Top 10 Biorxiv Papers Today


2.296 Mikeys
#1. How signals of calcium ions initiate the beats of cilia and flagella
Jack Adam Tuszynski, Miljko Satarić, Tomas Nemes, Dalibor L Sekulic
Cilia and flagella are cell organelles serving basic roles in cellular motility. Ciliary movement is performed by a sweeping-like repeated bending motion, which gives rise to a self-propagating "ciliary beat". The hallmark structure in cilia is the axoneme, a stable architecture of microtubule doublets. The motion of axoneme is powered by the axonemal dynein motor family powered by ATP hydrolysis. It is still unclear how the organized beat of cilium and flagella emerges from the combined action of hundreds of dynein molecules. It has been hypothesized that such coordination is mediated by mechanical stress due to transverse, radial or sliding deformations. The beating asymmetry is crucial for airway ciliary function and it requires tubulin glutamination a unique posttranslational modification of C-termini of constituent microtubules that is highly abundant in cilia and flagella. The exact role of tubulin glutamination in ciliary or flagellar function is still unclear. Here we examine the role of calcium (Ca2+) ions based on the...
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biorxivpreprint: How signals of calcium ions initiate the beats of cilia and flagella https://t.co/hs6U6eux7Z #bioRxiv
biorxiv_biophys: How signals of calcium ions initiate the beats of cilia and flagella https://t.co/0fczNxl6hK #biorxiv_biophys
EdoardoDImprima: RT @biorxiv_biophys: How signals of calcium ions initiate the beats of cilia and flagella https://t.co/0fczNxl6hK #biorxiv_biophys
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2.25 Mikeys
#2. IRE1β negatively regulates IRE1α signaling in response to endoplasmic reticulum stress
Michael J Grey, Eva Cloots, Mariska S Simpson, Nicole LeDuc, Yevgeniy Serebrenik, Heidi De Luca, Delphine De Sutter, Phi Luong, Jay R Thiagarajah, Adrienne W Paton, James C Paton, Markus Seeliger, Sven Eyckerman, Sophie Janssens, Wayne I Lencer
IRE1β is an ER stress sensor uniquely expressed in epithelial cells lining mucosal surfaces. Here, we show that intestinal epithelial cells expressing IRE1β have an attenuated response to ER stress. IRE1β assembles with and blocks activation of the closely related and most evolutionarily ancient stress-sensor IRE1α to suppress stress-induced xbp1 splicing, a key mediator of the unfolded protein response. In comparison, IRE1β has weak xbp1 splicing activity, largely explained by a non-conserved amino acid in the kinase domain that impairs its phosphorylation and restricts oligomerization. This enables IRE1β to act as a dominant negative suppressor of IRE1α. The inhibitory effect is amplified in cells by disrupting an XBP1-dependent feedback loop regulating stress-induced expression of IRE1α. Thus IRE1β functions to negatively regulate IRE1α signaling, perhaps enabling intestinal epithelial cells to manage the response to chronic stress stimuli at the host-environment interface.
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biorxivpreprint: IRE1β negatively regulates IRE1α signaling in response to endoplasmic reticulum stress https://t.co/dSjkRfSpuO #bioRxiv
biorxiv_cellbio: IRE1β negatively regulates IRE1α signaling in response to endoplasmic reticulum stress https://t.co/cVpm45b4mF #biorxiv_cellbio
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Authors: 15
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2.113 Mikeys
#3. Error, noise and bias in de novo transcriptome assemblies
Adam H Freedman, Michele Clamp, Timothy B Sackton
De novo transcriptome assembly is a powerful tool, widely used over the last decade for making evolutionary inferences. However, it relies on two implicit, untested assumptions: that the assembled transcriptome represents an unbiased, if incomplete, representation of the true underlying expressed transcriptome, and that the expression estimates from the assembly are good, if noisy approximations of the relative abundance of expressed transcripts. Using publicly available data for model organisms, we demonstrate that, across assembly algorithms, species, and data sets, these assumptions are consistently violated. Using standard filtering approaches, coverage of annotated genes by transcriptome assemblies falls far below complete coverage, even at the highest expression levels, and hundreds of expressed genes are not assembled by any of the algorithms we evaluated. Assembly contigs are compositionally biased towards non- coding bases relative to what is observed in the sequence reads, with a large fraction of contigs being entirely...
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biorxivpreprint: Error, noise and bias in de novo transcriptome assemblies https://t.co/6W6sYTYX5K #bioRxiv
biorxiv_bioinfo: Error, noise and bias in de novo transcriptome assemblies https://t.co/pnnLlNFsYT #biorxiv_bioinfo
razoralign: Error, noise and bias in de novo transcriptome assemblies https://t.co/CfAWrHzBa8 https://t.co/8uMGopPe7W
PromPreprint: Error, noise and bias in de novo transcriptome assemblies https://t.co/hABOLTamqt
methylnick: RT @biorxivpreprint: Error, noise and bias in de novo transcriptome assemblies https://t.co/6W6sYTYX5K #bioRxiv
prashbio: RT @biorxiv_bioinfo: Error, noise and bias in de novo transcriptome assemblies https://t.co/pnnLlNFsYT #biorxiv_bioinfo
mehrshmali: RT @biorxiv_bioinfo: Error, noise and bias in de novo transcriptome assemblies https://t.co/pnnLlNFsYT #biorxiv_bioinfo
eduocapa: RT @biorxiv_bioinfo: Error, noise and bias in de novo transcriptome assemblies https://t.co/pnnLlNFsYT #biorxiv_bioinfo
bibourokuabc: RT @biorxiv_bioinfo: Error, noise and bias in de novo transcriptome assemblies https://t.co/pnnLlNFsYT #biorxiv_bioinfo
hdeshmuk: RT @biorxiv_bioinfo: Error, noise and bias in de novo transcriptome assemblies https://t.co/pnnLlNFsYT #biorxiv_bioinfo
Github

