hoffmann, A. A. Snook, R. Price, T. 2020-04-18 doi:10.1101/2020.04.16.043265 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication ]]> https://biorxiv.org/content/10.1101/2020.04.17.033415v1?rss=1 Yurtman, E. Özer, O. Yüncü, E. Dagtas, N. D. Koptekin, D. Cakan, Y. G. Özkan, M. Akbaba, A. Kaptan, D. Atag, G. Vural, K. B. Gündem, C. Y. Martin, L. Kılınc, G. M. Ghalichi, A. Acan, S. C. Yaka, R. Saglıcan, E. Lagerholm, V. K. Krzewinska, M. Piskin, E. Sevketoglu, M. Bilgin, C. C. Atakuman, C. Erdal, Y. S. Sürer, E. Lenstra, J. A. Yorulmaz, S. Abazari, F. Sadati, J. H. Baird, D. Bıcakcı, E. Cevik, O. Gerritsen, F. Özbal, R. Götherström, A. Somel, M. Togan, I. Özer, F. 2020-04-18 doi:10.1101/2020.04.17.033415 Cold Spring Harbor Laboratory Press 2020-04-18 <![CDATA[ NMR backbone assignment and dynamics of Profilin from Heimdallarchaeota ]]> https://biorxiv.org/content/10.1101/2020.04.20.050468v1?rss=1 Haq, S. R. Survery, S. Hurtig, F. Lindas, A.-C. Chi, C. N. 2020-04-20 doi:10.1101/2020.04.20.050468 Cold Spring Harbor Laboratory Press 2020-04-20 <![CDATA[ Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism ]]> https://biorxiv.org/content/10.1101/2020.04.22.056440v1?rss=1 Horne, C. R. Venugoapl, H. Panjikar, S. Henrickson, A. Brookes, E. North, R. A. Murphy, J. M. Friemann, R. Griffin, M. D. W. Ramm, G. Demeler, B. Dobson, R. C. J. 2020-04-24 doi:10.1101/2020.04.22.056440 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ Heimdallarchaea encodes profilin with eukaryotic-like actin regulation and polyproline binding ]]> https://biorxiv.org/content/10.1101/2020.04.23.051748v1?rss=1 Survery, S. Hurtig, F. Haq, S. R. Lindas, A.-C. Chi, C. N. 2020-04-25 doi:10.1101/2020.04.23.051748 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Visualizing drug inhibitor binding interactions using microcrystal electron diffraction ]]> https://biorxiv.org/content/10.1101/2020.04.27.064188v1?rss=1 Clabbers, M. T. B. Fisher, Z. Coincon, M. Zou, X. Xu, H. 2020-04-29 doi:10.1101/2020.04.27.064188 Cold Spring Harbor Laboratory Press 2020-04-29 <![CDATA[ Shared safety abolishes the recovery of learned threat ]]> https://biorxiv.org/content/10.1101/2020.05.01.072827v1?rss=1 Pan, Y. Olsson, A. Golkar, A. 2020-05-03 doi:10.1101/2020.05.01.072827 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ Drosophila insulin-like peptide 8 (DILP8) in ovarian follicle cells regulates ovulation and metabolism ]]> https://biorxiv.org/content/10.1101/2020.05.02.073585v1?rss=1 Liao, S. Nassel, D. R. 2020-05-03 doi:10.1101/2020.05.02.073585 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ N-linked glycan sites on the influenza NA head domain are required for efficient IAV incorporation and replication ]]> https://biorxiv.org/content/10.1101/2020.05.05.080077v1?rss=1 Östbye, H. Gao, J. Rakic Martinez, M. Wang, H. de Gier, J.-W. Daniels, R. 2020-05-08 doi:10.1101/2020.05.05.080077 Cold Spring Harbor Laboratory Press 2020-05-08 <![CDATA[ The rise of the three-spined stickleback: eco-evolutionary consequences of a mesopredator release ]]> https://biorxiv.org/content/10.1101/2020.05.08.083873v1?rss=1 Eriksson, B. K. Yanos, C. Bourlat, S. Donadi, S. Fontaine, M. Hansen, J. Jakubaviciute, E. Kiragosyan, K. Maan, M. Merila, J. Austin, A. Olsson, J. Reiss, K. Sundblad, G. Bergstrom, U. Eklof, J. 2020-05-10 doi:10.1101/2020.05.08.083873 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ Spontaneous eye-movements during eyes-open rest reduce resting-state-network modularity by increasing visual-sensorimotor connectivity ]]> https://biorxiv.org/content/10.1101/2020.05.18.100669v1?rss=1 Koba, C. Notaro, G. Tamm, S. Nilsonne, G. Hasson, U. 2020-05-20 doi:10.1101/2020.05.18.100669 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ Sex-biased reduction in reproductive success drives selective constraint on human genes ]]> https://biorxiv.org/content/10.1101/2020.05.26.116111v1?rss=1 Gardner, E. J. Neville, M. D. Samocha, K. E. Barclay, K. Kolk, M. Niemi, M. E. Kirov, G. Martin, H. C. Hurles, M. E. 2020-05-28 doi:10.1101/2020.05.26.116111 Cold Spring Harbor Laboratory Press 2020-05-28 <![CDATA[ Ecology and population genetics of the parasitoid Phobocampe confusa (Hymenoptera: Ichneumonidae) in relation to its hosts, Aglais species (Lepidoptera: Numphalidae). ]]> https://biorxiv.org/content/10.1101/2020.05.27.115212v1?rss=1 Audusseau, H. Baudrin, G. Shaw, M. R. Keehnen, N. L. P. Schmucki, R. Dupont, L. 2020-05-27 doi:10.1101/2020.05.27.115212 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ Stop codon readthrough of a POU transcription factor regulates steroidogenesis and developmental transitions ]]> https://biorxiv.org/content/10.1101/2020.05.30.125401v1?rss=1 Zhao, Y. Lindberg, B. G. Esfahani, S. S. Tang, X. Piazza, S. Engstrom, Y. 2020-05-31 doi:10.1101/2020.05.30.125401 Cold Spring Harbor Laboratory Press 2020-05-31 <![CDATA[ Tracking the origin of Baker's yeast: Seven new long-read genomes of highly divergent, wild Saccharomyces cerevisiae strains from East Asia ]]> https://biorxiv.org/content/10.1101/2020.06.03.131607v1?rss=1 Bendixsen, D. P. Gettle, N. Gilchrist, C. Zhang, Z. Stelkens, R. 2020-06-03 doi:10.1101/2020.06.03.131607 Cold Spring Harbor Laboratory Press 2020-06-03 <![CDATA[ Seminal fluid protein divergence among populations exhibiting postmating prezygotic reproductive isolation ]]> https://biorxiv.org/content/10.1101/2020.06.08.140020v1?rss=1 Garlovsky, M. D. Evans, C. Rosenow, M. A. Karr, T. Snook, R. R. 2020-06-09 doi:10.1101/2020.06.08.140020 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ Bacterial protein domains with a novel Ig-like fold bind human CEACAM receptors ]]> https://biorxiv.org/content/10.1101/2020.06.09.141622v1?rss=1 van Sorge, N. M. Bonsor, D. A. Deng, L. Lindahl, E. Schmitt, V. Lyndin, M. Schmidt, A. Nilsson, O. R. Brizuela, J. Boero, E. Sundberg, E. J. van Strijp, J. Doran, K. S. Singer, B. S. Lindahl, G. McCarthy, A. J. 2020-06-10 doi:10.1101/2020.06.09.141622 Cold Spring Harbor Laboratory Press 2020-06-10 <![CDATA[ Characterization of the dynamic resting state of a pentameric ligand-gated ion channel by cryo-electron microscopy and simulations ]]> https://biorxiv.org/content/10.1101/2020.06.19.161356v1?rss=1 Rovsnik, U. Zhuang, Y. Axelsson, L. Forsberg, B. O. Lim, V. T. Carroni, M. Blau, C. Howard, R. J. Lindahl, E. 2020-06-20 doi:10.1101/2020.06.19.161356 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ Genetics of human gut microbiome composition ]]> https://biorxiv.org/content/10.1101/2020.06.26.173724v1?rss=1 Kurilshikov, A. Medina-Gomez, C. Bacigalupe, R. Radjabzadeh, D. Wang, J. Demirkan, A. Le Roy, C. I. Raygoza Garay, J. A. Finnicum, C. Liu, X. Zhernakova, D. Bonder, M. J. Hansen, T. H. Frost, F. Ruhlemann, M. C. Turpin, W. Moon, J.-Y. Kim, H.-N. Lull, K. Barkan, E. Shah, S. A. Fornage, M. Szopinska-Tokov, J. Wallen, Z. Borisevich, D. Agreus, L. Andreasson, A. Bang, C. Bedrani, L. Bell, J. T. Bisgaard, H. Boehnke, M. Boomsma, D. I. Burk, R. D. Claringbould, A. Croitoru, K. Davies, G. Van Duijn, C. Duijts, L. Falony, G. Fu, J. van der Graaf, A. Hansen, T 2020-06-28 doi:10.1101/2020.06.26.173724 Cold Spring Harbor Laboratory Press 2020-06-28 <![CDATA[ Impact of high-fat diet on lifespan, metabolism, fecundity and behavioral senescence in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.06.28.175794v1?rss=1 Liao, S. Amcoff, M. Nassel, D. 2020-06-28 doi:10.1101/2020.06.28.175794 Cold Spring Harbor Laboratory Press 2020-06-28 <![CDATA[ The ribosome modulates folding inside the ribosomal exit tunnel ]]> https://biorxiv.org/content/10.1101/2020.06.30.180224v1?rss=1 Wruck, F. Tian, P. Kudva, R. Best, R. B. von Heijne, G. Tans, S. J. Katranidis, A. 2020-07-01 doi:10.1101/2020.06.30.180224 Cold Spring Harbor Laboratory Press 2020-07-01 <![CDATA[ Viability and mitochondrial bioenergetic functions in human colon cancer cells are not affected by treatment with peptides mtCPP1, UPF25, mtgCPP, and mtCPP1gHO ]]> https://biorxiv.org/content/10.1101/2020.07.03.185967v1?rss=1 Timohhina, N. Cerrato, C. P. Kurrikoff, K. Chekulayev, V. Aid-Vanakova, J. Puurand, M. Tepp, K. Shevchuk, I. Langel, U. Kaambre, T. 2020-07-04 doi:10.1101/2020.07.03.185967 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ The ER membrane chaperone Shr3 co-translationally assists biogenesis of related plasma membrane transport proteins ]]> https://biorxiv.org/content/10.1101/2020.07.05.188557v1?rss=1 Ring, A. Myronidi, I. Ljungdahl, P. O. 2020-07-05 doi:10.1101/2020.07.05.188557 Cold Spring Harbor Laboratory Press 2020-07-05 <![CDATA[ Cotranslational folding of alkaline phosphatase in the periplasm of Escherichia coli ]]> https://biorxiv.org/content/10.1101/2020.07.06.189464v1?rss=1 Elfagieh, R. Karyolaimos, A. Kemp, G. deGier, J.-W. von Heijne, G. Kudva, R. 2020-07-06 doi:10.1101/2020.07.06.189464 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ Independence of 3D chromatin conformation and gene regulation during Drosophila dorsoventral patterning ]]> https://biorxiv.org/content/10.1101/2020.07.07.186791v1?rss=1 Ing-Simmons, E. Vaid, R. Mannervik, M. Vaquerizas, J. M. 2020-07-07 doi:10.1101/2020.07.07.186791 Cold Spring Harbor Laboratory Press 2020-07-07 <![CDATA[ Single-cell analysis of mosquito hemocytes identifies signatures of immune cell sub-types and cell differentiation ]]> https://biorxiv.org/content/10.1101/2020.07.11.197939v1?rss=1 Hyeogsun Kwon Oscar Franzen Mubasher Mohammed Johan Ankarklev Ryan C Smith 2020-07-11 doi:10.1101/2020.07.11.197939 Cold Spring Harbor Laboratory Press 2020-07-11 <![CDATA[ The evolution of social dominance through reinforcement learning ]]> https://biorxiv.org/content/10.1101/2020.07.23.218040v1?rss=1 Leimar, O. 2020-07-23 doi:10.1101/2020.07.23.218040 Cold Spring Harbor Laboratory Press 2020-07-23 <![CDATA[ The impact of microclimate and soil on the ecology and evolution of an arctic plant ]]> https://biorxiv.org/content/10.1101/2020.07.26.221721v1?rss=1 Wickander, N. J. Rasmussen, P. U. Marteinsdottir, B. Ehrlen, J. Tack, A. J. M. 2020-07-26 doi:10.1101/2020.07.26.221721 Cold Spring Harbor Laboratory Press 2020-07-26 <![CDATA[ Assembly and symmetry of the fungal E3BP-containing core of the Pyruvate Dehydrogenase Complex ]]> https://biorxiv.org/content/10.1101/2020.08.13.232140v1?rss=1 Forsberg, B. O. Aibara, S. Howard, R. J. Mortezaei, N. Lindahl, E. 2020-08-14 doi:10.1101/2020.08.13.232140 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Museomics of a rare taxon: placing Whalleyanidae in the Lepidoptera Tree of Life ]]> https://biorxiv.org/content/10.1101/2020.08.18.255182v1?rss=1 Twort, V. G. Minet, J. Wheat, C. W. Wahlberg, N. 2020-08-18 doi:10.1101/2020.08.18.255182 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ Neuronal death in pneumococcal meningitis is triggered by pneumolysin and pilus-1 interactions with β-actin ]]> https://biorxiv.org/content/10.1101/2020.08.20.258681v1?rss=1 Tabusi, M. Thorsdottir, S. Lysandrou, M. Narciso, A. R. Minoia, M. Henriques-Normark, B. Iovino, F. 2020-08-20 doi:10.1101/2020.08.20.258681 Cold Spring Harbor Laboratory Press 2020-08-20 <![CDATA[ Route following by one-eyed ants suggests a revised model of normal route following ]]> https://biorxiv.org/content/10.1101/2020.08.21.261354v1?rss=1 Collett, T. S. Woodgate, J. L. Perl, C. 2020-08-24 doi:10.1101/2020.08.21.261354 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Identification and characterization of distinct murine brown adipocyte lineages ]]> https://biorxiv.org/content/10.1101/2020.08.24.264416v1?rss=1 Ussar, S. Karlina, R. Lutter, D. Miok, V. Fischer, D. S. Altun, I. Schoettl, T. Schorpp, K. Israel, A. Cero, C. Johnson, J. W. Kapser-Fischer, I. Boettcher, A. Keipert, S. Feuchtinger, A. Graf, E. Strom, T. M. Walch, A. Lickert, H. Walzthoeni, T. Heinig, M. Theis, F. J. Garcia-Caceres, C. Cypess, A. M. 2020-08-25 doi:10.1101/2020.08.24.264416 Cold Spring Harbor Laboratory Press 2020-08-25 <![CDATA[ Accurate spliced alignment of long RNAsequencing reads ]]> https://biorxiv.org/content/10.1101/2020.09.02.279208v1?rss=1 Sahlin, K. Makinen, V. 2020-09-03 doi:10.1101/2020.09.02.279208 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ Evolutionarily conserved chaperone-mediated proteasomal degradation of a disease-linked aspartoacylase variant ]]> https://biorxiv.org/content/10.1101/2020.09.04.283028v1?rss=1 Gersing, S. K. Wang, Y. Gronbaek-Thygesen, M. Kampmeyer, C. Clausen, L. Andreasson, C. Stein, A. Lindorff-Larsen, K. Hartmann-Petersen, R. 2020-09-04 doi:10.1101/2020.09.04.283028 Cold Spring Harbor Laboratory Press 2020-09-04 <![CDATA[ Experimental evolution confirms signatures of sexual selection in genomic divergence. ]]> https://biorxiv.org/content/10.1101/2020.09.07.285650v1?rss=1 Wiberg, R. A. W. Veltsos, P. Snook, R. R. Ritchie, M. G. 2020-09-07 doi:10.1101/2020.09.07.285650 Cold Spring Harbor Laboratory Press 2020-09-07 <![CDATA[ Residue-by-residue analysis of cotranslational membrane protein integration in vivo ]]> https://biorxiv.org/content/10.1101/2020.09.27.315283v1?rss=1 Nicolaus, F. Metola, A. Mermans, D. Liljenstrom, A. Krc, A. Abdullahi, S. M. Zimmer, M. Miller, T. F. Von Heijne, G. 2020-09-28 doi:10.1101/2020.09.27.315283 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ Parallelized calculation of permutation tests ]]> https://biorxiv.org/content/10.1101/2020.10.01.321828v1?rss=1 Ekvall, M. Höhle, M. Käll, L. 2020-10-02 doi:10.1101/2020.10.01.321828 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Ecological specialisation and evolutionary reticulation in extant Hyaenidae ]]> https://biorxiv.org/content/10.1101/2020.10.14.338871v1?rss=1 Westbury, M. V. Le Duc, D. Duchene, D. A. Krishnan, A. Prost, S. Rutschmann, S. Grau, J. H. Weyrich, A. Noren, K. Werdelin, L. Dalerum, F. Schoeneberg, T. Hofreiter, M. 2020-10-14 doi:10.1101/2020.10.14.338871 Cold Spring Harbor Laboratory Press 2020-10-14 <![CDATA[ Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods ]]> https://biorxiv.org/content/10.1101/2020.10.17.343731v1?rss=1 2,000,000 images and >1,300 metagenomes in surface, deep chlorophyll maximum and mesopelagic samples across 6 size fractions (<0.2-2000 m). Imaging and PCR-free molecular data were remarkably congruent. Sequences from diazotrophs were detected from the ultrasmall bacterioplankton (<0.2 m) to mesoplankton (180-2000 m), while images predicted symbiotic and colonial-forming diazotrophs (>20 {micro}m). Imaging and molecular data estimated that polyploidy can significantly impact gene abundances of symbiotic vs colonial-forming diazotrophs. In general our results support the canonical view that larger sized diazotrophs (>10 m) dominate the tropical belts, while sequences from unicellular cyanobacterial and non-cyanobacterial diazotrophs were globally distributed in surface and the mesopelagic. Co-occurring diazotrophic lineages of different lifestyles were frequently encountered, and several new high density regions of diazotrophs were identified in the global ocean. Overall, this work provides an update of marine diazotroph biogeographical diversity and contributes a new bio-imaging-informatic workflow. ]]> Pierella Karlusich, J. J. Pelletier, E. Carsique, M. Dvorak, E. Colin, S. Picheral, M. Pepperkok, R. Karsenti, E. de Vargas, C. Lombard, F. Wincker, P. Bowler, C. Foster, R. A. 2020-10-17 doi:10.1101/2020.10.17.343731 Cold Spring Harbor Laboratory Press 2020-10-17 <![CDATA[ The evolution of social learning as phenotypic cue integration ]]> https://biorxiv.org/content/10.1101/2020.10.30.358028v1?rss=1 Kuijper, B. Leimar, O. Hammerstein, P. McNamara, J. M. Dall, S. R. X. 2020-10-31 doi:10.1101/2020.10.30.358028 Cold Spring Harbor Laboratory Press 2020-10-31 <![CDATA[ Improved chromosome level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) based on SMRT Sequencing and linkage map. ]]> https://biorxiv.org/content/10.1101/2020.11.03.364950v1?rss=1 Blande, D. Smolander, O.-P. Ahola, V. Rastas, P. Tanskanen, J. Kammonen, J. I. Oostra, V. Pellegrini, L. Ikonen, S. Dallas, T. DiLeo, M. F. Duplouy, A. Duru, I. C. Halimaa, P. Kahilainen, A. Kuwar, S. S. Karenlampi, S. O. Lafuente, E. Luo, S. Makkonen, J. Nair, A. Celorio-Mancera, M. d. l. P. Pennanen, V. Ruokolainen, A. Sundell, T. Tervahauta, A. I. Twort, V. van Bergen, E. Osterman-Udd, J. Paulin, L. Frilander, M. J. Auvinen, P. Saastamoinen, M. 2020-11-04 doi:10.1101/2020.11.03.364950 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ LyGo: A platform for rapid screening of lytic polysaccharide monooxygenase production ]]> https://biorxiv.org/content/10.1101/2020.11.04.368555v1?rss=1 Hernandez-Rollan, C. Falkenberg, K. B. Rennig, M. Bertelsen, A. B. Ipsen, J. O. Brander, S. Daley, D. O. Johansen, K. S. Norholm, M. H. H. 2020-11-04 doi:10.1101/2020.11.04.368555 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ Rapid compensatory evolution can rescue low fitness symbioses following partner-switching ]]> https://biorxiv.org/content/10.1101/2020.11.06.371401v1?rss=1 Sorensen, M. Wood, J. Cameron, D. Brockhurst, M. 2020-11-08 doi:10.1101/2020.11.06.371401 Cold Spring Harbor Laboratory Press 2020-11-08 <![CDATA[ The evolution of a placenta is not linked to increased brain size in poeciliid fishes ]]> https://biorxiv.org/content/10.1101/2020.11.07.372615v1?rss=1 Rowinski, P. K. Naslund, J. Sowersby, W. Eckerstrom-Liedholm, S. Rogell, B. 2020-11-08 doi:10.1101/2020.11.07.372615 Cold Spring Harbor Laboratory Press 2020-11-08 <![CDATA[ Bifurcations and mutation hot-spots in the SARS-CoV-2 spike protein ]]> https://biorxiv.org/content/10.1101/2020.11.11.378828v1?rss=1 Niemi, A. J. Peng, X. 2020-11-12 doi:10.1101/2020.11.11.378828 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ Comprehensive dataset of shotgun metagenomes from stratified freshwater lakes and ponds ]]> https://biorxiv.org/content/10.1101/2020.11.12.379446v1?rss=1 Buck, M. Garcia, S. L. Fernandez Vidal, L. Martin, G. Martinez Rodriguez, G. A. Saarenheimo, J. Zopfi, J. Bertilsson, S. Peura, S. 2020-11-12 doi:10.1101/2020.11.12.379446 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ Control of mitochondrial superoxide production includes programmed mtDNA deletion and restoration ]]> https://biorxiv.org/content/10.1101/2020.11.20.391110v1?rss=1 Stenberg, S. Li, J. Gjuvsland, A. B. Persson, K. Demitz-Helin, E. Yue, J.-X. Gilchrist, C. Ärengard, T. Ghiaci, P. Larsson-Berglund, L. Zackrisson, M. Höög, J. L. Molin, M. Liti, G. Omholt, S. W. Warringer, J. 2020-11-20 doi:10.1101/2020.11.20.391110 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ Conservation of glutathione S-transferase mRNA and protein sequences similar to human and horse Alpha class GST A3-3 across dog, goat, and opossum species ]]> https://biorxiv.org/content/10.1101/2020.11.25.396168v1?rss=1 Ing, N. H. Hubert, S. Samollow, P. B. Lindstrom, H. Mannervik, B. 2020-11-25 doi:10.1101/2020.11.25.396168 Cold Spring Harbor Laboratory Press 2020-11-25 <![CDATA[ Cryo-EM structure and kinetics reveal electron transfer by 2D diffusion of cytochrome c in the yeast III-IV respiratory supercomplex ]]> https://biorxiv.org/content/10.1101/2020.11.27.401935v1?rss=1 Moe, A. Di Trani, J. Rubinstein, J. L. Brzezinski, P. 2020-11-28 doi:10.1101/2020.11.27.401935 Cold Spring Harbor Laboratory Press 2020-11-28 <![CDATA[ Cholecystokinin-like Peptide Mediates Satiety by Inhibiting Sugar Attraction ]]> https://biorxiv.org/content/10.1101/2020.12.14.419390v1?rss=1 Guo, D. Zhang, Y.-j. Zhang, S. Li, J. Guo, C. Pan, Y. Liu, C.-X. Jia, Y.-L. Li, C.-Y. Ma, J.-Y. Nassel, D. Gao, C.-F. Wu, S.-F. 2020-12-15 doi:10.1101/2020.12.14.419390 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ InSegtCone: Interactive Segmentation of crystalline Cones in compound eyes ]]> https://biorxiv.org/content/10.1101/2020.12.15.422850v1?rss=1 Tichit, P. B. T. Zhou, T. Kjer, H. M. Andersen Dahl, V. Bjorholm Dahl, A. Baird, E. 2020-12-16 doi:10.1101/2020.12.15.422850 Cold Spring Harbor Laboratory Press 2020-12-16 <![CDATA[ The chaperonin GroESL facilitates Caulobacter crescentus cell division by supporting the function of the actin homologue FtsA ]]> https://biorxiv.org/content/10.1101/2020.12.17.423375v1?rss=1 Schroeder, K. Heinrich, K. Neuwirth, I. Jonas, K. 2020-12-18 doi:10.1101/2020.12.17.423375 Cold Spring Harbor Laboratory Press 2020-12-18 <![CDATA[ Bab2 activates JNK signaling to reprogram Drosophila wing disc development ]]> https://biorxiv.org/content/10.1101/2020.12.30.424794v1?rss=1 Zhao, Y. Duan, J. Dziedziech, A. Büttner, S. Engström, Y. 2020-12-30 doi:10.1101/2020.12.30.424794 Cold Spring Harbor Laboratory Press 2020-12-30 <![CDATA[ Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the liver ]]> https://biorxiv.org/content/10.1101/2021.01.11.426100v1?rss=1 Hildebrandt, F. F. A. Andersson, A. Saarenpaa, S. Larsson, L. Van Hul, N. Kanatani, S. Masek, J. Ellis, E. Barragan, A. Mollbrink, A. Andersson, E. R. Lundeberg, J. Ankarklev, J. 2021-01-12 doi:10.1101/2021.01.11.426100 Cold Spring Harbor Laboratory Press 2021-01-12 <![CDATA[ A genomic perspective on genome size distribution across Earth's microbiomes reveals a tendency to gene loss ]]> https://biorxiv.org/content/10.1101/2021.01.18.427069v1?rss=1 Rodriguez-Gijon, A. Nuy, J. K. Mehrshad, M. Buck, M. Schulz, F. Woyke, T. Garcia, S. L. 2021-01-18 doi:10.1101/2021.01.18.427069 Cold Spring Harbor Laboratory Press 2021-01-18 <![CDATA[ Trophic position derived from amino-acid nitrogen isotopes reflect physiological status of both predator and prey over four decades ]]> https://biorxiv.org/content/10.1101/2021.01.25.428045v1?rss=1 Karlson, A. M. Ek, C. Jones, D. 2021-01-26 doi:10.1101/2021.01.25.428045 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Experimental sexual selection reveals rapid divergence in male and female reproductive transcriptomes and their interactions ]]> https://biorxiv.org/content/10.1101/2021.01.29.428831v1?rss=1 Veltsos, P. Porcelli, D. Fang, Y. Cossins, A. R. Ritchie, M. G. Snook, R. R. 2021-01-31 doi:10.1101/2021.01.29.428831 Cold Spring Harbor Laboratory Press 2021-01-31 <![CDATA[ Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource ]]> https://biorxiv.org/content/10.1101/2021.02.01.428994v1?rss=1 20 countries on four continents based on a combination of 121 unpublished and 150 previously published genomic datasets. Several of these locations have been sampled at different seasons across multiple years. This dataset, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental meta-data. A web-based genome browser and web portal provide easy access to the SNP dataset. