Top 10 Biorxiv Papers Today in Biophysics


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#1. CryoEM structure of the Nipah virus nucleocapsid assembly
De-Sheng Ker, Huw T. Jenkins, Sandra J. Greive, Alfred A. Antson
Nipah virus is a highly pathogenic zoonotic RNA virus, causing fatal encephalitis in humans. Like other negative-strand RNA viruses including Ebola and measles, its genome is wrapped by the nucleocapsid (N) protein forming a helical assembly. Here we report the CryoEM structure of the Nipah nucleocapsid protein-RNA assembly, at near atomic resolution. The N protein wraps the RNA genome with a periodicity of six nucleotides per protomer, around the outer edge of the helical assembly, in common with other paramyxoviruses. This structure uncovers details of the nucleocapsid assembly, demonstrating the role of the N-terminal arm of the N protein in the formation of the helical assembly and revealing details of the sequence-independent coordination of RNA binding in the "3-bases-in, 3-bases-out" conformation. CryoEM analysis also reveals formation of clam-shaped assemblies of the N-protein, mediated by intersubunit interactions involving several N protein loop regions.
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biorxivpreprint: CryoEM structure of the Nipah virus nucleocapsid assembly https://t.co/GWtoTJC4QP #bioRxiv
biorxiv_biophys: CryoEM structure of the Nipah virus nucleocapsid assembly https://t.co/kJuzAYnHTJ #biorxiv_biophys
cryoEM_Papers: CryoEM structure of the Nipah virus nucleocapsid assembly https://t.co/ZtFrlziXun
DanielHurdiss: RT @cryoEM_Papers: CryoEM structure of the Nipah virus nucleocapsid assembly https://t.co/ZtFrlziXun
_socalledexpert: RT @cryoEM_Papers: CryoEM structure of the Nipah virus nucleocapsid assembly https://t.co/ZtFrlziXun
roponpallab: RT @biorxiv_biophys: CryoEM structure of the Nipah virus nucleocapsid assembly https://t.co/kJuzAYnHTJ #biorxiv_biophys
dmborek: RT @cryoEM_Papers: CryoEM structure of the Nipah virus nucleocapsid assembly https://t.co/ZtFrlziXun
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Authors: 4
Total Words: 0
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#2. Lipidomics of human adipose tissue reveals diversity between body areas
Naba Al-Sari, Tommi Suvitaival, Ismo Mattila, Ashfaq Ali, Linda Ahonen, Kajetan Trost, Trine Foged Henriksen, Flemming Pociot, Lars Ove Dragsted, Cristina Legido-Quigley
Background and aims: Adipose tissue plays a pivotal role in storing excess fat and its composition reflects the history of person's lifestyle and metabolic health. Broad profiling of lipids with mass spectrometry has potential for uncovering new knowledge on the pathology of obesity, metabolic syndrome, diabetes and other related conditions. Here, we developed a lipidomic method for analyzing human subcutaneous adipose biopsies. We applied the method to four body areas to understand the differences in lipid composition between these areas. Materials and methods: Adipose tissue biopsies from 10 participants were analyzed using ultra-high-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry. The method development included the optimization of the lipid extraction, the sample amount and the sample dilution factor to detect lipids in an appropriate concentration range. Lipidomic analyses were performed for adipose tissue collected from the abdomen, breast, thigh and lower back. Differences in lipid...
