Top 9 Biorxiv Papers Today in Biophysics


2.247 Mikeys
#1. Revisiting the Fisher-KPP equation to interpret the spreading-extinction dichotomy
Maud El-Hachem, Scott McCue, Wang Jin, Yihong Du, Matthew J Simpson
The Fisher-KPP model supports travelling wave solutions that are successfully used to model numerous invasive phenomena with applications in biology, ecology, and combustion theory. However, there are certain phenomena that the Fisher-KPP model cannot replicate, such as the extinction of invasive populations. The Fisher-Stefan model is an adaptation of the Fisher-KPP model to include a moving boundary whose evolution is governed by a Stefan condition. The Fisher-Stefan model also supports travelling wave solutions; however, a key additional feature of the Fisher-Stefan model is that it is able to simulate population extinction, giving rise to a spreading-extinction dichotomy . In this work, we revisit travelling wave solutions of the Fisher-KPP model and show that these results provide new insight into travelling wave solutions of the Fisher-Stefan model and the spreading-extinction dichotomy. Using a combination of phase plane analysis, perturbation analysis and linearisation, we establish a concrete relationship between...
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biorxivpreprint: Revisiting the Fisher-KPP equation to interpret the spreading-extinction dichotomy https://t.co/N9H2QzoMDA #bioRxiv
biorxiv_biophys: Revisiting the Fisher-KPP equation to interpret the spreading-extinction dichotomy https://t.co/lkO1ofa6wz #biorxiv_biophys
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Authors: 5
Total Words: 0
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2.0 Mikeys
#2. Robin Hood: non-fitting, non-smoothing image detrending for bleaching correction
Rory Nolan, Maro Iliopoulou, Christian Siebold, E Yvonne Jones, Sergi Padilla-Parra
Recent advances in protein labelling-gene tagging with CRIPSR-Cas9-have made it possible to label proteins of interest endogenously. This represents a major breakthrough in the field of quantitative microscopy, especially when quantifying protein-protein interactions. This is because over-expression of labelled proteins may cause a distortion in localization, function and perhaps artificially force protein-protein interactions due to crowding effects. A microscopy technique that is particularly well suited to detect protein interactions with low photon budgets is number and brightness (N&B). Detrending (removal of global trends in data) is a necessary pre-processing step to N&B calculations, but all current detrending methods perform poorly at low intensities. Here, we present the Robin Hood automatic detrending algorithm which performs well at low intensities, evaluating it with simulated and low photon budget live cell images. RH is available as an ImageJ plugin and as an R package.
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biorxivpreprint: Robin Hood: non-fitting, non-smoothing image detrending for bleaching correction https://t.co/jCiGitLg3D #bioRxiv
biorxiv_biophys: Robin Hood: non-fitting, non-smoothing image detrending for bleaching correction https://t.co/eXzTIOgdNw #biorxiv_biophys
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Simulate bounded Brownian motion.

Repository: brownded
User: rorynolan
Language: R
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Authors: 5
Total Words: 3589
Unqiue Words: 1266

1.998 Mikeys
#3. Demultiplexing overlapping signaling scaffold functions to probe lipid messenger coupling to cytoskeletal dynamics.
Nicholaus J Trenton, Robert Tyler McLaughlin, Satya Bellamkonda, David Tsao, Emily Mace, jordan orange, Volker Schweikhard, Michael R Diehl
The coordination of lipid messenger signaling with cytoskeletal regulation is central to many organelle-specific signaling and regulatory processes. While central to many aspects of cell physiology, this coupling often depends on the function of multi-domain scaffolds that orchestrate transient interactions and dynamic feedback among a spectrum of signaling intermediates and regulatory proteins on organelles. Understanding scaffold protein functions has remained challenging given this complexity. This work employs live-cell imaging and statistical analyses to deconvolve (demultiplex) how the multi-domain scaffold IQGAP1 coordinates phosphoinositide signaling with organelle-specific actin regulation and membrane processing events. Using actin-ensconced endosomes that localize to the basal cortex of polarized epithelial cells as a model system, we demonstrate abilities to dissect how IQGAP1 transitions between different actin and endosomal-membrane tethered states. We provide evidence IQGAP1 functions as a transient inhibitor of...
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biorxivpreprint: Demultiplexing overlapping signaling scaffold functions to probe lipid messenger coupling to cytoskeletal dynamics. https://t.co/4nXCUkAUOA #bioRxiv
biorxiv_biophys: Demultiplexing overlapping signaling scaffold functions to probe lipid messenger coupling to cytoskeletal dynamics. https://t.co/MDQyF3Y6Nc #biorxiv_biophys
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Sample Sizes : [45]
Authors: 8
Total Words: 9092
Unqiue Words: 2688

