Top 10 Biorxiv Papers Today in Microbiology


2.008 Mikeys
#1. Complete genome assembly of clinical multidrug resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial resistance genes and plasmids
Thomas Vognbjerg Sydenham, Soeren Overballe-Pedersen, Henrik Hasman, Hannah Wexler, Michael Kemp, Ulrik Stenz Justesen
Bacteroides fragilis constitutes a significant part of the normal human gut microbiota and can also act as an opportunistic pathogen. Antimicrobial resistance and the prevalence of antimicrobial resistance genes are increasing, and prediction of antimicrobial susceptibility based on sequence information could support targeted antimicrobial therapy in a clinical setting. Complete identification of insertion sequence (IS) elements carrying promoter sequences upstream of resistance genes is necessary for prediction of antimicrobial resistance. However, de novo assemblies from short reads alone are often fractured due to repeat regions and the presence multiple copies of identical IS elements. Identification of plasmids in clinical isolates can aid in the surveillance of the dissemination of antimicrobial resistance and comprehensive sequence databases support microbiome and metagenomic studies. Here we test several short-read, hybrid and long-lead assembly pipelines by assembling the type strain B. fragilis CCUG4856T...
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biorxivpreprint: Complete genome assembly of clinical multidrug resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial resistance genes and plasmids https://t.co/UDjpm65yqX #bioRxiv
biorxiv_micrbio: Complete genome assembly of clinical multidrug resistant Bacteroides fragilis isolates enables comprehensive identification of ... https://t.co/8MTAm1SrnO #biorxiv_micrbio
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Sample Sizes : None.
Authors: 6
Total Words: 3915
Unqiue Words: 2155

2.001 Mikeys
#2. Insights from the revised complete genome sequences of Acinetobacter baumannii strains AB307-0294 and ACICU belonging to global clone 1 and 2
Mohammad Hamidian, Ryan Wick, Rebecca M. Hartstein, Louise M. Judd, Kathryn Holt, Ruth M. Hall
The Acinetobacter baumannii global clone 1 (GC1) isolate AB307-0294, recovered in the USA in 1994, and the global clone 2 (GC2) isolate ACICU, isolated in 2005 in Italy, were among the first A. baumannii isolates to be completely sequenced. AB307-0294 is susceptible to most antibiotics and has been used in many genetic studies and ACICU belongs to a rare GC2 lineage. The complete genome sequences, originally determined using 454 pyrosequencing technology which is known to generate sequencing errors, were re-determined using Illumina MiSeq and MinION (ONT) technologies and a hybrid assembly generated using Unicycler. Comparison of the resulting new high-quality genomes to the earlier 454-sequenced version identified a large number of nucleotide differences affecting protein coding features, and allowed the sequence of the long and highly-repetitive bap and blp1 genes to be properly resolved for the first time in ACICU. Comparisons of the annotations of the original and revised genomes revealed a large number of differences in the...
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A script for comparing old vs new versions of genome annotations

Repository: Compare-annotations
User: rrwick
Language: Python
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Subscribers: 1
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Sample Sizes : [3568, 3494, 3387, 3336]
Authors: 6
Total Words: 7193
Unqiue Words: 2643

2.001 Mikeys
#3. Next-generation sequencing of double stranded RNA is greatly improved by treatment with the inexpensive denaturing reagent DMSO
Alexander H Wilcox, Eric Delwart, Samuel Diaz-Munoz
Double stranded RNA (dsRNA) is the genetic material of important viruses and a key component of RNA interference-based immunity in eukaryotes. Previous studies have noted difficulties in determining the sequence of dsRNA molecules that have affected studies of immune function and estimates of viral diversity in nature. Dimethyl sulfoxide (DMSO) has been used to denature dsRNA prior to the reverse transcription stage to improve RT-PCR and Sanger sequencing. We systematically tested the utility of DMSO to improve sequencing yield of a dsRNA virus (Φ6) in a short-read next generation sequencing platform. DMSO treatment improved sequencing read recovery by over two orders of magnitude, even when RNA and cDNA concentrations were below the limit of detection. We also tested the effects of DMSO on a mock eukaryotic viral community and found that dsRNA virus reads increased with DMSO treatment. Furthermore, we provide evidence that DMSO treatment does not adversely affect recovery of reads from a single-stranded RNA viral genome...
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pdmillett: Next-generation sequencing of double stranded RNA is greatly improved by treatment with the inexpensive denaturing reagent DMSO https://t.co/yIorTOuzVV
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Authors: 3
Total Words: 0
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1.997 Mikeys
#4. Regulation of the Erythrobacter litoralis DSM 8509 general stress response by visible light
Aretha Fiebig, Lydia M Varesio, Xiomarie Alejandro Navarreto, Sean Crosson
Extracytoplasmic function (ECF) sigma factors are a major class of environmentally-responsive transcriptional regulators. In Alphaproteobacteria the ECF sigma factor, σEcfG, activates general stress response (GSR) transcription and protects cells from multiple stressors. A phosphorylation-dependent protein partner switching mechanism, involving HWE/HisKA_2-family histidine kinases, underlies σEcfG activation. The identity of these sensor kinases and the signals that regulate them remain largely uncharacterized. We have developed the aerobic anoxygenic photoheterotrophic (AAP) bacterium, Erythrobacter litoralis DSM 8509, as a comparative genetic model to investigate GSR regulation. Using this system, we sought to define the contribution of visible light and a photosensory HWE kinase, LovK, to GSR transcription. We identified three HWE kinase genes that collectively regulate GSR: gsrK and lovK are activators, while gsrP is a repressor. GSR transcription is higher in the dark than light, and the opposing activities of gsrK and gsrP...
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biorxivpreprint: Regulation of the Erythrobacter litoralis DSM 8509 general stress response by visible light https://t.co/duTuXttqPf #bioRxiv
biorxiv_micrbio: Regulation of the Erythrobacter litoralis DSM 8509 general stress response by visible light https://t.co/IPyPIP4vlE #biorxiv_micrbio
sbotlite: RT @biorxivpreprint: Regulation of the Erythrobacter litoralis DSM 8509 general stress response by visible light https://t.co/duTuXttqPf #…
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Sample Sizes : [5]
Authors: 4
Total Words: 15838
Unqiue Words: 4265

