Top 10 Biorxiv Papers Today in Molecular Biology


2.018 Mikeys
#1. P granules protect RNA interference genes from silencing by piRNAs
John Paul Ouyang, Andrew Folkmann, Lauren Bernard, Chih-Yung Lee, Uri Seroussi, Amanda G Charlesworth, Julie M Claycomb, Geraldine Seydoux
P granules are perinuclear condensates in C. elegans germ cells proposed to serve as hubs for self/non-self RNA discrimination by Argonautes. We report that a mutant ( meg-3 meg-4 ) that does not assemble P granules in primordial germ cells loses competence for RNA-interference over several generations and accumulates silencing small RNAs against hundreds of endogenous genes, including the RNA-interference genes rde-11 and sid-1 . In wild-type, rde-11 and sid-1 transcripts are heavily targeted by piRNAs, accumulate in P granules, but maintain expression. In the primordial germ cells of meg-3 meg-4 mutants, rde-11 and sid-1 transcripts disperse in the cytoplasm with the small RNA biogenesis machinery, become hyper-targeted by secondary sRNAs, and are eventually silenced. Silencing requires the PIWI-class Argonaute PRG-1 and the nuclear Argonaute HRDE-1 that maintains trans-generational silencing of piRNA targets. These observations support a "safe harbor" model for P granules in protecting germline transcripts from piRNA-initiated...
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biorxivpreprint: P granules protect RNA interference genes from silencing by piRNAs https://t.co/Mns8H48t9q #bioRxiv
NeedhiBhalla: RT @biorxivpreprint: P granules protect RNA interference genes from silencing by piRNAs https://t.co/Mns8H48t9q #bioRxiv
jjdalzell: RT @biorxivpreprint: P granules protect RNA interference genes from silencing by piRNAs https://t.co/Mns8H48t9q #bioRxiv
grnfluoresceblg: RT @biorxivpreprint: P granules protect RNA interference genes from silencing by piRNAs https://t.co/Mns8H48t9q #bioRxiv
schraderlab: RT @biorxivpreprint: P granules protect RNA interference genes from silencing by piRNAs https://t.co/Mns8H48t9q #bioRxiv
l_stelzl: RT @biorxivpreprint: P granules protect RNA interference genes from silencing by piRNAs https://t.co/Mns8H48t9q #bioRxiv
ColinConine: RT @biorxivpreprint: P granules protect RNA interference genes from silencing by piRNAs https://t.co/Mns8H48t9q #bioRxiv
SharmaLab_UCSC: RT @biorxivpreprint: P granules protect RNA interference genes from silencing by piRNAs https://t.co/Mns8H48t9q #bioRxiv
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Sample Sizes : None.
Authors: 8
Total Words: 16809
Unqiue Words: 4560

2.01 Mikeys
#2. A unique lower X-gate in TASK channels traps inhibitors within the vestibule
Karin E J Rodstrom, Aytug K Kiper, Wei Zhang, Susanne Rinne, Ashley C W Pike, Matthias Goldstein, Linus Conrad, Martina Delbeck, Michael Hahn, Heinrich Meier, Magdalena Platzk, Andrew Quigley, David Speedman, Leela Shrestha, Shubhashish M M Mukhopadhyay, Nicola A Burgess-Brown, Stephen J Tucker, Thomas Mueller, Niels Decher, Elisabeth P Carpenter
TASK channels are unusual members of the two-pore domain potassium (K2P) channel family, with unique and unexplained physiological and pharmacological characteristics. TASKs are found in neurons, cardiomyocytes and vascular smooth muscle cells where they are involved in regulation of heart rate, pulmonary artery tone, sleep/wake cycles and responses to volatile anaesthetics. K2P channels regulate the resting membrane potential, providing background K+ currents controlled by numerous physiological stimuli. Unlike other K2P channels, TASK channels have the capacity to bind inhibitors with high affinity, exceptional selectivity and very slow compound washout rates. These characteristics make the TASK channels some of the the most easily druggable potassium channels, and indeed TASK-1 inhibitors are currently in clinical trials for obstructive sleep apnea (OSA) and atrial fibrillation (Afib) (The DOCTOS and SANDMAN Trials). Generally, potassium channels have an intramembrane vestibule with a selectivity filter above and a gate with...
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biorxivpreprint: A unique lower X-gate in TASK channels traps inhibitors within the vestibule https://t.co/bDPlZhdOW5 #bioRxiv
sbotlite: RT @biorxivpreprint: A unique lower X-gate in TASK channels traps inhibitors within the vestibule https://t.co/bDPlZhdOW5 #bioRxiv
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Authors: 20
Total Words: 0
Unqiue Words: 0

