Top 10 Biorxiv Papers Today in Biophysics


2.048 Mikeys
#1. Modelling heterogeneities in the cross-linked bacterial sacculus
Garima Rani, Issan Patri
Examining the design principles of biological materials, in particular the presence of inhomogeneities in their ultrastructure is the key to understanding the often remarkable mechanical properties possessed by them. In this work, motivated by the question of understanding the effect of variability in the material properties of the peptide cross-linkers on the bulk mechanical properties of the cell wall structure of bacteria, we study a spring system in which variability is encoded by assigning values of spring constants and rupture strengths of the constituent springs from appropriate probability distribution. Using analytical methods and computer simulations, we study the response of the spring system to shear loading and observe how heterogeneities inherent in the system can heighten the resistance to failure. We derive the force extension relation of the system and explore the effect that the disorder in values of spring constant and rupture strength has on load carrying capacity of the system and failure displacement. We also...
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biorxivpreprint: Modelling heterogeneities in the cross-linked bacterial sacculus https://t.co/iofs9reys6 #bioRxiv
biorxiv_biophys: Modelling heterogeneities in the cross-linked bacterial sacculus https://t.co/gy8F9qJrVc #biorxiv_biophys
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Authors: 2
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2.023 Mikeys
#2. Deep learning enables structured illumination microscopy with low light levels and enhanced speed
Luhong Jin, Bei Liu, Fenqiang Zhao, Stephen Hahn, Bowei Dong, Ruiyan Song, Timothy C. Elston, Yingke Xu, Klaus M. Hahn
Using deep learning to augment structured illumination microscopy (SIM), we obtained a fivefold reduction in the number of raw images required for super-resolution SIM, and generated images under extreme low light conditions (100X fewer photons). We validated the performance of deep neural networks on different cellular structures and achieved multi-color, live-cell super-resolution imaging with greatly reduced photobleaching.
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biorxivpreprint: Deep learning enables structured illumination microscopy with low light levels and enhanced speed https://t.co/1bXo7vQCIj #bioRxiv
biorxiv_biophys: Deep learning enables structured illumination microscopy with low light levels and enhanced speed https://t.co/yp8epc18ci #biorxiv_biophys
biophotonicat: Deep learning enables structured illumination microscopy with low light levels and enhanced speed (relevance: 88%) https://t.co/lbPhjaaSxN #biophotonics #biomedicaloptics https://t.co/NfaO5QKjlX
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Authors: 9
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2.011 Mikeys
#3. Sensing Traction Force on Matrix Induces Cell-Cell Distant Mechanical Communications for Self-assembly
Mingxing Ouyang, Zhili Qian, Bing Bu, Yang Jin, Jiajia Wang, Lei Liu, Yan Pan, Linhong Deng
The long-range biomechanical force propagating across large scale may reserve the capability to trigger coordinative responses within cell population such as during angiogenesis, epithelial tubulogenesis, and cancer metastasis. How cells communicate in a distant manner within the group for self-assembly remains largely unknown. Here we found that airway smooth muscle cells (ASMCs) rapidly self-assembled into well-constructed network on 3D Matrigel containing type I collagen (COL), which relied on long-range biomechanical force across the matrix to direct cell-cell distant interactions. Similar results happened by HUVEC cells to mimic angiogenesis. Interestingly, single ASMCs initiated multiple extended protrusions precisely pointing to neighboring cells in distance, depending on traction force sensing. Separate ASMCs sensed each other to move directionally on both non-fibrous Matrigel and more efficiently when containing fibrous COL, but lost mutual sensing on fixed gel or coated glass due to no long-range force transmission....
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biorxivpreprint: Sensing Traction Force on Matrix Induces Cell-Cell Distant Mechanical Communications for Self-assembly https://t.co/fnumgjJxgB #bioRxiv
biorxiv_biophys: Sensing Traction Force on Matrix Induces Cell-Cell Distant Mechanical Communications for Self-assembly https://t.co/AebEUjLVON #biorxiv_biophys
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Authors: 8
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2.011 Mikeys
#4. Determination of secretory granule maturation times in pancreatic islet beta-cells by serial block face scanning electron microscopy
Amith Rao, Emma L McBride, Guofeng Zhang, Tao Cai, Abner L Notkins, Maria A Aronova, Richard D Leapman
It is shown how serial block-face electron microscopy (SBEM) of insulin-secreting beta cells in wild-type mouse pancreatic islets of Langerhans can be used to determine maturation times of secretory granules. Although SBEM captures the beta cell structure at a snapshot in time, the observed ultrastructure can be considered representative of a dynamic equilibrium state of the cells since the pancreatic islets are maintained in culture in approximate homeostasis. It is found that 7.2±1.2% (±st. dev.) of the beta cell volume is composed of secretory granule dense-cores exhibiting angular shapes surrounded by wide (typically ≳100 nm) electron-lucent halos. These organelles are identified as mature granules that store insulin for regulated release through the plasma membrane, with a release time of 96±12 hours, as previously obtained from pulsed 35S-radiolabeling of cysteine and methionine. Analysis of beta cell 3D volumes reveals a subpopulation of secretory organelles without electron-lucent halos, identified as immature secretory...
