Top 10 Biorxiv Papers Today in Biophysics


2.368 Mikeys
#1. Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution
Xiao Fan, Jia Wang, Xing Zhang, Zi Yang, Jin-Can Zhang, Lingyun Zhao, Hai-Lin Peng, Jianlin Lei, Hong-Wei Wang
The fast development of single particle cryo-EM has made it more feasible to obtain the 3D structure of well-behaved macromolecules with molecular weight higher than 300 kDa at ~3 Å resolution. It remains a challenge to obtain high resolution structure of molecules smaller than 100 kDa using single particle cryo-EM, mainly due to the low contrast of the molecules embedded in vitreous ice. In this work, we applied the Cs-corrector-VPP coupled cryo-EM to study 52 kDa streptavidin (SA) protein supported on a thin layer of graphene film and embedded in vitreous ice. We were able to solve both the apo-SA and biotin-bound SA at near-atomic resolution using single particle cryo-EM. We demonstrated that the method is capable to determine the structure of molecule as small as 39 kDa and potentially even smaller molecules. Furthermore, we found that using the graphene film to avoid the adsorption to the air-water interface is critical to maintain the protein's high-resolution structural information.
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EdoardoDImprima: @DmitryLyumkis It seems so (https://t.co/ChIeUR7E8Q) thanks to @OliBClarke to point it out. However, they somehow gloss over how precisely they prepared the grids.
JGarciaNafria: Keeps getting smaller and smaller...https://t.co/l8SFvH6w71
FelipeIMerino: The smallest protein structure solved by #cryoEM to near-atomic resolution, support layer and all. 👇 https://t.co/i7QX28NyYt
cryoEM_Papers: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/WztVV1qRk1
cryoET: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/j4svVaOLKF
HattoriM: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
DanielHurdiss: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
PoulNissen: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
Paulino_Lab: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
BJ_Greber: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
OliBClarke: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
fronzes_lab: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
RuiZhangWUSTL: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
t2438: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
voorheeslab: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
analioj: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
moncourvoisier: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
xjtuhw: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
arshukla: RT @biorxivpreprint: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/qE69CkVeLp #bio…
KwiatBerlin: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
bwfalcon: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
LourduXavier14: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
tofayel_ahmed1: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
DebnathGhosal: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
CostaT_Lab: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
MitosisLab: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
ktr_nakanishi: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
danengw: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
ribo_doc: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
MarionPesenti: RT @cryoEM_Papers: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/WztVV1qRk1
scidave: RT @biorxivpreprint: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/qE69CkVeLp #bio…
clmpnino: RT @cryoET: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/j4svVaOLKF
biofiziksmama: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
TommiAWhite: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
M_Hospenthal: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
MGordonJoyce: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
GaneshaPitchai: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
The_Mbu: RT @biorxiv_biophys: Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution https://t.co/YFT7wHPwEf #bio…
matrappas: RT @JGarciaNafria: Keeps getting smaller and smaller...https://t.co/l8SFvH6w71
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Authors: 9
Total Words: 8252
Unqiue Words: 2110

2.032 Mikeys
#2. Heparin-induced tau filaments are polymorphic and differ from those in Alzheimer's and Pick's disease
Wenjuan Zhang, Benjamin Falcon, Alexey G Murzin, Juan Fan, R Anthony Crowther, Michel Goedert, Sjors H.W. Scheres
The assembly of microtubule-associated protein tau into abundant filamentous inclusions underlies a range of neurodegenerative diseases. The finding that tau filaments adopt different conformations in Alzheimer's and Pick's diseases raises the question of what kinds of structures of tau filaments form in vitro. Here, we used electron cryo-microscopy (cryo-EM) and negative-stain immuno-gold electron microscopy (immuno-EM) to characterise filaments that were assembled from recombinant full-length human tau with four (2N4R) or three (2N3R) microtubule-binding repeats in the presence of heparin. 4R tau assembles into at least four different types of filaments. Cryo-EM structures of three types of 4R filaments reveal similar "kinked hairpin" folds, in which the second and third repeats pack against each other. 3R tau filaments are structurally homogeneous, and adopt a dimeric core, where the third repeats of two tau molecules pack against each other in a parallel, yet asymmetric, manner. None of the heparin-induced tau filaments...
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SjorsScheres: Tau amyloids don't cease to surprise: in-vitro aggregation with heparin yields structures different from those in Alzheimer's or Pick's disease. With Wenjuan Zhang, @bfalcon and @MichelGoed; now on @biorxivpreprint https://t.co/fzBSlgega4 https://t.co/uRBsgDbBgA
cryoEM_Papers: Heparin-induced tau filaments are polymorphic and differ from those in Alzheimer\'s and Pick\'s disease https://t.co/UiBWDCW6mO
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Total Words: 13473
Unqiue Words: 3388