2.009 Mikeys
#3. RecO impedes RecG-SSB binding to impair the strand annealing recombination pathway in E.coli
Xuefeng Pan, Li Yang, Nan Jiang, Xifang Chen, Bo Li, Xinshen Yan, Yu Dou, Liang Ding, Fei Duan
Faithful duplication of genomic DNA relies not only on the fidelity of DNA replication itself, but also on fully functional DNA repair and homologous recombination machinery. We report a molecular mechanism responsible for deciding homologous recombinational repair pathways during replication dictated by binding of RecO and RecG to SSB in E.coli. Using a RecG-yfp fusion protein, we found that RecG-yfp foci appeared only in the ΔrecG, ΔrecO and ΔrecA, ΔrecO double mutants. Surprisingly, foci were not observed in wild-type ΔrecG, or double mutants where recG and either recF or, separately recR were deleted. In addition, formation of RecG-yfp foci in the ΔrecO::kanR required wildtype ssb, as ssb-113 could not substitute. This suggests that RecG and RecO binding to SSB is competitive. We also found that the UV resistance of recO alone mutant increased to certain extent by supplementing RecG. In an ssb-113 mutant, RecO and RecG worked following a different pattern. Both RecO and RecG were able to participate in repairing UV damages...
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biorxivpreprint: RecO impedes RecG-SSB binding to impair the strand annealing recombination pathway in E.coli https://t.co/qqFwurluQ6 #bioRxiv
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Authors: 9
Total Words: 9212
Unqiue Words: 2817

2.004 Mikeys
#4. Remodeling of the C. elegans Non-coding RNA Transcriptome by Heat Shock
William P Schreiner, Delaney C Pagliuso, Jacob M Garrigues, Jerry S Chen, Antti P Aalto, Amy E Pasquinelli
Elevated temperatures activate a Heat Shock Response (HSR) to protect cells from the pathological effects of protein mis-folding, cellular mis-organization, organelle dysfunction and altered membrane fluidity. This response includes activation of the conserved transcription factor Heat Shock Factor 1 (HSF-1), which binds Heat Shock Elements (HSEs) in the promoters of genes induced by heat shock (HS). The up-regulation of protein-coding genes (PCGs), such as Heat Shock Proteins (HSPs) and cytoskeletal regulators, is critical for cellular survival during elevated temperatures. While the transcriptional response of PCGs to heat shock has been comprehensively analyzed in a variety of organisms, the effect of this stress on the expression of non-coding RNAs (ncRNAs) has not been systematically examined. Here we show that in Caenorhabditis elegans HS induces up- and down-regulation of specific ncRNAs from multiple classes, including miRNA, piRNA, lincRNA, pseudogene, and repeat elements. Moreover, some ncRNA genes appear to be direct...
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biorxivpreprint: Remodeling of the C. elegans Non-coding RNA Transcriptome by Heat Shock https://t.co/fWzjBU9fpO #bioRxiv
Inannamarduk: RT @biorxivpreprint: Remodeling of the C. elegans Non-coding RNA Transcriptome by Heat Shock https://t.co/fWzjBU9fpO #bioRxiv
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Authors: 6
Total Words: 10614
Unqiue Words: 3088

