bioRxiv Channel: Micron Oxford https://biorxiv.org This feed contains articles for bioRxiv Channel "Micron Oxford" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Drosophila sensory cilia lacking MKS-proteins exhibit striking defects during development but only subtle defects in adults ]]> https://biorxiv.org/cgi/content/short/058081v1?rss=1" Metta B. Pratt Joshua S. Titlow Ilan Davis Amy R. Barker Helen R. Dawe Jordan W. Raff Helio Roque 2016-06-09 doi:10.1101/058081 Cold Spring Harbor Laboratory Press 2016-06-09 <![CDATA[ Single Molecule Fluorescence In Situ Hybridisation For Quantitating Post-Transcriptional Regulation In Drosophila Brains ]]> https://biorxiv.org/cgi/content/short/128785v1?rss=1" Yang, L. Titlow, J. Ennis, D. Smith, C. Mitchell, J. Young, F. L. Waddell, S. Ish-Horowicz, D. Davis, I. 2017-04-21 doi:10.1101/128785 Cold Spring Harbor Laboratory Press 2017-04-21 <![CDATA[ Imp/Syp Temporal Gradients Govern Decommissioning Of Drosophila Neural Stem Cells ]]> https://biorxiv.org/cgi/content/short/136655v1?rss=1" Yang, C.-P. Samuels, T. J. Huang, Y. Yang, L. Ish-Horowicz, D. Davis, I. Lee, T. 2017-05-10 doi:10.1101/136655 Cold Spring Harbor Laboratory Press 2017-05-10 <![CDATA[ Regulating prospero mRNA Stability Determines When Neural Stem Cells Stop Dividing ]]> https://biorxiv.org/cgi/content/short/135848v1?rss=1" Yang, L. Samuels, T. J. Arava, Y. Robertson, F. Jarvelin, A. I. Yang, C.-P. Lee, T. Ish-Horowicz, D. Davis, I. 2017-05-12 doi:10.1101/135848 Cold Spring Harbor Laboratory Press 2017-05-12 <![CDATA[ Brain Development: Machine Learning Analysis Of Individual Stem Cells In Live 3D Tissue ]]> https://biorxiv.org/cgi/content/short/137406v1?rss=1" nView larger version (93K):norg.highwire.dtl.DTLVardef@68912corg.highwire.dtl.DTLVardef@11300bdorg.highwire.dtl.DTLVardef@95810corg.highwire.dtl.DTLVardef@14b77a6_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LICytoCensus: machine learning quantitation of cell types in complex 3D tissuesnC_LIO_LISingle cell analysis of division rates from movies of living Drosophila brains in 3DnC_LIO_LIDiverse applications in the analysis of developing vertebrate tissues and organoidsnC_LIO_LIOutperforms other image analysis software on challenging, low SNR datasets testednC_LI ]]> Hailstone, M. Yang, L. Waithe, D. Samuels, T. J. Arava, Y. Dobrzycki, T. Parton, R. M. Davis, I. 2017-05-14 doi:10.1101/137406 Cold Spring Harbor Laboratory Press 2017-05-14 <![CDATA[ Antisense transcription-dependent chromatin signature modulates sense transcription and transcript dynamics ]]> https://biorxiv.org/cgi/content/short/187237v1?rss=1" nView larger version (52K):norg.highwire.dtl.DTLVardef@4f872corg.highwire.dtl.DTLVardef@1339662org.highwire.dtl.DTLVardef@1d62cc2org.highwire.dtl.DTLVardef@148f24_HPS_FORMAT_FIGEXP M_FIG Graphical AbstractnnC_FIG In this work, Brown et al. provide a mechanistic understanding of the effect of antisense transcription on the production and fate of sense transcripts. Antisense transcription buffers genes against the action of the Set3 lysine deacetylase, thus altering rates of transcript production, processing and stability. O_LIConserved antisense transcription-dependent chromatin architecture near promotersnC_LIO_LIAntisense transcription