2.0 Mikeys
#3. Cryo-EM structure of the receptor-activated TRPC5 ion channel at 2.9 angstrom resolution
Jingjing Duan, Jian Li, Gui-Lan Chen, Bo Zeng, David Clapham, Zongli Li, Jin Zhang
The transient receptor potential canonical subfamily member 5 (TRPC5) is a non-selective calcium-permeant cation channel. As a depolarizing channel, its function is studied in the central nervous system and kidney. TRPC5 forms heteromultimers with TRPC1, but also forms homomultimers. It can be activated by reducing agents through reduction of the extracellular disulfide bond. Here we present the 2.9 angstrom resolution electron cryo-microscopy (cryo-EM) structure of TRPC5. The structure of TRPC5 in its apo state is partially open, which may be related to the weak activation of TRPC5 in response to extracellular pH. We also report the conserved negatively charged residues of the cation binding site located in the hydrophilic pocket between S2 and S3. Comparison of the TRPC5 structure to previously determined structures of other TRPC and TRP channels reveals differences in the extracellular pore domain and in the length of the S3 helix. Together, these results shed light on the structural features that contribute to the specific...
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cryoEM_Papers: Cryo-EM structure of the receptor-activated TRPC5 ion channel at 2.9 angstrom resolution https://t.co/jSQkh2nqBT
AlexanderSobol6: Cryo-EM structure of the receptor-activated TRPC5 ion channel at 2.9 angstrom resolution https://t.co/YxsgrRNInb
grawoig: RT @biorxiv_biophys: Cryo-EM structure of the receptor-activated TRPC5 ion channel at 2.9 angstrom resolution https://t.co/oP0FICV0DR #bio…
ProfSharona: RT @AlexanderSobol6: Cryo-EM structure of the receptor-activated TRPC5 ion channel at 2.9 angstrom resolution https://t.co/YxsgrRNInb
OliBClarke: RT @biorxiv_biophys: Cryo-EM structure of the receptor-activated TRPC5 ion channel at 2.9 angstrom resolution https://t.co/oP0FICV0DR #bio…
osamaharraz: RT @AlexanderSobol6: Cryo-EM structure of the receptor-activated TRPC5 ion channel at 2.9 angstrom resolution https://t.co/YxsgrRNInb
cryoET: RT @AlexanderSobol6: Cryo-EM structure of the receptor-activated TRPC5 ion channel at 2.9 angstrom resolution https://t.co/YxsgrRNInb
analioj: RT @biorxiv_biophys: Cryo-EM structure of the receptor-activated TRPC5 ion channel at 2.9 angstrom resolution https://t.co/oP0FICV0DR #bio…
analioj: RT @cryoEM_Papers: Cryo-EM structure of the receptor-activated TRPC5 ion channel at 2.9 angstrom resolution https://t.co/jSQkh2nqBT
gqmartinez: RT @AlexanderSobol6: Cryo-EM structure of the receptor-activated TRPC5 ion channel at 2.9 angstrom resolution https://t.co/YxsgrRNInb
MartaUkleja: RT @AlexanderSobol6: Cryo-EM structure of the receptor-activated TRPC5 ion channel at 2.9 angstrom resolution https://t.co/YxsgrRNInb
coreyv87: RT @AlexanderSobol6: Cryo-EM structure of the receptor-activated TRPC5 ion channel at 2.9 angstrom resolution https://t.co/YxsgrRNInb
clmpnino: RT @AlexanderSobol6: Cryo-EM structure of the receptor-activated TRPC5 ion channel at 2.9 angstrom resolution https://t.co/YxsgrRNInb
rigbylab: RT @AlexanderSobol6: Cryo-EM structure of the receptor-activated TRPC5 ion channel at 2.9 angstrom resolution https://t.co/YxsgrRNInb
m_munari: RT @AlexanderSobol6: Cryo-EM structure of the receptor-activated TRPC5 ion channel at 2.9 angstrom resolution https://t.co/YxsgrRNInb
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1.995 Mikeys
#4. Oncogenic G12D mutation alters local conformations and dynamics of K-Ras
Sezen Vatansever, Burak Erman, Zeynep Gumus
K-Ras is the most frequently mutated oncoprotein in human cancers, and G12D is its most prevalent mutation. To understand how G12D mutation impacts K-Ras function, we need to understand how it alters the regulation of its dynamics. Here, we present local changes in K-Ras structure, conformation and dynamics upon G12D mutation, from long-timescale Molecular Dynamics simulations of active (GTP-bound) and inactive (GDP-bound) forms of wild-type and mutant K-Ras, with an integrated investigation of atomistic-level changes, local conformational shifts and correlated residue motions. Our results reveal that the local changes in K-Ras are specific to bound nucleotide (GTP or GDP), and we provide a structural basis for this. Specifically, we show that G12D mutation causes a shift in the population of local conformational states of K-Ras, especially in Switch-II (SII) and α3-helix regions, in favor of a conformation that is associated with a catalytically impaired state through structural changes; it also causes SII motions to...
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Authors: 3
Total Words: 8792
Unqiue Words: 2285