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biorxivpreprint: Lipidomics of human adipose tissue reveals diversity between body areas https://t.co/B36bx2WW41 #bioRxiv
biorxiv_biophys: Lipidomics of human adipose tissue reveals diversity between body areas https://t.co/bbzeJNYrw0 #biorxiv_biophys
HubBucket: RT @biorxivpreprint: Lipidomics of human adipose tissue reveals diversity between body areas https://t.co/B36bx2WW41 #bioRxiv
Astro_Erik: RT @biorxivpreprint: Lipidomics of human adipose tissue reveals diversity between body areas https://t.co/B36bx2WW41 #bioRxiv
AyalaTovy: RT @biorxivpreprint: Lipidomics of human adipose tissue reveals diversity between body areas https://t.co/B36bx2WW41 #bioRxiv
Jonatha14158813: RT @biorxivpreprint: Lipidomics of human adipose tissue reveals diversity between body areas https://t.co/B36bx2WW41 #bioRxiv
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Sample Sizes : [3, 4, 4, 10]
Authors: 10
Total Words: 6687
Unqiue Words: 2386

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#3. vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy
Alexander Spark, Alexandre Kitching, Daniel Esteban-Ferrer, Anoushka Handa, Alexander R. Carr, Lisa-Maria Needham, Aleks Ponjavic, Mafalda Da Cunha Santos, James McColl, Christophe Leterrier, Simon J. Davis, Ricardo Henriques, Steven F. Lee
Super-Resolution (SR) Microscopy based on 3D Single-Molecule Localization Microscopy (SMLM) is now well established and its wide-spread adoption has led to the development of more than 36 software packages, dedicated to quantitative evaluation of the spatial and temporal detection of fluorophore photoswitching. While the initial emphasis in the 3D SMLM field has clearly been on improving resolution and data quality, there is now a marked absence of 3D visualization approaches that enable the straightforward, high-fidelity exploration of this type of data. Inspired by the horological phosphorescence points that illuminate watch-faces in the dark, we present vLUME (Visualization of the Universe in a Micro Environment, pronounced 'volume') a free-for-academic-use immersive virtual reality-based (VR) visualization software package purposefully designed to render large 3D-SMLM data sets. vLUME enables robust visualization, segmentation and quantification of millions of fluorescence puncta from any 3D SMLM technique. vLUME has an...
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SteveTheChemist: Ever wanted to squish an immune cell, you need vLUME (pronounced 'volume'). VR for SMLM @lumeVR @AnoushkaHanda @SteveTheChemist @LisaMariaN91 @christlet @HenriquesLab pre-print now available, any questions please ask https://t.co/BsLkvCvI7d @biorxiv_biophys https://t.co/VUQoov0Gng
biophotonicat: vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy (relevance: 100%) https://t.co/0ukAuxpcmw #biophotonics #biomedicaloptics https://t.co/1FkJxBguwW
HubBucket: RT @biorxivpreprint: vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy https://t.co/2Zf1m2RyGE #bioRxiv
Olu_GH: RT @biorxiv_biophys: vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy https://t.co/dtNAh5HXI3 #biorxiv_biophys
Craggs_Lab: RT @biorxiv_biophys: vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy https://t.co/dtNAh5HXI3 #biorxiv_biophys
Nicolas26538817: RT @biorxiv_biophys: vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy https://t.co/dtNAh5HXI3 #biorxiv_biophys
kaaskac: RT @biorxiv_biophys: vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy https://t.co/dtNAh5HXI3 #biorxiv_biophys
AnoushkaHanda: RT @biorxiv_biophys: vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy https://t.co/dtNAh5HXI3 #biorxiv_biophys
nanxiaolin: RT @biorxiv_biophys: vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy https://t.co/dtNAh5HXI3 #biorxiv_biophys
Superresolved: RT @biorxiv_biophys: vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy https://t.co/dtNAh5HXI3 #biorxiv_biophys
DanielE42587767: RT @biorxiv_biophys: vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy https://t.co/dtNAh5HXI3 #biorxiv_biophys
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#4. Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge
Mehtap Işık, Teresa Danielle Bergazin, Thomas Fox, Andrea Rizzi, John D. Chodera, David L. Mobley
The SAMPL Challenges aim to focus the biomolecular and physical modeling community on issues that limit the accuracy of predictive modeling of protein-ligand binding for rational drug design. In the SAMPL5 log D Challenge, designed to benchmark the accuracy of methods for predicting drug-like small molecule transfer free energies from aqueous to nonpolar phases, participants found it difficult to make accurate predictions due to the complexity of protonation state issues. In the SAMPL6 log P Challenge, we asked participants to make blind predictions of the octanol-water partition coefficients of neutral species of 11 compounds and assessed how well these methods performed absent the complication of protonation state effects. This challenge builds on the SAMPL6 pKa Challenge, which asked participants to predict pKa values of a superset of the compounds considered in this log P challenge. Blind prediction sets of 91 prediction methods were collected from 27 research groups, spanning a variety of quantum mechanics (QM) or molecular...