Workflows and scripts used to perform analyses for de novo transcriptome assembly manuscript

Repository: TranscriptomeAssemblyEvaluation
User: harvardinformatics
Language: Python
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2.081 Mikeys
#4. Coolpup.py - a versatile tool to perform pile-up analysis of Hi-C data
Ilya M. Flyamer, Robert S. Illingworth, Wendy A. Bickmore
Hi-C is currently the method of choice to investigate the global 3D organisation of the genome. Of particular interest are looping interactions and topologically-associating domains (TADs), which have been implicated in genome functions, including both gene regulation and genome stability. However, a major limitation of Hi-C is the great sequencing depth required to robustly detect loops in the data. A popular approach used to mitigate this issue, even in extremely sparse single-cell Hi-C data, is genome-wide averaging (piling-up) of loops, or other features, annotated in high-resolution datasets, to measure their prominence in less deeply sequenced data. By carefully choosing the regions used for averaging, hypotheses about 3D genome organization can be tested genome-wide. Here we describe coolpup.py - a versatile tool to perform pile-up analysis on Hi-C data. We We demonstrate its utility by replicating previously published findings regarding the role of cohesin and CTCF in 3D genome organization, and to investigate the effect...
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biorxivpreprint: https://t.co/s8dtirl9wk - a versatile tool to perform pile-up analysis of Hi-C data https://t.co/tDfpCfPVu9 #bioRxiv
loops_enhancers: https://t.co/hgonOX8iXu - a versatile tool to perform pile-up analysis of Hi-C data https://t.co/sR8Q0dqUWt
biorxiv_bioinfo: https://t.co/85oNx1x9Bm - a versatile tool to perform pile-up analysis of Hi-C data https://t.co/UR022BLPPZ #biorxiv_bioinfo
thatdnaguy: RT @biorxivpreprint: https://t.co/s8dtirl9wk - a versatile tool to perform pile-up analysis of Hi-C data https://t.co/tDfpCfPVu9 #bioRxiv
4DNucleome: RT @loops_enhancers: https://t.co/hgonOX8iXu - a versatile tool to perform pile-up analysis of Hi-C data https://t.co/sR8Q0dqUWt
jpummil: RT @biorxiv_bioinfo: https://t.co/85oNx1x9Bm - a versatile tool to perform pile-up analysis of Hi-C data https://t.co/UR022BLPPZ #biorxiv_…
katatonikkat: RT @loops_enhancers: https://t.co/hgonOX8iXu - a versatile tool to perform pile-up analysis of Hi-C data https://t.co/sR8Q0dqUWt
nv1ctus: RT @loops_enhancers: https://t.co/hgonOX8iXu - a versatile tool to perform pile-up analysis of Hi-C data https://t.co/sR8Q0dqUWt
hdeshmuk: RT @biorxiv_bioinfo: https://t.co/85oNx1x9Bm - a versatile tool to perform pile-up analysis of Hi-C data https://t.co/UR022BLPPZ #biorxiv_…
GeorgeSpracklin: RT @loops_enhancers: https://t.co/hgonOX8iXu - a versatile tool to perform pile-up analysis of Hi-C data https://t.co/sR8Q0dqUWt
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2.077 Mikeys
#5. Cellular correlates of cortical thinning throughout the lifespan
Didac Vidal-Pineiro, Nadine Parker, Jean Shin, Leon French, Andrea Parolin Jackowski, Athanasia Monica Mowinckel, Yash Patel, Zdenka Pausova, Giovanni Salum, Oystein Sorensen, Kristine Beate Walhovd, Tomas Paus, Anders Martin Fjell, the Australian Imaging Biomarkers & Lifestyle flag
Changes in cortical thickness occur throughout the lifespan, but the neurobiological substrates are poorly understood. Here, we compared the regional patterns of cortical thinning (Magnetic Resonance Images; >4000 observations) with those of gene expression for several neuronal and non-neuronal cell types (Allen Human Brain Atlas). Inter-regional profiles of cortical thinning (estimated from MRIs) related to expression profiles for marker genes of CA1 pyramidal cells, astrocytes and microglia during development (less thinning, - greater gene expression). The same expression - thinning patterns were mirrored in aging, but in the opposite direction. The results were replicated in independent MRI datasets. Further analyses suggested that the cell type - thinning relationship is facilitated by astrocytic metabolic process in development and neural projection and synaptic changes in aging. Overall, these findings uncover the neurobiological mechanisms underlying cortical thinning across the lifespan, and may contribute to our...
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biorxivpreprint: Cellular correlates of cortical thinning throughout the lifespan https://t.co/lh4zQhcvrH #bioRxiv
biorxiv_neursci: Cellular correlates of cortical thinning throughout the lifespan https://t.co/Ed5lDhSLgK #biorxiv_neursci
VidalDidac: RT @biorxivpreprint: Cellular correlates of cortical thinning throughout the lifespan https://t.co/lh4zQhcvrH #bioRxiv
Github

ggplot-based graphics and useful functions for GAMs fitted using the mgcv package

Repository: schoenberg
User: gavinsimpson
Language: R
Stargazers: 19
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Forks: 2
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Total Words: 12041
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2.053 Mikeys
#6. Anchoring of actin to the plasma membrane enables tension production in the fission yeast cytokinetic ring
Shuyuan Wang, Ben O'Shaughnessy
The cytokinetic ring generates tensile force that drives cell division, but how tension emerges from the relatively disordered ring organization remains unclear. Long ago a muscle-like sliding filament mechanism was proposed, but evidence for sarcomeric order is lacking. Here we present quantitative evidence that in fission yeast ring tension originates from barbed-end anchoring of actin filaments to the plasma membrane, providing resistance to myosin forces which enables filaments to develop tension. The role of anchoring was highlighted by experiments on isolated fission yeast rings, where sections of ring unanchored from the membrane and shortened ~30-fold faster than normal [Mishra M., et al. (2013) Nat Cell Biol 15(7):853-859]. The dramatically elevated constriction rates are unexplained. Here we present a molecularly explicit simulation of constricting partially anchored rings as studied in these experiments. Simulations accurately reproduced the experimental constriction rates, and showed that following anchor release a...
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biorxivpreprint: Anchoring of actin to the plasma membrane enables tension production in the fission yeast cytokinetic ring https://t.co/ym8VcLDDcA #bioRxiv
biorxiv_cellbio: Anchoring of actin to the plasma membrane enables tension production in the fission yeast cytokinetic ring https://t.co/tBt8tUhxyG #biorxiv_cellbio
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Authors: 2
Total Words: 8327
Unqiue Words: 2117