1.997 Mikeys
#5. Comparative analysis of neuroinvasion by Japanese encephalitis virulent and vaccine strains in an in cellulo model of human blood-brain barrier
Cecile Khou, Marco Aurelio Diaz-Salinas, Anaelle da Costa, Christophe Prehaud, Patricia Jeannin, Philippe Afonso, Marco Vignuzzi, Monique Lafon, Nathalie Pardigon
Japanese encephalitis virus (JEV) is the major cause of viral encephalitis in South East Asia. It has been suggested that JEV gets access to the central nervous system (CNS) as a consequence of a preceding inflammatory process which leads to the blood-brain barrier (BBB) disruption and viral neuroinvasion. However, what happens at early times of JEV contact with the BBB is poorly understood. In the present work, we evaluated the ability of both a virulent and a vaccine strain of JEV (JEV RP9 and SA14-14-2, respectively) to cross an in cellulo human BBB model consisting of hCMEC/D3 human endothelial cells cultivated on permeable inserts above SK-N-SH human neuroblastoma cells. Using this system, we demonstrated that both JEV RP9 and SA14-14-2 are able to cross the BBB without disrupting it at early times post-addition. Furthermore, this BBB model was able to discriminate between the virulent RP9 and the vaccine SA14-14-2 strains, as demonstrated by the presence of almost 10 times more RP9 infectious particles that crossed the BBB...
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biorxivpreprint: Comparative analysis of neuroinvasion by Japanese encephalitis virulent and vaccine strains in an in cellulo model of human blood-brain barrier https://t.co/IeWAoXNMEX #bioRxiv
biorxiv_micrbio: Comparative analysis of neuroinvasion by Japanese encephalitis virulent and vaccine strains in an in cellulo model of human ... https://t.co/yXNi7yt82L #biorxiv_micrbio
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Authors: 9
Total Words: 9038
Unqiue Words: 2845

1.997 Mikeys
#6. Gateway mechanism confers ultrasensitivity on motor′s function
Oshri Afanzar, Diana Di Paolo, Miriam Eisenstein, Kohava Levi, Anne Plochowietz, Achillefs N. Kapanidis, Richard Michael Berry, Michael Eisenbach
In bacteria such as Escherichia coli, information from the chemotaxis system to the flagellar motor is transduced by a single protein, CheY. The motor responds to CheY by switching its direction of rotation from the default direction to the other. This response is ultrasensitive, but the mechanism underlying this ultrasensitive switching is unknown. Here we resolved this mechanism. We show that the motor employs three sequential steps of CheY binding to distinct sites at the motor, each with a different outcome. Binding to the first site activates CheY at the motor. Binding to the second site generates transient motor switching and enables binding to the third site, which stabilizes the switched state. We demonstrate by mathematical modeling that such a gateway mechanism provides ultrasensitivity. The unique combination of tight regulation and flexibility provided by this mechanism raises the possibility that similar mechanisms may be functional in other systems as well.
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Authors: 8
Total Words: 12943
Unqiue Words: 3620

1.997 Mikeys
#7. Estimating MIC distributions and cutoffs through mixture models: an application to establish M. Tuberculosis resistance.
CLARA GRAZIAN
Antimicrobial resistance is becoming a major threat to public health throughout the world. Researchers from around the world are attempting to contrast it by developing both new antibiotics and patient-specific treatments. It is, therefore, necessary to study these treatments, via phenotypic tests, and it is essential to have robust methods available to analyze the resistance patterns to medication, which could be applied to both new treatments and to new phenotypic tests. A general method is here proposed to study minimal inhibitory concentration (MIC) distributions and fixed breakpoints in order to separate sensible from resistant strains. The method has been applied to a new 96-well microtiter plate.
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Authors: 1
Total Words: 8552
Unqiue Words: 2048