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biorxivpreprint: Determination of secretory granule maturation times in pancreatic islet beta-cells by serial block face scanning electron microscopy https://t.co/tF9q1GrJI0 #bioRxiv
biorxiv_biophys: Determination of secretory granule maturation times in pancreatic islet beta-cells by serial block face scanning electron microscopy https://t.co/PpIwU3hMRC #biorxiv_biophys
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Authors: 7
Total Words: 9904
Unqiue Words: 2677

2.004 Mikeys
#5. The smfBox: an open-source platform for single-molecule FRET
Benjamin Ambrose, James Baxter, John Cully, Matthew Willmott, Elliot Steele, Benji C Bateman, Marisa L Martin-Fernandez, Ashley Cadby, Jonathan Shewring, Marleen Aaldering, Timothy D Craggs
Single-molecule Förster Resonance Energy Transfer (smFRET) is a powerful technique capable of resolving both relative and absolute distances within and between structurally dynamic biomolecules. High instrument costs, and a lack of open-source hardware and acquisition software have limited smFRET's broad application by non-specialists. Here, we present the smfBox, a cost-effective confocal smFRET platform, providing detailed build instructions, open-source acquisition software, and full validation, thereby democratising smFRET for the wider scientific community.
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Diego_official2: RT @biorxiv_biophys: The smfBox: an open-source platform for single-molecule FRET https://t.co/WMCFJ4mAr1 #biorxiv_biophys
CapitanioLab: RT @biorxiv_biophys: The smfBox: an open-source platform for single-molecule FRET https://t.co/WMCFJ4mAr1 #biorxiv_biophys
DinaGrohmann: RT @biorxiv_biophys: The smfBox: an open-source platform for single-molecule FRET https://t.co/WMCFJ4mAr1 #biorxiv_biophys
BarnabaCarlo: RT @biorxiv_biophys: The smfBox: an open-source platform for single-molecule FRET https://t.co/WMCFJ4mAr1 #biorxiv_biophys
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2.004 Mikeys
#6. Comparing current noise in biological and solid-state nanopores
Alessio Fragasso, Sonja Schmid, Cees Dekker
Nanopores bear great potential as single-molecule tools for bioanalytical sensing and sequencing, due to their exceptional sensing capabilities, high-throughput, and low cost. The detection principle relies on detecting small differences in the ionic current as biomolecules traverse the nanopore. A major bottleneck for the further progress of this technology is the noise that is present in the ionic current recordings, because it limits the signal-to-noise ratio and thereby the effective time resolution of the experiment. Here, we review the main types of noise at low and high frequencies and discuss the underlying physics. Moreover, we compare biological and solid-state nanopores in terms of the signal-to-noise ratio (SNR), the important figure of merit, by measuring free translocations of a short ssDNA through a selected set of nanopores under typical experimental conditions. We find that SiNx solid-state nanopores provide the highest SNR, due to the large currents at which they can be operated and the relatively low noise at...
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cees_dekker: Our latest #CDlab preprint: a review comparing noise in biological and solid-state nanopores, by #AlessioFragasso, @sciSonja and myself: https://t.co/SiiNR0KhxJ Surprising conclusions: MspA biological pores have lowest noise but solid-state SiN pores have best signal-to-noise. https://t.co/M4MaOA4Loy
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2.004 Mikeys
#7. Model for disordered proteins with strongly sequence-dependent liquid phase behavior
Antonia Statt, Helena Casademunt, Clifford P Brangwynne, Athanassios Z Panagiotopoulos
Phase separation of intrinsically disordered proteins is important for the formation of membraneless organelles, or biomolecular condensates, which play key roles in the regulation of biochemical processes within cells. In this work, we investigated the phase separation of different sequences of a coarse-grained model for intrinsically disordered proteins and discovered a surprisingly rich phase behavior. We studied both the fraction of total hydrophobic parts and the distribution of hydrophobic parts. Not surprisingly, sequences with larger hydrophobic fractions showed conventional liquid-liquid phase separation. The location of the critical point was systematically influenced by the terminal beads of the sequence, due to changes in interfacial composition and tension. For sequences with lower hydrophobicity, we observed not only conventional liquid-liquid phase separation, but also reentrant phase behavior, in which the liquid phase density decreases at lower temperatures. For some sequences, we observed formation of open phases...