1.984 Mikeys
#5. Lamina and Heterochromatin Direct Chromosome Organisation in Senescence and Progeria
Michael Chiang, Davide Michieletto, Chris A. Brackley, Nattaphong Rattanavirotkul, Hisham Mohammed, Davide Marenduzzo, Tamir Chandra
Lamina-associated domains (LADs) cover a large part of the human genome and are thought to play a major role in shaping the nuclear architectural landscape. Here, we use simulations based on concepts from polymer physics to dissect the roles played by heterochromatin- and lamina-mediated interactions in nuclear organisation. Our model explains the conventional organisation of heterochromatin and euchromatin in growing cells, as well as the pathological organisation found in oncogene-induced senescence and progeria. We show that the experimentally observed changes in the locality of contacts in senescent and progeroid cells can be explained naturally as arising due to phase transitions in the system. Our model predicts that LADs are highly stochastic, and that, once established, the senescent phenotype should be metastable even if lamina-mediated interactions were reinstated. Overall, our simulations uncover a universal physical mechanism that can regulate heterochromatin segregation and LAD formation in a wide range of mammalian nuclei.
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Total Words: 11886
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0.0 Mikeys
#6. Field induced cell proliferation and death in a thick epithelium
Niladri Sarkar, Jacques Prost, Frank Julicher
We study the dynamics of a thick polar epithelium subjected to the action of both an electric and a flow field in a planar geometry. We develop a generalized continuum hydrodynamic description and describe the tissue as a two component fluid system. The cells and the interstitial fluid are the two components and we keep all terms allowed by symmetry. In particular we keep track of the cell pumping activity for both solvent flow and electric current and discuss the corresponding orders of magnitude. We study the growth dynamics of tissue slabs, their steady states and obtain the dependence of the cell velocity, net cell division rate, and cell stress on the flow strength and the applied electric field. We find that finite thickness tissue slabs exist only in a restricted region of phase space and that relatively modest electric fields or imposed external flows can induce either proliferation or death.
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biorxivpreprint: Field induced cell proliferation and death in a thick epithelium https://t.co/d2Hc01ZXUS #bioRxiv
biorxiv_biophys: Field induced cell proliferation and death in a thick epithelium https://t.co/eXSwoHpKp7 #biorxiv_biophys
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Total Words: 10957
Unqiue Words: 2228

0.0 Mikeys
#7. MBIR: A Cryo-electron Tomography 3D Reconstruction Method that Effectively Minimizes Missing Wedge Artifacts and Restores Missing Information
Rui Yan, Singanallur V Venkatakrishnan, Jun Liu, Charles A Bouman, Wen Jiang
Cryo-Electron Tomography (cryo-ET) has become an essential technique in revealing cellular and macromolecular assembly structures in their native states. However, due to radiation damage and the limited tilt range, cryo-ET suffers from low contrast and missing wedge artifacts, which limits the tomograms to low resolution and hinders further biological interpretation. In this study, we applied the Model-Based Iterative Reconstruction (MBIR) method to obtain tomographic 3D reconstructions of experimental cryo-ET datasets and demonstrated the advantages of MBIR in contrast improvement, missing wedge artifacts reduction, and missing information restoration compared with other reconstruction approaches. Considering the outstanding reconstruction quality, MBIR has a great potential in the determination of high resolution biological structures with cryo-ET.
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Total Words: 6297
Unqiue Words: 2092