2.05 Mikeys
#7. The ability of single genes vs full genomes to resolve time and space in outbreak analysis
Gytis Dudas, Trevor Bedford
Inexpensive pathogen genome sequencing has had a transformative effect on the field of phylodynamics, where ever increasing volumes of data have promised real-time insight into outbreaks of infectious disease. As well as the sheer volume of pathogen isolates being sequenced, the sequencing of whole pathogen genomes, rather than select loci, has allowed phylogenetic analyses to be carried out at finer time scales, often approaching serial intervals for infections caused by rapidly evolving RNA viruses. Despite its utility, whole genome sequencing of pathogens has not been adopted universally and targeted sequencing of loci is common in some pathogen-specific fields. In this study we aim to highlight the utility of sequencing whole genomes of pathogens by re-analysing a well-characterised collection of Ebola virus sequences in the form of complete viral genomes (~19kb long) or the rapidly evolving glycoprotein (GP, ~2kb long) gene. We quantify changes in phylogenetic, temporal, and spatial inference resolution as a result of this...
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baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).

Repository: baltic
User: evogytis
Language: Jupyter Notebook
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2.047 Mikeys
#8. Untapped viral diversity in global soil metagenomes
Emily B Graham, David Paez-Espino, Colin Brislawn, Russell Y Neches, Kirsten S Hofmockel, Ruonan Wu, Nikos C Kyrpides, Janet K Jansson, Jason E McDermott
Viruses outnumber every other biological entity on Earth, and soil viruses are particularly diverse compared to other habitats. However, we have limited understanding of soil viruses because of the tremendous variation in soil ecosystems and because of the lack of appropriate screening tools. Here, we determined the global distribution of more than 24,000 soil viral sequences and their potential hosts, including >1,600 sequences associated with giant viruses. The viral sequences, derived from 668 terrestrial metagenomes, greatly extend existing knowledge of soil viral diversity and viral biogeographical distribution. We screened these sequences to identify a suite of cosmopolitan auxiliary metabolic genes (AMGs) encoding enzymes involved in soil organic carbon decomposition across soil biomes. Additionally, we provide evidence for viral facilitation of multi-domain linkages in soils by locating a fungal chitosanase in bacteriophages, generating a new paradigm of how viruses can serve as exchange vectors of carbon metabolism across...
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redpenblackpen: @KnEzmom wellllllll.... I'm going to make a comic (maybe a comic book) to go along with this paper that we just put up as a pre-print... https://t.co/U20athWSVk https://t.co/JchrmeSphE
biorxivpreprint: Untapped viral diversity in global soil metagenomes https://t.co/hqcTxHkFrW #bioRxiv
biorxiv_micrbio: Untapped viral diversity in global soil metagenomes https://t.co/WM6WcPgI8J #biorxiv_micrbio
lavik17: The fox guarding the henhouse... Once again JGI exploit the work of others 😡 #bioRxiv https://t.co/2ton9LdzRt
BioMickWatson: RT @biorxivpreprint: Untapped viral diversity in global soil metagenomes https://t.co/hqcTxHkFrW #bioRxiv
ctitusbrown: RT @biorxivpreprint: Untapped viral diversity in global soil metagenomes https://t.co/hqcTxHkFrW #bioRxiv