2.0 Mikeys
#5. Phazolicin – a Novel Thiazole/Oxazole-Modified Peptide Inhibiting the Bacterial Ribosome in a Species-Specific Way.
Dmitry Y. Travin, Zoe L. Watson, Mikhail Metelev, Fred R. Ward, Ilya A. Osterman, Irina M. Khven, Nelli F. Khabibullina, Marina Serebryakova, Peter Mergaert, Yury S. Polikanov, Jamie H.D. Cate, Konstantin Severinov
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a rapidly expanding and largely untapped class of natural products with various biological activities. Linear azol(in)e-containing peptides (LAPs) comprise a subclass of RiPPs that display an outstanding diversity of mechanisms of action while sharing common structural features. Here, we report the discovery of a new LAP biosynthetic gene cluster in the genome of Rhizobium sp. Pop5, which encodes the precursor peptide and modification machinery of phazolicin (PHZ) – an extensively modified peptide exhibiting narrow-spectrum antibacterial activity against some symbiotic bacteria of leguminous plants belonging to the Rhizobiales. PHZ inhibits prokaryotic translation through the obstruction of the passage of the nascent peptide through the ribosome exit channel. The cryo-EM structure of the Escherichia coli ribosome with bound PHZ revealed that the drug interacts with the 23S rRNA and ribosomal proteins uL4 and uL22 and obstructs the exit tunnel in a way...
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cryoEM_Papers: Phazolicin - a Novel Thiazole/Oxazole-Modified Peptide Inhibiting the Bacterial Ribosome in a Species-Specific Way. https://t.co/wG8bPckb9X
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Authors: 12
Total Words: 0
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2.0 Mikeys
#6. Nanopore direct RNA sequencing maps an Arabidopsis N6 methyladenosine epitranscriptome
Gordon Grant Simpson, Geoffrey John Barton, Matthew T Parker, Anna V Sherwood, Katarzyna Knop, Nicholas J E Schurch, Katarzyna Mackinnon, Peter D Gould, Anthony JW Hall
Understanding genome organization and gene regulation requires insight into RNA transcription, processing and modification. We adapted nanopore direct RNA sequencing to examine RNA from a wild-type accession of the model plant Arabidopsis thaliana and a mutant defective in mRNA methylation (m6A). Here we show that m6A can be mapped in full-length mRNAs transcriptome-wide and reveal the combinatorial diversity of cap-associated transcription start sites, splicing events, poly(A) site choice and poly(A) tail length. Loss of m6A from 3′ untranslated regions is associated with decreased relative transcript abundance and defective RNA 3′ end formation. A functional consequence of disrupted m6A is a lengthening of the circadian period. We conclude that nanopore direct RNA sequencing can reveal the complexity of mRNA processing and modification in full-length single molecule reads. These findings can refine Arabidopsis genome annotation. Further, applying this approach to less well-studied species could transform our understanding of...
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RiboHipster: RT @biorxivpreprint: Nanopore direct RNA sequencing maps an Arabidopsis N6 methyladenosine epitranscriptome https://t.co/UEotrs3TTA #bioRx…
nickschurch: RT @biorxivpreprint: Nanopore direct RNA sequencing maps an Arabidopsis N6 methyladenosine epitranscriptome https://t.co/UEotrs3TTA #bioRx…
pyglucksfall: RT @biorxivpreprint: Nanopore direct RNA sequencing maps an Arabidopsis N6 methyladenosine epitranscriptome https://t.co/UEotrs3TTA #bioRx…
1m1a2t: RT @biorxivpreprint: Nanopore direct RNA sequencing maps an Arabidopsis N6 methyladenosine epitranscriptome https://t.co/UEotrs3TTA #bioRx…
mkvalluru: RT @biorxivpreprint: Nanopore direct RNA sequencing maps an Arabidopsis N6 methyladenosine epitranscriptome https://t.co/UEotrs3TTA #bioRx…
kknop2: RT @biorxivpreprint: Nanopore direct RNA sequencing maps an Arabidopsis N6 methyladenosine epitranscriptome https://t.co/UEotrs3TTA #bioRx…
NZthRzXeiplAQA6: RT @biorxivpreprint: Nanopore direct RNA sequencing maps an Arabidopsis N6 methyladenosine epitranscriptome https://t.co/UEotrs3TTA #bioRx…
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Authors: 9
Total Words: 20347
Unqiue Words: 6052

1.998 Mikeys
#7. Automated sample preparation with SP3 for low-input clinical proteomics
Torsten Mueller, Mathias Kalxdorf, Rémi Longuespée, Daniel N Kazdal, Albrecht Stenzinger, Jeroen Krijgsveld
High-throughput and streamlined workflows are essential in clinical proteomics for standardized processing of samples originating from a variety of sources, including fresh frozen tissue, FFPE tissue, or blood. To reach this goal, we have implemented single-pot solid-phase-enhanced sample preparation (SP3) on a liquid handling robot for automated processing (autoSP3) of tissue lysates in a 96-well format, performing unbiased protein purification and digestion, and delivering peptides that can be directly analyzed by LCMS. AutoSP3 eliminates hands-on time and minimizes the risk of error, reduces variability in protein quantification and improves longitudinal performance and reproducibility. We demonstrate the distinguishing ability of autoSP3 to process low-input samples, reproducibly quantifying 500-1000 proteins from 100-1000 cells (<100 ng protein). Furthermore, we applied this approach to a cohort of clinical FFPE pulmonary adenocarcinoma (ADC) samples, and recapitulate their separation into known histological growth patterns...
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yanbopan: RT @biorxivpreprint: Automated sample preparation with SP3 for low-input clinical proteomics https://t.co/9JRSBuZ4Ov #bioRxiv
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Sample Sizes : [4, 8, 3750, 4, 8]
Authors: 6
Total Words: 19771
Unqiue Words: 4750