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan dataset. Our resource will enable population geneticists to analyze spatio-temporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail. ]]> Kapun, M. Nunez, J. C. B. Bogaerts-Marquez, M. Murga-Moreno, J. Paris, M. Outten, J. Coronado-Zamora, M. Tern, C. Rota-Stabelli, O. Garcia Guerreiro, M. P. P. Casillas, S. Orengo, D. J. Puerma, E. Kankare, M. Ometto, L. Loeschcke, V. V. Onder, B. S. Abbott, J. K. Schaeffer, S. W. Rajpurohit, S. Behrman, E. L. Schou, M. F. Merritt, T. J. S. Lazzaro, B. P. B. Glaser-Schmitt, A. Argyridou, E. Staubach, F. Wang, Y. Tauber, E. Serga, S. V. Fabian, D. K. Dyer, K. A. Wheat, C. W. Parsch, J. Grath, S. Savic Veselinovic, M. Stamenkovic-Radak, M. Jelic, M. Buendia-R 2021-02-01 doi:10.1101/2021.02.01.428994 Cold Spring Harbor Laboratory Press 2021-02-01 <![CDATA[ Spc1 regulates substrate selection for signal peptidase ]]> https://biorxiv.org/content/10.1101/2021.02.02.429376v1?rss=1 Yim, C. Chung, Y. Kim, J. Nilsson, I. Kim, J.-S. Kim, H. 2021-02-02 doi:10.1101/2021.02.02.429376 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Evolution of butterfly-plant networks over time, as revealed by Bayesian inference of host repertoire ]]> https://biorxiv.org/content/10.1101/2021.02.04.429735v1?rss=1 Braga, M. P. Janz, N. Nylin, S. Ronquist, F. Landis, M. J. 2021-02-05 doi:10.1101/2021.02.04.429735 Cold Spring Harbor Laboratory Press 2021-02-05 <![CDATA[ Cotranslational folding of a periplasmic protein domain in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2021.02.06.430026v1?rss=1 Sandhu, H. Hedman, R. Cymer, F. Kudva, R. Ismail, N. Von Heijne, G. 2021-02-06 doi:10.1101/2021.02.06.430026 Cold Spring Harbor Laboratory Press 2021-02-06 <![CDATA[ Relative brain size and cognitive equivalence in fishes ]]> https://biorxiv.org/content/10.1101/2021.02.09.430417v1?rss=1 Triki, Z. Aellen, M. Van Schaik, C. Bshary, R. 2021-02-09 doi:10.1101/2021.02.09.430417 Cold Spring Harbor Laboratory Press 2021-02-09 <![CDATA[ Widespread cryptic variation in genetic architecture between the sexes ]]> https://biorxiv.org/content/10.1101/2021.02.20.432102v1?rss=1 van der Bijl, W. Mank, J. E. 2021-02-20 doi:10.1101/2021.02.20.432102 Cold Spring Harbor Laboratory Press 2021-02-20 <![CDATA[ A spindle and thread-mechanism unblocks translation of N-terminally disordered proteins ]]> https://biorxiv.org/content/10.1101/2021.02.22.432221v1?rss=1 Kaldmae, M. Vosselman, T. Zhong, X. Lama, D. Chen, G. Saluri, M. Kronqvist, N. Siau, J. W. Ng, A. S. Ghadessy, F. J. Sabatier, P. Vojtesek, B. Sarr, M. Sahin, C. Osterlund, N. Ilag, L. I. Vaananen, V. A. Sedimbi, S. Zubarev, R. Nilsson, L. Koeck, P. J. Rising, A. Fritz, N. Johansson, J. Lane, D. P. Landreh, M. 2021-02-22 doi:10.1101/2021.02.22.432221 Cold Spring Harbor Laboratory Press 2021-02-22 <![CDATA[ Intra-helical salt bridge contribution to membrane protein insertion ]]> https://biorxiv.org/content/10.1101/2021.02.24.432724v1?rss=1 Duart, G. Lamb, J. Elofsson, A. Mingarro, I. 2021-02-25 doi:10.1101/2021.02.24.432724 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ Comprehensive analysis of chemical and biological problems associated with browning agents used in aquatic studies ]]> https://biorxiv.org/content/10.1101/2021.02.26.433092v1?rss=1 Scharnweber, K. Peura, S. Attermeyer, K. Bertilsson, S. Bolender, L. Buck, M. Einarsdottir, K. Garcia, S. L. Gollnisch, R. Grasset, C. Groeneveld, M. Hawkes, J. Lindstrom, E. S. Manthey, C. Overgaard, R. Rengefors, K. Nunez, V. S. Tranvik, L. J. Szekely, A. J. 2021-02-27 doi:10.1101/2021.02.26.433092 Cold Spring Harbor Laboratory Press 2021-02-27 <![CDATA[ Automated video tracking and flight analysis show how bumblebees solve a pattern discrimination task using active vision ]]> https://biorxiv.org/content/10.1101/2021.03.09.434580v1?rss=1 MaBouDi, H. Roper, M. Guiraud, M. Marshall, J. A. R. Chittka, L. 2021-03-10 doi:10.1101/2021.03.09.434580 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Epigenetic switching outcompetes genetic mutations during adaptation to fluctuating environments ]]> https://biorxiv.org/content/10.1101/2021.03.11.434930v1?rss=1 Stajic, D. Bank, C. Gordo, I. 2021-03-12 doi:10.1101/2021.03.11.434930 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Drug-bound and -free outward-facing structures of a multidrug ABC exporter point to a swing mechanism ]]> https://biorxiv.org/content/10.1101/2021.03.12.435132v1?rss=1 Chaptal, v. Zampieri, V. Wiseman, B. Orelle, C. Martin, J. Nguyen, K.-A. Magnard, S. Gobet, A. Di cesare, M. Javed, W. Kilburg, A. Peuchmaur, M. Marcoux, J. Hogbom, M. Jault, J.-M. Boumendjel, A. Falson, P. G. 2021-03-12 doi:10.1101/2021.03.12.435132 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ GABAergic signaling in human and murine NK cells upon challenge with Toxoplasma gondii ]]> https://biorxiv.org/content/10.1101/2021.03.19.435611v1?rss=1 Bhandage, A. K. Friedrich, L. M. Kanatani, S. Jakobsson-Bjoerken, S. Escrig-Larena, J. I. Wagner, A. K. Chambers, B. J. Barragan, A. 2021-03-20 doi:10.1101/2021.03.19.435611 Cold Spring Harbor Laboratory Press 2021-03-20 <![CDATA[ Seqpac: A New Framework for small RNA analysis in R using Sequence-Based Counts ]]> https://biorxiv.org/content/10.1101/2021.03.19.436151v1?rss=1 Skog, S. Orkenby, L. Tariq, K. Ostlund Farrants, A.-K. Ost, A. Natt, D. 2021-03-21 doi:10.1101/2021.03.19.436151 Cold Spring Harbor Laboratory Press 2021-03-21 <![CDATA[ Anti-fibrotic activity of an antimicrobial peptide in a Drosophila model. ]]> https://biorxiv.org/content/10.1101/2021.03.19.436168v1?rss=1 Khalili, D. Kalcher, C. Baumgartner, S. Theopold, U. 2021-03-19 doi:10.1101/2021.03.19.436168 Cold Spring Harbor Laboratory Press 2021-03-19 <![CDATA[ Sexual selection affects the evolution of physiological and life history traits ]]> https://biorxiv.org/content/10.1101/2021.03.23.436586v1?rss=1 Garlovsky, M. D. Holman, L. Brooks, A. L. Snook, R. R. 2021-03-23 doi:10.1101/2021.03.23.436586 Cold Spring Harbor Laboratory Press 2021-03-23 <![CDATA[ A nascent polypeptide sequence modulates DnaA translation elongation in response to nutrient availability ]]> https://biorxiv.org/content/10.1101/2021.03.31.437742v1?rss=1 Felletti, M. Romilly, C. Wagner, G. Jonas, K. 2021-03-31 doi:10.1101/2021.03.31.437742 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ Rapid mosaic brain evolution under artificial selection for relative telencephalon size in the guppy (Poecilia reticulata) ]]> https://biorxiv.org/content/10.1101/2021.03.31.437806v1?rss=1 Fong, S. Rogell, B. Amcoff, M. Kotrschal, A. van der Bijl, W. Buechel, S. D. Kolm, N. 2021-04-01 doi:10.1101/2021.03.31.437806 Cold Spring Harbor Laboratory Press 2021-04-01 <![CDATA[ Artificial mosaic brain evolution of relative telencephalon size improves cognitive performance in the guppy (Poecilia reticulata) ]]> https://biorxiv.org/content/10.1101/2021.04.03.438307v1?rss=1 Triki, Z. Fong, S. Amcoff, M. Kolm, N. 2021-04-04 doi:10.1101/2021.04.03.438307 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ The Up state of the SARS-COV-2 Spike homotrimer favors an increased virulence for new variants ]]> https://biorxiv.org/content/10.1101/2021.04.05.438465v1?rss=1 Correa Giron, C. Laaksonen, A. Barroso da Silva, F. L. 2021-04-06 doi:10.1101/2021.04.05.438465 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ Redetermination of the first unknown protein MicroED structure by high resolution X-ray diffraction ]]> https://biorxiv.org/content/10.1101/2021.04.07.438860v1?rss=1 Xu, H. Zou, X. Högbom, M. Lebrette, H. 2021-04-08 doi:10.1101/2021.04.07.438860 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ A large and diverse autosomal haplotype is associated with sex-linked colour polymorphism in the guppy ]]> https://biorxiv.org/content/10.1101/2021.04.08.437888v1?rss=1 Paris, J. R. Whiting, J. R. Daniel, M. J. Ferrer Obiol, J. Parsons, P. J. van der Zee, M. J. Wheat, C. W. Hughes, K. A. Fraser, B. A. 2021-04-09 doi:10.1101/2021.04.08.437888 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ Conformational clamping by a membrane ligand activates the EphA2 receptor ]]> https://biorxiv.org/content/10.1101/2021.04.08.439029v1?rss=1 Westerfield, J. M. Sahoo, A. Alves, D. S. Grau, B. Cameron, A. Maxwell, M. Schuster, J. Souza, P. C. T. Mingarro, I. Buck, M. Barrera, F. N. 2021-04-09 doi:10.1101/2021.04.08.439029 Cold Spring Harbor Laboratory Press 2021-04-09 <![CDATA[ The unresolved phylogenomic tree of butterflies and moths (Lepidoptera): assessing the potential causes and consequences ]]> https://biorxiv.org/content/10.1101/2021.04.09.439156v1?rss=1 Rota, J. Twort, V. G. Chiocchio, A. Pena, C. Wheat, C. W. Kaila, L. Wahlberg, N. 2021-04-11 doi:10.1101/2021.04.09.439156 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ Mitochondrial genomes of two parasitic Cuscuta species show little evidence of horizontal gene transfer and retain unusually fragmented ccmFC genes ]]> https://biorxiv.org/content/10.1101/2021.04.15.439983v1?rss=1 Anderson, B. M. Krause, K. Petersen, G. 2021-04-15 doi:10.1101/2021.04.15.439983 Cold Spring Harbor Laboratory Press 2021-04-15 <![CDATA[ Integrin-dependent migratory switches regulate the translocation of Toxoplasma-infected dendritic cells across brain endothelial monolayers ]]> https://biorxiv.org/content/10.1101/2021.04.21.440681v1?rss=1 Ross, E. .C. ten Hoeve, A. L. Barragan, A. 2021-04-21 doi:10.1101/2021.04.21.440681 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ Genome assemblies of three closely related leaf beetle species (Galerucella spp). ]]> https://biorxiv.org/content/10.1101/2021.04.28.441848v1?rss=1 Yang, X. Slotte, T. Hambäck, P. A. 2021-04-30 doi:10.1101/2021.04.28.441848 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Multi-animal pose estimation and tracking with DeepLabCut ]]> https://biorxiv.org/content/10.1101/2021.04.30.442096v1?rss=1 Lauer, J. Zhou, M. Ye, S. Menegas, W. Nath, T. Rahman, M. M. Di Santo, V. Soberanes, D. Feng, G. Murthy, V. N. Lauder, G. Dulac, C. Mathis, M. W. Mathis, A. 2021-04-30 doi:10.1101/2021.04.30.442096 Cold Spring Harbor Laboratory Press 2021-04-30 <![CDATA[ Rieske head domain dynamics and indazole-derivative inhibition of Candida albicans complex III ]]> https://biorxiv.org/content/10.1101/2021.05.18.444650v1?rss=1 Di Trani, J. Liu, Z. Whitesell, L. Brzezinski, P. Cowen, L. Rubinstein, J. L. 2021-05-18 doi:10.1101/2021.05.18.444650 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ A complex interplay between balancing selection and introgression maintains a genus-wide alternative life-history strategy. ]]> https://biorxiv.org/content/10.1101/2021.05.20.445023v1?rss=1 tunström, k. Woronik, A. Hanly, J. J. Rastas, P. Chichvarkhin, A. Warren, A. D. Kawahara, A. Schoville, S. D. Ficarrotta, V. Porter, A. H. Watt, W. B. Martin, A. Wheat, C. W. 2021-05-20 doi:10.1101/2021.05.20.445023 Cold Spring Harbor Laboratory Press 2021-05-20 <![CDATA[ A genetic switch for male UV-iridescence in an incipient species pair of sulphur butterflies ]]> https://biorxiv.org/content/10.1101/2021.05.21.445125v1?rss=1 Ficarrotta, V. Hanly, J. J. Loh, L. S. Francescutti, C. M. Ren, A. tunstrom, k. Wheat, C. W. Porter, A. H. Counterman, B. A. Martin, A. 2021-05-21 doi:10.1101/2021.05.21.445125 Cold Spring Harbor Laboratory Press 2021-05-21 <![CDATA[ SignalP 6.0 achieves signal peptide prediction across all types using protein language models ]]> https://biorxiv.org/content/10.1101/2021.06.09.447770v1?rss=1 Teufel, F. Armenteros, J. J. A. Johansen, A. R. Gislason, M. H. Pihl, S. I. Tsirigos, K. D. Winther, O. Brunak, S. Von Heijne, G. Nielsen, H. 2021-06-10 doi:10.1101/2021.06.09.447770 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ Complete loss of mitochondrial complex I genes in mistletoes (Viscaceae) and evidence of polyadenylated mitochondrial transcripts shown by whole transcriptome sequencing ]]> https://biorxiv.org/content/10.1101/2021.06.11.448138v1?rss=1 Zervas, A. Takenaka, M. Leebens-Mack, J. H. Seberg, O. Petersen, G. 2021-06-11 doi:10.1101/2021.06.11.448138 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Specific and dynamic lignification at the cell-type level controls plant physiology and adaptability ]]> https://biorxiv.org/content/10.1101/2021.06.12.447240v1?rss=1 Menard, D. Blaschek, L. Kriechbaum, K. Lee, C. C. Zhu, C. Nuoendagula, Bacsik, Z. Bergström, L. Mathew, A. Kajita, S. Pesquet, E. 2021-06-14 doi:10.1101/2021.06.12.447240 Cold Spring Harbor Laboratory Press 2021-06-14 <![CDATA[ The respiratory supercomplex from C. glutamicum ]]> https://biorxiv.org/content/10.1101/2021.06.16.448340v1?rss=1 Moe, A. Kovalova, T. Krol, S. Yanofsky, D. J. Bott, M. Sjöstrand, D. Rubinstein, J. L. Högbom, M. Brzezinski, P. 2021-06-16 doi:10.1101/2021.06.16.448340 Cold Spring Harbor Laboratory Press 2021-06-16 <![CDATA[ Reproductive skew, fitness costs, and winner-loser effects in social-dominance evolution ]]> https://biorxiv.org/content/10.1101/2021.06.22.449392v1?rss=1 Leimar, O. Bshary, R. 2021-06-22 doi:10.1101/2021.06.22.449392 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Probing interplays between human XBP1u translational arrest peptide and 80S ribosome ]]> https://biorxiv.org/content/10.1101/2021.06.22.449432v1?rss=1 Di Palma, F. Decherchi, S. Pardo-Avila, F. Succi, S. Levitt, M. von Heijne, G. Cavalli, A. 2021-06-22 doi:10.1101/2021.06.22.449432 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ The Lon protease temporally restricts polar cell differentiation events during the Caulobacter cell cycle ]]> https://biorxiv.org/content/10.1101/2021.06.29.450348v1?rss=1 Omnus, D. J. Fink, M. J. Szwedo, K. Jonas, K. 2021-06-29 doi:10.1101/2021.06.29.450348 Cold Spring Harbor Laboratory Press 2021-06-29 <![CDATA[ A supergene in seaweed flies modulates male traits and female perception ]]> https://biorxiv.org/content/10.1101/2021.06.30.450538v1?rss=1 Enge, S. Merot, C. Mozuraitis, R. Apsegaite, V. Bernatchez, L. Martens, G. A. Radziute, S. Pavia, H. Berdan, E. L. 2021-07-01 doi:10.1101/2021.06.30.450538 Cold Spring Harbor Laboratory Press 2021-07-01 <![CDATA[ Structure of mycobacterial CIII2CIV2 respiratory supercomplex bound to the tuberculosis drug candidate telacebec (Q203) ]]> https://biorxiv.org/content/10.1101/2021.07.06.451285v1?rss=1 Yanofsky, D. J. Di Trani, J. M. Krol, S. Abdelaziz, R. Bueler, S. A. Imming, P. Brzezinski, P. Rubinstein, J. L. 2021-07-06 doi:10.1101/2021.07.06.451285 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ Structure and lipid-mediated remodelling mechanism of the Na+/H+ exchanger NHA2 ]]> https://biorxiv.org/content/10.1101/2021.07.22.453398v1?rss=1 Matsuoka, R. Fudim, R. Jung, S. Zhang, C. Bazzone, A. Chatzikyriakidou, Y. Nomura, N. Iwata, S. Orellana, L. Beckstein, O. Drew, D. 2021-07-22 doi:10.1101/2021.07.22.453398 Cold Spring Harbor Laboratory Press 2021-07-22 <![CDATA[ Coordinated activation of both TGFβ and BMP canonical pathways regulates autophagy and tissue regeneration in acetaminophen induced liver injury ]]> https://biorxiv.org/content/10.1101/2021.07.23.453185v1?rss=1 Stavropoulos, A. Divolis, G. Manioudaki, M. Gavriil, A. Kloukina, I. Perrea, D. N. Sountoulidis, A. Ford, E. Doulou, A. Apostolidou, A. Katsantoni, E. Ritvos, O. Germanidis, G. Xilouri, M. Sideras, P. 2021-07-23 doi:10.1101/2021.07.23.453185 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ Microbiota-dependent and independent production of L-Dopa in the gut of Daphnia magna ]]> https://biorxiv.org/content/10.1101/2021.08.02.454848v1?rss=1 El-Shehawy, R. Luecke-Johansson, S. Ribbenstedt, A. Gorokhova, E. 2021-08-03 doi:10.1101/2021.08.02.454848 Cold Spring Harbor Laboratory Press 2021-08-03 <![CDATA[ Mg2+-dependent conformational equilibria in CorA: an integrated view on transport regulation ]]> https://biorxiv.org/content/10.1101/2021.08.20.457080v1?rss=1 Johansen, N. T. Bonaccorsi, M. Bengtsen, T. Larsen, A. H. Tidemand, F. G. Pedersen, M. C. Huda, P. Berndtsson, J. Darwish, T. Yepuri, N. R. Martel, A. Pomorski, T. Bertarello, A. Sansom, M. S. Rapp, M. Crehuet, R. Schubeis, T. Lindorff-Larsen, K. Pintacuda, G. Arleth, L. 2021-08-21 doi:10.1101/2021.08.20.457080 Cold Spring Harbor Laboratory Press 2021-08-21 <![CDATA[ The control of transcriptional memory by stable mitotic bookmarking ]]> https://biorxiv.org/content/10.1101/2021.08.30.458146v1?rss=1 Bellec, M. Dufourt, J. Hunt, G. Lenden-Hasse, H. Trullo, A. Zine El Aabidine, A. Lamarque, M. Gaskill, M. M. Faure-Gautron, H. Mannervik, M. Harrison, M. Andrau, J.-C. Favard, C. Radulescu, O. Lagha, M. 2021-08-30 doi:10.1101/2021.08.30.458146 Cold Spring Harbor Laboratory Press 2021-08-30 <![CDATA[ Genomic signatures of sexual selection on pollen-expressed genes in Arabis alpina ]]> https://biorxiv.org/content/10.1101/2021.09.02.457912v1?rss=1 Gutierrez-Valencia, J. Fracassetti, M. Horvath, R. Laenen, B. Desamore, A. Drouzas, A. D. Friberg, M. Kolar, F. Slotte, T. 2021-09-03 doi:10.1101/2021.09.02.457912 Cold Spring Harbor Laboratory Press 2021-09-03 <![CDATA[ PplD is a de-N-acetylase of the cell wall linkage unit of streptococcal rhamnopolysaccharides ]]> https://biorxiv.org/content/10.1101/2021.09.23.461590v1?rss=1 Rush, J. S. Parajuli, P. Ruda, A. Li, J. Pohane, A. A. Zamakhaeva, S. Rahman, M. M. Chang, J. C. Gogos, A. Kenner, C. W. Lambeau, G. Federle, M. J. Korotkov, K. V. Widmalm, G. Korotkova, N. 2021-09-23 doi:10.1101/2021.09.23.461590 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ Female fruit flies cannot protect stored sperm from high temperature damage ]]> https://biorxiv.org/content/10.1101/2021.09.30.462530v1?rss=1 Walsh, B. S. Parratt, S. R. Snook, R. R. Bretman, A. Atkinson, D. Price, T. A. R. 2021-10-01 doi:10.1101/2021.09.30.462530 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ A synthesis of senescence predictions for indeterminate growth, and support from multiple tests in wild lake trout ]]> https://biorxiv.org/content/10.1101/2021.10.05.463025v1?rss=1 Purchase, C. F. Rooke, A. C. Gaudry, M. J. Treberg, J. R. Mittell, E. A. Morrissey, M. B. Rennie, M. D. 2021-10-05 doi:10.1101/2021.10.05.463025 Cold Spring Harbor Laboratory Press 2021-10-05 <![CDATA[ Abnormal (hydroxy)prolines deuterium content redefines hydrogen chemical mass ]]> https://biorxiv.org/content/10.1101/2021.11.11.468216v1?rss=1 Gharibi, H. Chernobrovkin, A. L. Eriksson, G. Dibavar, A. S. Timmons, Z. Kitchener, A. C. Kalthoff, D. Liden, K. Makarov, A. A. Zubarev, R. 2021-11-12 doi:10.1101/2021.11.11.468216 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ Disentangling signatures of selection before and after European colonization in Latin Americans ]]> https://biorxiv.org/content/10.1101/2021.11.15.467418v1?rss=1 Mendoza-Revilla, J. Chacon-Duque, C. Fuentes-Guajardo, M. Ormond, L. Wang, K. Hurtado, M. Villegas, V. Granja, V. Acuna-Alonzo, V. Jaramillo, C. Barquera Lozano, R. Gomez-Valdes, J. Villamil-Ramirez, H. Silva de Cerqueira, C. C. Badillo Rivera, K. M. Nieves-Colon, M. A. Gignoux, C. R. Wojcik, G. L. Moreno-Estrada, A. Hunemeier, T. Ramallo, V. Schuler-Faccini, L. Gonzalez-Jose, R. Catira Bortolini, M. Canizales-Quinteros, S. Gallo, C. Poletti, G. Bedoya, G. Rothhammer, F. Balding, D. Fumagalli, M. Adhikari, K. Ruiz-Linares, A. Hellenthal, G. 2021-11-19 doi:10.1101/2021.11.15.467418 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ NUDT18 catalyzes hydrolysis of active metabolites of the antivirals Remdesivir and Ribavirin ]]> https://biorxiv.org/content/10.1101/2021.11.16.468802v1?rss=1 Jemth, A.