1.997 Mikeys
#8. Genome-wide identification of Pseudomonas syringae genes required for competitive fitness during colonization of the leaf surface and apoplast
Tyler C Helmann, Adam M Deutschbauer, Steven E Lindow
The foliar plant pathogen Pseudomonas syringae can establish large epiphytic populations on leaf surfaces before infection. However, the bacterial genes that contribute to these lifestyles have not been completely defined. The fitness contributions of most genes in P. syringae pv. syringae B728a were determined by genome-wide fitness profiling with a randomly barcoded transposon mutant library that was grown on the leaf surface and in the apoplast of the susceptible plant Phaseolus vulgaris . Genes within the functional categories of amino acid and polysaccharide (including alginate) biosynthesis contributed most to fitness both on the leaf surface (epiphytic) or in the leaf interior (apoplast), while genes in the type III secretion system and syringomycin synthesis were primarily important in the apoplast. Numerous other genes that had not been previously associated with in planta growth were also required for maximum epiphytic or apoplastic fitness. Many hypothetical proteins and uncategorized glycosyltransferases were also...
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Authors: 3
Total Words: 13925
Unqiue Words: 4085

1.996 Mikeys
#9. Extensive Transcriptional and Translational Regulation Occur During the Maturation of Malaria Parasite Sporozoites
Scott E Lindner, Kristian E Swearingen, Melanie J Shears, Michael P Walker, Erin N Vrana, Kevin J Hart, Allen M Minns, Photini Sinnis, Robert L. Moritz, Stefan H Kappe
Plasmodium sporozoites are transmitted from an infected mosquito to mammals in which they infect the liver. The infectivity profile of sporozoites changes as they egress from oocysts on the mosquito midgut into the hemocoel, and then invade the salivary glands, where they maintain a poised and infectious state until transmission occurs. Upon transmission, the sporozoite must then navigate the host skin, vasculature, and liver. All of these feats require distinct repertoires of proteins and capabilities that are coordinated in an appropriate temporal manner. Here, we report the comprehensive and dynamic transcriptomes and proteomes of both oocyst sporozoite and salivary gland sporozoite stages in both rodent-infectious Plasmodium yoelii parasites and human-infectious Plasmodium falciparum parasites. These data robustly define mRNAs and proteins that are Upregulated in Oocyst Sporozoites (UOS) or Upregulated in Infectious Sporozoites (UIS), which include critical gene products for sporozoite functions, as well as many of unknown...
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Authors: 10
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1.996 Mikeys
#10. Seven new Neocallimastigomycota genera from fecal samples of wild, zoo-housed, and domesticated herbivores: Description of Ghazallomyces constrictus gen. nov., sp. nov., Aklioshbomyces papillarum gen. nov., sp. nov., Agriosomyces longus gen. nov., sp. nov., Capellomyces foraminis gen. nov., sp. nov. and Capellomyces elongatus sp. nov., Joblinomyces apicalis gen. nov., sp. nov., Khoyollomyces ramosus gen. nov., sp. nov., and Tahromyces munnarensis gen. nov., sp. nov.
Radwa Hanafy, Vikram Lanjekar, Prashant Dhakephalkar, Tony Callaghan, Sumit S Dagar, Gareth W Griffith, Mostafa Elshahed, Noha H Youssef
We isolated and characterized sixty-five anaerobic gut fungi (AGF, Neocallimastigomycota) strains from fecal samples of five wild (W), one zoo-housed (Z), and three domesticated (D) herbivores in the US states of Texas (TX) and Oklahoma (OK), Wales (WA), and the Indian states of Kerala (KE) and Haryana (HA). Phylogenetic assessment based on D1-D2 region of the large rRNA subunit (LSU) identified seven distinct lineages, with strains recovered from Axis Deer (W-TX) clustering within the Orpinomyces-Neocallimastix-Pecoramyces-Feramyces clade; Boer Goat-domesticated Goat strains (W-TX, D-KE) clustering within the Oontomyces-Anaeromyces-Liebetanzomyces clade; and domesticated Goat and Sheep strains (D-HA) as well as Nilgiri Tahr strains (W-KE) forming two distinct clades associated with genus Buwchfawromyces. The remaining three lineages, represented by strains recovered from Mouflon-Boer Goat (W-TX), White Tailed Deer (W-OK), and Zebra-Horse (Z-OK, and D-WA), displayed no specific suprageneric affiliation. All strains displayed...
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Sample Sizes : [50, 15]
Authors: 8
Total Words: 18194
Unqiue Words: 4712

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