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Currently indexing 55,165 bioRxiv papers from 254,492 authors.

Most downloaded bioRxiv papers, since beginning of last month

Results 1 through 20 out of 2247

in category biophysics

 

1: HIV-1 Gag specifically restricts PI(4,5)P2 and cholesterol mobility in living cells creating a nanodomain platform for virus assembly.

Cyril Favard, Jakub Chojnacki et al.

1,244 downloads (posted 21 Feb 2019)

HIV-1 Gag protein self-assembles at the plasma membrane of infected cells for viral particle formation. Gag targets lipids, mainly the phosphatidylinositol (4,5) bisphosphate, at the inner leaflet of this membrane. Here, we address the question whether Gag is able to trap specifically PI(4,5)P2 or other lipids during HIV-1 assembly in the host CD4+ T lymphocytes. Lipid dynamics within and away from HIV-1 assembly sites was determined using super-resolution STED microscopy coupled with scanning Fluorescence Correlation Spectroscopy in living T cells. Analysis of HIV-1 infected cells revealed that, upon assembly, HIV-1 is able to specifically trap PI(4,5)P2, and cholesterol, but not phosphatidylethanolamine or sphingomyelin. Furthermore, our data show that Gag is the main driving force to restrict PI(4,5)P2 and cholesterol mobility at the cell plasma membrane. This is first direct evidence showing that HIV-1 creates its own specific lipid environment by selectively recruiting PI(4,5)P2 and cholesterol, as a membrane nano-platform for virus assembly.

https://rxivist.org/papers/44501
https://doi.org/10.1101/556308

2: Biophysical principles of choanoflagellate self-organization

Ben T. Larson, Teresa Ruiz-Herrero et al.

1,137 downloads (posted 04 Jun 2019)

Inspired by the patterns of multicellularity in choanoflagellates, the closest living relatives of animals, we quantify the biophysical processes underlying the morphogenesis of rosette colonies in the choanoflagellate Salpingoeca rosetta. We find that rosettes reproducibly transition from an early stage of 2D growth to a later stage of 3D growth, despite the underlying stochasticity of the cell lineages. We postulate that the extracellular matrix (ECM) exerts a physical constraint on the packing of proliferating cells,...

https://rxivist.org/papers/52443
https://doi.org/10.1101/659698

3: Surpassing the physical Nyquist limit to produce super-resolution cryo-EM reconstructions

J. Ryan Feathers, Katherine A. Spoth et al.

929 downloads (posted 19 Jun 2019)

Recent advances in single-particle cryo-electron microscopy (cryo-EM) methods have led to the determination of hundreds of high-resolution (< 4.0 Å) macromolecular structures. However, access to high-end instrumentation can be scarce and expensive. The resolution of cryo-EM reconstructions is fundamentally limited by the Nyquist frequency, which is half the sampling frequency of the detector and depends upon the magnification used. In principle, super-resolution imaging should enable reconstructions to surpass the physi...

https://rxivist.org/papers/53696
https://doi.org/10.1101/675397

4: DNA-loop extruding condensin complexes can traverse one another

Eugene Kim, Jacob W.J. Kerssemakers et al.

820 downloads (posted 26 Jun 2019)

Condensin, a key member of the Structure Maintenance of Chromosome (SMC) protein complexes, has recently been shown to be a motor that extrudes loops of DNA. It remains unclear, however, how condensin complexes work together to collectively package DNA into the chromosomal architecture. Here, we use time-lapse single-molecule visualization to study mutual interactions between two DNA-loop-extruding yeast condensins. We find that these one-side-pulling motor proteins are able to dynamically change each other's DNA loop s...

https://rxivist.org/papers/54205
https://doi.org/10.1101/682864

5: Single molecule localization microscopy with autonomous feedback loops for ultrahigh precision

Simao Coelho, Jongho baek et al.

697 downloads (posted 05 Dec 2018)

Single-molecule localization microscopy (SMLM) promises to provide truly molecular scale images of biological specimens. However, mechanical instabilities in the instrument, readout errors and sample drift constitute significant challenges and severely limit both the useable data acquisition length and the localization accuracy of single molecule emitters. Here, we developed an actively stabilized total internal fluorescence (TIRF) microscope that performs 3D real-time drift corrections and achieves a stability of ≤1 nm...

https://rxivist.org/papers/38078
https://doi.org/10.1101/487728

6: Structural insights into ligand efficacy and activation of the glucagon receptor

Daniel Hilger, Kaavya Krishna Kumar et al.