-S. Scaletti, E. R. Homan, E. J. Stenmark, P. Helleday, T. Michel, M. 2021-11-17 doi:10.1101/2021.11.16.468802 Cold Spring Harbor Laboratory Press 2021-11-17 <![CDATA[ Phylogeny of the ingoid clade (Caesalpinioideae, Fabaceae), based on nuclear and plastid data ]]> https://biorxiv.org/content/10.1101/2021.11.23.469677v1?rss=1 Ferm, J. Wikstrom, N. Staahl, B. Rydin, C. 2021-11-25 doi:10.1101/2021.11.23.469677 Cold Spring Harbor Laboratory Press 2021-11-25 <![CDATA[ What can the cold-induced transcriptomes of Arctic Brassicaceae tell us about the evolution of cold tolerance? ]]> https://biorxiv.org/content/10.1101/2021.12.04.471218v1?rss=1 Birkeland, S. Slotte, T. Brysting, A. K. Gustafsson, A. L. S. Hvidsten, T. R. Brochmann, C. Nowak, M. D. 2021-12-05 doi:10.1101/2021.12.04.471218 Cold Spring Harbor Laboratory Press 2021-12-05 <![CDATA[ The Prion Protein Octarepeat Domain Forms Transient β-sheet Structures Upon Residue-Specific Cu(II) and Zn(II) Binding ]]> https://biorxiv.org/content/10.1101/2021.12.12.472308v1?rss=1 Gielnik, M. Szymanska, A. Dong, X. Jarvet, J. Svedruzic, Z. M. Graslund, A. Kozak, M. Warmlander, S. K. T. S. 2021-12-13 doi:10.1101/2021.12.12.472308 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ Can associative learning be the general process for intelligent behavior in non-human animals? ]]> https://biorxiv.org/content/10.1101/2021.12.15.472737v1?rss=1 Lind, J. Vinken, V. 2021-12-16 doi:10.1101/2021.12.15.472737 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Amino acid substitutions in human growth hormone affect coiled-coil content and receptor binding ]]> https://biorxiv.org/content/10.1101/2021.12.16.473085v1?rss=1 Rajkovic, A. Kanchugal, S. Abdurakhmanov, E. Howard, R. Gräslund, A. Wärmländer, S. Erwin, J. Danielson, H. U. Flores, S. C. 2021-12-17 doi:10.1101/2021.12.16.473085 Cold Spring Harbor Laboratory Press 2021-12-17 <![CDATA[ Dynamic localisation of DamX regulates bacterial filamentation and division during UPEC dispersal from host cells ]]> https://biorxiv.org/content/10.1101/2021.12.17.473257v1?rss=1 Soderstrom, B. Daley, D. O. Duggin, I. G. 2021-12-18 doi:10.1101/2021.12.17.473257 Cold Spring Harbor Laboratory Press 2021-12-18 <![CDATA[ HSP70-binding motifs function as protein quality control degrons ]]> https://biorxiv.org/content/10.1101/2021.12.22.473789v1?rss=1 Abildgaard, A. B. Petersen, S. D. Larsen, F. B. Kampmeyer, C. Johansson, K. E. Stein, A. Ravid, T. Andreasson, C. Jensen, M. K. Lindorff-Larsen, K. Hartmann-Petersen, R. 2021-12-22 doi:10.1101/2021.12.22.473789 Cold Spring Harbor Laboratory Press 2021-12-22 <![CDATA[ Functional design of bacterial superoxide:quinone oxidoreductase ]]> https://biorxiv.org/content/10.1101/2021.12.23.473985v1?rss=1 von Ballmoos, C. Abou-Hamdan, A. Mahler, R. Grossenbacher, P. Biner, O. Sjöstrand, D. Lochner, M. Högbom, M. 2021-12-23 doi:10.1101/2021.12.23.473985 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Upstream charged and hydrophobic residues impact the timing of membrane insertion of transmembrane helices ]]> https://biorxiv.org/content/10.1101/2021.12.23.474019v1?rss=1 Nicolaus, F. Ibrahimi, F. den Besten, A. von Heijne, G. 2021-12-24 doi:10.1101/2021.12.23.474019 Cold Spring Harbor Laboratory Press 2021-12-24 <![CDATA[ Towards an optimal monoclonal antibody with higher binding affinity to the receptor-binding domain of SARS-CoV-2 spike proteins from different variants ]]> https://biorxiv.org/content/10.1101/2022.01.04.474958v1?rss=1 Neamtu, A. Mocci, F. Laaksonen, A. Barroso da Silva, F. L. 2022-01-05 doi:10.1101/2022.01.04.474958 Cold Spring Harbor Laboratory Press 2022-01-05 <![CDATA[ Developmental origins of cell heterogeneity in the human lung ]]> https://biorxiv.org/content/10.1101/2022.01.11.475631v1?rss=1 Sountoulidis, A. Marco Salas, S. Braun, E. Avenel, C. Bergenstrahle, J. Vicari, M. Czarnewski Barenco, P. V. Theelke, J. Liontos, A. Abalo, X. Andrusivova, Z. Asp, M. Li, X. Hu, L. Sariyar, S. Martinez Casals, A. Ayoglu, B. Firsova, A. B. Michaelsson, J. Lundberg, E. Wählby, C. Sundström, E. Linnarsson, S. Lundeberg, J. Nilsson, M. Samakovlis, C. 2022-01-12 doi:10.1101/2022.01.11.475631 Cold Spring Harbor Laboratory Press 2022-01-12 <![CDATA[ An essential function for autocrine Hedgehog signaling in epithelial proliferation and differentiation in the trachea ]]> https://biorxiv.org/content/10.1101/2022.01.13.476169v1?rss=1 Yin, W. Liontos, A. Koepke, J. Ghoul, M. Mazzocchi, L. Liu, X. Lu, C. Wu, H. Fysikopoulos, A. Sountoulidis, A. Seeger, W. Ruppert, C. Gunther, A. Stainier, D. Y. R. Samakovlis, C. 2022-01-14 doi:10.1101/2022.01.13.476169 Cold Spring Harbor Laboratory Press 2022-01-14 <![CDATA[ Whole genome analysis sheds light on the genetic origin of Huns, Avars and conquering Hungarians ]]> https://biorxiv.org/content/10.1101/2022.01.19.476915v1?rss=1 Maroti, Z. Neparaczki, E. Schutz, O. Maar, K. Varga, G. I. B. Kovacs, B. Kalmar, T. Nyerki, E. Nagy, I. Latinovics, D. Tihanyi, B. Marcsik, A. Palfi, G. Bernert, Z. Gallina, Z. Horvath, C. Varga, S. Kolto, L. Rasko, I. Nagy, P. L. Balogh, C. Zink, A. Maixner, F. Gotherstrom, A. George, R. Szalontai, C. Szenthe, G. Gall, E. Kiss, A. P. Racz, Z. Gulyas, B. Kovacsoczy, B. N. Gaal, S. S. Tomka, P. Torok, T. 2022-01-20 doi:10.1101/2022.01.19.476915 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Biogenic methane cycling is controlled by microbial cohorts ]]> https://biorxiv.org/content/10.1101/2022.01.24.477581v1?rss=1 Mondav, R. Martin, G. Peura, S. Garcia, S. L. 2022-01-25 doi:10.1101/2022.01.24.477581 Cold Spring Harbor Laboratory Press 2022-01-25 <![CDATA[ Fgfr2b signaling is essential for the maintenance of the alveolar epithelial type 2 lineage during lung homeostasis in mice ]]> https://biorxiv.org/content/10.1101/2022.01.26.477823v1?rss=1 Ahmadvand, N. Lingampally, A. Khosravi, F. Vazquez-Armendariz, A. Rivetti, S. Wilhelm, J. Herold, S. Barreto, G. Koepke, J. Samakovlis, C. Carraro, G. Zhang, J. Al Alam, D. Bellusci, S. 2022-01-28 doi:10.1101/2022.01.26.477823 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Differences between Omicron SARS-CoV-2 RBD and other variants in their ability to interact with cell receptors and monoclonal antibodies ]]> https://biorxiv.org/content/10.1101/2022.01.29.478316v1?rss=1 Correa Giron, C. Laaksonen, A. Barroso da Silva, F. L. 2022-01-31 doi:10.1101/2022.01.29.478316 Cold Spring Harbor Laboratory Press 2022-01-31 <![CDATA[ Reproductive strategies in a complex of simultaneously hermaphroditic species, the Allolobophora chlorotica case study ]]> https://biorxiv.org/content/10.1101/2022.01.31.475338v1?rss=1 Dupont, L. Audusseau, H. Porco, D. Butt, K. R. 2022-01-31 doi:10.1101/2022.01.31.475338 Cold Spring Harbor Laboratory Press 2022-01-31 <![CDATA[ A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition ]]> https://biorxiv.org/content/10.1101/2022.01.31.478487v1?rss=1 Altinisik, N. E. Kazanci, D. D. Aydogan, A. Gemici, H. C. Erdal, O. D. Sarialtun, S. Vural, K. B. Koptekin, D. Gurun, K. Saglican, E. Cakan, G. Koruyucu, M. M. Lagerholm, V. K. Karamurat, C. Ozkan, M. Klinc, G. M. Sevkar, A. Surer, E. Gotherstrom, A. Atakuman, C. Erdal, Y. S. Ozer, F. Erim-Ozdogan, A. Somel, M. 2022-02-01 doi:10.1101/2022.01.31.478487 Cold Spring Harbor Laboratory Press 2022-02-01 <![CDATA[ Novel methodology for localizing and studying the insect dorsal rim area morphology in 2D and 3D ]]> https://biorxiv.org/content/10.1101/2022.02.07.479135v1?rss=1 Jie, V. W. Miettinen, A. Baird, E. 2022-02-09 doi:10.1101/2022.02.07.479135 Cold Spring Harbor Laboratory Press 2022-02-09 <![CDATA[ Allometric scaling of a superposition eye optimises sensitivity and acuity in large and small hawkmoths ]]> https://biorxiv.org/content/10.1101/2022.02.08.479593v1?rss=1 Stöckl, A. L. Grittner, R. Taylor, G. J. Rau, C. Bodey, A. J. Baird, E. 2022-02-11 doi:10.1101/2022.02.08.479593 Cold Spring Harbor Laboratory Press 2022-02-11 <![CDATA[ Structure and mechanism of the tripartite ATP-independent periplasmic (TRAP) transporter ]]> https://biorxiv.org/content/10.1101/2022.02.13.480285v1?rss=1 Davies, J. Currie, M. J. North, R. A. Wright, J. D. Scalise, M. Copping, J. Remus, D. Gulati, A. Morado, D. R. Jamieson, S. A. Abeysekera, G. S. Subramanian, R. Friemann, R. Wakatsuki, S. Allison, J. R. Indiveri, C. Drew, D. Mace, P. D. Dobson, R. 2022-02-14 doi:10.1101/2022.02.13.480285 Cold Spring Harbor Laboratory Press 2022-02-14 <![CDATA[ Distinct physiological responses of Coccolithus braarudii life cycle phases to light intensity and nutrient availability ]]> https://biorxiv.org/content/10.1101/2022.02.17.480838v1?rss=1 Langer, G. Jie, V. W. Kottmeier, D. Flori, S. Sturm, D. de Vries, J. Harper, G. Brownlee, C. Wheeler, G. L. 2022-02-17 doi:10.1101/2022.02.17.480838 Cold Spring Harbor Laboratory Press 2022-02-17 <![CDATA[ Practical application of indicators for genetic diversity in CBD post-2020 Global Biodiversity Framework implementation ]]> https://biorxiv.org/content/10.1101/2022.02.18.481087v1?rss=1 500, 33% of 22557 investigated species had a population estimate. For herptiles and mammals, 70% and 49%, respectively likely had Ne>500. For indicator 2, the proportion of populations or range remaining within species, 20% of all species evaluated for the Red-List have data. Meanwhile, 32% of the herptile and 84% of the mammal populations are maintaining their populations/range. For indicator 3, the number of species/populations in which genetic diversity is monitored using DNA-based methods, there are studies on 3% of species, and 0.3% are monitored. In contrast 68% of mammals and 29% of herptiles are studied using DNA, and 8% of mammals and 24% of herptiles are genetically monitored. We conclude that the Red List provide data suitable for evaluating the genetic indicators, but the data quality can be improved. There is a synergy in estimating the genetic indicators in parallel with the Red-Listing process. We propose that indicator values could be included in national Red-Listing as a new category - "genetically threatened", based on the genetic indicators. ]]> Thurfjell, H. Laikre, L. Ekblom, R. Hoban, S. Sjogren-Gulve, P. 2022-02-23 doi:10.1101/2022.02.18.481087 Cold Spring Harbor Laboratory Press 2022-02-23 <![CDATA[ Sexual deprivation induces a CRF independent stress response and decreases resistance to stressors in Drosophila via a subpopulation of Neuropeptide F receptor-expressing neurons ]]> https://biorxiv.org/content/10.1101/2022.03.02.482596v1?rss=1 Ryvkin, J. Shmueli, A. Jacob, A. Shalit, T. Bentzur, A. Agranovich, B. Abramovich, I. Gottlieb, E. Nassel, D. R. Shohat-Ophir, G. 2022-03-04 doi:10.1101/2022.03.02.482596 Cold Spring Harbor Laboratory Press 2022-03-04 <![CDATA[ FGF10 triggers de novo alveologenesis in a BPD model: impact on the resident mesenchymal niche cells ]]> https://biorxiv.org/content/10.1101/2022.03.14.484213v1?rss=1 Taghizadeh, S. Chao, C.-M. Guenther, S. Glaser, L. Gersmann, L. Michel, G. Kraut, S. Goth, K. Koepke, J. Herold, S. Samakovlis, C. Weissmann, N. Aquila, g. Ricci, F. Boyer, L. Erhardt, H. Minoo, P. Bellusci, S. Rivetti, S. 2022-03-16 doi:10.1101/2022.03.14.484213 Cold Spring Harbor Laboratory Press 2022-03-16 <![CDATA[ Expressed therapeutic protein yields are predicted by transiently transfected mammalian cell population ]]> https://biorxiv.org/content/10.1101/2022.03.15.484372v1?rss=1 Porosk, L. Nebogatova, J. Hark, H. H. Vunk, B. Arukuusk, P. Toots, U. Toots, M. Langel, U. Kurrikoff, K. 2022-03-15 doi:10.1101/2022.03.15.484372 Cold Spring Harbor Laboratory Press 2022-03-15 <![CDATA[ Selection on the fly: short term adaptation to an altered sexual selection regime in Drosophila pseudoobscura ]]> https://biorxiv.org/content/10.1101/2022.03.16.484639v1?rss=1 Barata, C. Snook, R. Ritchie, M. G. Kosiol, C. 2022-03-17 doi:10.1101/2022.03.16.484639 Cold Spring Harbor Laboratory Press 2022-03-17 <![CDATA[ Harnessing the power of technical and natural variation in 116 yeast datasets to benchmark long read assembly pipelines ]]> https://biorxiv.org/content/10.1101/2022.03.17.484703v1?rss=1 Gettle, N. Gallone, B. Verstrepen, K. Stelkens, R. 2022-03-19 doi:10.1101/2022.03.17.484703 Cold Spring Harbor Laboratory Press 2022-03-19 <![CDATA[ Taxonomic and functional diversity of aquatic heterotrophs is sustained by dissolved organic matter chemodiversity ]]> https://biorxiv.org/content/10.1101/2022.03.21.485019v1?rss=1 Garcia, S. L. Nuy, J. K. Mehrshad, M. Hampel, J. J. Sedano-Nunez, V. T. Buck, M. Divne, A.-M. Lindström, E. S. Petras, D. Hawkes, J. Bertilsson, S. 2022-03-22 doi:10.1101/2022.03.21.485019 Cold Spring Harbor Laboratory Press 2022-03-22 <![CDATA[ The dynamics of adaptation to stress from standing genetic variation and de novo mutations ]]> https://biorxiv.org/content/10.1101/2022.03.26.485920v1?rss=1 Ament-Velasquez, S. L. Gilchrist, C. Rego, A. Bendixsen, D. P. Brice, C. Grosse-Sommer, J. M. Rafati, N. Stelkens, R. 2022-03-28 doi:10.1101/2022.03.26.485920 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ CRISPR-induced exon skipping of β-catenin reveals tumorigenic mutants driving distinct subtypes of liver cancer ]]> https://biorxiv.org/content/10.1101/2022.03.27.485965v1?rss=1 Mou, H. Yue, J. Jin, Y. Wang, Z. Gao, Y. Janowitz, T. Meyer, H. V. Kucukural, A. Wilkinson, J. E. Ozata, D. M. Beyaz, S. 2022-03-27 doi:10.1101/2022.03.27.485965 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Cotranslational folding and assembly of the dimeric E. coli inner membrane protein EmrE ]]> https://biorxiv.org/content/10.1101/2022.04.02.486806v1?rss=1 Mermans, D. Nicolaus, F. Fleisch, K. von Heijne, G. 2022-04-02 doi:10.1101/2022.04.02.486806 Cold Spring Harbor Laboratory Press 2022-04-02 <![CDATA[ Single-cell transcriptomics to define Plasmodium falciparum stage-transition in the mosquito midgut ]]> https://biorxiv.org/content/10.1101/2022.04.05.487115v1?rss=1 Mohammed, M. Dziedziech, A. Sekar, V. Ernest, M. Alves E Silva, T. L. Balan, B. Emami, S. N. Biryukova, I. Friedlander, M. R. Jex, A. Jacobs-Lorena, M. Henriksson, J. Vega-Rodriguez, J. Ankarklev, J. 2022-04-05 doi:10.1101/2022.04.05.487115 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Differential interactions of resting, activated, and desensitized states of the α7 nicotinic acetylcholine receptor with lipidic modulators ]]> https://biorxiv.org/content/10.1101/2022.04.08.487470v1?rss=1 Zhuang, Y. Noviello, C. M. Hibbs, R. E. Howard, R. J. Lindahl, E. 2022-04-08 doi:10.1101/2022.04.08.487470 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ Effects of local versus global competition on reproductive skew and sex differences in social dominance behaviour ]]> https://biorxiv.org/content/10.1101/2022.04.13.488121v1?rss=1 Leimar, O. Bshary, R. 2022-04-14 doi:10.1101/2022.04.13.488121 Cold Spring Harbor Laboratory Press 2022-04-14 <![CDATA[ Structural basis of mammalian Complex IV inhibition by steroids ]]> https://biorxiv.org/content/10.1101/2022.04.13.488242v1?rss=1 Di Trani, J. Moe, A. Riepl, D. Saura, P. Kaila, V. R. I. Brzezinski, P. Rubinstein, J. L. 2022-04-14 doi:10.1101/2022.04.13.488242 Cold Spring Harbor Laboratory Press 2022-04-14 <![CDATA[ Redox-controlled structural reorganization and flavin strain within the ribonucleotide reductase R2b-NrdI complex monitored by serial femtosecond crystallography ]]> https://biorxiv.org/content/10.1101/2022.04.14.488295v1?rss=1 John, J. Aurelius, O. Srinivas, V. Kim, I.-S. Bhowmick, A. Simon, P. S. Dasgupta, M. Pham, C. Gul, S. Sutherlin, K. D. Aller, P. Butryn, A. Orville, A. M. Cheah, M. H. Owada, S. Tono, K. Fuller, F. D. Batyuk, A. Brewster, A. S. Sauter, N. K. Yachandra, V. K. Yano, J. Kern, J. Lebrette, H. Hogbom, M. 2022-04-14 doi:10.1101/2022.04.14.488295 Cold Spring Harbor Laboratory Press 2022-04-14 <![CDATA[ Different combinations of laccase paralogs non-redundantly control the lignin amount and composition of specific cell types and cell wall layers in Arabidopsis ]]> https://biorxiv.org/content/10.1101/2022.05.04.490011v1?rss=1 Blaschek, L. Murozuka, E. Menard, D. Pesquet, E. 2022-05-05 doi:10.1101/2022.05.04.490011 Cold Spring Harbor Laboratory Press 2022-05-05 <![CDATA[ Biophysical characterization of calcium-binding and modulatory-domain dynamics in a pentameric ligand-gated ion channel ]]> https://biorxiv.org/content/10.1101/2022.05.06.490775v1?rss=1 Lycksell, M. Rovsnik, U. Hanke, A. Martel, A. Howard, R. J. Lindahl, E. 2022-05-06 doi:10.1101/2022.05.06.490775 Cold Spring Harbor Laboratory Press 2022-05-06 <![CDATA[ Multi-Omic Integration by Machine Learning (MIMaL) Reveals Protein-Metabolite Connections and New Gene Functions ]]> https://biorxiv.org/content/10.1101/2022.05.11.491527v1?rss=1 Dickinson, Q. Aufschnaiter, A. Ott, M. Meyer, J. G. 2022-05-11 doi:10.1101/2022.05.11.491527 Cold Spring Harbor Laboratory Press 2022-05-11 <![CDATA[ Differential effect of Fas activation on spinal muscular atrophy motoneuron death and induction of axonal growth ]]> https://biorxiv.org/content/10.1101/2022.05.12.491475v1?rss=1 Benlefki, S. Younes, R. Challuau, D. Bernard-Marissal, N. Hilaire, C. Scamps, F. Bowerman, M. Kothary, R. Schneider, B. L. Raoul, C. 2022-05-16 doi:10.1101/2022.05.12.491475 Cold Spring Harbor Laboratory Press 2022-05-16 <![CDATA[ A survey of mapping algorithms in the long-reads era ]]> https://biorxiv.org/content/10.1101/2022.05.21.492932v1?rss=1 Sahlin, K. Baudeau, T. Cazaux, B. Marchet, C. 2022-05-22 doi:10.1101/2022.05.21.492932 Cold Spring Harbor Laboratory Press 2022-05-22 <![CDATA[ Gene losses resulting in specialized metabolism in the earliest divergent symbiotic Frankia clade can be linked to its low saprotrophic capabilities ]]> https://biorxiv.org/content/10.1101/2022.05.25.493452v1?rss=1 Berckx, F. Nguyen, T. V. Hilker, R. Wibberg, D. Battenberg, K. Kalinowski, J. Berry, A. M. Pawlowski, K. 2022-05-26 doi:10.1101/2022.05.25.493452 Cold Spring Harbor Laboratory Press 2022-05-26 <![CDATA[ Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level ]]> https://biorxiv.org/content/10.1101/2022.05.27.493681v1?rss=1 Gutierrez-Valencia, J. Fracassetti, M. Berdan, E. L. Bunikis, I. Soler, L. Dainat, J. Kutschera, V. E. Losvik, A. Desamore, A. Hughes, W. Foroozani, A. Laenen, B. Pesquet, E. Abdelaziz, M. Vinnere Pettersson, O. Nystedt, B. Brennan, A. Arroyo, J. Slotte, T. 2022-05-29 doi:10.1101/2022.05.27.493681 Cold Spring Harbor Laboratory Press 2022-05-29 <![CDATA[ Separation of transcriptional repressor and activator functions in HDAC3 ]]> https://biorxiv.org/content/10.1101/2022.06.11.495646v1?rss=1 Tang, M. Regadas, I. Belikov, S. Shilkova, O. Xu, L. Wernersson, E. Liu, X. Wu, H. Bienko, M. Mannervik, M. 2022-06-11 doi:10.1101/2022.06.11.495646 Cold Spring Harbor Laboratory Press 2022-06-11 <![CDATA[ Electrostatic features for the Receptor binding domain of SARS-COV-2 wildtype and its variants. Compass to the severity of the future variants with the charge rule. ]]> https://biorxiv.org/content/10.1101/2022.06.16.496458v1?rss=1 Barroso da Silva, F. L. Giron, C. C. Laaksonen, A. 2022-06-17 doi:10.1101/2022.06.16.496458 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Determinants of sugar-induced influx in the mammalian fructose transporter GLUT5 ]]> https://biorxiv.org/content/10.1101/2022.06.17.495601v1?rss=1 McComas, S. Mitrovic, D. Alleva, C. Bonaccorsi, M. Drew, D. Delemotte, L. 2022-06-18 doi:10.1101/2022.06.17.495601 Cold Spring Harbor Laboratory Press 2022-06-18 <![CDATA[ Optimizing insect metabarcoding using replicated mock communities ]]> https://biorxiv.org/content/10.1101/2022.06.20.496906v1?rss=1 Iwaszkiewicz-Eggebrecht, E. Granqvist, E. Buczek, M. Prus, M. Roslin, T. Tack, A. J. M. Andersson, A. F. Miraldo, A. Ronquist, F. Lukasik, P. 2022-06-22 doi:10.1101/2022.06.20.496906 Cold Spring Harbor Laboratory Press 2022-06-22 <![CDATA[ Linking microenvironment modification to species interactions and demography in an alpine plant community ]]> https://biorxiv.org/content/10.1101/2022.06.21.497097v1?rss=1 Ray, C. A. Kapas, R. E. Opedal, O. H. Blonder, B. W. 2022-06-26 doi:10.1101/2022.06.21.497097 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Increased glycolysis and functional mitochondria fuel acinar-ductal metaplasia in the pancreas ]]> https://biorxiv.org/content/10.1101/2022.06.27.495427v1?rss=1 Neuss, T. Wirges, N. Chen, M.-C. Usluer, S. Oellinger, R. Lier, S. Dudek, M. Madl, T. Jastroch, M. Steiger, K. Schmitz, W. Einwaechter, H. Schmid, R. M. 2022-06-29 doi:10.1101/2022.06.27.495427 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Autocrine Sfrp1 inhibits lung fibroblast invasion during transition to injury induced myofibroblasts ]]> https://biorxiv.org/content/10.1101/2022.07.11.499594v1?rss=1 Mayr, C. H. Sengupta, A. Ansari, M. Pestoni, J. Ogar, P. Angelidis, I. Liontos, A. Rodriguez, J. A. Lang, N. J. Strunz, M. Ashgarpour, S. Gonzalez, D. Gerckens, M. Oehrle, B. Viteri, V. Fernandez, I. Tallquist, M. V. Irmler, M. Beckers, J. Eickelberg, O. Stoleriu, G. M. Behr, J. Kneidinger, N. Yildirim, O. A. Ahlbrecht, K. Morty, R. Samakovlis, C. Theis, F. J. Burgstaller, G. Schiller, H. B. 2022-07-12 doi:10.1101/2022.07.11.499594 Cold Spring Harbor Laboratory Press 2022-07-12 <![CDATA[ Positive indirect effects more than balance negative direct effects of ungulate grazers on population growth of a grassland herb ]]> https://biorxiv.org/content/10.1101/2022.07.24.501324v1?rss=1 Richards, T. Thomann, M. Ehrlen, J. Agren, J. 2022-07-24 doi:10.1101/2022.07.24.501324 Cold Spring Harbor Laboratory Press 2022-07-24 <![CDATA[ Cold-induced expression of a truncated Adenylyl Cyclase 3 acts as rheostat to brown fat function. ]]> https://biorxiv.org/content/10.1101/2022.08.01.502156v1?rss=1 Khani, S. Topel, H. Josephrajan, A. Larsen, B. D. M. Tavanez, A. R. A. d. A. Gaudry, M. J. Leyendecker, P. Stanic, N. Gaziano, I. Hansmeier, N. R. Schmidt, E. Klemm, P. Vagliano, L.-M. Engelhard, C. A. Nielsen, S. Jespersen, N. Z. Rehimi, R. Gohlke, S. Frommolt, P. Gnad, T. Rada-Iglesias, A. Pradas-Juni, M. Schulz, T. J. Wunderlich, F. T. Pfeifer, A. Jastroch, M. Wachten, D. Kornfeld, J.