Top 10 Biorxiv Papers Today in Microbiology


2.007 Mikeys
#1. Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome.
Damien Farrell, Joseph Crispell, Stephen V. Gordon
Mycobacterium bovis AF2122/97 is the reference strain for the bovine tuberculosis bacillus. We here report an update to the M. bovis AF2122/97 genome annotation to reflect 616 new protein identifications which replace many of the old hypothetical coding sequences and proteins of unknown function in the genome. These changes integrate information from functional assignments of orthologous coding sequences in the Mycobacterium tuberculosis H37Rv genome. We have also added 69 additional new gene names.
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biorxivpreprint: Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome. https://t.co/mQ1cjFzc68 #bioRxiv
biorxiv_micrbio: Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome. https://t.co/gCVH7iZ70p #biorxiv_micrbio
ZaminIqbal: RT @biorxiv_micrbio: Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome. https://t.co/gCVH7iZ70p #biorxiv…
con_meehan: RT @biorxiv_micrbio: Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome. https://t.co/gCVH7iZ70p #biorxiv…
steve_myco: RT @biorxiv_micrbio: Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome. https://t.co/gCVH7iZ70p #biorxiv…
icoes: RT @biorxiv_micrbio: Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome. https://t.co/gCVH7iZ70p #biorxiv…
david_machugh: RT @biorxiv_micrbio: Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome. https://t.co/gCVH7iZ70p #biorxiv…
danielkein: RT @biorxiv_micrbio: Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome. https://t.co/gCVH7iZ70p #biorxiv…
mglopez76: RT @biorxiv_micrbio: Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome. https://t.co/gCVH7iZ70p #biorxiv…
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Authors: 3
Total Words: 1876
Unqiue Words: 816

1.998 Mikeys
#2. A Conserved Mechanism of APOBEC3 Relocalization by Herpesviral Ribonucleotide Reductase Large Subunits
Adam Z Cheng, Sofia Nóbrega de Moraes, Claire Attarian, Jaime Yockteng-Melgar, Matthew Carter Jarvis, Matteo Biolatti, Ganna Galitska, Valentina Dell'Oste, Lori Frappier, Craig J. Bierle, Stephen A. Rice, Reuben S Harris
An integral part of the antiviral innate immune response is the APOBEC3 family of single-stranded DNA cytosine deaminases, which inhibits virus replication through deamination-dependent and -independent activities. Viruses have evolved mechanisms to counteract these enzymes such as HIV-1 Vif-mediated formation of a ubiquitin ligase to degrade virus-restrictive APOBEC3 enzymes. A new example is Epstein-Barr virus (EBV) ribonucleotide reductase (RNR)-mediated inhibition of cellular APOBEC3B (A3B). The large subunit of the viral RNR, BORF2, causes A3B relocalization from the nucleus to cytoplasmic bodies and thereby protects viral DNA during lytic replication. Here, we use co-immunoprecipitation and immunofluorescent microscopy approaches to ask whether this mechanism is shared with the closely related g-herpesvirus Kaposi's sarcoma-associated herpesvirus (KSHV) and the more distantly related α-herpesvirus, herpes simplex virus-1 (HSV-1). The large RNR subunit of KSHV, ORF61, co-precipitated multiple APOBEC3s including A3B and...
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Authors: 12
Total Words: 10424
Unqiue Words: 3579

1.997 Mikeys
#3. Whole genome sequence analysis reveals broad distribution of the RtxA type 1 secretion system and four novel type 1 secretion systems throughout the Legionella genus
Connor L. Brown, Emily Garner, Guillaume Jospin, David A. Coil, David O. Schwake, Jonathan A. Eisen, Biswarup Mukhopadhyay, Amy Pruden
Type 1 secretion systems (T1SSs) are broadly distributed among bacteria and translocate effectors with diverse function across the bacterial cell membrane. Legionella pneumophila, the species most commonly associated with Legionellosis, encodes a T1SS at the lssXYZABD locus which is responsible for the secretion of the virulence factor RtxA. Many investigations have failed to detect lssD, the gene encoding the membrane fusion protein of the RtxA T1SS, in non- pneumophila Legionella, suggesting that this system is a conserved virulence factor in L. pneumophila. Here we discovered RtxA and its associated T1SS in a novel Legionella taurinensis strain, leading us to question whether this system may be more widespread than previously thought. Through a bioinformatic analysis of publicly available data, we classified and determined the distribution of four T1SSs including the RtxA T1SS and four novel T1SSs among diverse Legionella spp. The ABC transporter of the novel Legionella T1SS Legonella repeat protein secretion system (LRPSS)...
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Authors: 8
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1.997 Mikeys
#4. Diverse flanking sequence types of blaNDM in IncX3 and IncB/O/K/Z plasmids in Escherichia coli isolated from poultry
JiaHang Zhu, Run-Mao Cai, Li-Juan Zhang, Xing-Run Zheng, Yue-Wei Lu, Qiu-Yun Zhao, Man-Xia Chang, Hongxia Jiang
We identified 33 blaNDM-harboring Escherichia coli in 470 poultry samples from Shandong and Guangdong provinces during 2016 to 2017 and included the subtypes blaNDM-1, blaNDM-5 and blaNDM-9. The blaNDM gene possessed by all strains was plasmid-borne and ranged in size from 46 to 265 kb. The plasmids included the replicon types IncX3, IncY, IncB/O/K/Z and IncHI2 and most were transferable and stable in recipient host bacteria. Sequences flanking blaNDM in IncX3 and IncB/O/K/Z plasmids were diverse and the mobile element IS26 played an important role in the evolution of the IncB/O/K/Z blaNDM plasmids.
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Authors: 8
Total Words: 4240
Unqiue Words: 1648