1.998 Mikeys
#4. Chromatin nanoscale compaction in live cells visualized by acceptor-donor ratio corrected FRET between DNA dyes
Simone Pelicci, Alberto Diaspro, Luca Lanzanò
Chromatin nanoscale architecture in live cells can be studied by Forster Resonance Energy Transfer (FRET) between fluorescently labeled chromatin components, such as histones. A higher degree of nanoscale compaction is detected as a higher FRET level, since this corresponds to a higher degree of proximity between donor and acceptor molecules. However, in such a system the stoichiometry of the donors and acceptors engaged in the FRET process is not well defined and, in principle, FRET variations could be caused by variations in the acceptor-donor ratio rather than distance. Here we show that a FRET value independent of the acceptor-donor ratio can be obtained by Fluorescence Lifetime Imaging (FLIM) detection of FRET combined with a normalization of the FRET level to a pixel-wise estimation of the acceptor-donor ratio. We use this method to study FRET between two DNA binding dyes staining the nuclei of live cells. We show that acceptor-donor ratio corrected FRET imaging reveals variations of nanoscale compaction in different...
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biorxivpreprint: Chromatin nanoscale compaction in live cells visualized by acceptor-donor ratio corrected FRET between DNA dyes https://t.co/LDMJG8ZT4d #bioRxiv
biorxiv_biophys: Chromatin nanoscale compaction in live cells visualized by acceptor-donor ratio corrected FRET between DNA dyes https://t.co/zdXGgMzusP #biorxiv_biophys
biophotonicat: Chromatin nanoscale compaction in live cells visualized by acceptor-donor ratio corrected FRET between DNA dyes (relevance: 100%) https://t.co/MFgNJbcDvz #biophotonics #biomedicaloptics https://t.co/1JjP1D3vhT
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Authors: 3
Total Words: 8952
Unqiue Words: 2482

1.997 Mikeys
#5. Extensive Evaluation of Weighted Ensemble Strategies for Calculating Rate Constants and Binding Affinities of Molecular Association/Dissociation Processes
AJ Pratt, Ernesto Suarez, Daniel Zuckerman, Lillian Chong
The weighted ensemble (WE) path sampling strategy is highly efficient in generating pathways and rate constants for rare events using atomistic molecular dynamics simulations. Here we extensively evaluated the impact of several advances to the WE strategy on the efficiency of computing association and dissociation rate constants (kon, koff) as well as binding affinities (KD) for a set of benchmark systems, listed in order of increasing timescales of molecular association/dissociation processes: methane/methane, Na+/Cl-, and K+/18-crown-6 ether. In particular, we assessed the advantages of carrying out (i) a large set of light-weight WE simulations that each consist of a small number of trajectories vs. a single heavy-weight WE simulation that consists of a relatively large number of trajectories, (ii) equilibrium vs. steady-state WE simulations, (iii) history augmented Markov State Model (haMSM) post-simulation analysis of equilibrium sets of trajectories, and (iv) tracking of trajectory history (the state last visited) during the...
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biorxivpreprint: Extensive Evaluation of Weighted Ensemble Strategies for Calculating Rate Constants and Binding Affinities of Molecular Association/Dissociation Processes https://t.co/gjkbS5MVJX #bioRxiv
biorxiv_biophys: Extensive Evaluation of Weighted Ensemble Strategies for Calculating Rate Constants and Binding Affinities of Molecular ... https://t.co/Ng1pELUFYm #biorxiv_biophys
razoralign: Extensive Evaluation of Weighted Ensemble Strategies for Calculating Rate Constants and Binding Affinities of Molecular Association/Dissociation Processes https://t.co/0kG13GFMxk
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1.997 Mikeys
#6. Magnetic-alignment of polymer macro-nanodiscs enable residual dipolar couplings based high-resolution structural studies by NMR
Thirupathi Ravula, Ayyalusamy Ramamoorthy
Residual dipolar couplings (RDCs) have been shown to be valuable for the structural studies of systems ranging from small molecules to large proteins. Here we demonstrate the lyotropic liquid crystal behavior of polymer macro-nanodiscs (> 20 nm in diameter) and enable the measurement of RDCs using high resolution NMR.
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biorxivpreprint: Magnetic-alignment of polymer macro-nanodiscs enable residual dipolar couplings based high-resolution structural studies by NMR https://t.co/iRAaPoOVTu #bioRxiv
biorxiv_biophys: Magnetic-alignment of polymer macro-nanodiscs enable residual dipolar couplings based high-resolution structural studies by NMR https://t.co/sBdbvAefOv #biorxiv_biophys
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Authors: 2
Total Words: 2795
Unqiue Words: 1138