-W. 2022-08-01 doi:10.1101/2022.08.01.502156 Cold Spring Harbor Laboratory Press 2022-08-01 <![CDATA[ Imputed genomes and haplotype-based analyses of the Picts of early medieval Scotland reveal fine-scale relatedness between Iron Age, early medieval and the modern people of the UK. ]]> https://biorxiv.org/content/10.1101/2022.08.01.502257v1?rss=1 8,300 previously published ancient and modern genomes. Using allele frequency and haplotype-based approaches, we can firmly place the Pictish genomes within the Iron Age gene pool in Britain and demonstrate local biological affinity. We also demonstrate the presence of population structure within Pictish groups, with Orcadian Picts being genetically distinct from their mainland contemporaries. When investigating Identity-By-Descent (IBD) with present-day genomes, we observe broad affinities between the mainland Pictish genomes and the present-day people living in western Scotland, Wales, Northern Ireland and Northumbria, but less with the rest of England, the Orkney islands and eastern Scotland - where the political centres of Pictland were located. The pre-Viking Age Orcadian Picts evidence a high degree of IBD sharing across modern Scotland, Wales, Northern Ireland, and the Orkney islands, demonstrating substantial genetic continuity in the Orkney for the last ~2,000 years. Analysis of mitochondrial DNA diversity at the Pictish cemetery of Lundin Links (n = 7) reveals absence of female endogamy, with implications for broader social organisation. Overall, our study provides novel insights into the genetic affinities and population structure of the Picts and direct relationships between ancient and present-day groups of the UK. ]]> Morez, A. Britton, K. Noble, G. Günther, T. Götherström, A. Rodriguez-Varela, R. Kashuba, N. Martiniano, R. Talamo, S. Evans, N. J. Irish, J. D. Donald, C. Girdland Flink, L. 2022-08-03 doi:10.1101/2022.08.01.502257 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ Cotranslational folding of human growth hormone in vitro and in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2022.08.08.503169v1?rss=1 Mermans, D. Nicolaus, F. Baygin, A. von Heijne, G. 2022-08-08 doi:10.1101/2022.08.08.503169 Cold Spring Harbor Laboratory Press 2022-08-08 <![CDATA[ ENGRAILED-1 transcription factor exerts a paracrine neurotrophic activity on adult spinal cord α-motoneurons. ]]> https://biorxiv.org/content/10.1101/2022.08.16.504081v1?rss=1 Leboeuf, M. Vargas-Abonce, S. E. Peze-Hedsieck, E. Dupont, E. Jimenez-Alonso, L. MOYA, K. L. Prochiantz, A. 2022-08-16 doi:10.1101/2022.08.16.504081 Cold Spring Harbor Laboratory Press 2022-08-16 <![CDATA[ Probe set selection for targeted spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2022.08.16.504115v1?rss=1 Kuemmerle, L. B. Luecken, M. D. Firsova, A. B. Barros de Andrade e Sousa, L. Strasser, L. Heumos, L. Mekki, I. I. Mahbubani, K. T. Sountoulidis, A. Balassa, T. Kovacs, F. Horvath, P. Piraud, M. Erturk, A. Samakovlis, C. Theis, F. J. 2022-08-17 doi:10.1101/2022.08.16.504115 Cold Spring Harbor Laboratory Press 2022-08-17 <![CDATA[ Chitinase-like protein promotes tumorigenesis through disruption of cell polarity via enlarged vesicles. ]]> https://biorxiv.org/content/10.1101/2022.08.17.504232v1?rss=1 Khalili, D. Kunc, M. Herbrich, S. Mueller, A. M. Theopold, U. 2022-08-17 doi:10.1101/2022.08.17.504232 Cold Spring Harbor Laboratory Press 2022-08-17 <![CDATA[ Microchip-based electrokinetic biosensor: microfabrication and application in membrane protein profiling of extracellular vesicles ]]> https://biorxiv.org/content/10.1101/2022.08.17.504250v1?rss=1 Talebian Gevari, M. Sahu, S. S. Mitra, D. Haag, P. Viktorsson, K. Zhang, S. Linnros, J. Dev, A. 2022-08-17 doi:10.1101/2022.08.17.504250 Cold Spring Harbor Laboratory Press 2022-08-17 <![CDATA[ A scenario-guided strategy for the future management of biological invasions ]]> https://biorxiv.org/content/10.1101/2022.09.07.506838v1?rss=1 Roura-Pascual, N. Saul, W.-C. Perez-Granados, C. Rutting, L. Peterson, G. D. Latombe, G. Essl, F. Adriaens, T. Aldridge, D. C. Bacher, S. Bernardo-Madrid, R. Brotons, L. Diaz, F. Gallardo, B. Genovesi, P. Golivets, M. Gonzalez-Moreno, P. Hall, M. Kutlesa, P. Lenzner, B. Liu, C. Pagitz, K. Pastor, T. Rabitsch, W. Robertson, P. Roy, H. E. Seebens, H. Solarz, W. Starfinger, U. Tanner, R. Vila, M. Leung, B. Garcia-Lozano, C. Jeschke, J. M. 2022-09-08 doi:10.1101/2022.09.07.506838 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ Diversification of neuropil organization in specialized and broadly tuned olfactory glomerular circuits in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2022.09.30.510181v1?rss=1 Gruber, L. Cantera, R. Pleijzier, M. W. Hansson, B. S. Rybak, J. 2022-10-02 doi:10.1101/2022.09.30.510181 Cold Spring Harbor Laboratory Press 2022-10-02 <![CDATA[ Contrasting genomic consequences of anthropogenic reintroduction and natural recolonisation in high-arctic wild reindeer ]]> https://biorxiv.org/content/10.1101/2022.11.25.517957v1?rss=1 Burnett, H. A. Bieker, V. C. Le Moullec, M. Peeters, B. Rosvold, J. Pedersen, A. O. Dalen, L. Loe, L. E. Jensen, H. Hansen, B. B. Martin, M. D. 2022-11-27 doi:10.1101/2022.11.25.517957 Cold Spring Harbor Laboratory Press 2022-11-27 <![CDATA[ A versatile synaptotagmin-1 nanobody provides perturbation-free live synaptic imaging and low linkage-error in super-resolution microscopy ]]> https://biorxiv.org/content/10.1101/2023.01.30.525828v1?rss=1 Queiroz Zetune Villa Real, K. Mougios, N. Rehm, R. Sograte-Idrissi, S. Albert, L. Rahimi, A. M. Maidorn, M. Martinez-Carranza, M. Hosseini, H. Saal, K. A. Oleksiievets, N. Prigge, M. Tsukanov, R. Stenmark, P. Fornasiero, E. F. Opazo, F. 2023-02-01 doi:10.1101/2023.01.30.525828 Cold Spring Harbor Laboratory Press 2023-02-01 <![CDATA[ phylopath: Easy phylogenetic path analysis in R. ]]> https://biorxiv.org/content/10.1101/212068v1?rss=1 van der Bijl, W. 2017-10-31 doi:10.1101/212068 Cold Spring Harbor Laboratory Press 2017-10-31 <![CDATA[ Competitive ability of a tetraploid selfing species (Capsella bursa-pastoris) across its expansion range and comparison with its sister species ]]> https://biorxiv.org/content/10.1101/214866v1?rss=1 Yang, X. Lascoux, M. Glemin, S. 2017-11-06 doi:10.1101/214866 Cold Spring Harbor Laboratory Press 2017-11-06 <![CDATA[ A butterfly chromonome reveals selection dynamics during extensive and cryptic chromosomal reshuffling ]]> https://biorxiv.org/content/10.1101/233700v1?rss=1 Hill, J. A. Neethiraj, R. Rastas, P. Clark, N. Morehouse, N. Celorio, M. Cols, J. C. Dircksen, H. Meslin, C. Sikkink, K. Vives, M. Vogel, H. Wiklund, C. Kingsolver, J. Boggs, C. Nylin, S. Wheat, C. 2017-12-13 doi:10.1101/233700 Cold Spring Harbor Laboratory Press 2017-12-13 <![CDATA[ The Viral protein Corona Directs Viral Pathogenesis and Amyloid Aggregation ]]> https://biorxiv.org/content/10.1101/246785v1?rss=1 Ezzat, K. Pernemalm, M. Palsson, S. Roberts, T. C. Jarver, P. Dondalska, A. Bestas, B. Sobkowiak, M. J. Levanen, B. Skold, M. Thompson, E. A. Wood, M. J. A. Power, U. F. Masich, S. Linden, A. Sandberg, J. K. Lehtio, J. Spetz, A.-L. Andaloussi, S. E. 2018-01-16 doi:10.1101/246785 Cold Spring Harbor Laboratory Press 2018-01-16 <![CDATA[ The Folding Pathway of an Ig Domain is Conserved On and Off the Ribosome ]]> https://biorxiv.org/content/10.1101/253013v1?rss=1 Tian, P. Steward, A. Kudva, R. Su, T. Shilling, P. J. Nickson, A. A. Hollins, J. J. Beckmann, R. Von Heijne, G. Best, R. Clarke, J. 2018-01-24 doi:10.1101/253013 Cold Spring Harbor Laboratory Press 2018-01-24 <![CDATA[ Cotranslational folding of a pentarepeat β-helix protein ]]> https://biorxiv.org/content/10.1101/255810v1?rss=1 Notari, L. Martinez-Carranza, M. Stenmark, P. Von Heijne, G. 2018-01-29 doi:10.1101/255810 Cold Spring Harbor Laboratory Press 2018-01-29 <![CDATA[ The Shape of the Ribosome Exit Tunnel Affects Cotranslational Protein Folding ]]> https://biorxiv.org/content/10.1101/274191v1?rss=1 Kudva, R. Pardo-Avila, F. Sandhu, H. Carroni, M. Bernstein, H. D. Von Heijne, G. 2018-03-01 doi:10.1101/274191 Cold Spring Harbor Laboratory Press 2018-03-01 <![CDATA[ Mercury-methylating bacteria are associated with zooplankton: a proof-of-principle survey in the Baltic Sea ]]> https://biorxiv.org/content/10.1101/279976v1?rss=1 Gorokhova, E. Soerensen, A. L. Motwani, N. H. 2018-03-12 doi:10.1101/279976 Cold Spring Harbor Laboratory Press 2018-03-12 <![CDATA[ Measuring Endoplasmic Reticulum Signal Sequences Translocation Efficiency Using the Xbp1 Arrest Peptide ]]> https://biorxiv.org/content/10.1101/281535v1?rss=1 Kriegler, T. Magoulopoulou, A. Amate Marchal, R. Hessa, T. 2018-03-14 doi:10.1101/281535 Cold Spring Harbor Laboratory Press 2018-03-14 <![CDATA[ Imaging the evolution of visual specializations in fungus gnats ]]> https://biorxiv.org/content/10.1101/290841v1?rss=1 Taylor, G. J. Hall, S. A. Gren, J. A. Baird, E. 2018-03-28 doi:10.1101/290841 Cold Spring Harbor Laboratory Press 2018-03-28 <![CDATA[ Ecological genetic conflict between specialism and plasticity through genomic islands of divergence ]]> https://biorxiv.org/content/10.1101/298554v1?rss=1 Leimar, O. Dall, S. R. X. McNamara, J. M. Kuijper, B. Hammerstein, P. 2018-04-11 doi:10.1101/298554 Cold Spring Harbor Laboratory Press 2018-04-11 <![CDATA[ Revisiting the social brain hypothesis: contest duration depends on loser’s brain size ]]> https://biorxiv.org/content/10.1101/300335v1?rss=1 van der Bijl, W. Buechel, S. D. Kotrschal, A. Kolm, N. 2018-04-12 doi:10.1101/300335 Cold Spring Harbor Laboratory Press 2018-04-12 <![CDATA[ Effects of protein size, thermodynamic stability, and net charge on cotranslational folding on the ribosome ]]> https://biorxiv.org/content/10.1101/303784v1?rss=1 Farias-Rico, J. A. Ruud Selin, F. Myronidi, I. Von Heijne, G. 2018-04-18 doi:10.1101/303784 Cold Spring Harbor Laboratory Press 2018-04-18 <![CDATA[ Intersection of phosphate transport, oxidative stress and TOR signalling in Candida albicans virulence ]]> https://biorxiv.org/content/10.1101/317933v1?rss=1 Liu, N.-N. Uppuluri, P. Broggi, A. Besold, A. Ryman, K. Kambara, H. Solis, N. Lorenz, V. Qi, W. Acosta Zaldivar, M. Emami, S. N. Bao, B. An, D. Bonilla, F. Sola-Visner, M. Filler, S. Luo, H. R. Engstrom, Y. Ljungdahl, P. O. Culotta, V. C. Zanoni, I. Lopez-Ribot, J. L. Koehler, J. R. 2018-05-11 doi:10.1101/317933 Cold Spring Harbor Laboratory Press 2018-05-11 <![CDATA[ Genetic insight into zinc and antimicrobial toxicity uncovers a glycerol phosphate modification on streptococcal rhamnose polysaccharides ]]> https://biorxiv.org/content/10.1101/337519v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@6d7598org.highwire.dtl.DTLVardef@435695org.highwire.dtl.DTLVardef@e9515corg.highwire.dtl.DTLVardef@1dc78b7_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Edgar, R. J. van Hensbergen, V. P. Ruda, A. Turner, A. Deng, P. Le Breton, Y. El-Sayed, N. M. Belew, A. T. McIver, K. S. McEwan, A. G. Morris, A. J. Lambeau, G. Walker, M. J. Rush, J. S. Korotkov, K. V. Widmalm, G. van Sorge, N. M. Korotkova, N. 2018-06-04 doi:10.1101/337519 Cold Spring Harbor Laboratory Press 2018-06-04 <![CDATA[ Getting more from heterogeneous HIV-1 surveillance data in a high immigration country: estimation of incidence and undiagnosed population size using multiple biomarkers ]]> https://biorxiv.org/content/10.1101/345710v1?rss=1 Giardina, F. Romero-Severson, E. Axelsson, M. Svedhem, V. Leitner, T. Britton, T. Albert, J. 2018-06-17 doi:10.1101/345710 Cold Spring Harbor Laboratory Press 2018-06-17 <![CDATA[ Metal-independent ribonucleotide reduction powered by a DOPA radical in Mycoplasma pathogens ]]> https://biorxiv.org/content/10.1101/348268v1?rss=1 Srinivas, V. Lebrette, H. Lundin, D. Kutin, Y. Sahlin, M. Lerche, M. Eirich, J. Branca, R. Cox, N. Sjöberg, B.-M. Högbom, M. 2018-06-15 doi:10.1101/348268 Cold Spring Harbor Laboratory Press 2018-06-15 <![CDATA[ Orchestration of Drosophila post-feeding physiology and behavior by the neuropeptide leucokinin ]]> https://biorxiv.org/content/10.1101/355107v1?rss=1 Zandawala, M. Yurgel, M. E. Liao, S. Texada, M. J. Rewitz, K. F. Keene, A. C. Nassel, D. R. 2018-06-26 doi:10.1101/355107 Cold Spring Harbor Laboratory Press 2018-06-26 <![CDATA[ Hydrophobic organic contaminants are not linked to microplastic uptake in Baltic Sea herring ]]> https://biorxiv.org/content/10.1101/363127v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@4cb5b6org.highwire.dtl.DTLVardef@2de3c8org.highwire.dtl.DTLVardef@c58baborg.highwire.dtl.DTLVardef@154b828_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ogonowski, M. Wenman, V. Danielsson, S. Gorokhova, E. 2018-07-06 doi:10.1101/363127 Cold Spring Harbor Laboratory Press 2018-07-06 <![CDATA[ Fusion of a functional glutaredoxin to the radical-generating subunit of ribonucleotide reductase ]]> https://biorxiv.org/content/10.1101/373563v1?rss=1 Rozman Grinberg, I. Lundin, D. Sahlin, M. Crona, M. Berggren, G. Hofer, A. Sjöberg, B.-M. 2018-07-20 doi:10.1101/373563 Cold Spring Harbor Laboratory Press 2018-07-20 <![CDATA[ Mitochondrial proline catabolism activates Ras1/cAMP/PKA-induced filamentation in Candida albicans ]]> https://biorxiv.org/content/10.1101/374777v1?rss=1 Silao, F. G. S. Ward, M. Ryman, K. Wallstrom, A. Brindefalk, B. Udekwu, K. Ljungdahl, P. O. 2018-07-23 doi:10.1101/374777 Cold Spring Harbor Laboratory Press 2018-07-23 <![CDATA[ Hierarchical multiscale simulation of DNA condensation ]]> https://biorxiv.org/content/10.1101/375626v1?rss=1 Sun, T. Mirzoev, A. Korolev, N. Lyubartsev, A. P. Nordenskioeld, L. 2018-07-24 doi:10.1101/375626 Cold Spring Harbor Laboratory Press 2018-07-24 <![CDATA[ Drosophila insulin-like peptide dilp1 increases lifespan and glucagon-like Akh expression epistatic to dilp2 ]]> https://biorxiv.org/content/10.1101/380410v1?rss=1 Post, S. Liao, S. Yamamoto, R. Vennstra, J. A. Nässel, D. R. Tatar, M. 2018-07-30 doi:10.1101/380410 Cold Spring Harbor Laboratory Press 2018-07-30 <![CDATA[ A serial dilution method for assessment of microplastic toxicity in suspension ]]> https://biorxiv.org/content/10.1101/401331v1?rss=1 nView larger version (40K):norg.highwire.dtl.DTLVardef@13e1153org.highwire.dtl.DTLVardef@1e37652org.highwire.dtl.DTLVardef@6d3efborg.highwire.dtl.DTLVardef@420d7a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gerdes, Z. Hermann, M. Ogonowski, M. Gorokhova, E. 2018-08-27 doi:10.1101/401331 Cold Spring Harbor Laboratory Press 2018-08-27 <![CDATA[ Dogs, but not wolves, lose their sensitivity towards novelty with age ]]> https://biorxiv.org/content/10.1101/405480v1?rss=1 Hansen Wheat, C. van der Bijl, W. Temrin, H. 2018-08-31 doi:10.1101/405480 Cold Spring Harbor Laboratory Press 2018-08-31 <![CDATA[ Alterations in swimming behavior of Daphnia exposed to polymer and mineral particles: towards understanding effects of microplastics on planktonic filtrators ]]> https://biorxiv.org/content/10.1101/406587v1?rss=1 Gorokhova, E. Konnecke, O. Ogonowski, M. Gerdes, Z. Eriksson Wiklund, A.-K. 2018-09-03 doi:10.1101/406587 Cold Spring Harbor Laboratory Press 2018-09-03 <![CDATA[ Viewing pictures triggers rapid morphological enlargement in the human visual cortex ]]> https://biorxiv.org/content/10.1101/408658v1?rss=1 Mansson, K. N. T. Cortes, D. S. Manzouri, A. Hau, S. Fischer, H. 2018-09-05 doi:10.1101/408658 Cold Spring Harbor Laboratory Press 2018-09-05 <![CDATA[ Drosophila insulin-like peptide 1 (DILP1) promotes organismal growth during non-feeding stages ]]> https://biorxiv.org/content/10.1101/421669v1?rss=1 Liao, S. Post, S. Veenstra, J. A. Tatar, M. Nassel, D. R. 2018-09-19 doi:10.1101/421669 Cold Spring Harbor Laboratory Press 2018-09-19 <![CDATA[ Sexual selection rewires reproductive protein networks ]]> https://biorxiv.org/content/10.1101/422410v1?rss=1 Karr, T. Southern, H. Rosenow, M. A. Gossmann, T. I. Snook, R. R. 2018-09-21 doi:10.1101/422410 Cold Spring Harbor Laboratory Press 2018-09-21 <![CDATA[ Genetic basis and timing of a major mating system shift in Capsella ]]> https://biorxiv.org/content/10.1101/425389v1?rss=1 Bachmann, J. A. Tedder, A. Laenen, B. Fracassetti, M. Desamore, A. Lafon-Placette, C. Steige, K. A. Callot, C. Marande, W. Neuffer, B. Berges, H. Köhler, C. Castric, V. Slotte, T. 2018-09-24 doi:10.1101/425389 Cold Spring Harbor Laboratory Press 2018-09-24 <![CDATA[ Complex responses of global insect pests to climate change ]]> https://biorxiv.org/content/10.1101/425488v1?rss=1 Lehmann, P. Ammunet, T. Barton, M. Battisti, A. Eigenbrode, S. D. Jepsen, J. U. Kalinkat, G. Neuvonen, S. Niemela, P. Okland, B. Terblanche, J. S. Bjorkman, C. 2018-09-24 doi:10.1101/425488 Cold Spring Harbor Laboratory Press 2018-09-24 <![CDATA[ Microplastic-mediated transport of PCBs? A depuration study with Daphnia magna ]]> https://biorxiv.org/content/10.1101/428151v1?rss=1 Gerdes, Z. Ogonowski, M. Nybom, I. Ek, C. Adolfsson-Erici, M. Barth, A. Gorokhova, E. 2018-09-26 doi:10.1101/428151 Cold Spring Harbor Laboratory Press 2018-09-26 <![CDATA[ Is there a BMAA transfer in the pelagic and benthic food webs in the Baltic Sea? ]]> https://biorxiv.org/content/10.1101/430330v1?rss=1 Zguna, N. Karlson, A. Ilag, L. L. Garbaras, A. Gorokhova, E. 2018-09-29 doi:10.1101/430330 Cold Spring Harbor Laboratory Press 2018-09-29 <![CDATA[ NanoJ: a high-performance open-source super-resolution microscopy toolbox ]]> https://biorxiv.org/content/10.1101/432674v1?rss=1 Laine, R. Tosheva, K. Gustafsson, N. Gray, R. D. M. Almada, P. Albrecht, D. Risa, G. T. Hurtig, F. Lindas, A.-C. Baum, B. Mercer, J. Leterrier, C. Pereira, P. M. Culley, S. Henriques, R. 2018-10-01 doi:10.1101/432674 Cold Spring Harbor Laboratory Press 2018-10-01 <![CDATA[ Using micro-CT techniques to explore the role of sex and hair in the functional morphology of bumblebee (Bombus terrestris) ocelli ]]> https://biorxiv.org/content/10.1101/433979v1?rss=1 Wilby, D. Aarts, T. Tichit, P. Bodey, A. Rau, C. Taylor, G. Baird, E. 2018-10-03 doi:10.1101/433979 Cold Spring Harbor Laboratory Press 2018-10-03 <![CDATA[ Growth-driven displacement of protein aggregates along the cell length ensures partitioning to both daughter cells in Caulobacter crescentus ]]> https://biorxiv.org/content/10.1101/436394v1?rss=1 Schramm, F. D. Schroeder, K. Alvelid, J. Testa, I. Jonas, K. 2018-10-05 doi:10.1101/436394 Cold Spring Harbor Laboratory Press 2018-10-05 <![CDATA[ Social learning through associative processes: A computational theory ]]> https://biorxiv.org/content/10.1101/446906v1?rss=1 Lind, J. Ghirlanda, S. Enquist, M. 2018-10-18 doi:10.1101/446906 Cold Spring Harbor Laboratory Press 2018-10-18 <![CDATA[ Ecosystem tipping points in an evolving world ]]> https://biorxiv.org/content/10.1101/447227v1?rss=1 Dakos, V. Matthews, B. Hendry, A. Levine, J. Loeuille, N. Norberg, J. Nosil, P. Scheffer, M. De Meester, L. 2018-10-24 doi:10.1101/447227 Cold Spring Harbor Laboratory Press 2018-10-24 <![CDATA[ Whatever You Want: Inconsistent Results Is The Rule, Not The Exception, In The Study Of Primate Brain Evolution ]]> https://biorxiv.org/content/10.1101/454132v1?rss=1 Wartel, A. Lindenfors, P. Lind, J. 2018-10-26 doi:10.1101/454132 Cold Spring Harbor Laboratory Press 2018-10-26 <![CDATA[ Dynamic modelling of hepatitis C transmission among people who inject drugs: A tool to support WHO elimination targets ]]> https://biorxiv.org/content/10.1101/460550v1?rss=1 Stocks, T. J. S. Martin, L. J. Kühlmann-Berenzon, S. Britton, T. 2018-11-08 doi:10.1101/460550 Cold Spring Harbor Laboratory Press 2018-11-08 <![CDATA[ Ensemble projections of global ocean animal biomass with climate change ]]> https://biorxiv.org/content/10.1101/467175v1?rss=1 Lotze, H. K. Tittensor, D. P. Bryndum-Buchholz, A. Eddy, T. D. Cheung, W. W. Galbraith, E. D. Barange, M. Barrier, N. Bianchi, D. Blanchard, J. L. Bopp, L. Buechner, M. Bulman, C. Carozza, D. A. Christensen, V. Coll, M. Dunne, J. Fulton, E. A. Jennings, S. Jones, M. Mackinson, S. Maury, O. Niiranen, S. Oliveros-Ramos, R. Roy, T. Fernandes, J. A. Schewe, J. Shin, Y.-J. Silva, T. A. Steenbeek, J. Stock, C. A. Verley, P. Volkholz, J. Walker, N. D. 2018-11-09 doi:10.1101/467175 Cold Spring Harbor Laboratory Press 2018-11-09 <![CDATA[ Force-profile analysis of the cotranslational folding of HemK and filamin domains: Comparison of biochemical and biophysical folding assays ]]> https://biorxiv.org/content/10.1101/470831v1?rss=1 Kemp, G. Kudva, R. de la Rosa, A. von Heijne, G. 2018-11-15 doi:10.1101/470831 Cold Spring Harbor Laboratory Press 2018-11-15 <![CDATA[ Long-term balancing selection drives evolution of immunity genes in Capsella ]]> https://biorxiv.org/content/10.1101/477612v1?rss=1 Koenig, D. Hagmann, J. Li, R. Bemm, F. Slotte, T. Nueffer, B. Wright, S. Weigel, D. 2018-11-26 doi:10.1101/477612 Cold Spring Harbor Laboratory Press 2018-11-26 <![CDATA[ Astrotactins 1 and 2 have similar membrane topology and mature via endoproteolytic cleavage catalyzed by signal peptidase ]]> https://biorxiv.org/content/10.1101/493858v1?rss=1 Lara, P. Tellgren-Roth, A. Behesti, H. Horn, Z. Schiller, N. Enquist, K. Cammenberg, M. Liljenström, A. Hatten, M. E. Von Heijne, G. Nilsson, I. 2018-12-11 doi:10.1101/493858 Cold Spring Harbor Laboratory Press 2018-12-11 <![CDATA[ Conformational changes in Apolipoprotein N-acyltransferase (Lnt) ]]> https://biorxiv.org/content/10.1101/497412v1?rss=1 nView larger version (55K):norg.highwire.dtl.DTLVardef@318596org.highwire.dtl.DTLVardef@139463corg.highwire.dtl.DTLVardef@13213ecorg.highwire.dtl.DTLVardef@ba011b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Wiseman, B. Hogbom, M. 2018-12-16 doi:10.1101/497412 Cold Spring Harbor Laboratory Press 2018-12-16 <![CDATA[ Generation of Transgenic Human Malaria Parasites With Strong Fluorescence in the Transmission Stages ]]> https://biorxiv.org/content/10.1101/500793v1?rss=1 McLean, K. J. Straimer, J. Hopp, C. S. Vega-Rodriguez, J. Tripathi, A. Mlambo, G. Doumolin, P. C. Harris, C. T. Tong, X. Shears, M. J. Ankarklev, J. Kafsack, B. Fidock, D. A. Sinnis, P. 2018-12-18 doi:10.1101/500793 Cold Spring Harbor Laboratory Press 2018-12-18 <![CDATA[ Increase in stable isotope ratios driven by metabolic alterations in amphipods exposed to the beta-blocker propranolol ]]> https://biorxiv.org/content/10.1101/520205v1?rss=1 Ek, C. Yu, Z. Garbaras, A. Oskarsson, H. Wiklund, A.-K. E. Kumblad, L. Gorokhova, E. 2019-01-14 doi:10.1101/520205 Cold Spring Harbor Laboratory Press 2019-01-14 <![CDATA[ Corazonin neuroendocrine pathway orchestrates stress-associated physiology in Drosophila ]]> https://biorxiv.org/content/10.1101/522441v1?rss=1 Zandawala, M. Nguyen, T. Johard, H. Amcoff, M. Paluzzi, J.