1.997 Mikeys
#5. Plasmid transmitted small multidrug resistant (SMR) efflux pumps differ in gene regulation and enhance tolerance to quaternary ammonium compounds (QAC) when grown as biofilms
Carmine J Slipski, Taylor R Jamieson, Amy Lam, Vanessa Leung Shing, Kelli Bell, George G Zhanel, Denice C. Bay
Small multidrug resistance (SMR) efflux pump genes are commonly identified from integrons carried by multidrug-resistant (MDR) plasmids. SMR pumps are annotated as 'qac' for their ability to confer resistance to quaternary ammonium compounds (QACs) but few qac are characterized to date. Hence, we have examined SMR sequence diversity, antimicrobial susceptibility, and gene expression from >500 sequenced proteobacterial plasmids. SMR sequence diversity from plasmid database surveys identified 20 unique SMR sequences annotated as qacE/EΔ1/F/G/H/I/L, or sugE. Phylogenetic analysis shows 'Qac' sequences are homologous to archetypical SMR member EmrE, and share a single sequence origin. In contrast, SugE sequences are homologous to archetypical member Gdx/SugE and likely originate from different species. SMR genes, qacE, qacEΔ1, qacF, qacG, qacH, and sugE(p), were over-expressed in Escherichia coli to determine their QAC antimicrobial susceptibility as planktonic, colony, and biofilms. SMRs (except qacEΔ1/sugE) expressed in biofilms...
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Authors: 7
Total Words: 0
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1.997 Mikeys
#6. Two uptake hydrogenases differentially interact with the aerobic respiratory chain during mycobacterial growth and persistence
Paul RF Cordero, Rhys Grinter, Kiel Hards, Max J Cryle, Coral G Warr, Gregory M Cook, Chris Greening
Aerobic soil bacteria metabolize atmospheric hydrogen (H2) to persist when nutrient sources are limited. This process is the primary sink in the global H2 cycle and supports the productivity of microbes in oligotrophic environments. To mediate this function, bacteria possess [NiFe]-hydrogenases capable of oxidising H2 to subatmospheric concentrations. The soil saprophyte Mycobacterium smegmatis has two such [NiFe]-hydrogenases, designated Huc and Hhy, which belong to different phylogenetic subgroups. Huc and Hhy exhibit similar characteristics: both are oxygen-tolerant, oxidise H2 to subatmospheric concentrations, and enhance survival during hypoxia and carbon limitation. These shared characteristics pose the question: Why does M. smegmatis require two hydrogenases mediating a seemingly similar function? In this work we resolve this question by showing that Huc and Hhy are differentially expressed, localised, and integrated into the respiratory chain. Huc is active in late exponential and early stationary phase, supporting energy...
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biorxivpreprint: Two uptake hydrogenases differentially interact with the aerobic respiratory chain during mycobacterial growth and persistence https://t.co/0GNSNf41V5 #bioRxiv
biorxiv_micrbio: Two uptake hydrogenases differentially interact with the aerobic respiratory chain during mycobacterial growth and persistence https://t.co/kkKG9s5DaG #biorxiv_micrbio
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1.997 Mikeys
#7. Lyb-2-4, a unique genomic region of hypervirulent carbapenem-resistant Acinetobacter baumannii
Chao Zheng, Jinyong Zhang, Min Zhang, Zhou Liu, Yuxin Zhong, Shiyi Liu, Ruiqin Cui, Qiuyang Deng, Yanji Xu, Yun Shi, Hao Zeng, Xiyao Yang, Chuchu Lin, Yutian Luo, Huaisheng Chen, Weiyuan Wu, Jingsong Wu, Tianle Zhang, Yuemei Lu, Xueyan Liu, Quanming Zou, Wei Huang
Acinetobacter baumannii is an important human pathogen due to its multi-drug resistance, but is usually with low-grade virulence. Although a mouse model revealed different virulence grades of clinical carbapenem-resistant A. baumannii (CRAB) strains, the genetic basis remains unknown. We collected 61 CRAB isolates from intensive care unit of Shenzhen People's Hospital (Shenzhen, China), and analyzed them used whole genome sequencing (WGS), multilocus sequence typing (MLST) and core genome MLST (cgMLST), transmission chain reconstruction and Comparative genomic tools. A mouse pneumonia model was used to confirm the hypervirulent phenotype. Eleven complex types (CT) were identified based on core genome multilocus sequence typing scheme. CT512 showed higher transmissibility and bloodstream infection rates than other CTs. A genomic region Lyb-2-4 was shared by CT512 and CT2092 but not CT2085. The mortality rates of patient infected with CRAB harboring Lyb-2-4 was significantly higher than those infected with CRAB isolates without...
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biorxivpreprint: Lyb-2-4, a unique genomic region of hypervirulent carbapenem-resistant Acinetobacter baumannii https://t.co/cbk5nTaD1z #bioRxiv
biorxiv_micrbio: Lyb-2-4, a unique genomic region of hypervirulent carbapenem-resistant Acinetobacter baumannii https://t.co/FamO9Xvgb8 #biorxiv_micrbio
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Sample Sizes : [61, 227]
Authors: 22
Total Words: 6412
Unqiue Words: 2435