1.998 Mikeys
#8. C6orf203 controls OXPHOS function through modulation of mitochondrial protein biosynthesis
Sara Palacios-Zambrano, Luis Vazquez-Fonseca, Cristina Gonzalez-Paramos, Laura Mamblona, Laura Sanchez-Caballero, Leo G.J. Nijtmans, Rafael Garesse, Miguel Angel Fernandez-Moreno
Mitochondria are essential organelles present in the vast majority of eukaryotic cells. Their central function is to produce cellular energy through the OXPHOS system, and functional alterations provoke so-called mitochondrial OXPHOS diseases. It is estimated that several hundred mitochondrial proteins have unknown functions. Very recently, C6orf203 was described to participate in mitochondrial transcription under induced mitochondrial DNA depletion stress conditions. Here, we describe another role for C6orf203, specifically in OXPHOS biogenesis under regular culture conditions. HEK293T C6orf203-Knockout (KO) cells generated by CRISPR/Cas9 genome editing showed both reduced grow in galactose, as a carbon source, and in their oxygen consumption capability, strongly suggesting an OXPHOS dysfunction. C6orf203-KO also provoked a depletion of OXPHOS proteins and decreased the activity of the mitochondrial respiratory chain complexes. C6orf203 was present in high molecular weight complexes compatible with mitoribosomes, and in vivo...
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Authors: 8
Total Words: 0
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1.998 Mikeys
#9. In silico identification of a molecular circadian system with novel features in the crustacean model organism Parhyale hawaiensis
Benjamin Hunt, Eamonn Mallon, Ezio Rosato
The amphipod Parhyale hawaiensis is a model organism of growing importance in the fields of evolutionary development and regeneration. A small, hardy marine crustacean that breeds year-round with a short generation time, it has simple lab culture requirements and an extensive molecular toolkit including the ability to generate targeted genetic mutant lines. Here we identify canonical core and regulatory clock genes using genomic and transcriptomic resources as a first step in establishing this species as a model in the field of chronobiology. The molecular clock of P. hawaiensis lacks orthologs of the canonical circadian genes cryptochrome 1 and timeless , in common with the mammalian system but in contrast to many arthropods including Drosophila melanogaster . Furthermore the predicted CLOCK peptide is atypical and CRY2 shows an extended 5' region of unknown function. These results appear to be shared by two other amphipod species.
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biorxivpreprint: In silico identification of a molecular circadian system with novel features in the crustacean model organism Parhyale hawaiensis https://t.co/1e46hL3hTy #bioRxiv
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Authors: 3
Total Words: 0
Unqiue Words: 0

1.997 Mikeys
#10. Feeding intensity and molecular prey identification of the common long-armed octopus, Octopus minor (Mollusca: Octopodidae) in the wild
Qi-Kang Bo, Xiao-Dong Zheng, Zhi-Wei Chen
The common long-armed octopus, Octopus minor, is an important component of systems and supports the local fisheries in the coastal areas of northern China. And because of the overfishing, the national germplasm reserve was established as conservation area at the Moon Lake for the genetic resource of O.minor in 2012. For the fishery management and artificial breeding, especially for the management of exclusive conservation reserves, its role in the ecosystem requires assessment. Therefore, the feeding intensity of O. minor was studied from April to July 2014 when females reaching maturation, and prey composition was identified from stomach contents using a DNA barcoding method. Of the 172 sampled octopuses, 66 had stomach contents that were nearly digested into pulp. Maximum feeding intensity occurred during the month of April and the feeding intensity of the females was greater than that of the males in April and May. A considerable overall reduction of feeding intensity in both sexes occurred from April to July. A total of 8...
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Authors: 3
Total Words: 6869
Unqiue Words: 2734

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