-P. Nassel, D. R. 2019-01-16 doi:10.1101/522441 Cold Spring Harbor Laboratory Press 2019-01-16 <![CDATA[ Dynamic membrane topology in an unassembled membrane protein ]]> https://biorxiv.org/content/10.1101/548537v1?rss=1 Seurig, M. Ek, M. Von Heijne, G. Fluman, N. 2019-02-13 doi:10.1101/548537 Cold Spring Harbor Laboratory Press 2019-02-13 <![CDATA[ Developmental plasticity in metabolism but not in energy reserve accumulation in a seasonally polyphenic butterfly ]]> https://biorxiv.org/content/10.1101/556969v1?rss=1 Kivelä, S. Gotthard, K. Lehmann, P. 2019-02-21 doi:10.1101/556969 Cold Spring Harbor Laboratory Press 2019-02-21 <![CDATA[ PRDM16 establishes lineage-specific transcriptional program to promote temporal progression of neural progenitors in the mouse neocortex ]]> https://biorxiv.org/content/10.1101/573857v1?rss=1 He, L. Jones, J. He, W. Bjork, B. Wen, J. Dai, Q. 2019-03-11 doi:10.1101/573857 Cold Spring Harbor Laboratory Press 2019-03-11 <![CDATA[ Supramodal sentence processing in the human brain: fMRI evidence for the influence of syntactic complexity in more than 200 participants ]]> https://biorxiv.org/content/10.1101/576769v1?rss=1 Udden, J. Hulten, A. Schoffelen, J. M. Lam, N. Harbusch, K. van den Bosch, A. Kempen, G. Petersson, K. M. Hagoort, P. 2019-03-14 doi:10.1101/576769 Cold Spring Harbor Laboratory Press 2019-03-14 <![CDATA[ Structural basis for the delivery of activated sialic acid into Golgi for sialyation ]]> https://biorxiv.org/content/10.1101/580449v1?rss=1 Nji, E. Gulati, A. Qureshi, A. A. Coincon, M. Drew, D. 2019-03-17 doi:10.1101/580449 Cold Spring Harbor Laboratory Press 2019-03-17 <![CDATA[ Disparate effects of antibiotic-induced microbiome change and enhanced fitness in Daphnia magna ]]> https://biorxiv.org/content/10.1101/586669v1?rss=1 Motiei, A. Brindefalk, B. Ogonowski, M. El-Shehawy, R. Pastuszek, P. Ek, K. Liewenborg, B. Udekwu, K. Gorokhova, E. 2019-03-22 doi:10.1101/586669 Cold Spring Harbor Laboratory Press 2019-03-22 <![CDATA[ Structural and mutational analysis of the ribosome-arresting human XBP1u ]]> https://biorxiv.org/content/10.1101/588681v1?rss=1 Shanmuganathan, V. Schiller, N. Magoulopoulou, A. Cheng, J. Braunger, K. Cymer, F. Berninghausen, O. Beatrix, B. Kohno, K. Heijne, G. v. Beckmann, R. 2019-03-25 doi:10.1101/588681 Cold Spring Harbor Laboratory Press 2019-03-25 <![CDATA[ BEN-solo factors partition active chromatin to ensure proper gene activation in Drosophila ]]> https://biorxiv.org/content/10.1101/593830v1?rss=1 Ueberschar, M. Wang, H. Zhang, C. Guo, E. Lai, E. Wen, J. Dai, Q. 2019-03-31 doi:10.1101/593830 Cold Spring Harbor Laboratory Press 2019-03-31 <![CDATA[ DNA epigenetic marks are linked to reproductive aberrations in amphipods ]]> https://biorxiv.org/content/10.1101/594788v1?rss=1 Gorokhova, E. Martella, G. Motwani, N. H. Tretyakova, N. Y. Sundelin, B. Motwani, H. V. 2019-03-31 doi:10.1101/594788 Cold Spring Harbor Laboratory Press 2019-03-31 <![CDATA[ Solving the first novel protein structure by 3D micro-crystal electron diffraction ]]> https://biorxiv.org/content/10.1101/600387v1?rss=1 Xu, H. Lebrette, H. Clabbers, M. T. B. Zhao, J. Griese, J. Zou, X. Hogbom, M. 2019-04-05 doi:10.1101/600387 Cold Spring Harbor Laboratory Press 2019-04-05 <![CDATA[ Environmental variation mediates the evolution of anticipatory parental effects ]]> https://biorxiv.org/content/10.1101/606103v1?rss=1 Lind, M. I. Zwoinska, M. K. Andersson, J. Carlsson, H. Krieg, T. Larva, T. Maklakov, A. A. 2019-04-18 doi:10.1101/606103 Cold Spring Harbor Laboratory Press 2019-04-18 <![CDATA[ Recombining your way out of trouble: The genetic architecture of hybrid fitness under environmental stress ]]> https://biorxiv.org/content/10.1101/622845v1?rss=1 Zhang, Z. Bendixsen, D. Janzen, T. Nolte, A. Greig, D. Stelkens, R. 2019-04-30 doi:10.1101/622845 Cold Spring Harbor Laboratory Press 2019-04-30 <![CDATA[ Detecting Novel Sequence Signals in Targeting Peptides Using Deep Learning ]]> https://biorxiv.org/content/10.1101/639203v1?rss=1 Almagro Armenteros, J. J. Salvatore, M. Winther, O. Emanuelsson, O. von Heijne, G. Elofsson, A. Nielsen, H. 2019-05-17 doi:10.1101/639203 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ A rationally designed and highly versatile epitope tag for nanobody-based purification, detection and manipulation of proteins ]]> https://biorxiv.org/content/10.1101/640771v1?rss=1 Goetzke, H. Kilisch, M. Martinez-Carranza, M. Sograte-Idrissi, S. Rajavel, A. Schlichthaerle, T. Engels, N. Jungmann, R. Stenmark, P. Opazo, F. Frey, S. 2019-05-17 doi:10.1101/640771 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ Mutators drive evolution of multi-resistance to antibiotics ]]> https://biorxiv.org/content/10.1101/643585v1?rss=1 Gifford, D. R. Berrios, E. Joerres, C. Galla, T. Knight, C. G. 2019-05-21 doi:10.1101/643585 Cold Spring Harbor Laboratory Press 2019-05-21 <![CDATA[ Cotranslational folding cooperativity of contiguous domains of α-spectrin ]]> https://biorxiv.org/content/10.1101/653360v1?rss=1 Kemp, G. Nilsson, O. B. Tian, P. Best, R. B. Von Heijne, G. 2019-05-29 doi:10.1101/653360 Cold Spring Harbor Laboratory Press 2019-05-29 <![CDATA[ Membrane integration and topology of RIFIN and STEVOR proteins of the Plasmodium falciparum parasite ]]> https://biorxiv.org/content/10.1101/653998v1?rss=1 Andersson, A. Kudva, R. Magoulopoulou, A. Lejarre, Q. Lara, P. Xu, P. Goel, S. Pissi, J. Ru, X. Hessa, T. Wahlgren, M. Von Heijne, G. Nilsson, I. Tellgren-Roth, A. 2019-05-29 doi:10.1101/653998 Cold Spring Harbor Laboratory Press 2019-05-29 <![CDATA[ Dogs defy the domestication syndrome: morphology does not covary with predicted behavioural correlations within dog breeds ]]> https://biorxiv.org/content/10.1101/660829v1?rss=1 Hansen Wheat, C. van der Bijl, W. Wheat, C. W. 2019-06-10 doi:10.1101/660829 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ Species-specific recognition of Sulfolobales mediated by UV inducible pili and S-layer glycosylation patterns ]]> https://biorxiv.org/content/10.1101/663898v1?rss=1 van Wolferen, M. Shajahan, A. Heinrich, K. Brenziger, S. Black, I. Wagner, A. Briegel, A. Azadi, P. Albers, S.-V. 2019-06-08 doi:10.1101/663898 Cold Spring Harbor Laboratory Press 2019-06-08 <![CDATA[ A simple pressure-assisted method for cryo-EM specimen preparation ]]> https://biorxiv.org/content/10.1101/665448v1?rss=1 Zhao, J. Xu, H. Carroni, M. Lebrette, H. Wallden, K. Moe, A. Matsuoka, R. Hogbom, M. Zou, X. 2019-06-10 doi:10.1101/665448 Cold Spring Harbor Laboratory Press 2019-06-10 <![CDATA[ Bayesian inference of ancestral host-parasite interactions under a phylogenetic model of host repertoire evolution ]]> https://biorxiv.org/content/10.1101/675017v1?rss=1 Braga, M. P. Landis, M. J. Nylin, S. Janz, N. Ronquist, F. 2019-06-18 doi:10.1101/675017 Cold Spring Harbor Laboratory Press 2019-06-18 <![CDATA[ Depression, GABA and age correlate with the plasma levels of inflammatory markers. ]]> https://biorxiv.org/content/10.1101/689984v1?rss=1 Bhandage, A. K. Cunningham, J. L. Jin, Z. Shhen, Q. Bongiovanni, S. Korol, S. V. Syk, M. Kamali-Moghaddam, M. Ekselius, L. Birnir, B. 2019-07-02 doi:10.1101/689984 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Coevolution between life-history and metabolic rate depends on ontogenetic stage ]]> https://biorxiv.org/content/10.1101/705707v1?rss=1 Sowersby, W. Morozov, S. Eckerstrom-Liedholm, S. Lehmann, P. Rowinski, P. Naslund, J. Gonzalez-Voyer, A. Rogell, B. 2019-07-18 doi:10.1101/705707 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ Intrinsically ball retrieving wolf puppies reveal standing ancestral variation for human-directed play behaviour ]]> https://biorxiv.org/content/10.1101/744862v1?rss=1 Hansen Wheat, C. Temrin, H. 2019-08-23 doi:10.1101/744862 Cold Spring Harbor Laboratory Press 2019-08-23 <![CDATA[ Proteasome-mediated protein degradation resets the cell division cycle and triggers ESCRT-III-mediated cytokinesis in an archaeon ]]> https://biorxiv.org/content/10.1101/774273v1?rss=1 Tarrason Risa, G. Hurtig, F. Bray, S. Hafner, A. Harker-Kirschneck, L. Faull, P. Davis, C. Papatziamou, D. Mutavchiev, D. R. Fan, C. Meneguello, L. Arashiro Pulschen, A. Dey, G. Culley, S. Kilkenny, M. L. Pellegrini, L. de Bruin, R. A. M. Henriques, R. Snijders, A. P. Saric, A. Lindas, A.-C. Robinson, N. Baum, B. 2019-09-18 doi:10.1101/774273 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ A histone methyltransferase inhibitor can reverse epigenetically acquired drug resistance in the malaria parasite Plasmodium falciparum ]]> https://biorxiv.org/content/10.1101/775734v1?rss=1 Chan, A. Dziedziech, A. Kirkman, L. Deitsch, K. Ankarklev, J. 2019-09-19 doi:10.1101/775734 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ Inherited Causes of Clonal Hematopoiesis of Indeterminate Potential in TOPMed Whole Genomes ]]> https://biorxiv.org/content/10.1101/782748v1?rss=1 Bick, A. G. Weinstock, J. Nandakumar, S. K. Fulco, C. P. Leventhal, M. J. Bao, E. L. Nasser, J. Zekavat, S. M. Szeto, M. D. Laurie, C. Taub, M. Mitchell, B. Barnes, K. Moscati, A. Fornage, M. Redline, S. Psaty, B. M. Silverman, E. Weiss, S. Palmer, N. Ramachandran, V. Burchard, E. Kardia, S. He, J. Kaplan, R. Smith, N. L. Arnett, D. Schwartz, D. Correa, A. de Andrade, M. Guo, X. Konkle, B. A. Custer, B. Peralta, J. Gui, H. Meyers, D. McGarvey, S. T. Chen, I. Shoemaker, M. B. Peyser, P. A. Broome, J. Gogarten, S. Wang, F. F. Wong, Q. Montasser, M. Da 2019-09-27 doi:10.1101/782748 Cold Spring Harbor Laboratory Press 2019-09-27 <![CDATA[ Tissue-autonomous immune response regulates stress signalling during hypertrophy ]]> https://biorxiv.org/content/10.1101/787226v1?rss=1 Krautz, R. Khalili, D. Theopold, U. 2019-09-30 doi:10.1101/787226 Cold Spring Harbor Laboratory Press 2019-09-30 <![CDATA[ Geographic variation in hemocyte diversity and phagocytic propensity shows a diffuse genomic signature in the green veined white butterfly ]]> https://biorxiv.org/content/10.1101/790782v1?rss=1 Keehnen, N. L. P. Fors, L. Jarver, P. Spetz, A.-L. Nylin, S. Theopold, U. Wheat, C. W. 2019-10-03 doi:10.1101/790782 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ The consequences of surviving infection across the metamorphic boundary: tradeoff insights from RNAseq and life history measures ]]> https://biorxiv.org/content/10.1101/792176v1?rss=1 Keehnen, N. L. P. Kucerova, L. Nylin, S. Theopold, U. Wheat, C. W. 2019-10-04 doi:10.1101/792176 Cold Spring Harbor Laboratory Press 2019-10-04 <![CDATA[ Adaptive resetting of tuberoinfundibular dopamine (TIDA) network activity during lactation in mice ]]> https://biorxiv.org/content/10.1101/797159v1?rss=1 Thorn Perez, C. Ferraris, J. van Lunteren, J. A. Hellysaz, A. Iglesias, M. J. Broberger, C. 2019-10-08 doi:10.1101/797159 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals ]]> https://biorxiv.org/content/10.1101/806166v1?rss=1 Vaga, S. Lee, S. Ji, B. Andreasson, A. Talley, N. J. Agreus, L. Bidkhori, G. Kovatcheva-Datchary, P. Park, J. Lee, D. Proctor, G. Ehrlich, D. Nielsen, J. Engstrand, L. Shoaie, S. 2019-10-16 doi:10.1101/806166 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Network-based metrics of community resilience and dynamics in lake ecosystems ]]> https://biorxiv.org/content/10.1101/810762v1?rss=1 Armstrong McKay, D. I. Dyke, J. G. Dearing, J. A. Doncaster, C. P. Wang, R. 2019-10-24 doi:10.1101/810762 Cold Spring Harbor Laboratory Press 2019-10-24 <![CDATA[ Localized axolemma deformations suggest mechanoporation as axonal injury trigger ]]> https://biorxiv.org/content/10.1101/816108v1?rss=1 Montanino, A. Saeedimasine, M. Villa, A. Kleiven, S. 2019-10-23 doi:10.1101/816108 Cold Spring Harbor Laboratory Press 2019-10-23 <![CDATA[ Sex identification of ancient pinnipeds using the dog genome ]]> https://biorxiv.org/content/10.1101/838797v1?rss=1 Bro-Joergensen, M. H. Keighley, X. Ahlgren, H. Scharff-Olsen, C. H. Rosing-Asvid, A. Dietz, R. Ferguson, S. H. Gotfredsen, A. B. Jordan, P. Glykou, A. Liden, K. Olsen, M. T. 2019-11-12 doi:10.1101/838797 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ Amplitude and timescale of metacommunity trait-lag response to climate change ]]> https://biorxiv.org/content/10.1101/850289v1?rss=1 Norberg, J. Moor, H. 2019-11-21 doi:10.1101/850289 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ The SWI/SNF subunits BRG1 affects alternative splicing by changing RNA binding factor interactions with RNA ]]> https://biorxiv.org/content/10.1101/858852v1?rss=1 Ganez Zapater, A. Mackowiak, S. D. Guo, Y. Jordan Pla, A. Friedländer, M. R. Visa, N. Östlund Farrants, A.-K. 2019-11-28 doi:10.1101/858852 Cold Spring Harbor Laboratory Press 2019-11-28 <![CDATA[ Adverse caregiving in infancy blunts neural processing of the mother: Translating across species ]]> https://biorxiv.org/content/10.1101/870261v1?rss=1 Opendak, M. M. Theisen, E. Blomkvist, A. Hollis, K. Lind, T. Sarro, E. Lundstrom, J. N. Tottenham, N. Dozier, M. Wilson, D. Sullivan, R. 2019-12-10 doi:10.1101/870261 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ Quantitative Real-Time PCR assays for species-specific detection and quantification of Baltic Sea spring bloom dinoflagellates ]]> https://biorxiv.org/content/10.1101/871020v1?rss=1 Brink, A. M. Kremp, A. Gorokhova, E. 2019-12-10 doi:10.1101/871020 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ Pragmatic Language Processing in the Adolescent Brain ]]> https://biorxiv.org/content/10.1101/871343v1?rss=1 Asaridou, S. S. Demir-Lira, E. Udden, J. S. Goldin-Meadow, S. Small, S. L. 2019-12-11 doi:10.1101/871343 Cold Spring Harbor Laboratory Press 2019-12-11 <![CDATA[ Optimized design and in vivo application of optogenetically functionalized Drosophila dopamine receptors ]]> https://biorxiv.org/content/10.1101/2023.05.20.541404v1?rss=1 Zhou, F. Tichy, A.-M. Imambocus, B. N. Rodriguez Jimenez, F. J. Gonzalez Martinez, M. Jahan, I. Habib, M. Wilhelmy, N. Bräuler, V. Lömker, T. Sauter, K. Helfrich-Förster, C. Pielage, J. Grunwald Kadow, I. C. Janovjak, H. Soba, P. 2023-05-21 doi:10.1101/2023.05.20.541404 Cold Spring Harbor Laboratory Press 2023-05-21 <![CDATA[ The Alk receptor tyrosine kinase regulates Sparkly, a novel activity regulating neurosecretory protein in the Drosophila CNS. ]]> https://biorxiv.org/content/10.1101/2023.06.02.543395v1?rss=1 Sukumar, S. K. Antonydhason, V. Molander, L. Sandakly, J. Umapathy, G. Mendoza-Garcia, P. Masudi, T. Schlosser, A. Nassel, D. R. Wegener, C. Shirinian, M. Palmer, R. 2023-06-05 doi:10.1101/2023.06.02.543395 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Flexibility of learning in complex worlds ]]> https://biorxiv.org/content/10.1101/2023.06.12.544544v1?rss=1 Leimar, O. Quinones, A. E. Bshary, R. 2023-06-12 doi:10.1101/2023.06.12.544544 Cold Spring Harbor Laboratory Press 2023-06-12 <![CDATA[ Notes on the diet composition of Anoles lizards, Anolis (Dactyloidae), in the Yasuni National Park (Ecuador) ]]> https://biorxiv.org/content/10.1101/2023.06.15.545064v1?rss=1 Pinto, J. 2023-06-15 doi:10.1101/2023.06.15.545064 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ Structure and dynamics of differential ligand binding in the human {rho}-type GABA(A) receptor ]]> https://biorxiv.org/content/10.1101/2023.06.16.545288v1?rss=1 Cowgill, J. Fan, C. Haloi, N. Tobiasson, V. Zhuang, Y. Howard, R. J. Lindahl, E. 2023-06-17 doi:10.1101/2023.06.16.545288 Cold Spring Harbor Laboratory Press 2023-06-17 <![CDATA[ Single-cell sequencing of tumor-associated macrophages in a Drosophila model. ]]> https://biorxiv.org/content/10.1101/2023.06.17.545411v1?rss=1 Khalili, D. Mohammed, M. Kunc, M. Ankarklev, J. Theopold, U. 2023-06-18 doi:10.1101/2023.06.17.545411 Cold Spring Harbor Laboratory Press 2023-06-18 <![CDATA[ Activity modulation in anaerobic ribonucleotide reductases: nucleotide binding to the ATP-cone mediates long-range order-disorder transitions in the active site ]]> https://biorxiv.org/content/10.1101/2023.06.20.545753v1?rss=1 Bimai, O. Banerjee, I. Grinberg, I. R. Huang, P. Lundin, D. Sjöberg, B.-M. Logan, D. T. 2023-06-20 doi:10.1101/2023.06.20.545753 Cold Spring Harbor Laboratory Press 2023-06-20 <![CDATA[ Pesticide-induced resurgence of the brown planthopper is mediated by diverse actors that promote juvenile hormone biosynthesis and female fecundity ]]> https://biorxiv.org/content/10.1101/2023.06.21.545881v1?rss=1 Gao, Y. Su, S.-C. Liu, Z.-Y. Dick, N. Bass, C. Gao, C.-F. Wu, S.-F. 2023-06-24 doi:10.1101/2023.06.21.545881 Cold Spring Harbor Laboratory Press 2023-06-24 <![CDATA[ Ancient Sheep Genomes reveal four Millennia of North European Short-Tailed Sheep in the Baltic Sea region ]]> https://biorxiv.org/content/10.1101/2023.06.26.544912v1?rss=1 Larsson, M. N. Morell Miranda, P. Pan, L. Basak Vural, K. Kaptan, D. Rodrigues Soares, A. E. Kivikero, H. Kantanen, J. Somel, M. Ozer, F. Johansson, A. M. Stora, J. Gunther, T. 2023-06-26 doi:10.1101/2023.06.26.544912 Cold Spring Harbor Laboratory Press 2023-06-26 <![CDATA[ Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample ]]> https://biorxiv.org/content/10.1101/2023.06.30.547175v1?rss=1 Sandoval-Velasco, M. Dudchenko, O. Antonio Rodriguez, J. Perez Estrada, C. Dehasque, M. Fontsere, C. Mak, S. S. T. Plotnikov, V. Khan, R. Weisz, D. Contessoto, V. G. Oliveira Junior, A. B. Kalluchi, A. Omer, A. D. Batra, S. S. Shamim, M. S. Durand, N. C. O'Connell, B. Roca, A. L. Gnirke, A. Garcia-Trevino, I. Coke, R. Flanagan, J. P. Pletch, K. Ruiz-Herrera, A. Lander, E. S. Rowley, M. J. Onuchic, J. N. Dalen, L. Marti-Renom, M. A. Gilbert, M. T. P. Aiden, E. L. 2023-06-30 doi:10.1101/2023.06.30.547175 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Conversational production and comprehension: fMRI-evidence reminiscent of the classic Broca-Wernicke model ]]> https://biorxiv.org/content/10.1101/2023.07.05.547796v1?rss=1 Arvidsson, C. Torubarova, E. Pereira, A. Udden, J. 2023-07-06 doi:10.1101/2023.07.05.547796 Cold Spring Harbor Laboratory Press 2023-07-06 <![CDATA[ Geographic population structure and distinct population dynamics of globally abundant freshwater bacteria ]]> https://biorxiv.org/content/10.1101/2023.07.13.548520v1?rss=1 Hoetzinger, M. Hahn, M. W. Andersson, L. Y. Buckley, N. Ramsin, C. Buck, M. Nuy, J. K. Garcia, S. L. Puente-Sanchez, F. Bertilsson, S. 2023-07-14 doi:10.1101/2023.07.13.548520 Cold Spring Harbor Laboratory Press 2023-07-14 <![CDATA[ Measuring RBC deformability and its heterogeneity using a fast microfluidic device ]]> https://biorxiv.org/content/10.1101/2023.07.18.549500v1?rss=1 Kumari, S. Mehendale, N. Roy, T. Sen, S. Mitra, D. Paul, D. 2023-07-19 doi:10.1101/2023.07.18.549500 Cold Spring Harbor Laboratory Press 2023-07-19 <![CDATA[ The Genomic Legacy of Human Management and sex-biased Aurochs hybridization in Iberian Cattle ]]> https://biorxiv.org/content/10.1101/2023.07.19.548914v1?rss=1 Günther, T. Chisausky, J. Galindo-Pellicena, M. A. Iriarte, E. Cortes Gardyn, O. Eusebi, P. G. Garcia-Gonzalez, R. Urena, I. Moreno, M. Alday, A. Rojo, M. Perez, A. Tejedor Rodriguez, C. Garcia Martinez de Lagran, I. Arsuaga, J. L. Carretero, J.-M. Götherström, A. Smith, C. Valdiosera, C. 2023-07-20 doi:10.1101/2023.07.19.548914 Cold Spring Harbor Laboratory Press 2023-07-20 <![CDATA[ Sources of prey availability data alter interpretation of outputs from prey choice null networks ]]> https://biorxiv.org/content/10.1101/2023.07.25.549927v1?rss=1 Cuff, J. P. Tercel, M. P. Windsor, F. M. Hawthorne, B. S. Hamback, P. A. Bell, J. R. Symondson, W. O. Vaughan, I. P. 2023-07-26 doi:10.1101/2023.07.25.549927 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ Phosphate starvation decouples cell differentiation from DNA replication control in the dimorphic bacterium Caulobacter crescentus ]]> https://biorxiv.org/content/10.1101/2023.07.26.550773v1?rss=1 Hallgren, J. Koonce, K. Felletti, M. Mortier, J. Turco, E. Jonas, K. 2023-07-27 doi:10.1101/2023.07.26.550773 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ Diverse mechanisms control amino acid-dependent environmental alkalization by Candida albicans ]]> https://biorxiv.org/content/10.1101/2023.08.04.551922v1?rss=1 Silao, F. G. S. Valeriano, V. D. Uddström, E. Falconer, E. Ljungdahl, P. O. 2023-08-04 doi:10.1101/2023.08.04.551922 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ Methanolobus use unspecific methyltransferases to produce methane from dimethylsulfide ]]> https://biorxiv.org/content/10.1101/2023.08.04.551946v1?rss=1 Tsola, S. L. Chen, Y. Sanders, I. A. Economou, C. K. Bruchert, V. Eyice, O. 2023-08-04 doi:10.1101/2023.08.04.551946 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ AI in Paleontology ]]> https://biorxiv.org/content/10.1101/2023.08.07.552217v1?rss=1 Yu, C. Qin, F. Watanabe, A. Yao, W. Li, Y. Qin, Z. Liu, Y. Wang, H. Jiangzuo, Q. Hsiang, A. Y. Ma, C. Rayfield, E. Benton, M. J. Xu, X. 2023-08-08 doi:10.1101/2023.08.07.552217 Cold Spring Harbor Laboratory Press 2023-08-08 <![CDATA[ Does urbanization lead to parallel demographic shifts across the world in a cosmopolitan plant? ]]> https://biorxiv.org/content/10.1101/2023.08.14.552623v1?rss=1 Caizergues, A. E. Santangelo, J. S. Ness, R. W. Angeoletto, F. Anstett, D. N. Anstett, J. Baena-Diaz, F. Carlen, E. J. Chaves, J. A. Comerford, M. S. Dyson, K. Falahati-Anbaran, M. Fellowes, M. D. E. Hodgins, K. A. Hood, G. R. Iniguez-Armijos, C. Kooyers, N. J. Lazaro-Lobo, A. Moles, A. T. Munshi-South, J. Paule, J. Porth, I. M. Santiago-Rosario, L. Y. Stack Whitney, K. Tack, A. J. M. Johnson, M. T. J. 2023-08-14 doi:10.1101/2023.08.14.552623 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Extracellular vesicles stimulate smooth muscle cell migration by presenting collagen VI. ]]> https://biorxiv.org/content/10.1101/2023.08.17.551257v1?rss=1 View larger version (43K): org.highwire.dtl.DTLVardef@1355004org.highwire.dtl.DTLVardef@1186e9forg.highwire.dtl.DTLVardef@106ad30org.highwire.dtl.DTLVardef@1543518_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kapustin, A. N. Tsakali, S. S. Whitehead, M. Chennell, G. Wu, M.-Y. Molenaar, C. Kutikhin, A. Bogdanov, L. Sinitsky, M. Rubina, K. Clayton, A. Verweij, F. J. Pegtel, D. M. Zingaro, S. Lobov, A. Zainullina, B. Owen, D. Parsons, M. Cheney, R. E. Warren, D. Humphries, M. J. Iskratsch, T. Holt, M. Shanahan, C. M. 2023-08-18 doi:10.1101/2023.08.17.551257 Cold Spring Harbor Laboratory Press 2023-08-18 <![CDATA[ Validation of the sleep EEG headband ZMax ]]> https://biorxiv.org/content/10.1101/2023.08.18.553744v1?rss=1 Jafarzadeh Esfahani, M. D. Weber, F. Boon, M. Anthes, S. Almazova, T. van Hal, M. Keuren, Y. Heuvelmans, C. Simo, E. Bovy, L. Adelhofer, N. ter Avest, M. M. Perslev, M. ter Horst, R. Harous, C. Sundelin, T. Axelsson, J. Dresler, M. 2023-08-21 doi:10.1101/2023.08.18.553744 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Social complexity affects cognitive abilities but not brain structure in a Poecilid fish ]]> https://biorxiv.org/content/10.1101/2023.08.20.554009v1?rss=1 Triki, Z. Zhou, T. Argyriou, E. Sousa de Novais, E. Servant, O. Kolm, N. 2023-08-21 doi:10.1101/2023.08.20.554009 Cold Spring Harbor Laboratory Press 2023-08-21 <![CDATA[ Reply to: Contribution of carbon inputs to soil carbon accumulation cannot be neglected ]]> https://biorxiv.org/content/10.1101/2023.08.20.552557v1?rss=1 Tao, F. Houlton, B. Z. Frey, S. D. Lehmann, J. Manzoni, S. Huang, Y. Jiang, L. Mishra, U. Hungate, B. A. Schmidt, M. W. I. Reichstein, M. Carvalhais, N. Ciais, P. Wang, Y.