alters sense transcription dynamics and transcript stabilitynC_LIO_LIAntisense transcription functions in a chromatin-dependent mannernC_LIO_LIIncreased acetylation by set3{Delta} mimics high antisense transcriptional dynamicsnC_LI ]]> Brown, T. Howe, F. S. Murray, S. C. Seward, E. Rata, S. Angel, A. Mellor, J. 2017-09-11 doi:10.1101/187237 Cold Spring Harbor Laboratory Press 2017-09-11 <![CDATA[ Cohesin Can Remain Associated With Chromosomes During DNA Replication ]]> https://biorxiv.org/cgi/content/short/124107v1?rss=1" Rhodes, J. Haarhuis, J. Grimm, J. Rowland, B. Lavis, L. Nasmyth, K. 2017-04-04 doi:10.1101/124107 Cold Spring Harbor Laboratory Press 2017-04-04 <![CDATA[ Scc2/Nipbl Hops Between Chromosomal Cohesin Rings After Loading ]]> https://biorxiv.org/cgi/content/short/136754v1?rss=1" Rhodes, J. Mazza, D. Nasmyth, K. Uphoff, S. 2017-05-11 doi:10.1101/136754 Cold Spring Harbor Laboratory Press 2017-05-11 <![CDATA[ Asymmetric MukB ATPases are regulated independently by the N- and C-terminal domains of MukF kleisin ]]> https://biorxiv.org/cgi/content/short/180729v1?rss=1" Zawadzka, K. Zawadzki, P. Baker, R. Rajasekar, K. Sherratt, D. J. Arciszewska, L. 2017-08-25 doi:10.1101/180729 Cold Spring Harbor Laboratory Press 2017-08-25 <![CDATA[ Diffusion of lipids and GPI-anchored proteins in actin-free plasma membrane vesicles measured by STED-FCS ]]> https://biorxiv.org/cgi/content/short/076109v1?rss=1" Falk Schneider Mathias P Clausen Dominic Waithe Thomas Koller Gunes Ozhan Christian Eggeling Erdinc Sezgin 2016-09-19 doi:10.1101/076109 Cold Spring Harbor Laboratory Press 2016-09-19 <![CDATA[ Advanced processing and analysis of conventional confocal microscopy generated scanning FCS data ]]> https://biorxiv.org/cgi/content/short/163766v1?rss=1" Waithe, D. Schneider, F. Chojnacki, J. Shrestha, D. Bernardino de la Serna, J. Eggeling, C. 2017-07-14 doi:10.1101/163766 Cold Spring Harbor Laboratory Press 2017-07-14 <![CDATA[ Polarity sensitive probes for super resolution STED microscopy ]]> https://biorxiv.org/cgi/content/short/107334v1?rss=1" Sezgin, E. Schneider, F. Zilles, V. Garcia, E. Waithe, D. Klymchenko, A. S. Eggeling, C. 2017-02-09 doi:10.1101/107334 Cold Spring Harbor Laboratory Press 2017-02-09 <![CDATA[ FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET ]]> https://biorxiv.org/cgi/content/short/039198v1?rss=1" Antonino Ingargiola Eitan Lerner SangYoon Chung Shimon Weiss Xavier Michalet 2016-02-09 doi:10.1101/039198 Cold Spring Harbor Laboratory Press 2016-02-09 <![CDATA[ Laurdan and di-4-ANEPPDHQ probe different properties of the membrane ]]> https://biorxiv.org/cgi/content/short/076752v1?rss=1" Mariana Amaro Francesco Reina Martin Hof Christian Eggeling Erdinc Sezgin 2016-09-22 doi:10.1101/076752 Cold Spring Harbor Laboratory Press 2016-09-22 <![CDATA[ IsoSense: frequency enhanced sensorless adaptive optics through structured illumination ]]> https://biorxiv.org/cgi/content/short/448613v1?rss=1" Zurauskas, M. Dobbie, I. M. Parton, R. M. Phillips, M. A. Gohler, A. Davis, I. Booth, M. 2018-10-22 doi:10.1101/448613 Cold Spring Harbor Laboratory Press 2018-10-22 <![CDATA[ Testing models of mRNA localization reveals robustness regulated by reducing transport between cells ]]> https://biorxiv.org/cgi/content/short/533133v1?rss=1" Harrison, J. U. Parton, R. M. Davis, I. Baker, R. E. 2019-02-01 doi:10.1101/533133 Cold Spring Harbor Laboratory Press 2019-02-01 <![CDATA[ Syncrip/hnRNPQ is required for activity-induced Msp300/Nesprin-1 expression and new synapse formation ]]> https://biorxiv.org/cgi/content/short/585679v1?rss=1" Titlow, J. Robertson, F. Jarvelin, A. Ish-Horowicz, D. Smith, C. Gratton, E. Davis, I. 2019-03-22 doi:10.1101/585679 Cold Spring Harbor Laboratory Press 2019-03-22 <![CDATA[ Scc2-Mediated Loading Of Cohesin Onto Chromosomes In G1 Yeast Cells Is Insufficient To Build Cohesion During S Phase ]]> https://biorxiv.org/cgi/content/short/123596v1?rss=1" Nasmyth, K. 2017-04-03 doi:10.1101/123596 Cold Spring Harbor Laboratory Press 2017-04-03 <![CDATA[ The cohesin ring uses its hinge to organize DNA using non-topological as well as topological mechanisms ]]> https://biorxiv.org/cgi/content/short/197848v1?rss=1" Srinivasan, M. Scheinost, J. Petela, N. Gligoris, T. Wissler, M. Ogushi, S. Collier, J. Voulgaris, M. Kurze, A. Chan, K.-L. Hu, B. Costanzo, V. Nasmyth, K. 2017-10-03 doi:10.1101/197848 Cold Spring Harbor Laboratory Press 2017-10-03 <![CDATA[ Multiple interactions between Scc1 and Scc2 activate cohesin’s DNA dependent ATPase and replace Pds5 during loading ]]> https://biorxiv.org/cgi/content/short/205914v1?rss=1" Petela, N. Gligoris, T. G. Metson, J. S. Lee, B.-G. Voulgaris, M. Hu, B. Kikuchi, S. Chapard, C. Chen, W. Rajendra, E. Srinivisan, M. Yu, H. Löwe, J. Nasmyth, K. 2017-10-19 doi:10.1101/205914 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ The topology of DNA entrapment by cohesin rings. ]]> https://biorxiv.org/cgi/content/short/495762v1?rss=1" Chapard, C. Jones, R. van Oepen, T. Scheinost, J. C. Nasmyth, K. 2018-12-13 doi:10.1101/495762 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Scc2 counteracts a Wapl-independent mechanism that releases cohesin from chromosomes during G1 but is unnecessary during S phase for establishing cohesion ]]> https://biorxiv.org/cgi/content/short/513960v1?rss=1" Nasmyth, K. A. Srinivasan, M. Petela, N. J. Scheinost, J. C. Collier, J. Voulgaris, M. Brunet-Roig, M. Beckouët, F. Hu, B. 2019-01-09 doi:10.1101/513960 Cold Spring Harbor Laboratory Press 2019-01-09 <![CDATA[ Pathways of DNA unlinking: A story of stepwise simplification ]]> https://biorxiv.org/cgi/content/short/188722v1?rss=1" Stolz, R. Yoshida, M. Brasher, R. Flanner, M. Ishihara, K. Sherratt, D. J. Shimokawa, K. Vazquez, M. 2017-09-14 doi:10.1101/188722 Cold Spring Harbor Laboratory Press 2017-09-14 <![CDATA[ Self-organised segregation of bacterial chromosomal origins ]]> https://biorxiv.org/cgi/content/short/304600v1?rss=1" Murray, S. M. Sourjik, V. 2018-04-20 doi:10.1101/304600 Cold Spring Harbor Laboratory Press 2018-04-20 <![CDATA[ Single-molecule imaging of DNA gyrase activity in living Escherichia coli ]]> https://biorxiv.org/cgi/content/short/460006v1?rss=1" Stracy, M. Wollman, A. Kaja, E. Gapinski, J. Lee, J.