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ShorterLabGroup: RT @biorxiv_biophys: Model for disordered proteins with strongly sequence-dependent liquid phase behavior https://t.co/DutILOIB8U #biorxiv…
BioCondensates: RT @biorxiv_biophys: Model for disordered proteins with strongly sequence-dependent liquid phase behavior https://t.co/DutILOIB8U #biorxiv…
Vegaismyname: RT @biorxiv_biophys: Model for disordered proteins with strongly sequence-dependent liquid phase behavior https://t.co/DutILOIB8U #biorxiv…
mike27072: RT @biorxiv_biophys: Model for disordered proteins with strongly sequence-dependent liquid phase behavior https://t.co/DutILOIB8U #biorxiv…
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2.002 Mikeys
#8. Nanometric axial localization of single fluorescent molecules with modulated excitation
Pierre Jouchet, Clement Cabriel, Nicolas Bourg, Marion Bardou, Christian Pous, Emmanuel FORT, Sandrine LEVEQUE-FORT
Strategies have been developed in LIDAR to perform distance measurements for non-coherent emission in sparse samples based on excitation modulation. Super-resolution fluorescence microscopy is also striving to perform axial localization but through entirely different approaches. Here we revisit the amplitude modulated LIDAR approach to reach nanometric localization precision and we successfully adapt it to bring distinct advantages to super-resolution microscopy. The excitation pattern is performed by interference enabling the decoupling between spatial and time modulation. The localization of a single emitter is performed by measuring the relative phase of its linear fluorescent response to the known shifting excitation field. Taking advantage of a tilted interfering configuration, we obtain a typical axial localization precision of 7.5 nm over the entire field of view and the axial capture range, without compromising on the acquisition time, the emitter density or the lateral localization precision. The interfering pattern being...
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biophotonicat: Nanometric axial localization of single fluorescent molecules with modulated excitation (relevance: 94%) https://t.co/s9Nh0W3VkW #biophotonics #biomedicaloptics https://t.co/baoWz0CvOn
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1.999 Mikeys
#9. Hidden dynamic signatures drive substrate selectivity in the disordered phosphoproteome
Min Hyung Cho, James O. Wrabl, James Taylor, Vincent J. Hilser
Phosphorylation sites are hyper-abundant in the disordered proteins of eukaryotes, suggesting that conformational dynamics (or heterogeneity) may play a major role in determining to what extent a kinase interacts with a particular substrate. In biophysical terms, substrate selectivity may be determined not just by the structural and chemical complementarity between the kinase and its protein substrates, but also by the free energy difference between the conformational ensembles that are recognized by the kinase and those that are not. To test this hypothesis, we developed an informatics framework based on statistical thermodynamics, which allows us to probe for dynamic contributions to phosphorylation, as evaluated by the ability to predict Ser/Thr/Tyr phosphorylation sites in the disordered proteome. Essential to this framework is a decomposition of substrate sequence information into two types: vertical information encoding conserved kinase specificity motifs and horizontal (distributed) information encoding substrate...
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MattChallacombe: RT @biorxiv_biophys: Hidden dynamic signatures drive substrate selectivity in the disordered phosphoproteome https://t.co/9J6WJnsjVk #bior…
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1.998 Mikeys
#10. Quantifying the heterogeneity of macromolecular machines by mass photometry
Adar Sonn Segev, Katarina Belacic, Tatyana Bodrug, Gavin Young, Ryan T. VanderLinden, Brenda Schulman, Johannes Schimpf, Thorsten Friedrich, Phat Vinh Dip, Thomas Schwartz, Benedikt Bauer, Jan-Michael Peters, Weston B. Struwe, Justin LP Benesch, Nicholas G. Brown, David Haselbach, Philipp Kukura
Sample purity is central to in vitro studies of protein function and regulation, as well as to the efficiency and success of structural studies requiring crystallization or computational alignment of individual molecules. Here, we show that mass photometry (MP) accurately reports on sample heterogeneity using minimal volumes with molecular resolution within minutes. We benchmark our approach by negative stain electron microscopy (nsEM), including workflows involving chemical crosslinking and multi-step purification of a multi-subunit ubiquitin ligase. When applied to proteasome stability, we detect and quantify assemblies invisible to nsEM. Our results illustrate the unique advantages of MP for rapid sample characterization, prioritization and optimization.
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HaselbachLab: RT @biorxivpreprint: Quantifying the heterogeneity of macromolecular machines by mass photometry https://t.co/AB1msFGiav #bioRxiv
Jan_Soro: RT @biorxivpreprint: Quantifying the heterogeneity of macromolecular machines by mass photometry https://t.co/AB1msFGiav #bioRxiv
JulienMarcoux2: RT @biorxivpreprint: Quantifying the heterogeneity of macromolecular machines by mass photometry https://t.co/AB1msFGiav #bioRxiv
SnowWhiteGretel: RT @biorxivpreprint: Quantifying the heterogeneity of macromolecular machines by mass photometry https://t.co/AB1msFGiav #bioRxiv
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Authors: 17
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