-P. Ahrens, B. Hugelius, G. Hocking, T. D. Lu, X. Shi, Z. Viatkin, K. Vargas, R. Yigini, Y. Omuto, C. Malik, A. A. Peralta, G. Cuevas-Corona, R. Di Paolo, L. E. Luotto, I. Liao, C. Liang, Y.-S. Saynes, V. S. Huang, X. Luo, Y. 2023-08-29 doi:10.1101/2023.08.20.552557 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ Structural and biophysical analysis of a Haemophilus influenzae tripartite ATP-independent periplasmic (TRAP) transporter ]]> https://biorxiv.org/content/10.1101/2023.08.28.549404v1?rss=1 Currie, M. Davies, J. Scalise, M. Gulati, A. Wright, J. Newton-Vesty, M. Abeysekera, G. Subramanian, R. Wahlgren, W. Friemann, R. Allison, J. Mace, P. Griffin, M. Demeler, B. Wakatsuki, S. Drew, D. Indiveri, C. Dobson, R. North, R. 2023-08-29 doi:10.1101/2023.08.28.549404 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ Pigment Binding in The Light-Dependent Protochlorophyllide Oxidoreductase ]]> https://biorxiv.org/content/10.1101/2023.08.28.555081v1?rss=1 Pesara, P. Szafran, K. Nguyen, H. C. Sirohiwal, A. Pantazis, D. A. Gabruk, M. 2023-08-29 doi:10.1101/2023.08.28.555081 Cold Spring Harbor Laboratory Press 2023-08-29 <![CDATA[ Parkin is not required to sustain OXPHOS function in adult mammalian tissues ]]> https://biorxiv.org/content/10.1101/2023.09.02.556020v1?rss=1 Filograna, R. Gerlach, J. Choi, H.-N. Rigoni, G. Barbaro, M. Oscarson, M. Lee, S. Tiklova, K. Ringner, M. Koolmeister, C. Wibom, R. Riggare, S. Nennesmo, I. Perlmann, T. Wredenberg, A. Wedell, A. Motori, E. Svenningsson, P. Larsson, N.-G. 2023-09-02 doi:10.1101/2023.09.02.556020 Cold Spring Harbor Laboratory Press 2023-09-02 <![CDATA[ PI-(3,5)P2-mediated oligomerization of the endosomal sodium/proton exchanger NHE9 ]]> https://biorxiv.org/content/10.1101/2023.09.10.557050v1?rss=1 Kokane, S. Meier, P. Gulati, A. Matsuoka, R. Pipatpolkai, T. Delemotte, L. Drew, D. 2023-09-10 doi:10.1101/2023.09.10.557050 Cold Spring Harbor Laboratory Press 2023-09-10 <![CDATA[ The geometry of admixture in population genetics: the blessing of dimensionality ]]> https://biorxiv.org/content/10.1101/2023.09.08.556908v1?rss=1 Oteo, J. A. Oteo-Garcia, G. 2023-09-12 doi:10.1101/2023.09.08.556908 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics ]]> https://biorxiv.org/content/10.1101/2023.09.25.559365v1?rss=1 Mc Cartney, A. M. Formenti, G. Mouton, A. Ciofi, C. Waterhouse, R. M. Mazzoni, C. J. De Panis, D. Schlude Marins, L. S. Leitao, H. G. Diedericks, G. Kirangwa, J. Morselli, M. Salces, J. Escudero, N. Iannucci, A. Natali, C. Svardal, H. Fernandez, R. De Pooter, T. Joris, G. Strazisar, M. Wood, J. Herron, K. E. Seehausen, O. Watts, P. C. Shaw, F. Davey, R. P. Minotto, A. Fernandez Gonzalez, J. M. Bohne, A. Alegria, C. Alioto, T. Alves, P. C. Amorim, I. R. Aury, J.-M. Backstrom, N. Baldrian, P. Ballarin, L. Baltrunaite, L. Barta, E. BedHom, B. Belser, C. B 2023-09-28 doi:10.1101/2023.09.25.559365 Cold Spring Harbor Laboratory Press 2023-09-28 <![CDATA[ Deep learning reveals the role of copy number variation in the genetic architecture of a highly polymorphic sexual trait ]]> https://biorxiv.org/content/10.1101/2023.09.29.560175v1?rss=1 van der Bijl, W. Shu, J. Goberdhan, V. S. Sherin, L. Cortazar-Chinarro, M. Corral-Lopez, A. Mank, J. E. 2023-09-30 doi:10.1101/2023.09.29.560175 Cold Spring Harbor Laboratory Press 2023-09-30 <![CDATA[ Sentinels for future coral reef conditions: assessment of environmental variability and water quality in semi-enclosed inland bays in the southern Caribbean ]]> https://biorxiv.org/content/10.1101/2023.10.04.560694v1?rss=1 20 abiotic parameters characterizing two mangrove- and seagrass-dominated inland bays and two nearby coral reefs in Curacao (southern Caribbean) during the cool, dry season and warm, wet season. This was combined with time-integrated pollution monitoring using bioindicators to assess nutrients and trace metal pollution (inland bays only), and passive samplers and bioassays to assess organic chemical pollution (all four sites) during the wet season. This approach revealed a previously undocumented extent of strong diel and seasonal environmental variability in the two inland bays, with temperature, pH and dissolved oxygen frequently reaching values predicted under moderate-to-severe future climate scenarios. In addition, the inland bays had greater nutrient concentrations (especially ammonium) and ecotoxicological risks than the nearby reefs during the wet season due to run-off, industrial- and wastewater effluents, ports and boating. Overall, our findings show that Curacaos inland bays have significant potential to serve as natural laboratories to study the effects of future ocean conditions on resident taxa in situ. This however applies within the context of strong diel fluctuations and with the caveat of co-occurring stressors. Our work confirms the important role of mangrove and seagrass habitats as resilience hotspots for climate-sensitive taxa but also highlights the urgent need to improve monitoring, water quality and protection of these valuable habitats along the mangrove-seagrass-coral reef continuum. ]]> de Jong, C. van Os, I. Sepulveda-Rodriguez, G. de Baat, M. L. Schoepf, V. 2023-10-06 doi:10.1101/2023.10.04.560694 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Social bond dynamics and the evolution of helping ]]> https://biorxiv.org/content/10.1101/2023.10.11.561838v1?rss=1 Leimar, O. Bshary, R. 2023-10-11 doi:10.1101/2023.10.11.561838 Cold Spring Harbor Laboratory Press 2023-10-11 <![CDATA[ Relative Homoplasy Index: A New Cross-comparable Metric for Quantifying Homoplasy in Discrete Character Datasets ]]> https://biorxiv.org/content/10.1101/2023.10.10.561677v1?rss=1 Steell, E. M. Hsiang, A. Y. Field, D. J. 2023-10-13 doi:10.1101/2023.10.10.561677 Cold Spring Harbor Laboratory Press 2023-10-13 <![CDATA[ Early Neolithic forest farming at Seven Springs, Martlesham, Suffolk from sedaDNA and pollen ]]> https://biorxiv.org/content/10.1101/2023.10.11.561859v1?rss=1 Hudson, S. M. Allen, S. J. Alsos, I. G. Curl, J. Heintzman, P. D. Hughes, P. Gardiner, L. Lloyd-Smith, L. Pears, B. R. Scaife, R. Stoof-Leichsenring, K. R. Brown, A. 2023-10-16 doi:10.1101/2023.10.11.561859 Cold Spring Harbor Laboratory Press 2023-10-16 <![CDATA[ Scalable distance-based phylogeny inference using divide-and-conquer ]]> https://biorxiv.org/content/10.1101/2023.10.11.561902v1?rss=1 Arvestad, L. 2023-10-16 doi:10.1101/2023.10.11.561902 Cold Spring Harbor Laboratory Press 2023-10-16 <![CDATA[ Species-specific dynamics may cause deviations from general biogeographical predictions - evidence from a population genomics study of a New Guinean endemic passerine bird family (Melampittidae). ]]> https://biorxiv.org/content/10.1101/2023.10.19.563072v1?rss=1 Müller, I. A. Thörn, F. Rajan, S. Ericson, P. Dumbacher, J. P. Maiah, G. Blom, M. P. K. Jonsson, K. A. Irestedt, M. 2023-10-22 doi:10.1101/2023.10.19.563072 Cold Spring Harbor Laboratory Press 2023-10-22 <![CDATA[ Growth couples temporal and spatial fluctuations of tissue properties during morphogenesis ]]> https://biorxiv.org/content/10.1101/2023.10.23.563640v1?rss=1 Fruleux, A. Hong, L. Roeder, A. H. K. Li, C.-B. Boudaoud, A. 2023-10-25 doi:10.1101/2023.10.23.563640 Cold Spring Harbor Laboratory Press 2023-10-25 <![CDATA[ High-quality genome assemblies of four members of the Podospora anserina species complex ]]> https://biorxiv.org/content/10.1101/2023.10.24.563784v1?rss=1 Ament-Velasquez, S. L. Vogan, A. A. Wallerman, O. Hartmann, F. E. Gautier, V. Silar, P. Giraud, T. Johannesson, H. 2023-10-28 doi:10.1101/2023.10.24.563784 Cold Spring Harbor Laboratory Press 2023-10-28 <![CDATA[ Unveiling Driver Modules in Lung Cancer: A Clustering-Based Gene-Gene Interaction Network Analysis ]]> https://biorxiv.org/content/10.1101/2023.11.01.565104v1?rss=1 Taheri, G. 2023-11-03 doi:10.1101/2023.11.01.565104 Cold Spring Harbor Laboratory Press 2023-11-03 <![CDATA[ Robust organ size in Arabidopsis is primarily governed by cell growth rather than cell division patterns ]]> https://biorxiv.org/content/10.1101/2023.11.11.566685v1?rss=1 Burda, I. Li, C.-B. Clark, F. K. Roeder, A. H. 2023-11-14 doi:10.1101/2023.11.11.566685 Cold Spring Harbor Laboratory Press 2023-11-14 <![CDATA[ Genomic analyses elucidate the causes and consequences of breakdown of distyly in Linum trigynum ]]> https://biorxiv.org/content/10.1101/2023.11.16.567348v1?rss=1 Gutierrez-Valencia, J. Zervakis, P.-I. Postel, Z. Fracassetti, M. Losvik, A. Mehrabi, S. Bunikis, I. Soler, L. Hughes, P. W. Desamore, A. Laenen, B. Abdelaziz, M. Vinnere Pettersson, O. Arroyo, J. Slotte, T. 2023-11-17 doi:10.1101/2023.11.16.567348 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Distinct Functions for Beta and Alpha Bursts in Gating of Human Working Memory ]]> https://biorxiv.org/content/10.1101/2023.11.17.566386v1?rss=1 Liljefors, J. Almeida, R. Rane, G. Lundstrom, J. N. Herman, P. A. Lundqvist, M. 2023-11-17 doi:10.1101/2023.11.17.566386 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Facilitated introgression from domestic goat into Alpine ibex at immune loci ]]> https://biorxiv.org/content/10.1101/2023.11.23.568345v1?rss=1 Muenger, X. Robin, M. Dalen, L. Grossen, C. 2023-11-23 doi:10.1101/2023.11.23.568345 Cold Spring Harbor Laboratory Press 2023-11-23 <![CDATA[ Kinetic and structural characterization of human NUDIX hydrolase NUDT15 and NUDT18 as catalysts of isoprene pyrophosphate hydrolysis ]]> https://biorxiv.org/content/10.1101/2023.11.29.569174v1?rss=1 Scaletti, E. R. Unterlass, J. E. Almlof, I. Koolmeister, T. Vallin, K. S. Kapsitidou, D. Helleday, T. Stenmark, P. Jemth, A.-S. 2023-11-29 doi:10.1101/2023.11.29.569174 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ Evolution of hybrid inviability associated with chromosome fusions ]]> https://biorxiv.org/content/10.1101/2023.11.30.569355v1?rss=1 Boman, J. Näsvall, K. Vila, R. Wiklund, C. Backström, N. 2023-12-01 doi:10.1101/2023.11.30.569355 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Constant-pH molecular dynamics simulations of progressive activation in a proton-gated ion channel ]]> https://biorxiv.org/content/10.1101/2023.11.30.569372v1?rss=1 Jansen, A. Bauer, P. Howard, R. J. Hess, B. Lindahl, E. 2023-12-01 doi:10.1101/2023.11.30.569372 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Strong cascading impacts of micropollutants on planktonic food web in urban river ]]> https://biorxiv.org/content/10.1101/2023.12.03.569813v1?rss=1 Adyari, B. Zhang, L. Nascimento, F. J. d. A. Zhang, Y. Cao, M. Wang, J. Li, H. Sun, Q. Yu, C. Hu, A. 2023-12-05 doi:10.1101/2023.12.03.569813 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Symmetry-adapted Markov state models of closing, opening, and desensitizing in α7 nicotinic acetylcholine receptors ]]> https://biorxiv.org/content/10.1101/2023.12.04.569956v1?rss=1 Zhuang, Y. Howard, R. J. Lindahl, E. 2023-12-05 doi:10.1101/2023.12.04.569956 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Postnatal FGF-signalling establishes gradients of cell-identities along the proximal-distal axis of the lung airways ]]> https://biorxiv.org/content/10.1101/2023.12.11.571142v1?rss=1 Sountoulidis, A. Firsova, A. B. Liontos, A. Theelke, J. Koepke, J. Millar-Buchner, P. Manneras-Holm, L. Bjorklund, A. K. Fysikopoulos, A. Gaengel, K. Backhed, F. Betsholtz, C. Seeger, W. Bellusci, S. Samakovlis, C. 2023-12-12 doi:10.1101/2023.12.11.571142 Cold Spring Harbor Laboratory Press 2023-12-12 <![CDATA[ Hybrid adaptation is hampered by Haldane's sieve ]]> https://biorxiv.org/content/10.1101/2023.12.15.571924v1?rss=1 Bautista, C. Gagnon-Arsenault, I. Utrobina, M. Fijarczyk, A. Bendixsen, D. P. Stelkens, R. Landry, C. 2023-12-16 doi:10.1101/2023.12.15.571924 Cold Spring Harbor Laboratory Press 2023-12-16 <![CDATA[ Divergent mechanisms of steroid inhibition in the human {rho}1 GABA(A) receptor ]]> https://biorxiv.org/content/10.1101/2024.01.23.576874v1?rss=1 Fan, C. Cowgill, J. Howard, R. J. Lindahl, E. 2024-01-26 doi:10.1101/2024.01.23.576874 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ Meiotic drive against chromosome fusions in butterfly hybrids ]]> https://biorxiv.org/content/10.1101/2024.02.02.578558v1?rss=1 Boman, J. Wiklund, C. Vila, R. Backström, N. 2024-02-07 doi:10.1101/2024.02.02.578558 Cold Spring Harbor Laboratory Press 2024-02-07 <![CDATA[ Hypermigration of macrophages through the concerted action of GRA effectors on NF-κB/p38 signaling and host chromatin accessibility potentiates Toxoplasma dissemination ]]> https://biorxiv.org/content/10.1101/2024.02.06.579146v1?rss=1 ten Hoeve, A. L. Rodriguez, M. E. Säflund, M. Michel, V. Magimel, L. Ripoll, A. Yu, T. Hakimi, M.-A. Saeij, J. P. Ozata, D. M. Barragan, A. 2024-02-07 doi:10.1101/2024.02.06.579146 Cold Spring Harbor Laboratory Press 2024-02-07 <![CDATA[ Anti-diuretic hormone ITP signals via a guanylate cyclase receptor to modulate systemic homeostasis in Drosophila ]]> https://biorxiv.org/content/10.1101/2024.02.07.579245v1?rss=1 Gera, J. Agard, M. Nave, H. Sajadi, F. Thorat, L. Kondo, S. Nassel, D. Paluzzi, J.-P. V. Zandawala, M. 2024-02-10 doi:10.1101/2024.02.07.579245 Cold Spring Harbor Laboratory Press 2024-02-10 <![CDATA[ Lineage-tracing of Acta2+ cells in aged mice during lung fibrosis formation and resolution supports the lipofibroblasts to myofibroblast reversible switch ]]> https://biorxiv.org/content/10.1101/2024.02.19.580952v1?rss=1 Lingampally, A. Truchi, M. Mauduit, O. Delcroix, V. Hadzic, S. Koepke, J. Vazquez-Armendariz, A.-I. Herold, S. Samakovlis, C. Makarenkova, H. El Agha, E. Chen, C. Mari, B. Bellusci, S. 2024-02-22 doi:10.1101/2024.02.19.580952 Cold Spring Harbor Laboratory Press 2024-02-22 <![CDATA[ Survival of tardigrades (Hypsibius exemplaris) to subzero temperatures depends on exposure intensity, duration, and ice-nucleation--as shown by large-scale mortality dye-based assays ]]> https://biorxiv.org/content/10.1101/2024.02.28.582259v1?rss=1 Lyons, A. M. Roberts, K. T. Williams, C. M. 2024-03-02 doi:10.1101/2024.02.28.582259 Cold Spring Harbor Laboratory Press 2024-03-02 <![CDATA[ A platform for the recombinant production of Group A Streptococcus glycoconjugate vaccines ]]> https://biorxiv.org/content/10.1101/2024.03.01.582896v1?rss=1 Ajay Castro, S. Passmore, I. J. Ndeh, D. Shaw, H. A. Ruda, A. Burns, K. Thomson, S. Nagar, R. Alagesan, K. Lucas, K. Abouelhadid, S. Reglinski, M. Schwarz- Linek, U. Mawas, F. Widmalm, G. Wren, B. W. Dorfmueller, H. C. 2024-03-02 doi:10.1101/2024.03.01.582896 Cold Spring Harbor Laboratory Press 2024-03-02 <![CDATA[ An Allosteric Cholesterol Site in Glycine Receptors Characterized Through Molecular Simulations ]]> https://biorxiv.org/content/10.1101/2024.03.05.583408v1?rss=1 Jalalypour, F. Howard, R. J. Lindahl, E. 2024-03-06 doi:10.1101/2024.03.05.583408 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Circular RNA circASH1L(4,5) protects microRNA-129-5p from target-directed microRNA degradation in human skin wound healing ]]> https://biorxiv.org/content/10.1101/2024.03.12.584463v1?rss=1 Wang, Q. Niu, G. Liu, Z. Toma, M. A. Geara, J. Bian, X. Zhang, L. Piipponen, M. Li, D. Sommar, P. Xu Landen, N. 2024-03-14 doi:10.1101/2024.03.12.584463 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ An unsupervised deep learning framework encodes super-resolved image features to decode bacterial cell cycle ]]> https://biorxiv.org/content/10.1101/2024.03.13.584804v1?rss=1 Griffie, J. Zhang, C. Denereaz, J. Pham, T.-A. M. Weissbart, G. Sieben, C. Lambert, A. Veening, J.-W. Manley, S. 2024-03-14 doi:10.1101/2024.03.13.584804 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ High-resolution genomic ancestry reveals mobility in early medieval Europe ]]> https://biorxiv.org/content/10.1101/2024.03.15.585102v1?rss=1 Speidel, L. Silva, M. Booth, T. Raffield, B. Anastasiadou, K. Barrington, C. Gotherstrom, A. Heather, P. Skoglund, P. 2024-03-19 doi:10.1101/2024.03.15.585102 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ Malaria-derived hemozoin alters chromatin remodelling and skews dendritic cell responses to subsequent bacterial infections ]]> https://biorxiv.org/content/10.1101/2024.03.18.585548v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@1573c58org.highwire.dtl.DTLVardef@3aeb6forg.highwire.dtl.DTLVardef@36f4bdorg.highwire.dtl.DTLVardef@1fddcd2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Lasaviciute, G. Tariq, K. Sugathan, A. Quin, J. E. Bujila, I. Skorokhod, O. Troye-Blomberg, M. Sverremark-Ekstrom, E. Ostlund Farrants, A.-K. 2024-03-19 doi:10.1101/2024.03.18.585548 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ Profiling trace organic chemical biotransformation genes, enzymes and associated bacteria in microbial model communities ]]> https://biorxiv.org/content/10.1101/2024.03.25.586518v1?rss=1 Cao, L. Garcia, S. L. Wurzbacher, C. 2024-03-25 doi:10.1101/2024.03.25.586518 Cold Spring Harbor Laboratory Press 2024-03-25 <![CDATA[ Altered empathy processing in frontotemporal dementiaA task-based fMRI study ]]> https://biorxiv.org/content/10.1101/2024.03.21.586051v1?rss=1 Lindberg, O. Li, T.-Q. Lind, C. Vest, S. Alm, O. Stiernstedt, M. Ericson, A. B, N. Hansson, O. Harper, L. Westman, E. Graff, C. Tsevis, T. Mannfolk, P. Fischer, H. Nilsonne, G. Petrovic, P. Nyberg, L. Wahlund, L.-O. Santillo, A. 2024-03-26 doi:10.1101/2024.03.21.586051 Cold Spring Harbor Laboratory Press 2024-03-26 <![CDATA[ The PR factor Hamlet controls heterotypic epithelial tissue assembly in Drosophila reproduction system ]]> https://biorxiv.org/content/10.1101/2024.04.05.588322v1?rss=1 Wang, H. Bertonnier-Brouty, L. Artner, I. Wen, J. Dai, Q. 2024-04-10 doi:10.1101/2024.04.05.588322 Cold Spring Harbor Laboratory Press 2024-04-10 <![CDATA[ Worldwide soundscape ecology patterns across realms ]]> https://biorxiv.org/content/10.1101/2024.04.10.588860v1?rss=1 Darras, K. F. Rountree, R. Van Wilgenburg, S. Dong, L. Gasc, A. Chen, Y. Lin, T.-H. Diaz, P. M. Wu, S.-H. Salton, M. Marley, S. Cord, A. F. Aparecido Do Nascimento, L. Astaras, C. Barbaro, L. Bellisario, K. Ben David, A. Berger-Tal, O. Bhalla, I. Bolgan, M. Bradfer-Lawrence, T. Briers, R. A. Budka, M. Cerezo-Araujo, M. Cerwen, G. Desjonqueres, C. Diniz, P. Duarte, A. Enari, H. Enari, H. S. Freitas, B. Friedman, N. Froidevaux, J. Gogoleva, S. Goodale, E. Greenhalgh, J. Hagge, J. Jacot, A. Jahn, O. Kepfer Rojas, S. Lloyd, K. J. Mammides, C. Marcacci, G. 2024-04-14 doi:10.1101/2024.04.10.588860 Cold Spring Harbor Laboratory Press 2024-04-14 <![CDATA[ Single-nuclei histone modification profiling of the adult human central nervous system unveils epigenetic memory of developmental programs ]]> https://biorxiv.org/content/10.1101/2024.04.15.589512v1?rss=1 Kabbe, M. Agirre, E. Carlstrom, K. E. Baldivia Pohl, F. Ruffin, N. van Bruggen, D. Meijer, M. Seeker, L. A. Bestard-Cuche, N. Lederer, A. R. Zhang, J. Ahola, V. Goldman, S. A. Bartosovic, M. Jagodic, M. Williams, A. Castelo-Branco, G. 2024-04-16 doi:10.1101/2024.04.15.589512 Cold Spring Harbor Laboratory Press 2024-04-16 <![CDATA[ Partial Fitch Graphs: Characterization, Satisfiability and Complexity ]]> https://biorxiv.org/content/10.1101/2024.04.30.591842v1?rss=1 Korchmaros, A. Hellmuth, M. Ramirez-Rafael, J. A. Schmidt, B. Stadler, P. F. Thekkumpadan Puthiyaveedu, S. 2024-05-03 doi:10.1101/2024.04.30.591842 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Survival, Movement, and Lifespan: Decoding the Roles of Patched-Related (Ptr) in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2024.05.07.592982v1?rss=1 Parada, C. Cantera, R. Prieto, D. 2024-05-08 doi:10.1101/2024.05.07.592982 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ Cotranslational membrane insertion of the voltage-sensitive K+ channel KvAP ]]> https://biorxiv.org/content/10.1101/2024.05.28.596144v1?rss=1 Westerfield, J. Kozojedova, P. Juli, C. Metola, A. von Heijne, G. 2024-05-29 doi:10.1101/2024.05.28.596144 Cold Spring Harbor Laboratory Press 2024-05-29 <![CDATA[ Nuclear phylogenomics of grasses (Poaceae) supports current classification and reveals repeated reticulation ]]> https://biorxiv.org/content/10.1101/2024.05.28.596153v1?rss=1 Grass Phylogeny Working Group 3, Arthan, W. Baker, W. J. Barrett, M. D. Barrett, R. L. Bennetzen, J. Besnard, G. Bianconi, M. E. Birch, J. L. Catalan, P. Chen, W. Christenhusz, M. Christin, P.-A. Clark, L. G. Couch, C. A. Columbus, J. T. Crayn, D. M. Davidse, G. Dunning, L. T. Duvall, M. R. Dransfield, S. Ficinski, S. Z. Fisher, A. E. Fjellheim, S. Forest, F. Gillespie, L. J. Hackel, J. Haevermans, T. Hodkinson, T. R. Huang, C.-H. Huang, W. Humphreys, A. M. Jobson, R. W. Kayombo, C. J. Kellogg, E. A. Kimeu, J. M. Larridon, I. Letsara, R. Li, D.-Z. Liu, 2024-06-02 doi:10.1101/2024.05.28.596153 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ Molecular principles of redox-coupled sodium pumping of the ancient Rnf machinery ]]> https://biorxiv.org/content/10.1101/2024.06.21.599731v1?rss=1 Kumar, A. Roth, J. Kim, H. Saura, P. Bohn, S. Reif-Trauttmansdorff, T. Schubert, A. Kaila, V. R. I. Schuller, J. Mueller, V. 2024-06-21 doi:10.1101/2024.06.21.599731 Cold Spring Harbor Laboratory Press 2024-06-21 <![CDATA[ Drought tolerance as an evolutionary precursor to frost and winter tolerance in grasses ]]> https://biorxiv.org/content/10.1101/2024.06.29.601311v1?rss=1 Schat, L. Schubert, M. Fjellheim, S. Humphreys, A. M. 2024-07-02 doi:10.1101/2024.06.29.601311 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Ancient tree-topologies and gene-flow processes among human lineages in Africa ]]> https://biorxiv.org/content/10.1101/2024.07.15.603519v1?rss=1 Breton, G. Sjodin, P. Zervakis, P. I. Laurent, R. Froment, A. Sjostrand, A. E. Hewlett, B. S. Barreiro, L. B. Perry, G. H. Soodyall, H. Heyer, E. Schlebusch, C. M. Jakobsson, M. Verdu, P. 2024-07-16 doi:10.1101/2024.07.15.603519 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Atypical soluble guanylyl cyclases control brain size in Drosophila ]]> https://biorxiv.org/content/10.1101/2024.07.17.603894v1?rss=1 Prieto, D. Egger, B. Cantera, R. 2024-07-22 doi:10.1101/2024.07.17.603894 Cold Spring Harbor Laboratory Press 2024-07-22 <![CDATA[ Bursts of rapid diversification, dispersals out of southern Africa, and two origins of dioecy punctuate the evolution of Asparagus ]]> https://biorxiv.org/content/10.1101/2024.07.25.605174v1?rss=1 Bentz, P. C. Burrows, J. E. Burrows, S. M. Mizrachi, E. Liu, Z. Yang, J.