virome_girl: RT @biorxiv_micrbio: Untapped viral diversity in global soil metagenomes https://t.co/WM6WcPgI8J #biorxiv_micrbio
msmjetten: RT @biorxiv_micrbio: Untapped viral diversity in global soil metagenomes https://t.co/WM6WcPgI8J #biorxiv_micrbio
ryneches: RT @biorxivpreprint: Untapped viral diversity in global soil metagenomes https://t.co/hqcTxHkFrW #bioRxiv
mehrshmali: RT @biorxiv_micrbio: Untapped viral diversity in global soil metagenomes https://t.co/WM6WcPgI8J #biorxiv_micrbio
Phages_fr: RT @biorxiv_micrbio: Untapped viral diversity in global soil metagenomes https://t.co/WM6WcPgI8J #biorxiv_micrbio
socialpathologi: RT @biorxiv_micrbio: Untapped viral diversity in global soil metagenomes https://t.co/WM6WcPgI8J #biorxiv_micrbio
aadjiep: RT @biorxiv_micrbio: Untapped viral diversity in global soil metagenomes https://t.co/WM6WcPgI8J #biorxiv_micrbio
ilnam_kang: RT @biorxivpreprint: Untapped viral diversity in global soil metagenomes https://t.co/hqcTxHkFrW #bioRxiv
asbhattac: RT @biorxivpreprint: Untapped viral diversity in global soil metagenomes https://t.co/hqcTxHkFrW #bioRxiv
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Total Words: 9926
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2.04 Mikeys
#9. Characterization of genes and alleles involved in the control of flowering time in grapevine
Nadia Kamal, Iris Ochßner, Anna Schwandner, Prisca Viehöver, Ludger Hausmann, Reinhard Töpfer, Bernd Weisshaar, Daniela Luise Holtgräwe
Grapevine (Vitis vinifera) is one of the most important perennial crop plants in worldwide. Understanding of developmental processes like flowering, which impact quality and quantity of yield in this species is therefore of high interest. This gets even more important when considering some of the expected consequences of climate change. Earlier bud burst and flowering, for example, may result in yield loss due to spring frost. Berry ripening under higher temperatures will impact wine quality. Knowledge of interactions between a genotype or allele combination and the environment can be used for the breeding of genotypes that are better adapted to new climatic conditions. To this end, we have generated a list of more than 500 candidate genes that may play a role in the timing of flowering. The grapevine genome was exploited for flowering time control gene homologs on the basis of functional data from model organisms like A. thaliana. In a previous study, a mapping population derived from early flowering GF.GA-47-42 and late...
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biorxivpreprint: Characterization of genes and alleles involved in the control of flowering time in grapevine https://t.co/yeE0RNi64F #bioRxiv
biorxiv_genetic: Characterization of genes and alleles involved in the control of flowering time in grapevine https://t.co/u1jGRUfxMP #biorxiv_genetic
boas_pucker: Characterization of genes and alleles involved in the control of flowering time in grapevine https://t.co/h5OZRrAad5 #bioRxiv #genetics #plants @CeBiTec @JKI_Bund https://t.co/FAk59woZeL
JKI_Bund: RT @boas_pucker: Characterization of genes and alleles involved in the control of flowering time in grapevine https://t.co/h5OZRrAad5 #…
tomilloberlin: RT @boas_pucker: Characterization of genes and alleles involved in the control of flowering time in grapevine https://t.co/h5OZRrAad5 #…
swagayathri: RT @biorxivpreprint: Characterization of genes and alleles involved in the control of flowering time in grapevine https://t.co/yeE0RNi64F…
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Authors: 8
Total Words: 16980
Unqiue Words: 5166