1.997 Mikeys
#8. Establishing RPTE-derived cell lines expressing hTERT for studying BK polyomavirus
Linbo Zhao, Michael Imperiale
We previously established an infection model for BKPyV in primary human renal proximal tubule epithelial (RPTE) cells. Use of these cells is limited by their inability to be passaged extensively. We describe RPTE cells immortalized with hTERT, which can serve as a model system for acute or persistent BKPyV infection.
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Authors: 2
Total Words: 2067
Unqiue Words: 1059

1.997 Mikeys
#9. RNA-dependent RNA polymerase speed and fidelity are not the only determinants of the mechanism or efficiency of recombination.
Hyejeong Kim, Victor D. Ellis, Andrew Woodman, Yan Zhao, Jamie Arnold, Craig Cameron
Using the RNA-dependent RNA polymerase (RdRp) from poliovirus (PV) as our model system, we have shown that Lys-359 in motif-D functions as a general acid in the mechanism of nucleotidyl transfer. A K359H (KH) RdRp derivative is slow and faithful relative to wild-type enzyme. In the context of the virus, RdRp-coding sequence evolves, selecting for the following substitutions: I331F (IF, motif-C) and P356S (PS, motif-D). We have evaluated IF-KH, PS-KH, and IF-PS-KH viruses and enzymes. The speed and fidelity of each double mutant are equivalent. Each exhibits a unique recombination phenotype, with IF-KH being competent for copy-choice recombination and PS-KH being competent for forced-copy-choice recombination. Although the IF-PS-KH RdRp exhibits biochemical properties within twofold of wild type, the virus is impaired substantially for recombination in cells. We conclude that there are biochemical properties of the RdRp in addition to speed and fidelity that determine the mechanism and efficiency of recombination. The interwoven...
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Authors: 6
Total Words: 0
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1.997 Mikeys
#10. Aggregatibacter actinomycetemcomitans LtxA hijacks endocytic trafficking pathways in human lymphocytes
Edward Lally, Kathleen Boesze-Battaglia, Anuradha Dhingra, Nestor M Gomez, Claire H Mitchell, Alexander Giannakakis, Syed A Fahim, Roland Benz, Nataliya Balashova
Abstract: Leukotoxin (LtxA) from oral pathogen Aggregatibacter actinomycetemcomitans is a secreted membrane-damaging protein. LtxA is internalized by β2 integrin LFA-1 (CD11a/CD18) expressing leukocytes and ultimately causes cell death; however toxin localization in the host cell is poorly understood and these studies fill this void. We investigated LtxA trafficking using multi-fluor confocal imaging, flow cytometry and Rab5 knockdown in human T lymphocyte Jurkat cells. Planar lipid bilayers were used to characterize LtxA pore-forming activity at different pH. Our results demonstrate that LtxA/LFA-1 complex gains an access to the cytosol of Jurkat cells without evidence of plasma membrane damage utilizing dynamin-dependent and clathrin-independent mechanism. Upon internalization LtxA follows the LFA-1 endocytic trafficking pathways as identified by co-localization experiments with endosomal and lysosomal markers (Rab5, Rab11A, Rab7, and Lamp2) and CD11a. Knockdown of Rab5a resulted in loss of susceptibility of Jurkat cells to LtxA...
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Authors: 9
Total Words: 0
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