-B. Mao, Z. Popecki, M. Seberg, O. Petersen, G. Leebens-Mack, J. 2024-07-25 doi:10.1101/2024.07.25.605174 Cold Spring Harbor Laboratory Press 2024-07-25 <![CDATA[ A common pathway controls cell size in the sepal and leaf epidermis leading to a non-random pattern of giant cells ]]> https://biorxiv.org/content/10.1101/2024.07.26.605215v1?rss=1 Clark, F. K. Weissbart, G. Wang, X. Harline, K. Li, C.-B. Formosa-Jordan, P. Roeder, A. H. K. 2024-07-29 doi:10.1101/2024.07.26.605215 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ Cryo-EM structures of {rho}1 GABA(A) receptors with antagonist and agonist drugs ]]> https://biorxiv.org/content/10.1101/2024.07.30.605774v1?rss=1 Fan, C. Cowgill, J. Howard, R. J. Lindahl, E. 2024-07-30 doi:10.1101/2024.07.30.605774 Cold Spring Harbor Laboratory Press 2024-07-30 <![CDATA[ Multipartite complexity of the lichen symbiosis revealed by metagenome and transcriptome analysis of Xanthoria parietina ]]> https://biorxiv.org/content/10.1101/2024.08.16.608140v1?rss=1 Tagirdzhanova, G. Scharnagl, K. Sahu, N. Yan, X. Bucknell, A. Bentham, A. R. Jegousse, C. Ament-Velasquez, S. L. Brännström, I. O. Johannesson, H. MacLean, D. Talbot, N. J. 2024-08-17 doi:10.1101/2024.08.16.608140 Cold Spring Harbor Laboratory Press 2024-08-17 <![CDATA[ Single-residue effects on the behavior of a nascent polypeptide chain inside the ribosome exit tunnel ]]> https://biorxiv.org/content/10.1101/2024.08.20.608737v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@d61d3forg.highwire.dtl.DTLVardef@11a3fa3org.highwire.dtl.DTLVardef@47e7ecorg.highwire.dtl.DTLVardef@cb4fb7_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Pardo Avila, F. Kudva, R. Levitt, M. Von Heijne, G. 2024-08-20 doi:10.1101/2024.08.20.608737 Cold Spring Harbor Laboratory Press 2024-08-20 <![CDATA[ Investigating the impact of the interstitial fluid flow and hypoxia interface on cancer biology using a spheroid-on-chip perfusion system ]]> https://biorxiv.org/content/10.1101/2024.08.21.608919v1?rss=1 Pyne, E. Reardon, M. Christensen, M. Rodriguez-Mateos, P. Taylor, S. Iles, A. Choudhury, A. Pamme, N. M. Pires, I. M. 2024-08-22 doi:10.1101/2024.08.21.608919 Cold Spring Harbor Laboratory Press 2024-08-22 <![CDATA[ Caveolin assemblies displace one bilayer leaflet to organize and bend membranes ]]> https://biorxiv.org/content/10.1101/2024.08.28.610209v1?rss=1 Doktorova, M. Daum, S. Ebenhan, J. Neudorf, S. Han, B. Sharma, S. Kasson, P. Levental, K. Bacia, K. Kenworthy, A. K. Levental, I. 2024-08-30 doi:10.1101/2024.08.28.610209 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Posterior specification of multi-lineage axial assembloids from human pluripotent stem cells. ]]> https://biorxiv.org/content/10.1101/2024.08.29.610410v1?rss=1 Kee, N. Leboeuf, M. Gomez, S. Petipre, C. Mei, I. Benlefki, S. Hagey, D. W. Dias, J. Lallemend, F. EL Andaloussi, S. Ericson, J. Hedlund, E. 2024-08-30 doi:10.1101/2024.08.29.610410 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ A Distinct Alternative mRNA Splicing Profile Identifies the Oncogenic CD44 Transcript Variant 3 in KMT2A-Rearranged Pediatric T-cell Acute Lymphoblastic Leukemia Cells ]]> https://biorxiv.org/content/10.1101/2024.09.05.611385v1?rss=1 Ramilo Amor, A. Enlund, S. Sinha, I. Jiang, Q. Hermanson, O. Nilsson, A. Shirazi Fard, S. Holm, F. 2024-09-06 doi:10.1101/2024.09.05.611385 Cold Spring Harbor Laboratory Press 2024-09-06 <![CDATA[ Bacterial transcriptional repressor NrdR - a flexiblemultifactorial nucleotide sensor ]]> https://biorxiv.org/content/10.1101/2024.09.04.609659v1?rss=1 Rozman Grinberg, I. Bimai, O. Shahid, S. Philipp, L. Martinez-Carranza, M. Banerjee, I. Lundin, D. Stenmark, P. Sjoberg, B.-M. Logan, D. T. 2024-09-08 doi:10.1101/2024.09.04.609659 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ Inkjet-printed graphene multielectrode arrays: an accessible platform for in vitro cardiac electrophysiology ]]> https://biorxiv.org/content/10.1101/2024.09.09.611887v1?rss=1 Lumpuy-Castillo, J. Fu, Y. Avila, A. Solodka, K. Li, J. Lorenzo, O. Zeglio, E. Garma, L. D. 2024-09-13 doi:10.1101/2024.09.09.611887 Cold Spring Harbor Laboratory Press 2024-09-13 <![CDATA[ Multiplexed spatial mapping of chromatin features, transcriptome, and proteins in tissues ]]> https://biorxiv.org/content/10.1101/2024.09.13.612892v1?rss=1 Guo, P. Mao, L. Chen, Y. Lee, C. N. Cardilla, A. Li, M. Bartosovic, M. Deng, Y. 2024-09-19 doi:10.1101/2024.09.13.612892 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ The long-term evolutionary potential of four yeast species and their hybrids in extreme temperature conditions ]]> https://biorxiv.org/content/10.1101/2024.09.27.615317v1?rss=1 Pinto, J. Stelkens, R. 2024-09-28 doi:10.1101/2024.09.27.615317 Cold Spring Harbor Laboratory Press 2024-09-28 <![CDATA[ Genomic stability in the Galapagos Scalesia adaptive radiation: Consistent transposable element accumulation despite hybridization and ecological niche shifts ]]> https://biorxiv.org/content/10.1101/2024.09.30.614436v1?rss=1 Cerca, J. Jaramillo Diaz, P. Goubert, C. Yang, H. Bieke, V. C. Fernandez-Mazuecos, M. Vargas, P. Schley, R. J. Li, S. Guevara-Andino, J. E. Petersen, B. Petersen, G. Sinha, N. Nielsen, L. R. Leebens-Mack, J. Rivas-Torres, G. Rieseberg, L. H. Martin, M. 2024-10-01 doi:10.1101/2024.09.30.614436 Cold Spring Harbor Laboratory Press 2024-10-01 <![CDATA[ Catalytic-dependent and independent functions of the histone acetyltransferase CBP promote pioneer factor-mediated zygotic genome activation ]]> https://biorxiv.org/content/10.1101/2024.10.04.616638v1?rss=1 Marsh, A. J. Pirogov, S. Ruffridge, A. J. Sajwan, S. Gibson, T. J. Hunt, G. Kaur, Y. Harrison, M. M. Mannervik, M. 2024-10-05 doi:10.1101/2024.10.04.616638 Cold Spring Harbor Laboratory Press 2024-10-05 <![CDATA[ The ambiguity of "hybrid swarm": inconsistent definitions and applications in existing research ]]> https://biorxiv.org/content/10.1101/2024.10.11.617831v1?rss=1 Campbell, J. N. Mandeville, E. G. Lewis, N. C. Meuser, A. V. 2024-10-12 doi:10.1101/2024.10.11.617831 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Medieval genomes from eastern Iberia illuminate the role of Morisco mass deportations in dismantling a long-standing genetic bridge with North Africa ]]> https://biorxiv.org/content/10.1101/2024.10.09.617385v1?rss=1 Oteo-Garcia, G. Silva, M. Foody, M. G. B. Yau, B. Fichera, A. Alapont, L. Justeau, P. Rodrigues, S. Monteiro, R. Gandini, F. Rovira, M. Ribera i Lacomba, A. Beneyto, J. P. Mattiangeli, V. Bradley, D. G. Edwards, C. J. Pala, M. Richards, M. B. 2024-10-13 doi:10.1101/2024.10.09.617385 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ Ancient DNA analyses of two Early Chalcolithic Individuals from the West Mound ]]> https://biorxiv.org/content/10.1101/2024.10.22.619570v1?rss=1 Dogu, A. Kaptan, D. Yuncu, E. Gurun, K. Vural, K. B. Chylenski, M. Byrnes, J. Gotherstrom, A. Ozer, F. Somel, M. 2024-10-23 doi:10.1101/2024.10.22.619570 Cold Spring Harbor Laboratory Press 2024-10-23 <![CDATA[ Sequence-dependent scale for translocon-mediated insertion of interfacial helices in membranes ]]> https://biorxiv.org/content/10.1101/2024.10.23.619793v1?rss=1 Grau, B. Kormos, R. Bano-Polo, M. Chen, K. Garcia-Murria, M. J. Hajredini, F. Sanchez del Pino, M. Jo, H. Martinez-Gil, L. Von Heijne, G. DeGrado, W. Mingarro, I. 2024-10-25 doi:10.1101/2024.10.23.619793 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ A novel male accessory gland peptide reduces female post-mating receptivity in the brown planthopper ]]> https://biorxiv.org/content/10.1101/2024.10.26.620448v1?rss=1 Zhang, Y.-J. Zhang, N. Bu, R.-T. Nassel, D. R. Gao, C.-F. Wu, S.-F. 2024-10-27 doi:10.1101/2024.10.26.620448 Cold Spring Harbor Laboratory Press 2024-10-27 <![CDATA[ Data of the Insect Biome Atlas: a metabarcoding survey of the terrestrial arthropods of Sweden and Madagascar ]]> https://biorxiv.org/content/10.1101/2024.10.24.619818v1?rss=1 Miraldo, A. Sundh, J. Iwaszkiewicz-Eggebrecht, E. Buczek, M. Goodsell, R. Johansson, H. Fisher, B. L. Raharinjanahary, D. Rajoelison, E. T. Ranaivo, C. Randrianandrasana, C. E. Rafanomezantsoa, J.-J. Manoharan, L. Granqvist, E. van Dijk, L. J. A. Ahlberg, L. Ahlen, D. Aspebo, M. Aström, S. Bellviken, A. Bergman, P.-E. Björklund, S. Björkman, M. P. Deng, J. Desborough, L. Dolff, E. Eliasson, A. Elmquist, H. Emanuelsson, H. Z. S. Erixon, R. Fahlen, L. Frogner, C. Fürst, P. Grabs, A. Grudd, H. Guasconi, D. Gunnarsson, M. Häggqvist, S. Hed, A. Hörnströ 2024-10-28 doi:10.1101/2024.10.24.619818 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ De novo clustering of extensive long-read transcriptome datasets with isONclust3 ]]> https://biorxiv.org/content/10.1101/2024.10.29.620862v1?rss=1 Petri, A. J. Sahlin, K. 2024-11-03 doi:10.1101/2024.10.29.620862 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ Clock genes period and timeless control synaptogenesis in Drosophila motor terminals ]]> https://biorxiv.org/content/10.1101/2024.11.15.621522v1?rss=1 Ferreiro, M. J. Astrada, S. Cantera, R. Ruiz, S. 2024-11-17 doi:10.1101/2024.11.15.621522 Cold Spring Harbor Laboratory Press 2024-11-17 <![CDATA[ Systematic exploration of domain assortments in NOD-like receptors uncovers two types of NACHT domains in Sordariales fungi ]]> https://biorxiv.org/content/10.1101/2024.11.26.625400v1?rss=1 bonometti, l. charriat, f. hensen, n. Minana Posada, S. johannesson, h. Gladieux, P. 2024-11-28 doi:10.1101/2024.11.26.625400 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ A novel menthol-DCMU bleaching method for foraminifera: Generating aposymbiotic hosts for symbiosis research ]]> https://biorxiv.org/content/10.1101/2024.12.09.627035v1?rss=1 Schmidt, C. Puerto Rueda, D. N. Nusser, M. Oakley, C. A. Pochon, X. Stuhr, M. Raposo, D. S. Davy, S. K. 2024-12-10 doi:10.1101/2024.12.09.627035 Cold Spring Harbor Laboratory Press 2024-12-10 <![CDATA[ ColBuilder: Flexible structure generation of crosslinked collagen fibrils ]]> https://biorxiv.org/content/10.1101/2024.12.10.627782v1?rss=1 Monego, D. Brosz, M. Buck, J. Viliuga, V. Jung, J. Stuehn, T. Schmies, M. Sugita, Y. Gräter, F. 2024-12-12 doi:10.1101/2024.12.10.627782 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ HAPP: High-Accuracy Pipeline for Processing deep metabarcoding data ]]> https://biorxiv.org/content/10.1101/2024.12.20.629441v1?rss=1 Sundh, J. Granqvist, E. Iwaszkiewicz-Eggebrecht, E. Manoharan, L. van Dijk, L. J.- A. Goodsell, R. Godeiro, N. Bellini, B. Lukasik, P. Miraldo, A. Roslin, T. Tack, A. J. M. Andersson, A. A. Ronquist, F. 2024-12-22 doi:10.1101/2024.12.20.629441 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ QUANTIFYING ACYL CHAIN INTERDIGITATION IN SIMULATED BILAYERS VIA DIRECT TRANSBILAYER INTERACTIONS ]]> https://biorxiv.org/content/10.1101/2024.12.20.629658v1?rss=1 Chaisson, E. H. Heberle, F. A. Doktorova, M. 2024-12-22 doi:10.1101/2024.12.20.629658 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Whole-genome duplication increases genetic diversity and load in outcrossing Arabidopsis ]]> https://biorxiv.org/content/10.1101/2025.01.12.632621v1?rss=1 Vlcek, J. Hamala, T. Cobo, C. V. Curran, E. Sramkova, G. Slotte, T. Schmickl, R. Yant, L. Kolar, F. 2025-01-15 doi:10.1101/2025.01.12.632621 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Genomic studies in Linum shed light on the evolution of the distyly supergene and the molecular basis of convergent floral evolution ]]> https://biorxiv.org/content/10.1101/2025.04.11.648331v1?rss=1 30 Mya in Linum. In combination with findings from other systems, our results suggest that the brassinosteroid pathway frequently contributes to style length polymorphism. C_LI ]]> Zervakis, P.-I. Postel, Z. Losvik, A. Fracassetti, M. Soler, L. Proux-Wera, E. Bunikis, I. Churcher, A. Slotte, T. 2025-04-17 doi:10.1101/2025.04.11.648331 Cold Spring Harbor Laboratory Press 2025-04-17 <![CDATA[ The effect of Shifts in Fish Community Structure on PCDD/F temporal variability in common guillemot (Baltic Sea) ]]> https://biorxiv.org/content/10.1101/2025.04.14.648406v1?rss=1 Ammar, Y. olsson, j. Gorokhova, E. Skold, M. Faxneld, S. Hentati-Sundberg, J. Soerensen, A. L. 2025-04-19 doi:10.1101/2025.04.14.648406 Cold Spring Harbor Laboratory Press 2025-04-19 <![CDATA[ A Novel Model for Proton Transport Mediated by Uncoupling Protein 1 ]]> https://biorxiv.org/content/10.1101/2025.04.28.650983v1?rss=1 Jacobsen, L. Menon, S. Gaudry, M. J. Hakami Zanjani, A. A. Reinholdt, P. Jastroch, M. Khandelia, H. 2025-05-01 doi:10.1101/2025.04.28.650983 Cold Spring Harbor Laboratory Press 2025-05-01 <![CDATA[ Patterns and drivers of genome-wide codon usage bias in the fungal order Sordariales ]]> https://biorxiv.org/content/10.1101/2025.05.07.652452v1?rss=1 Hensen, N. Hiltunen Thoren, M. Johannesson, H. 2025-05-10 doi:10.1101/2025.05.07.652452 Cold Spring Harbor Laboratory Press 2025-05-10 <![CDATA[ Transcription factor NFYA directs male meiotic entry by facilitating accessible chromatin at meiotic promoters in mice ]]> https://biorxiv.org/content/10.1101/2025.05.09.653044v1?rss=1 Saflund, M. Askari, M. Eghbali, A. Abdi, M. M. Östlund Farrants, A.-K. Yu, T. Ozata, D. M. 2025-05-14 doi:10.1101/2025.05.09.653044 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ AI4CellFate: Interpretable Early Cell Fate Prediction with Generative AI ]]> https://biorxiv.org/content/10.1101/2025.05.12.653464v1?rss=1 Cunha, I. Panconi, L. Bauer, S. Gestin, M. Latron, E. Sahai, E. Le Marois, A. Griffie, J. 2025-05-14 doi:10.1101/2025.05.12.653464 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ Widespread potential for phototrophy and convergent reduction of lifecycle complexity in the dimorphic order Caulobacterales ]]> https://biorxiv.org/content/10.1101/2025.05.26.656076v1?rss=1 Hallgren, J. Dharamshi, J. E. Rodriguez-Gijon, A. Nuy, J. Garcia, S. L. Jonas, K. 2025-05-26 doi:10.1101/2025.05.26.656076 Cold Spring Harbor Laboratory Press 2025-05-26 <![CDATA[ Beneficial and detrimental consequences of AHR activation in intestinal infection ]]> https://biorxiv.org/content/10.1101/2025.05.28.656570v1?rss=1 Diaz, O. P. zhou, L. Barrington, C. Lindquist, D. Graelmann, F. Wincent, E. Stockinger, B. 2025-06-01 doi:10.1101/2025.05.28.656570 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ A conserved glycan motif overcomes antigenic variation inducing broadly reactive antibodies against the zoonotic pathogen Streptococcus suis ]]> https://biorxiv.org/content/10.1101/2025.06.02.656523v1?rss=1 Shi, Y. Widmalm, G. Sorieul, C. Roodsant, T. J. Rush, J. S. Korotkova, N. Jacobs, A. A. C. Spaninks, M. Grommen, R. Dominguez-Medina, C. C. Schimmel, I. M. van der Wel, N. N. Kenner, C. W. Heiss, C. Azadi, P. Tan, L. Codee, J. D. C. Stegeman, A. Schultsz, C. Benedictus, L. van Sorge, N. M. 2025-06-03 doi:10.1101/2025.06.02.656523 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Microbial hydrocarbon degradation potential of the Baltic Sea ecosystem ]]> https://biorxiv.org/content/10.1101/2025.06.02.657333v1?rss=1 10 reads per kilobase million). Aerobic degradation was the predominant pathway for hydrocarbon degradation across environmental samples. Hydrocarbon degradation gene abundances varied among samples and Baltic Sea subbasins, with long-chain alkanes and dibenzothiophene compounds being the preferred substrates. Species richness and diversity of both benthic and pelagic microorganisms positively correlated with hydrocarbon degradation gene diversity, with the pelagic ecosystem exhibiting significantly higher richness and diversity compared to the benthic ecosystem. Additionally, the composition of the hydrocarbon degradation genes across the Baltic Sea subbasins was influenced by oil spill history, with areas that experienced higher spill volumes showing lower microbial diversity, suggesting potential enrichment of specific hydrocarbon degraders. Among the environmental factors assessed, depth played a significant role in shaping the composition of genes involved in hydrocarbon degradation within the Baltic Sea. ConclusionsUsing metagenomics, we profiled the native microorganisms associated with hydrocarbon degradation in the Baltic Sea. This knowledge will aid in understanding the natural capacities of microbial communities, potentially linked to the natural attenuation of hydrocarbon pollutants in the area. Insights into microbial degradation potential can enhance predictions of petroleum pollutant persistence and accumulation, support mitigation strategies for marine pollution, and reveal the ecological resilience of native microbial communities in marine ecosystems. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/657333v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@1ba6e59org.highwire.dtl.DTLVardef@a2c000org.highwire.dtl.DTLVardef@eb7bd2org.highwire.dtl.DTLVardef@e4dce_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Serrana, J. M. Dessirier, B. Nascimento, F. J. A. Broman, E. Posselt, M. 2025-06-04 doi:10.1101/2025.06.02.657333 Cold Spring Harbor Laboratory Press 2025-06-04 <![CDATA[ Pasta, an age-shift transcriptomic clock, maps the chemical and genetic determinants of aging and rejuvenation ]]> https://biorxiv.org/content/10.1101/2025.06.04.657785v1?rss=1 Salignon, J. Tsiokou, M. Marques, P. Rodriguez-Diaz, E. Ang, H. Pietrocola, F. Riedel, C. G. 2025-06-04 doi:10.1101/2025.06.04.657785 Cold Spring Harbor Laboratory Press 2025-06-04 <![CDATA[ Neural adolescent pragmatic development mirrors pragmatic differences in adulthood: an fMRI-study ]]> https://biorxiv.org/content/10.1101/2025.06.27.661903v1?rss=1 Forbes Schieche, C. Udden, J. 2025-07-01 doi:10.1101/2025.06.27.661903 Cold Spring Harbor Laboratory Press 2025-07-01 <![CDATA[ Disruption of hemocyte differentiation and distribution in Drosophila Ptr23c mutants ]]> https://biorxiv.org/content/10.1101/2025.07.03.662979v1?rss=1 Parada, C. Silvera, M. C. de los Campos, T. Cantera, R. Bolatto, C. Prieto, D. 2025-07-03 doi:10.1101/2025.07.03.662979 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ Evolutionary constraints in host shifts: limited adaptation of Plutella xylostella to cardenolide-defended Erysimum cheiranthoides ]]> https://biorxiv.org/content/10.1101/2025.07.04.663117v1?rss=1 Biswas, B. van Bergen, E. Vaello, T. Daellenbach, L. J. Wheat, C. W. Zuest, T. 2025-07-07 doi:10.1101/2025.07.04.663117 Cold Spring Harbor Laboratory Press 2025-07-07 <![CDATA[ Extensive multi-species hybridization between Leuciscidae minnow species ]]> https://biorxiv.org/content/10.1101/2025.07.14.664671v1?rss=1 Meuser, A. V. Pitura, A. R. McFarlane, S. E. Mandeville, E. G. 2025-07-18 doi:10.1101/2025.07.14.664671 Cold Spring Harbor Laboratory Press 2025-07-18 <![CDATA[ AEMB: a computationally efficient abundance estimation method for metagenomic binning ]]> https://biorxiv.org/content/10.1101/2025.07.30.667338v1?rss=1 Pan, S. Tolstoganov, I. Sahlin, K. Martin, M. Zhao, X.-M. Coelho, L. P. 2025-08-01 doi:10.1101/2025.07.30.667338 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ A ventral striatal learning signal reflecting individual differences in the success of fear extinction ]]> https://biorxiv.org/content/10.1101/2025.08.26.672387v1?rss=1 Andres, E. Chuan-Peng, H. Gerlicher, A. M. V. Tuescher, O. Kalisch, R. 2025-08-27 doi:10.1101/2025.08.26.672387 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ Cotranslational folding and maturation of HIV-1 protease ]]> https://biorxiv.org/content/10.1101/2025.08.27.672612v1?rss=1 Westerfield, J. M. Nicolaus, F. Swanstrom, R. M. von Heijne, G. 2025-08-27 doi:10.1101/2025.08.27.672612 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ A Quantitative Polymerase Chain Reaction Protocol for Sex Identification of Zebra Finch and Chicken Using Blood Samples ]]> https://biorxiv.org/content/10.1101/2025.08.27.671803v1?rss=1 Subba, P. Adeniran-Obey, S. O. Kraft, F.-L. H. Chapman, S. C. Shay, N. A. Liedl, S. R. Wild, M. D. Wolcott, S. A. George, J. M. 2025-08-28 doi:10.1101/2025.08.27.671803 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ Endogenous corazonin signaling modulates the post-mating switch in behavior and physiology in females of the brown planthopper and Drosophila ]]> https://biorxiv.org/content/10.1101/2025.09.07.674776v1?rss=1 Zhang, N. Su, S.-C. Bu, R.-T. Zhang, Y.-J. Yang, L. Chen, J. Nassel, D. R. Gao, C.-F. Wu, S.-F. 2025-09-12 doi:10.1101/2025.09.07.674776 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ Interplay between purging and admixture shapes genetic load in an invasive guppy population ]]> https://biorxiv.org/content/10.1101/2025.09.12.675788v1?rss=1 Burda, K. Janecka, M. J. Mohammed, R. S. Clark, D. R. Kramp, R. Stephenson, J. F. Radwan, J. Konczal, M. 2025-09-16 doi:10.1101/2025.09.12.675788 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Aggregation in experimental studies with microparticles: Bacterial communities in the exposure system affect animal responses to the test particles ]]> https://biorxiv.org/content/10.1101/2025.09.13.676006v1?rss=1 Reichelt, S. El-Shehawy, R. Gorokhova, E. 2025-09-17 doi:10.1101/2025.09.13.676006 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Continuous Serial Electron Diffraction for High Quality Protein Structures ]]> https://biorxiv.org/content/10.1101/2025.09.14.676192v1?rss=1 Hofer, G. Wang, L. Pacoste, L. Hager, P. Fonjallaz, A. Williams, L. Scaletti Hutchinson, E. Di Palma, M. Stenmark, P. Worral, J. Steiner, R. A. Xu, H. Zou, X. 2025-09-17 doi:10.1101/2025.09.14.676192 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Eastern Baltic cod larvae in a salinity gradient: choice of salinity and the role of neutral buoyancy ]]> https://biorxiv.org/content/10.1101/2025.09.18.677118v1?rss=1 Garate-Olaizola, M. Frojd, J. Behrens, J. W. Sorensen, S. R. Cortazar-Chinarro, M. Laurila, A. 2025-09-20 doi:10.1101/2025.09.18.677118 Cold Spring Harbor Laboratory Press 2025-09-20 <![CDATA[ CryoEM of ATP-driven dynamics and itraconazole binding in a fungal ABC pump ]]> https://biorxiv.org/content/10.1101/2025.09.22.677697v1?rss=1 Pata, J. Wiseman, B. Zarkadas, E. Baccouch, R. Samrouth, N. Desbois, C. Moissonier, L. Moreno, A. Banerjee, A. Aguerro, S. Bettler, E. Dujardin, M. Terreux, R. Schoehn, G. Hogbom, M. Boumendjel, A. Lamping, E. Cannon, R. Prasad, R. Chaptal, V. Falson, P. 2025-09-22 doi:10.1101/2025.09.22.677697 Cold Spring Harbor Laboratory Press 2025-09-22 <![CDATA[ Internal mechanosensory feedback modulates central pattern generation to coordinate ovulation in Drosophila ]]> https://biorxiv.org/content/10.1101/2025.09.22.677773v1?rss=1 Su, S. Zhang, N. Li, C.