0.0 Mikeys
#8. Red muscle activity in bluegill sunfish Lepomis macrochirus during forward accelerations
Margot A. B. Schwalbe, Alexandra Leigh Boden, Tyler N. Wise, Eric Daniel Tytell
Fishes generate force to swim by activating muscles on either side of their flexible bodies. To accelerate, they must produce higher muscle forces, which leads to higher reaction forces back on their bodies from the environment. If their bodies are too flexible, the forces during acceleration could not be transmitted effectively to the environment. Here, we investigate whether fish can use their red muscle to stiffen their body during acceleration. We used high-speed video, electromyographic recordings, and a new digital inertial measurement unit to quantify body kinematics, red muscle activity, and 3D orientation and centre of mass acceleration during forward accelerations and steady swimming over several speeds. During acceleration, fish co-activated anterior muscle on the left and right side, and activated all muscle sooner and kept it active for a larger fraction of the tail beat cycle. These activity patterns are consistent with our hypothesis that fish use their red muscle to stiffen their bodies during acceleration. We...
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biorxivpreprint: Red muscle activity in bluegill sunfish Lepomis macrochirus during forward accelerations https://t.co/JVmqtSop2F #bioRxiv
biorxiv_biophys: Red muscle activity in bluegill sunfish Lepomis macrochirus during forward accelerations https://t.co/sT9nzoigln #biorxiv_biophys
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Total Words: 11038
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0.0 Mikeys
#9. Dynamic Graphical Models of Molecular Kinetics
Simon Olsson, Frank Noe
Most current molecular dynamics simulation and analysis methods rely on the idea that the molecular system can be characterized by a single global state, e.g., a Markov State in a Markov State Model (MSM). In this approach, molecules can be extensively sampled and analyzed when they only possess a few metastable states, such as small to medium-sized proteins. However this approach breaks down in frustrated systems and in large protein assemblies, where the number of global meta-stable states may grow exponentially with the system size. Here, we introduce Dynamic Graphical Models (DGMs), which build upon the idea of Ising models, and describe molecules as assemblies of coupled subsystems. The switching of each sub-system state is only governed by the states of itself and its neighbors. DGMs need many fewer parameters than MSMs or other global-state models, in particular we do not need to observe all global system configurations to estimate them. Therefore, DGMs can predict new, previously unobserved, molecular configurations. Here,...
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biorxivpreprint: Dynamic Graphical Models of Molecular Kinetics https://t.co/pXATOOHpWn #bioRxiv
biorxiv_biophys: Dynamic Graphical Models of Molecular Kinetics https://t.co/ZLpjh3xY3a #biorxiv_biophys
MattChallacombe: RT @biorxiv_biophys: Dynamic Graphical Models of Molecular Kinetics https://t.co/ZLpjh3xY3a #biorxiv_biophys
jsci: RT @biorxiv_biophys: Dynamic Graphical Models of Molecular Kinetics https://t.co/ZLpjh3xY3a #biorxiv_biophys
habibhobo: RT @biorxiv_biophys: Dynamic Graphical Models of Molecular Kinetics https://t.co/ZLpjh3xY3a #biorxiv_biophys
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0.0 Mikeys
#10. Reconstitution of a flexible SYCP3-DNA fibre suggests a mechanism for SYCP3 coating of the meiotic chromosome axis
Daniel Bollschweiler, Laura Radu, Juergen M Plitzko, Robert M Henderson, Ioanna Mela, Luca Pellegrini
The synaptonemal complex (SC) keeps homologous chromosomes in close alignment during meiotic crossover. A hallmark of SC formation is the presence of its protein component SYCP3 on the chromosome axis. As SC assembly progresses, SYCP3 is deposited on both axes of the homologue pair, forming the lateral element (LE) in the tripartite structure of the mature SC. We have used cryo-electron tomography and atomic force microscopy to study the mechanism of assembly and DNA binding of the SYCP3 fibre. We find that the three-dimensional architecture of the fibre is built on a highly irregular arrangement of SYCP3 molecules displaying very limited local geometry. Interaction between SYCP3 molecules is driven by the intrinsically disordered tails of the protein, with no contact between the helical cores, resulting in a flexible fibre assembly. We demonstrate that the SYCP3 fibre can engage in extensive interactions with DNA, indicative of an efficient mechanism for incorporation of DNA within the fibre. Taken together, our findings suggest...
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biorxivpreprint: Reconstitution of a flexible SYCP3-DNA fibre suggests a mechanism for SYCP3 coating of the meiotic chromosome axis https://t.co/e40INKC7yH #bioRxiv
biorxiv_biophys: Reconstitution of a flexible SYCP3-DNA fibre suggests a mechanism for SYCP3 coating of the meiotic chromosome axis https://t.co/L8qM5ZvXko #biorxiv_biophys
meiosis_papers: Reconstitution of a flexible SYCP3-DNA fibre suggests a mechanism for S…|Bollschweiler, D https://t.co/6cOZ9vxbZV
PellegriniLab: Check out our latest paper on BioRxiv: Reconstitution of a flexible SYCP3-DNA fibre suggests a mechanism for SYCP3 coating of the meiotic chromosome axis https://t.co/LFz43ZtQ0x
Spo11Rulz: RT @meiosis_papers: Reconstitution of a flexible SYCP3-DNA fibre suggests a mechanism for S…|Bollschweiler, D https://t.co/6cOZ9vxbZV
biobosie: RT @meiosis_papers: Reconstitution of a flexible SYCP3-DNA fibre suggests a mechanism for S…|Bollschweiler, D https://t.co/6cOZ9vxbZV
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Total Words: 8517
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Assert is a website where the best academic papers on arXiv (computer science, math, physics), bioRxiv (biology), BITSS (reproducibility), EarthArXiv (earth science), engrXiv (engineering), LawArXiv (law), PsyArXiv (psychology), SocArXiv (social science), and SportRxiv (sport research) bubble to the top each day.

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