684 downloads (posted 05 Jun 2019)

The glucagon receptor family comprises Class B G protein-coupled receptors (GPCRs) that play a crucial role in regulating blood sugar levels. Receptors of this family represent important therapeutic targets for the treatment of diabetes and obesity. Despite intensive structural studies, we only have a poor understanding of the mechanism of peptide hormone-induced Class B receptor activation. This process involves the formation of a sharp kink in transmembrane helix 6 that moves out to allow formation of the nucleotide-f...

https://rxivist.org/papers/52524
https://doi.org/10.1101/660837

7: RELION-3: new tools for automated high-resolution cryo-EM structure determination

Jasenko Zivanov, Takanori Nakane et al.

669 downloads (posted 19 Sep 2018)

Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations. Reference-free autopicking with Laplacian-of-Gaussian filtering and execution of jobs from python allows non-interactive processing during acquisition, including 2D-classification, de novo model generation and 3D-classification. Per-particle refinement of CTF parameters and correction of estimated beam tilt provides hig...

https://rxivist.org/papers/32792
https://doi.org/10.1101/421123

8: General and robust covalently linked graphene oxide affinity grids for high-resolution cryo-EM

Feng Wang, Yanxin Liu et al.

648 downloads (posted 02 Jun 2019)

Despite their great potential to facilitate rapid preparation of quite impure samples, affinity grids have not yet been widely employed in single particle cryo-EM. Here, we chemically functionalize graphene oxide coated grids and use a highly specific covalent affinity tag system. Importantly, our polyethylene glycol spacer keeps particles away from the air-water interface and graphene oxide surface, protecting them from denaturation or aggregation and permits high-resolution reconstructions of small particles.

https://rxivist.org/papers/52216
https://doi.org/10.1101/657411

9: Motility induced fracture reveals a ductile to brittle crossover in the epithelial tissues of a simple animal

Vivek N. Prakash, Matthew Storm Bull et al.

563 downloads (posted 19 Jun 2019)

Animals are characterized by their movement, and their tissues are continuously subjected to dynamic force loading while they crawl, walk, run or swim [1]. Tissue mechanics fundamentally determine the ecological niches that can be endured by a living organism [2]. While epithelial tissues provide an important barrier function in animals, they are subjected to extreme strains during day to day physiological activities, such as breathing [1], feeding [3], and defense response [4]. However, failure or inability to withstan...

https://rxivist.org/papers/53692
https://doi.org/10.1101/676866

10: Multi-scale spatial heterogeneity enhances particle clearance in airway ciliary arrays

Guillermina R. Ramirez-San Juan, Arnold Mathijssen et al.

515 downloads (posted 09 Jun 2019)

Mucus clearance constitutes the primary defence of the respiratory system against viruses, bacteria and environmental insults. This transport across the entire airway emerges from the integrated activity of thousands of multiciliated cells, each containing hundreds of cilia, which together must coordinate their spatial arrangement, alignment and motility. The mechanisms of fluid transport have been studied extensively at the level of an individual cilium, collectively moving metachronal waves, and more generally the hyd...

https://rxivist.org/papers/52809
https://doi.org/10.1101/665125

11: Alternative transcription cycle for bacterial RNA polymerase

Timothy T Harden, Karina S. Herlambang et al.

417 downloads (posted 11 Jun 2019)

RNA polymerases (RNAPs) transcribe genes through a cycle of recruitment to promoter DNA, initiation, elongation, and termination. After termination, RNAP is thought to initiate the next round of transcription by detaching from DNA and rebinding a new promoter. We used single-molecule fluorescence microscopy to observe individual RNAP molecules after transcript release at a terminator. Following termination, RNAP almost always remained bound to DNA and sometimes exhibited one-dimensional sliding over thousands of basepai...

https://rxivist.org/papers/53026
https://doi.org/10.1101/663534

12: OptiJ: Open-source optical projection tomography of large organ samples

Pedro P Vallejo Ramirez, Joseph Zammit et al.

373 downloads (posted 02 Jun 2019)

The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 μm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plug...

https://rxivist.org/papers/52223
https://doi.org/10.1101/656488

13: Organization and Regulation of Chromatin by Liquid-Liquid Phase Separation

Bryan A Gibson, Lynda K Doolittle et al.

370 downloads (posted 18 Jan 2019)

Genomic DNA is highly compacted in the nucleus of eukaryotic cells as a nucleoprotein assembly called chromatin. The basic unit of chromatin is the nucleosome, where ~146 base pair increments of the genome are wrapped and compacted around the core histone proteins. Further genomic organization and compaction occur through higher order assembly of nucleosomes. This organization regulates many nuclear processes, and is controlled in part by histone post-transtranslational modifications and chromatin-binding proteins. Mech...

https://rxivist.org/papers/41939
https://doi.org/10.1101/523662

14: An RNA-binding region regulates CTCF clustering and chromatin looping

Anders Sejr Hansen, Tsung-Han S Hsieh et al.

