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Sunday, July 7, 2019

Comparative genomic analysis of two clonally related multidrug resistant Mycobacterium tuberculosis by Single Molecule Real Time Sequencing.

Background: Multidrug-resistant tuberculosis (MDR-TB) is posing a major threat to global TB control. In this study, we focused on two consecutive MDR-TB isolated from the same patient before and after the initiation of anti-TB treatment. To better understand the genomic characteristics of MDR-TB, Single Molecule Real-Time (SMRT) Sequencing and comparative genomic analyses was performed to identify mutations that contributed to the stepwise development of drug resistance and growth fitness in MDR-TB underin vivochallenge of anti-TB drugs.Result:Both pre-treatment and post-treatment strain demonstrated concordant phenotypic and genotypic susceptibility profiles toward rifampicin, pyrazinamide, streptomycin, fluoroquinolones, aminoglycosides, cycloserine, ethionamide, and para-aminosalicylic acid. However, although…

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Sunday, July 7, 2019

Filling in the gap of human chromosome 4: Single Molecule Real Time sequencing of macrosatellite repeats in the facioscapulohumeral muscular dystrophy locus.

A majority of facioscapulohumeral muscular dystrophy (FSHD) is caused by contraction of macrosatellite repeats called D4Z4 that are located in the subtelomeric region of human chromosome 4q35. Sequencing the FSHD locus has been technically challenging due to its long size and nearly identical nature of repeat elements. Here we report sequencing and partial assembly of a BAC clone carrying an entire FSHD locus by a single molecule real time (SMRT) sequencing technology which could produce long reads up to about 18 kb containing D4Z4 repeats. De novo assembly by Hierarchical Genome Assembly Process 1 (HGAP.1) yielded a contig of 41…

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Sunday, July 7, 2019

Evolutionary history of the global emergence of the Escherichia coli epidemic clone ST131.

Escherichia colisequence type 131 (ST131) has emerged globally as the most predominant extraintestinal pathogenic lineage within this clinically important species, and its association with fluoroquinolone and extended-spectrum cephalosporin resistance impacts significantly on treatment. The evolutionary histories of this lineage, and of important antimicrobial resistance elements within it, remain unclearly defined. This study of the largest worldwide collection (n= 215) of sequenced ST131E. coliisolates to date demonstrates that the clonal expansion of two previously recognized antimicrobial-resistant clades, C1/H30R and C2/H30Rx, started around 25 years ago, consistent with the widespread introduction of fluoroquinolones and extended-spectrum cephalosporins in clinical medicine. These two clades appear to…

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Sunday, July 7, 2019

Exploring structural variants in environmentally sensitive gene families.

Environmentally sensitive plant gene families like NBS-LRRs, receptor kinases, defensins and others, are known to be highly variable. However, most existing strategies for discovering and describing structural variation in complex gene families provide incomplete and imperfect results. The move to de novo genome assemblies for multiple accessions or individuals within a species is enabling more comprehensive and accurate insights about gene family variation. Earlier array-based genome hybridization and sequence-based read mapping methods were limited by their reliance on a reference genome and by misplacement of paralogous sequences. Variant discovery based on de novo genome assemblies overcome the problems arising from…

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Sunday, July 7, 2019

Gene duplication confers enhanced expression of 27-kDa ?-zein for endosperm modification in quality protein maize.

The maizeopaque2(o2) mutant has a high nutritional value but it develops a chalky endosperm that limits its practical use. Genetic selection foro2modifiers can convert the normally chalky endosperm of the mutant into a hard, vitreous phenotype, yielding what is known as quality protein maize (QPM). Previous studies have shown that enhanced expression of 27-kDa ?-zein in QPM is essential for endosperm modification. Taking advantage of genome-wide association study analysis of a natural population, linkage mapping analysis of a recombinant inbred line population, and map-based cloning, we identified a quantitative trait locus (q?27) affecting expression of 27-kDa ?-zein.q?27was mapped to the…

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Sunday, July 7, 2019

Complete genome sequence of a CTX-M-15-producing Escherichia coli strain from the H30Rx subclone of sequence type 131 from a patient with recurrent urinary tract infections, closely related to a lethal urosepsis isolate from the patient’s sister.

We report here the complete genome sequence, including five plasmid sequences, of Escherichia coli sequence type 131 (ST131) strain JJ1887. The strain was isolated in 2007 in the United States from a patient with recurrent cystitis, whose caregiver sister died from urosepsis caused by a nearly identical strain. Copyright © 2016 Johnson et al.