2.033 Mikeys
#10. The shift to life on land selected for planning
Ugurcan Mugan, Malcolm A MacIver
It is uncontroversial that land animals have developed more elaborated cognitive abilities than aquatic animals, with the possible exception of formerly land-based mammals like whales and dolphins that have returned to an aquatic existence. Yet there is no apparent a-priori reason for aquatic and land animals to have different evolutionary capacities for the rise of cognition. One possibility is that investigators have been anthropocentric in their definition of cognition, rather than attuned to cognitive phenomena as appropriate to the broader ethological and ecological context of each species. However, this concern may not apply to the paradigmatically cognitive faculty of being able to imagine multiple complete sequences of actions to accomplish a goal and select one to enact, or planning. Although planning over space requires cognitive maps--which exist in many species including fish--behavioral and neural evidence for planning is presently restricted to birds and mammals. Here, we present evidence that a reason for the...
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biorxivpreprint: The shift to life on land selected for planning https://t.co/gF578LiHyX #bioRxiv
biorxiv_neursci: The shift to life on land selected for planning https://t.co/EO2oVObW33 #biorxiv_neursci
__exa__: RT @biorxivpreprint: The shift to life on land selected for planning https://t.co/gF578LiHyX #bioRxiv
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Total Words: 14655
Unqiue Words: 3867

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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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