-E. Leek, V. McKie, S. Mitchenall, L. Maxwell, A. Sherratt, D. Leake, M. Zawadzki, P. 2018-11-01 doi:10.1101/460006 Cold Spring Harbor Laboratory Press 2018-11-01 <![CDATA[ Choosing the right label for single-molecule tracking in live bacteria: Side-by-side comparison of photoactivatable fluorescent protein and Halo tag dyes ]]> https://biorxiv.org/cgi/content/short/381665v1?rss=1" Banaz, N. Makela, J. Uphoff, S. 2018-08-10 doi:10.1101/381665 Cold Spring Harbor Laboratory Press 2018-08-10 <![CDATA[ Gene expression noise randomizes the adaptive response to DNA alkylation damage in E. coli ]]> https://biorxiv.org/cgi/content/short/551911v1?rss=1" Uphoff, S. 2019-02-18 doi:10.1101/551911 Cold Spring Harbor Laboratory Press 2019-02-18 <![CDATA[ Drosophila PLP forms centriolar-clouds that promote centriole stability, cohesion and MT nucleation ]]> https://biorxiv.org/cgi/content/short/161554v1?rss=1" Roque, H. Pratt, M. Johnson, E. Raff, J. 2017-07-10 doi:10.1101/161554 Cold Spring Harbor Laboratory Press 2017-07-10 <![CDATA[ Paleo-Eskimo genetic legacy across North America ]]> https://biorxiv.org/cgi/content/short/203018v1?rss=1" Flegontov, P. Altinisik, N. E. Changmai, P. Rohland, N. Mallick, S. Bolnick, D. A. Candilio, F. Flegontova, O. Jeong, C. Harper, T. K. Keating, D. Kennett, D. J. Kim, A. M. Lamnidis, T. C. Olalde, I. Raff, J. Sattler, R. A. Skoglund, P. Vajda, E. J. Vasilyev, S. Veselovskaya, E. Hayes, M. G. O'Rourke, D. H. Pinhasi, R. Krause, J. Reich, D. Schiffels, S. 2017-10-13 doi:10.1101/203018 Cold Spring Harbor Laboratory Press 2017-10-13 <![CDATA[ A free-running oscillator times and executes centriole biogenesis ]]> https://biorxiv.org/cgi/content/short/510875v1?rss=1" Aydogan, M. G. Steinacker, T. L. Mofatteh, M. Gartenmann, L. Wainman, A. Saurya, S. Conduit, P. T. Zhou, F. Y. Boemo, M. A. Raff, J. W. 2019-01-03 doi:10.1101/510875 Cold Spring Harbor Laboratory Press 2019-01-03 <![CDATA[ Constraining CD45 exclusion at close-contacts provides a mechanism for discriminatory T-cell receptor signalling ]]> https://biorxiv.org/cgi/content/short/109785v1?rss=1" Fernandes, R. A. Ganzinger, K. A. Tzou, J. Jonsson, P. Lee, S. F. Palayret, M. Santos, A. M. Chang, V. T. Macleod, C. Lagerholm, B. C. Lindsay, A. E. Dushek, O. Tilevik, A. Davis, S. J. Klenerman, D. 2017-02-19 doi:10.1101/109785 Cold Spring Harbor Laboratory Press 2017-02-19 <![CDATA[ A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions ]]> https://biorxiv.org/cgi/content/short/234427v1?rss=1" Brown, J. M. Roberts, N. A. Graham, B. Waithe, D. Lagerholm, C. Telenius, J. M. De Ornellas, S. Oudelaar, M. Szczerbal, I. Babbs, C. Kassouf, M. T. Hughes, J. R. Higgs, D. R. Buckle, V. J. 2017-12-15 doi:10.1101/234427 Cold Spring Harbor Laboratory Press 2017-12-15 <![CDATA[ Complementary studies of lipid membrane dynamics using iSCAT and STED microscopy ]]> https://biorxiv.org/cgi/content/short/235564v1?rss=1" 40 nm) and temporal (50 [≤] t [≤] 100 ms) scales probed, the diffussion coefficient was reduced by 20- to 60-fold when tagging with 20 and 40 nm large gold particles as compared to when using dye-tagged lipid analogues. These FCS measurements of hybrid fluorescent tag - gold nanoparticle labeled lipids also revealed that commercially supplied streptavidin-coated gold nanoparticles contain large quantities of free streptavidin. Finally, the values of apparent diffusion coefficients obtained by STED-FCS and iSCAT differed by a factor of 2-3 across the techniques, while relative differences