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Sunday, July 7, 2019

Isolation and genomic characterization of ‘Desulfuromonas soudanensis WTL’, a metal- and electrode-respiring bacterium from anoxic deep subsurface brine.

Reaching a depth of 713 m below the surface, the Soudan Underground Iron Mine (Soudan, MN, USA) transects a massive Archaean (2.7 Ga) banded iron formation, providing a remarkably accessible window into the terrestrial deep biosphere. Despite organic carbon limitation, metal-reducing microbial communities are present in potentially ancient anoxic brines continuously emanating from exploratory boreholes on Level 27. Using graphite electrodes deposited in situ as bait, we electrochemically enriched and isolated a novel halophilic iron-reducing Deltaproteobacterium, ‘Desulfuromonas soudanensis’ strain WTL, from an acetate-fed three-electrode bioreactor poised at +0.24 V (vs. standard hydrogen electrode). Cyclic voltammetry revealed that ‘D. soudanensis’ releases…

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Sunday, July 7, 2019

Conservation genetics of an endangered grassland butterfly (Oarisma poweshiek) reveals historically high gene flow despite recent and rapid range loss

1. In poorly dispersing species gene flow can be facilitated when suitable habitat is widespread, allowing for increased dispersal between neighbouring locations. The Poweshiek skipperling [Oarisma poweshiek (Parker)], a federally endangered butterfly, has undergone a rapid, recent demographic decline following the loss of tallgrass prairie and fen habitats range wide. The loss of habitat, now restricted geographic range, and poor dispersal ability have left O. poweshiek at increased risk of extinction. 2. We studied the population genetics of six remaining populations of O. poweshiek in order to test the hypothesis that gene flow was historically high despite limited long-distance dispersal…

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Sunday, July 7, 2019

Highlights of the 11th International Bordetella Symposium: from basic biology to vaccine development.

Pertussis is a severe respiratory disease caused by infection with the bacterial pathogen Bordetella pertussis The disease affects individuals of all ages but is particularly severe and sometimes fatal in unvaccinated young infants. Other Bordetella species cause diseases in humans, animals, and birds. Scientific, clinical, public health, vaccine company, and regulatory agency experts on these pathogens and diseases gathered in Buenos Aires, Argentina from 5 to 8 April 2016 for the 11th International Bordetella Symposium to discuss recent advances in our understanding of the biology of these organisms, the diseases they cause, and the development of new vaccines and other…

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Sunday, July 7, 2019

Complete genome sequence of Celeribacter baekdonensis strain LH4, a thiosulfate-oxidizing alphaproteobacterial isolate from Gulf of Mexico continental slope sediments.

We report here the closed genome sequences of Celeribacter baekdonensis strain LH4 and five unnamed plasmids obtained through PacBio sequencing with 99.99% consensus concordance. The genomes contained several distinctive features not found in other published Celeribacter genomes, including the potential to aerobically degrade styrene and other phenolic compounds. Copyright © 2018 Flood et al.

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Sunday, July 7, 2019

Complete genome sequence of Klebsiella quasipneumoniae strain S05, a fouling-causing bacterium isolated from a membrane bioreactor.

We report here the complete genome sequence of Klebsiella quasipneumoniae strain S05, a bacterium capable of producing membrane fouling-causing soluble substances and capable of respiring on oxygen, nitrate, and an anodic electrode. The genomic information of strain S05 should help predict metabolic pathways associated with these unique biological properties of this bacterium. Copyright © 2018 Kitajima et al.

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Sunday, July 7, 2019

Identification of different putative outer membrane electron conduits necessary for Fe(III) citrate, Fe(III) oxide, Mn(IV) oxide, or electrode reduction by Geobacter sulfurreducens.

At least five gene clusters in the Geobacter sulfurreducens genome encode putative “electron conduits” implicated in electron transfer across the outer membrane, each containing a periplasmic multiheme c-type cytochrome, integral outer membrane anchor, and outer membrane redox lipoprotein(s). Markerless single-gene-cluster deletions and all possible multiple-deletion combinations were constructed and grown with soluble Fe(III) citrate, Fe(III) and Mn(IV) oxides, and graphite electrodes poised at +0.24 V and -0.1 V versus the standard hydrogen electrode (SHE). Different gene clusters were necessary for reduction of each electron acceptor. During metal oxide reduction, deletion of the previously described omcBC cluster caused defects, but deletion…

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