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biorxivpreprint: Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge https://t.co/jzTjR3DZgT #bioRxiv
biorxiv_biophys: Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge https://t.co/ASEBLPqrGg #biorxiv_biophys
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Total Words: 32644
Unqiue Words: 8155

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#5. Middle-level IM-MS and CIU experiments for improved therapeutic immunoglobulin isotype fingerprinting
Thomas Botzanowski, Oscar HERNANDEZ-ALBA, Martine Malissard, Elsa Wagner-Rousset, Evolene Desligniere, Olivier Colas, Jean-Francois Haeuw, Alain Beck, Sarah CIANFERANI
Currently approved therapeutic monoclonal antibodies (mAbs) are based on immunoglobulin G (IgG) 1, 2 or 4 isotypes, which differ in their specific inter-chains disulfide bridge connectivities. Different analytical techniques have been reported for mAb isotyping, among which native ion mobility mass spectrometry (IM-MS) and collision induced unfolding (CIU) experiments. However, mAb isotyping by these approaches is based on detection of subtle differences and thus remains challenging at the intact-level. We report here on middle-level (after IdeS digestion) IM-MS and CIU approaches to afford better differentiation of mAb isotypes. Our method provides simultaneously CIU patterns of F(ab)2 and Fc domains within a single run. Middle-level CIU patterns of F(ab)2 domains enable more reliable classification of mAb isotypes compared to intact level CIU, while CIU fingerprints of Fc domains are overall less informative for mAb isotyping. F(ab)2 regions can thus be considered as diagnostic domains providing specific CIU signatures for mAb...
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biorxivpreprint: Middle-level IM-MS and CIU experiments for improved therapeutic immunoglobulin isotype fingerprinting https://t.co/AKzCi6lboW #bioRxiv
biorxiv_biophys: Middle-level IM-MS and CIU experiments for improved therapeutic immunoglobulin isotype fingerprinting https://t.co/zlwavbyqZj #biorxiv_biophys
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#6. Effect of flagellar beating pattern on sperm rheotaxis and boundary-dependent navigation
Meisam Zaferani, Farhad Javi, Amir Mokhtare, Alireza Abbaspourrad
The study of navigational mechanisms used by mammalian sperm inside a microenvironment yields better understanding of sperm locomotion during the insemination process, which aids in the design of tools for overcoming infertility. Near- and far-field hydrodynamic interactions with nearby boundaries and rheotaxis are known to be some of the steering strategies that keep sperm on the correct path toward the egg. However, it is not known how the beating patterns of sperm may influence these navigational strategies. In this study, we investigate the effect of flagellar beating pattern on navigation of sperm cells both theoretically and experimentally using a two-step approach. We first isolate bovine sperm based on their rheotactic behavior in a zone with quiescent medium using a microfluidic system. This step ensures that the swimmers are able to navigate upstream and have motilities higher than a selected value, even though they feature various flagellar beating patterns. We then explore the flagellar beating pattern of these...
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biorxivpreprint: Effect of flagellar beating pattern on sperm rheotaxis and boundary-dependent navigation https://t.co/Mif23rlRbp #bioRxiv
biorxiv_biophys: Effect of flagellar beating pattern on sperm rheotaxis and boundary-dependent navigation https://t.co/cIgE9YvmO1 #biorxiv_biophys
biophotonicat: Effect of flagellar beating pattern on sperm rheotaxis and boundary-dependent navigation (relevance: 46%) https://t.co/HyX4VqqSqD #biophotonics #biomedicaloptics https://t.co/tdglwojRUp
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Total Words: 12865
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#7. Intrinsic fluorescence in non-aromatic peptide structures is induced by collective vibrations, charge reorganisation and short hydrogen bonds, as shown in a new glutamine-related structure
Amberley D Stephens, Muhammad Nawaz Qaisrani, Michael T Ruggiero, Saul T E Jones, Emiliano Poli, Andrew D Bond, Philippa J Woodhams, Elyse M Kleist, Luca Grisanti, Ralph Gebauer, J Axel Zeitler, Dan Credgington, Ali Hassanali, Gabriele S Kaminski Schierle
Disentangling the origin of the optical activity of non-aromatic proteins is challenging due to their size and thus their high computational requisites. Here we show, in a much smaller model system, that the single amino acid glutamine undergoes a chemical transformation leading to an unreported glutamine-like structure which has a similar broad absorption spectrum reported previously for non-aromatic proteins. We further show computationally that the optical activity of the glutamine-like structure is directly coupled to short-hydrogen bonds, but also displays charge and vibrational fluctuations, the latter of which are also present in less optically active structures such as in L-glutamine. Since experimentally the glutamine-like structure is the brightest structure, we conclude that short-hydrogen bonds are the ones responsible for the large Stokes shift observed in optically active non-aromatic proteins.