1.997 Mikeys
#7. Preferential phosphatidylinositol 5-phosphate binding contributes to a destabilization of the VHS domain structure of Tom1
Wen Xiong, Tuo-Xian Tang, Evan Littleton, Arba Karcini, Iulia M. Lazar, Daniel G. S. Capelluto
Tom1 transports endosomal ubiquitinated proteins that are targeted for degradation in the lysosomal pathway. Infection of eukaryotic cells by Shigella flexneri boosts oxygen consumption and promotes the synthesis of phosphatidylinositol-5-phosphate [PtdIns5P], which triggers Tom1 translocation to signaling endosomes. Removing Tom1 from its cargo trafficking function hinders protein degradation in the host and, simultaneously, enables bacterial survival. Tom1 preferentially binds PtdIns5P via its VHS domain, but the effects of a reducing environment as well as PtdIns5P on the domain structure and function are unknown. Thermal denaturation studies demonstrate that, under reducing conditions, the monomeric Tom1 VHS domain switches from a three-state to a two-state transition behavior. PtdIns5P reduced thermostability, interhelical contacts, and conformational compaction of Tom1 VHS, suggesting that the phosphoinositide destabilizes the protein domain. Destabilization of Tom1 VHS structure was also observed with other phospholipids....
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biorxivpreprint: Preferential phosphatidylinositol 5-phosphate binding contributes to a destabilization of the VHS domain structure of Tom1 https://t.co/loHsRztxlM #bioRxiv
biorxiv_biophys: Preferential phosphatidylinositol 5-phosphate binding contributes to a destabilization of the VHS domain structure of Tom1 https://t.co/LU3J2AAIlB #biorxiv_biophys
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Authors: 6
Total Words: 8952
Unqiue Words: 3086

1.997 Mikeys
#8. Geometrical constraints greatly hinder formin mDia1 activity
Emiko L. Suzuki, Bérengère Guichard, Guillaume Romet-Lemonne, Antoine Jegou
Formins are one of the central players in the assembly of most actin networks in cells. The sensitivity of these processive molecular machines to mechanical tension is now well established. However, how the activity of formins is affected by geometrical constraints related to network architecture, such as filament crosslinking and formin spatial confinement, remains largely unknown. Combining microfluidics and micropatterning, we reconstituted in vitro mDia1 formin-elongated filament bundles induced by fascin, with different geometrical constraints on the formins, and measured the impact of these constraints on formin elongation rates and processivity. When filaments are not bundled, formins can be anchored to static or fluid surfaces, by either end of the proteins, without affecting their activity. We show that filament bundling by fascin reduces both unanchored formin elongation rate and processivity. Strikingly, when filaments elongated by surface-anchored formins are cross-linked together, formin elongation rate immediately...
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biorxivpreprint: Geometrical constraints greatly hinder formin mDia1 activity https://t.co/GqfGfTkwUp #bioRxiv
biorxiv_biophys: Geometrical constraints greatly hinder formin mDia1 activity https://t.co/E1iKj0SUUH #biorxiv_biophys
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Sample Sizes : [80, 34, 28, 8, 8, 15, 48, 78, 53, 18, 18, 15, 35]
Authors: 4
Total Words: 7868
Unqiue Words: 2112

1.995 Mikeys
#9. A mechanical model reveals that non-axisymmetric buckling lowers the energy barrier associated with membrane neck constriction
Ritvik Vasan, Shiva Rudraraju, Matthew Akamatsu, Krishna Garikipati, Padmini Rangamani
Membrane neck formation is essential for scission, which, as recent experiments on tubules have demonstrated, can be location dependent. The diversity of biological machinery that can constrict a neck such as dynamin, actin, ESCRTs and BAR proteins, and the range of forces and deflection over which they operate, suggest that the constriction process is functionally mechanical and robust to changes in biological environment. In this study, we used a mechanical model of the lipid bilayer to systematically investigate the influence of location, symmetry constraints, and helical forces on membrane neck constriction. Simulations from our model demonstrated that the energy barriers associated with constriction of a membrane neck are location-dependent. Importantly, if symmetry restrictions are relaxed, then the energy barrier for constriction is dramatically lowered and the membrane buckles at lower values of forcing parameters. Our simulations also show that constriction due to helical proteins further reduces the energy barrier for...
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