330 downloads (posted 13 Dec 2018)

Mammalian genomes are folded into Topologically Associating Domains (TADs), consisting of cell-type specific chromatin loops anchored by CTCF and cohesin. Since CTCF and cohesin are expressed ubiquitously, how cell-type specific CTCF-mediated loops are formed poses a paradox. Here we show RNase-sensitive CTCF self-association in vitro and that an RNA-binding region (RBR) mediates CTCF clustering in vivo. Intriguingly, deleting the RBR abolishes or impairs almost half of all chromatin loops in mouse embryonic stem cells....

https://rxivist.org/papers/38814
https://doi.org/10.1101/495432

15: Real-time cryo-EM data pre-processing with Warp

Dimitry Tegunov, Patrick Cramer

325 downloads (posted 14 Jun 2018)

The acquisition of cryo-electron microscopy (cryo-EM) data from biological specimens is currently largely uncoupled from subsequent data evaluation, correction and processing. Therefore, the acquisition strategy is difficult to optimize during data collection, often leading to suboptimal microscope usage and disappointing results. Here we provide Warp, a software for real-time evaluation, correction, and processing of cryo-EM data during their acquisition. Warp evaluates and monitors key parameters for each recorded mic...

https://rxivist.org/papers/17549
https://doi.org/10.1101/338558

16: Automated cryo-EM sample preparation by pin-printing and jet vitrification

Raimond B.G. Ravelli, Frank J.T. Nijpels et al.

311 downloads (posted 28 May 2019)

The increasing demand for cryo-electron microscopy (cryo-EM) reveals drawbacks in current sample preparation protocols, such as sample waste and lack of reproducibility. Here, we present several technical developments that provide controlled and efficient sample preparation for cryo-EM studies. Pin printing substantially reduces sample waste by depositing only a sub-nanoliter volume of sample on the carrier surface. Sample evaporation is mitigated by dewpoint control feedback loops. The deposited sample is vitrified by ...

https://rxivist.org/papers/51812
https://doi.org/10.1101/651208

17: Allosteric Motions of the CRISPR-Cas9 HNH Nuclease Probed by NMR and Molecular Dynamics

Kyle W. East, Jocelyn C. Newton et al.

309 downloads (posted 05 Jun 2019)

CRISPR-Cas9 is a widely employed genome-editing tool with functionality reliant on the ability of the Cas9 endonuclease to introduce site-specific breaks in double-stranded DNA. In this system, an intriguing allosteric communication has been suggested to control its DNA cleavage activity through flexibility of the catalytic HNH domain. Here, solution NMR experiments and Gaussian accelerated Molecular Dynamics (GaMD) simulations - flanked by mixed machine learning and structure-based prediction of NMR chemical shifts - a...

https://rxivist.org/papers/52511
https://doi.org/10.1101/660613

18: The unjamming transition is distinct from the epithelial-to-mesenchymal transition.

Jennifer A. Mitchel, Amit Das et al.

291 downloads (posted 10 Jun 2019)

Every organ surface and body cavity is lined by a confluent collective of epithelial cells. In homeostatic circumstances the epithelial collective remains effectively solid-like and sedentary. But during morphogenesis, remodeling or repair, as well as during malignant invasion or metastasis, the epithelial collective becomes fluid-like and migratory. This conversion from sedentary to migratory behavior has traditionally been understood as a manifestation of the epithelial-to-mesenchymal transition (EMT) or the partial E...

https://rxivist.org/papers/52919
https://doi.org/10.1101/665018

19: The effectiveness of glass beads for plating cell cultures

Alidivinas Prusokas, Michelle Hawkins et al.

284 downloads (posted 01 Jan 2018)

Cell plating and subsequent colony growth is an important laboratory procedure in microbiology. A common protocol for cell culture plating in Petri dishes uses glass beads to spread cells on the surface of the solid growth media. Here we perform an experimental analysis and mathematical modelling of cell plating. We introduce a new class of billiard - shifting billiard, which serves as a conceptual abstraction of the cell plating with glass beads. Numerical analysis of the dynamics of this simple yet efficient billiard,...

https://rxivist.org/papers/30501
https://doi.org/10.1101/241752

20: Divide and Conquer: Real-time maximum likelihood fitting of multiple emitters for super-resolution localization microscopy

Luchang Li, Bo Xin et al.

277 downloads (posted 04 Jun 2019)

Multi-emitter localization has great potential for maximizing the imaging speed of super-resolution localization microscopy. However, the slow image analysis speed of reported multi-emitter localization algorithms limits their usage in mostly off-line image processing with small image size. Here we adopt the well-known divide and conquer strategy in computer science and present a fitting-based method called QC-STORM for fast multi-emitter localization. Using simulated and experimental data, we verify that QC-STORM is ca...

https://rxivist.org/papers/52428
https://doi.org/10.1101/659631