in mobility between different species of lipid analogues considered were identical in both approaches. In conclusion, our experiments reveal that large and potentially crosslinking scattering tags introduce a significant slow-down in diffusion on SLBs but no additional bias, and our labeling approach creates a new way of exploiting complementary information from STED-FCS and iSCAT measurements. ]]> Reina, F. Galiani, S. Shrestha, D. Sezgin, E. de Wit, G. Cole, D. Lagerholm, B. C. Kukura, P. Eggeling, C. 2017-12-16 doi:10.1101/235564 Cold Spring Harbor Laboratory Press 2017-12-16 <![CDATA[ Understanding RNP remodelling uncovers RBPs functionally required for viral replication ]]> https://biorxiv.org/cgi/content/short/350686v1?rss=1" Garcia-Moreno, M. Noerenberg, M. Ni, S. Jarvelin, A. I. Gonzalez-Almela, E. Lenz, C. Bach-Pages, M. Cox, V. Avolio, R. Davis, T. Hester, S. Sohier, T. J. Li, B. Sanz, M. A. Carrasco, L. Ricci, E. P. Pelechano, V. Fischer, B. Mohammed, S. Castello, A. 2018-06-20 doi:10.1101/350686 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ A thorough RNA-seq characterization of the porcine sperm transcriptome and its seasonal changes ]]> https://biorxiv.org/cgi/content/short/506899v1?rss=1" Godia, M. Estill, M. Castello, A. Balasch, S. Rodriguez-Gil, J. E. Krawetz, S. A. Sanchez, A. Clop, A. 2018-12-27 doi:10.1101/506899 Cold Spring Harbor Laboratory Press 2018-12-27 <![CDATA[ Correlative cryo-structured illumination fluorescence microscopy and soft X-ray tomography elucidates reovirus intracellular release pathway ]]> https://biorxiv.org/cgi/content/short/2020.01.13.904623v1?rss=1" Harkiolaki, M. Kounatidis, I. Stanifer, M. L. Phillips, M. A. Paul-Gilloteau, P. Helligenstein, X. Wang, H. Okolo, C. A. Fish, T. Spink, M. C. Stuart, D. I. Davis, I. Boulant, S. Grimes, J. M. Dobbie, I. M. 2020-01-14 doi:10.1101/2020.01.13.904623 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ CryoSIM: super resolution 3D structured illumination cryogenic fluorescence microscopy for correlated ultra-structural imaging ]]> https://biorxiv.org/cgi/content/short/2020.03.09.980334v1?rss=1" Phillips, M. A. Harkiolaki, M. Pinto, D. M. S. Parton, R. M. Palanca, A. Garcia-Moreno, M. Sedat, J. Stuart, D. I. Castello, A. Booth, M. J. Davis, I. Dobbie, I. M. 2020-03-11 doi:10.1101/2020.03.09.980334 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ BeamDelta: simple alignment tool for optical systems ]]> https://biorxiv.org/cgi/content/short/833368v1?rss=1" Hall, N. J. Pinto, D. M. S. Dobbie, I. M. 2019-11-07 doi:10.1101/833368 Cold Spring Harbor Laboratory Press 2019-11-07 <![CDATA[ Democratising "Microscopi": a 3D printed automated XYZT fluorescence imaging system for teaching, outreach and fieldwork ]]> https://biorxiv.org/cgi/content/short/2020.05.21.108894v1?rss=1" Wincott, M. B. Jefferson, A. Dobbie, I. M. Booth, M. J. Davis, I. Parton, R. M. 2020-05-24 doi:10.1101/2020.05.21.108894 Cold Spring Harbor Laboratory Press 2020-05-24 <![CDATA[ Microscope-AOtools: A generalised adaptive optics implementation ]]> https://biorxiv.org/cgi/content/short/2020.06.18.158972v1?rss=1" Hall, N. J. Titlow, J. Booth, M. J. Dobbie, I. M. 2020-06-18 doi:10.1101/2020.06.18.158972 Cold Spring Harbor Laboratory Press 2020-06-18