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#8. Are Maize Stalks Efficiently Tapered to Withstand Wind Induced Bending Stresses?
Christopher J Stubbs, Kate Seegmiller, Rajandeep S Sekhon, Daniel J Robertson
Stalk lodging (breaking of agricultural plant stalks prior to harvest) results in millions of dollars in lost revenue each year. Despite a growing body of literature on the topic of stalk lodging, the structural efficiency of maize stalks has not been investigated previously. In this study, we investigate the morphology of mature maize stalks to determine if rind tissues, which are the major load bearing component of corn stalks, are efficiently organized to withstand wind induced bending stresses that cause stalk lodging. 945 fully mature, dried commercial hybrid maize stem specimens (48 hybrids, ~2 replicates, ~10 samples per plot) were subjected to: (1) three-point-bending tests to measure their bending strength and (2) rind penetration tests to measure the cross-sectional morphology at each internode. The data were analyzed through an engineering optimization algorithm to determine the structural efficiency of the specimens. Hybrids with higher average bending strengths were found to allocate rind tissue more efficiently than...
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#9. Epithelial organ shape is generated by patterned actomyosin contractility and maintained by the extracellular matrix
Ali Nematbakhsh, Megan Levis, Nilay Kumar, Weitao Chen, Jeremiah J Zartman, Mark Alber
Epithelial sheets play important roles in defining organ architecture during development. Here, we employed an iterative experimental and multi-scale computational modeling approach to decouple direct and indirect effects of actomyosin-generated forces, nuclear positioning, extracellular matrix (ECM), and cell-cell adhesion in shaping Drosophila wing imaginal discs, a powerful system for elucidating general principles of epithelial morphogenesis. Basally generated actomyosin forces are found to regulate apically biased nuclear positioning and are required for generating epithelial bending and cell elongation of the wing disc pouch. Surprisingly, however, short-term pharmacological inhibition of ROCK-driven actomyosin contractility does not impact the maintenance of tissue height or curved shape. In comparison, the relative tautness of the extracellular basement membrane is also patterned between regions of the wing disc. However, computational simulations show that patterning of ECM tautness provides only a minor contribution to...
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#10. Geometric models for robust encoding of dynamical information into embryonic patterns
Laurent Jutras-Dubé, Ezzat El-Sherif, Paul François
During development, cells gradually assume specialized fates via changes of transcriptional dynamics, sometimes even within the same developmental stage. For anterior-posterior patterning in metazoans, it has been suggested that the gradual transition from a dynamic genetic regime to a static one is encoded by different transcriptional modules. In that case, the static regime has an essential role in pattern formation in addition to its maintenance function. In this work, we introduce a geometric approach to study such transition. We exhibit two types of genetic regime transitions, respectively arising through local or global bifurcations. We find that the global bifurcation type is more generic, more robust, and better preserves dynamical information. This could parsimoniously explain common features of metazoan segmentation, such as changes of periods leading to waves of gene expressions, "speed/frequency-gradient" dynamics, and changes of wave patterns. Geometric approaches appear as possible alternatives to gene regulatory...
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Alexis_Lomakin: RT @biorxivpreprint: Geometric models for robust encoding of dynamical information into embryonic patterns https://t.co/JbCJvjNxGt #bioRxiv
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