-Y. Nassel, D. R. Gao, C.-F. Wu, S.-F. 2025-09-22 doi:10.1101/2025.09.22.677773 Cold Spring Harbor Laboratory Press 2025-09-22 <![CDATA[ 6S RNA facilitates bacterial virulence and adaptation at the epithelial barrier ]]> https://biorxiv.org/content/10.1101/2025.10.07.681022v1?rss=1 Sarigoz, O. Valeriano, V. D. Avican, U. Wang, H. Nilsson, K. Hasanzade, N. Mahmood, F. Fahlgren, A. Bauer, S. griffie, J. Fallman, M. Avican, K. 2025-10-08 doi:10.1101/2025.10.07.681022 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ Universal Hyb-Seq kits capture considerable intraspecific variation: Less is more in herbarium-inclusive molecular ecology ]]> https://biorxiv.org/content/10.1101/2025.10.14.682325v1?rss=1 Woudstra, Y. Quatela, A.-S. Wagemaker, N. C. Ivanovic, S. Meirmans, P. Slotte, T. Gravendeel, B. Verhoeven, K. J. 2025-10-15 doi:10.1101/2025.10.14.682325 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ 2000-year fish bone record reveals transition to commercial fisheries during climatic change ]]> https://biorxiv.org/content/10.1101/2025.10.14.682357v1?rss=1 Buss, D. L. Parker, A. K. Falahati-Anbaran, M. Zliobaite, I. Connolly, R. Royle, T. C. A. Ballantyne, R. Boethuis, A. Dutting, M. K. Enehaug, M. N. Enghoff, I. B. Ervynck, A. Hamilton-Dyer, S. Harland, J. F. Hoffmann, R. C. Holm, P. Hufthammer, A. K. van der Jagt, I. Krooks, B. Kuchelmann, H. C. Ljungqvist, F. C. Lougas, L. Magnell, O. Makowiecki, D. Maltin, E. Meijer, H. Mills, W. F. Nicholson, R. Quinlan, L. Russ, H. Ritchie, K. Seim, A. Van Neer, W. Wouters, W. Barrett, J. H. 2025-10-15 doi:10.1101/2025.10.14.682357 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Male social dominance affects access to mates but not female mate choice in a livebearing fish ]]> https://biorxiv.org/content/10.1101/2025.10.16.682567v1?rss=1 Goncalves, A. Reuland, C. Daupagne, L. Wheatcroft, D. Kolm, N. Fitzpatrick, J. L. 2025-10-16 doi:10.1101/2025.10.16.682567 Cold Spring Harbor Laboratory Press 2025-10-16 <![CDATA[ Sexually antagonistic co-evolution at the molecular level predicts phenotypic outcomes of mating interactions. ]]> https://biorxiv.org/content/10.1101/2025.11.04.686516v1?rss=1 Thorson, A. Snook, R. Wiberg, R. A. W. 2025-11-05 doi:10.1101/2025.11.04.686516 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ The mRNA architecture of the termination site primes programmed stop codon readthrough events in Drosophila ]]> https://biorxiv.org/content/10.1101/2025.11.07.685291v1?rss=1 View larger version (36K): org.highwire.dtl.DTLVardef@dbccf6org.highwire.dtl.DTLVardef@6d53f3org.highwire.dtl.DTLVardef@1a27deborg.highwire.dtl.DTLVardef@f8e5ae_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kansara, L. Wolfstetter, G. Wintermayr, D. Alexopoulos, I. Escos, A. Friedländer, M. R. Engström, Y. 2025-11-07 doi:10.1101/2025.11.07.685291 Cold Spring Harbor Laboratory Press 2025-11-07 <![CDATA[ Ancient balanced polymorphism underlies long-standing adaptation for seasonal camouflage in the least weasel ]]> https://biorxiv.org/content/10.1101/2025.11.14.688436v1?rss=1 Miranda, I. Ruivo, R. Farelo, L. Alvarenga, M. Borowski, Z. Elmeros, M. Kalthoff, D. C. Merilä, J. Müller, J. P. Schley, L. Suchentrunk, F. Sundell, J. Rodrigues, M. Santos-Reis, M. Fernandes, C. R. Zub, K. Good, J. M. Mills, L. S. Castro, L. F. C. Dalen, L. Melo-Ferreira, J. 2025-11-15 doi:10.1101/2025.11.14.688436 Cold Spring Harbor Laboratory Press 2025-11-15 <![CDATA[ Tangerine: a Starship-like element in the genomes of Xanthoria lichen-forming fungi ]]> https://biorxiv.org/content/10.1101/2025.11.25.690456v1?rss=1 Tagirdzhanova, G. Bucknell, A. Cameron, E. S. Finn, R. D. Blaxter, M. McDonald, M. C. Talbot, N. J. 2025-11-27 doi:10.1101/2025.11.25.690456 Cold Spring Harbor Laboratory Press 2025-11-27 <![CDATA[ Reevaluating the Role of Beta2-Microglobulin: New Insights on Selective Vulnerability in ALS Pathology ]]> https://biorxiv.org/content/10.1101/2025.11.27.690988v1?rss=1 Leboeuf, M. Nijssen, J. Comley, L. H. Benitez, J. C. A. Mei, I. Alcalde, S. G. Radoi, V. Nichterwitz, S. Schweingruber, C. Hedlund, E. Cullheim, S. 2025-12-01 doi:10.1101/2025.11.27.690988 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ A linear regression model predicts human brain ageing and reveals differential neuronal biological ageing relevant for Parkinson's disease susceptibility ]]> https://biorxiv.org/content/10.64898/2025.12.01.691179v1?rss=1 Cheng, S. Aguila Benitez, J. C. Leboeuf, M. Wang, M. Mei, I. Gomez Alcalde, S. Deng, Q. Sanchez Pernaute, R. Hedlund, E. 2025-12-02 doi:10.64898/2025.12.01.691179 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ A recent shift in centromere size and DNA content in Podospora pseudocomata co-occurs with the loss of a fungal genome defense system ]]> https://biorxiv.org/content/10.64898/2025.12.02.690432v1?rss=1 Westerberg, I. Li, M. Mercier, E. Ament-Velasquez, S. L. Sandell, L. Silar, P. Vogan, A. Grognet, P. Malagnac, F. Johannesson, H. 2025-12-02 doi:10.64898/2025.12.02.690432 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Brain size reduction in dogs was already established at least by the Late Neolithic of western Europe, 5,000 years ago ]]> https://biorxiv.org/content/10.64898/2025.12.12.693870v1?rss=1 Cucchi, T. Hays, L.-M. Veneziano, A. Michaud, M. Brassard, C. Arbogast, R.-M. Petrequin, P. Germonpre, M. B. Cregut-Bonnoure, E. Elleboudt, F. Czeibert, K. Garamszegi, L. Z. Kubinyi, E. Kolm, N. Csorgo, T. Joseph, J. Leroy, S. Guintard, C. Fusellier, M. Duchamp, C. Herrel, A. Koungoulos, L. G. Peachey, T. J. Scarsbrook, L. Frantz, L. Madurell-Malapeira, J. Ladeveze, S. 2025-12-12 doi:10.64898/2025.12.12.693870 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ Gill-associated microbiome as indicators of population stress and condition in Eastern Baltic Cod ]]> https://biorxiv.org/content/10.64898/2025.12.16.694594v1?rss=1 Chinarro, M. C. OLAIZOLA, M. G. FROJD, J. HEIMBRAND, Y. BEHRENS, J. w. LAURILA, A. 2025-12-18 doi:10.64898/2025.12.16.694594 Cold Spring Harbor Laboratory Press 2025-12-18 <![CDATA[ A Non-Transcriptional Mitotic Function of POU/Oct Factors Ensures Spindle Stability and Chromosome Segregation ]]> https://biorxiv.org/content/10.64898/2025.12.19.695428v1?rss=1 Gohel, P. Tsarouhas, V. Kansara, L. Sajwan, S. Engström, Y. 2025-12-21 doi:10.64898/2025.12.19.695428 Cold Spring Harbor Laboratory Press 2025-12-21 <![CDATA[ Atomic resolution structure of spinach rubisco reveals protons and dynamics ]]> https://biorxiv.org/content/10.64898/2025.12.22.696010v1?rss=1 Croy, N. A. Gaullier, G. Saura, P. Masiulis, S. Bhowmick, A. Kern, J. Raschdorf, O. Andersson, I. Kaila, V. R. I. Blikstad, C. Messinger, J. 2025-12-23 doi:10.64898/2025.12.22.696010 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Wastewater-impacted Skagerrak Sea microbiomes anaerobically demethylate micropollutants ]]> https://biorxiv.org/content/10.64898/2026.01.06.697959v1?rss=1 Gilevska, T. Rotaru, A.-E. Anestis, K. Fonseca, A. Kuemmel, S. Krauss, M. Inostroza, P. A. Bonaglia, S. 2026-01-06 doi:10.64898/2026.01.06.697959 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ Mechanism of Alkaline Gating in a Pentameric Ion Channel ]]> https://biorxiv.org/content/10.64898/2026.01.07.698087v1?rss=1 Karlsson, E. Ygland, I. Jansen, A. Plumley, J. Lindahl, E. Howard, R. J. Hess, B. 2026-01-08 doi:10.64898/2026.01.07.698087 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Whole-genome profiling of native 5-hydroxymethylation in human neurons with long-read sequencing ]]> https://biorxiv.org/content/10.64898/2026.01.11.695537v1?rss=1 60%) were enriched in neuron-related terms, with functional variety when stratifying across chromatin states. Analysis of transcription factor motifs in highly methylated regions, demonstrated 5hmC- and 5mC-specific enrichment affecting downstream regulatory networks. Altogether, our study demonstrates the potential of ONT to characterize whole-genome, native 5hmC and 5mC DNA modifications in human neurons, specifically highlighting the enrichment of 5hmC in actively transcribed regions and enhancers in the human brain. ]]> Klose, D. Sepehri, M. H. Olsen, R.-A. Vu, H. Ernst, J. Kular, L. Needhamsen, M. Jagodic, M. 2026-01-12 doi:10.64898/2026.01.11.695537 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ Pollutant biodegradation profile mediated by multi-trophic microbial dynamics in rivers ]]> https://biorxiv.org/content/10.64898/2026.01.14.699447v1?rss=1 Serrana, J. M. Tian, R. Nascimento, F. J. A. Broman, E. Dessirier, B. Posselt, M. 2026-01-14 doi:10.64898/2026.01.14.699447 Cold Spring Harbor Laboratory Press 2026-01-14 <![CDATA[ Assessing local adaptation and divergence at early life stages within Eastern Baltic cod ]]> https://biorxiv.org/content/10.64898/2026.01.20.700346v1?rss=1 Garate-Olaizola, M. Fröjd, J. Larsson Aberg, V. Hodzic-Vazquez, A. Heimbrand, Y. Nissling, A. Behrens, J. W. Cortazar-Chinarro, M. Bergström, U. Laurila, A. 2026-01-22 doi:10.64898/2026.01.20.700346 Cold Spring Harbor Laboratory Press 2026-01-22 <![CDATA[ The marine microbiome can accurately predict its chemical and biological environment ]]> https://biorxiv.org/content/10.64898/2026.01.25.701552v1?rss=1 Bell, E. Garefelt, K. Jurdzinski, K. T. Delgado, L. F. Johansson, F. Karlson, B. Andersson, A. F. 2026-01-25 doi:10.64898/2026.01.25.701552 Cold Spring Harbor Laboratory Press 2026-01-25 <![CDATA[ A Carboxylate Switch Point Controls Long-Range Energy Transduction in Respiratory Complex I ]]> https://biorxiv.org/content/10.64898/2026.01.27.702182v1?rss=1 300 [A]) proton-coupled electron transfer (PCET) reaction. Here, we investigate the unknown coupling mechanism of Complex I by probing the charge transfer reaction along its functionally central carboxylate pathway (E-channel). By combining biophysical and site-directed mutagenesis experiments with high-resolution (2.6-2.7 [A]) cryo-electron microscopy (cryo-EM) and multiscale simulations, we identify a conserved carboxylate switch point (D79NuoA) that mediates proton transfer by establishing a kinetic gate that couples the redox chemistry to proton pumping. We find that mutation of the identified site, as found in patients suffering from severe neurodegenerative disorders, perturbs the charge transfer mechanism, and results in a drastic (>80%) reduction of the long-range PCET activity. Our combined findings illustrate mechanistic principles of molecular gates underlying long-range charge transfer reactions, and show how disease mutations perturb the function of conserved switch points in energy transduction. ]]> Beghiah, A. Saura, P. Kovalova, T. Hoeser, F. Friedrich, T. Kaila, V. R. I. 2026-01-30 doi:10.64898/2026.01.27.702182 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Timing of reproduction modulates fitness effects of local seasonal adaptation in a range expanding butterfly ]]> https://biorxiv.org/content/10.64898/2026.01.28.702196v1?rss=1 Bovolenta, M. Ittonen, M. Gotthard, K. 2026-01-30 doi:10.64898/2026.01.28.702196 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ RNA degradation by DIS3 is a necessary step in the resolution of backtracked transcription complexes ]]> https://biorxiv.org/content/10.64898/2026.02.02.703186v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@c080dorg.highwire.dtl.DTLVardef@1e4b375org.highwire.dtl.DTLVardef@1c1f575org.highwire.dtl.DTLVardef@d9d640_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDIS3 depletion leads to severely reduced rates of RNA synthesis in human cells. C_LIO_LITranscription-blocking lesions reveal a critical role for DIS3 in RNA polymerase II elongation. C_LIO_LIThe 3 to 5 exoribonuclease activity of DIS3 is necessary for transcription elongation. C_LIO_LIDIS3-mediated degradation of backtracked RNA is required for the resolution of stalled transcription complexes. C_LI ]]> Enervald, E. Tarbier, M. Jain, S. Sinha, I. Jain, A. Planells, J. McHugh, T. Visa, N. 2026-02-02 doi:10.64898/2026.02.02.703186 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Repeated heat waves trigger divergent transcriptional responses in cold- and warm-adapted yeast species ]]> https://biorxiv.org/content/10.64898/2026.02.02.703184v1?rss=1 Haberkorn, C. Molinet, J. Stelkens, R. 2026-02-03 doi:10.64898/2026.02.02.703184 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Structural basis of canonical TIR-NLR activation in plant innate immunity ]]> https://biorxiv.org/content/10.64898/2026.02.03.703613v1?rss=1 Maruta, N. Gu, W. Lim, B. Y. J. Sorbello, M. Ngu, D. Jobichen, C. Nanson, J. D. Li, Y. Chen, J. Outram, M. Bernoux, M. P. Rahman, M. M. Vu, T. D. Xu, H. Wang, L. Kwah, K. Burdett, H. Mobli, M. Ve, T. Ellis, J. G. Anderson, P. A. Williams, S. J. Dodds, P. Kobe, B. 2026-02-06 doi:10.64898/2026.02.03.703613 Cold Spring Harbor Laboratory Press 2026-02-06 <![CDATA[ From constraint to opportunity: Relaxing sexual antagonism reveals adaptive potential maintained by balancing selection ]]> https://biorxiv.org/content/10.64898/2026.02.04.703537v1?rss=1 Zwoinska, M. K. Wiberg, R. A. W. Trabert, M. Kaufmann, P. Immonen, E. 2026-02-06 doi:10.64898/2026.02.04.703537 Cold Spring Harbor Laboratory Press 2026-02-06 <![CDATA[ Quasi-continuous cotranslational compaction and folding of a multidomain protein ]]> https://biorxiv.org/content/10.64898/2026.02.04.703729v1?rss=1 Mitsikosta, S. Westerfield, J. M. Pardo-Avila, F. Levitt, M. von Heijne, G. Metola, A. 2026-02-06 doi:10.64898/2026.02.04.703729 Cold Spring Harbor Laboratory Press 2026-02-06 <![CDATA[ Structural basis of caveolin-driven membrane bending ]]> https://biorxiv.org/content/10.64898/2026.02.05.703862v1?rss=1 Connelly, S. M. Bergner, L. Tiwari, A. Brant, T. S. Medford, S. Ramesh, S. Tidwell, E. D. Yoo, Y. Xiao, K. Gentry, J. Chang, L. Han, B. Rangamani, P. Doktorova, M. Kenworthy, A. K. Mosalaganti, S. Ohi, M. D. 2026-02-08 doi:10.64898/2026.02.05.703862 Cold Spring Harbor Laboratory Press 2026-02-08 <![CDATA[ Mitochondrial COX4I2 drives pericyte-dependent inflammation and emphysema ]]> https://biorxiv.org/content/10.64898/2026.02.09.703513v1?rss=1 View larger version (39K): org.highwire.dtl.DTLVardef@83bca4org.highwire.dtl.DTLVardef@d5ebaborg.highwire.dtl.DTLVardef@632d1borg.highwire.dtl.DTLVardef@1267a13_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Garcia Castro, C. F. Balasubramanian Lakshmi, V. S. Hadzic, S. Nardiello, C. Glaser, R. D. Huttemann, M. Grossman, L. I. Kojonazarov, B. Li, M. Jash, S. Koepke, J. Gredic, M. Wu, C.-Y. Giordano, L. Hecker, M. Samakovlis, C. Loku, E. Cilic, A. Better, J. Matt, U. Mueller, B. Stieger, K. Lytvynchuk, L. Pervizaj-Oruqaj, L. Guenther, A. Wilhelm, J. Herold, S. Crnkovic, S. Kwapiszewska, G. Murphy, M. P. Grimminger, F. Bartkuhn, M. Seeger, W. Weissmann, N. Pak, O. Sommer, N. 2026-02-09 doi:10.64898/2026.02.09.703513 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Benchmarking the quantitative performance of metabarcoding and shotgun sequencing using mock communities of marine nematodes ]]> https://biorxiv.org/content/10.64898/2026.02.09.704827v1?rss=1 Izabel-Shen, D. Sandberg, H. Ahmed, M. Broman, E. Holovachov, O. Nascimento, F. J. A. 2026-02-09 doi:10.64898/2026.02.09.704827 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Testing for trait lability at macroevolutionary scales: is life history evolution labile in grasses? ]]> https://biorxiv.org/content/10.64898/2026.02.13.705712v1?rss=1 Schat, L. Humphreys, A. M. 2026-02-16 doi:10.64898/2026.02.13.705712 Cold Spring Harbor Laboratory Press 2026-02-16 <![CDATA[ Accuracy of occurrence and abundance estimates from insect metabarcoding ]]> https://biorxiv.org/content/10.64898/2026.02.20.707016v1?rss=1 Iwaszkiewicz-Eggebrecht, E. Granqvist, E. Nowak, K. H. Valdivia, C. Buczek, M. Srivathsan, A. Hartop, E. Miraldo, A. Roslin, T. Tack, A. J. M. Lukasik, P. Meier, R. Ronquist, F. 2026-02-22 doi:10.64898/2026.02.20.707016 Cold Spring Harbor Laboratory Press 2026-02-22 <![CDATA[ Evolutionary consequences of repeated loss of distyly in Linum ]]> https://biorxiv.org/content/10.64898/2026.03.03.709227v1?rss=1 Postel, Z. Zervakis, P.-I. Fracassetti, M. Losvik, A. Wanntorp, M. Soler, L. Churcher, A. Humphrey, A. M. Slotte, T. 2026-03-04 doi:10.64898/2026.03.03.709227 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Low-barrier hydrogen-bond powers long-range radical transfer in the metal-free ribonucleotide reductase ]]> https://biorxiv.org/content/10.64898/2026.03.06.710006v1?rss=1 30 [A]) proton-coupled electron transfer (PCET) by mechanistic principles that remain much debated. By combing multiscale quantum and classical simulations with directed mutagenesis, x-ray crystallography, and vibrational and electron paramagnetic resonance spectroscopy, we elucidate here the molecular principles underlying how metal-free RNRs initiate the long-range PCET process by creating a highly stable DOPA initiator radical. We show that DOPA* is redox-tuned by a low-barrier hydrogen bond (LBHB), with a delocalized proton that provides the catalytic power for the ribonucleotide reduction. We find that the LBHB couples to an extended hydrogen-bonded network, with distant mutations resulting in the loss of radical formation, and providing key molecular insight into the long-range radical transport mechanism in RNRs. On a general level, our findings support the direct involvement of LBHB in protein chemistry and the importance of quantum effects in enzyme catalysis. Significance StatementRibonucleotide reductases (RNRs) are ancient enzymes responsible for the synthesis of deoxyribonucleotides from ribonucleotides. RNRs catalyze this reaction via a long-range proton-coupled electron transfer (PCET) process, involving the formation of a stable protein radical. Yet, despite decades of detailed structural, biochemical, spectroscopic and computational studies, the mechanistic principles of this process remain unclear and much debated. Here, we show that metal-free RNRs power the reduction of RNA building blocks by a highly stable organic DOPA initiator radical, arising from a unique low-barrier hydrogen bonding (LBHB) network that enables the radical transport by strong redox-tuning effects. Our findings reveal mechanistic principles underlying the elusive PCET reactions of metal-free RNRs, and provide evidence for the involvement of quantum effects in enzyme catalysis. ]]> Sirohiwal, A. John, J. Kutin, Y. Kumar, R. Baserga, F. Srinivas, V. Lebrette, L. Poverlein, M. C. Gamiz-Hernandez, A. P. Heberle, J. Kasanmascheff, M. Hogbom, M. Kaila, V. R. I. 2026-03-09 doi:10.64898/2026.03.06.710006 Cold Spring Harbor Laboratory Press 2026-03-09 <![CDATA[ Aging-associated endo-lysosomal dysfunction drives inflammaging and neurodegeneration through the STING-IFN-I axis ]]> https://biorxiv.org/content/10.64898/2026.03.15.711864v1?rss=1 Oberg, M. Maric, I. P. Stromberg, A. Myers, C. Saffarzadeh, N. Fabrikova, D. Fabrik, I. Rivas Gavalez, L. Skibicka, K. Kurzawa-Akanbi, M. Paul, G. Gekara, N. O. Hartlova, A. 2026-03-18 doi:10.64898/2026.03.15.711864 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ Infauna selectively enhance DNA virus diversity and activity in marine sediments ]]> https://biorxiv.org/content/10.64898/2026.03.17.711404v1?rss=1 Fonseca, A. Middelboe, M. Holmfeldt, K. Bell, E. Humborg, C. Norkko, A. Nascimento, F. J. A. 2026-03-18 doi:10.64898/2026.03.17.711404 Cold Spring Harbor Laboratory Press 2026-03-18 <![CDATA[ Functional definition of the Drosophila airway progenitor field through overlapping compensatory regulators ]]> https://biorxiv.org/content/10.64898/2026.03.18.712720v1?rss=1 Matsuda, R. Hosono, C. Saigo, K. Samkovlis, C. 2026-03-20 doi:10.64898/2026.03.18.712720 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ Convergent targeting of conserved regulatory networks during thermal evolution across Saccharomyces ]]> https://biorxiv.org/content/10.64898/2026.03.23.708575v1?rss=1 Molinet, J. Gierer, C. Villarreal, P. Stelkens, R. 2026-03-25 doi:10.64898/2026.03.23.708575 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Single-cell, clonal and spatial atlases of cranial placodes illuminate their specification and evolution ]]> https://biorxiv.org/content/10.64898/2026.04.01.715621v1?rss=1 Murtazina, A. Fatieieva, Y. Waern, F. Maunsell, H. R. Thawani, A. Semsch, B. Bostrom, J. Reagor, C. C. Kameneva, P. Araslanova, K. Isaev, S. Schelb, F. Fried, K. Erickson, A. G. Klimovich, A. Streit, A. Kutscher, L. M. Kozmikova, I. Kozmik, Z. Andersson, E. R. Schlosser, G. Groves, A. K. Adameyko, I. 2026-04-03 doi:10.64898/2026.04.01.715621 Cold Spring Harbor Laboratory Press 2026-04-03 <![CDATA[ Several multiple sequence alignment perturbation methods enhance AlphaFold3 sampling of alternative protein states ]]> https://biorxiv.org/content/10.64898/2026.04.02.716037v1?rss=1 Eriksson Lidbrink, S. Nissen, I. Ahrlind, J. K. Howard, R. J. Lindahl, E. 2026-04-03 doi:10.64898/2026.04.02.716037 Cold Spring Harbor Laboratory Press 2026-04-03