Letter to the Editor, BJOG Exchange Borgogna, JLC; Shardell, MD; Santori, EK ...
BJOG : an international journal of obstetrics and gynaecology,
03/2020, Letnik:
127, Številka:
6
Journal Article
Pseudomonas fluorescens Pf-5 is a plant commensal bacterium that inhabits the rhizosphere and produces secondary metabolites that suppress soilborne plant pathogens. The complete sequence of the ...7.1-Mb Pf-5 genome was determined. We analyzed repeat sequences to identify genomic islands that, together with other approaches, suggested P. fluorescens Pf-5's recent lateral acquisitions include six secondary metabolite gene clusters, seven phage regions and a mobile genomic island. We identified various features that contribute to its commensal lifestyle on plants, including broad catabolic and transport capabilities for utilizing plant-derived compounds, the apparent ability to use a diversity of iron siderophores, detoxification systems to protect from oxidative stress, and the lack of a type III secretion system and toxins found in related pathogens. In addition to six known secondary metabolites produced by P. fluorescens Pf-5, three novel secondary metabolite biosynthesis gene clusters were also identified that may contribute to the biocontrol properties of P. fluorescens Pf-5.
Fanconi anaemia (FA) is an autosomal recessive disorder associated with diverse developmental abnormalities, bone-marrow failure and predisposition to cancer. FA cells show increased chromosome ...breakage and hypersensitivity to DNA cross-linking agents such as diepoxybutane and mitomycin C. Somatic-cell hybridisation analysis of FA cell lines has demonstrated the existence of at least five complementation groups (FA-A to FA-E), the most common of which is FA-A. This genetic heterogeneity has been a major obstacle to the positional cloning of FA genes by classical linkage analysis. The FAC gene was cloned by functional complementation, and localised to chromosome 9q22.3 (ref. 2), but this approach has thus far failed to yield the genes for the other complementation groups. We have established a panel of families classified as FA-A by complementation analysis, and used them to search for the FAA gene by linkage analysis. We excluded the previous assignment by linkage of an FA gene to chromosome 20q, and obtained conclusive evidence for linkage of FAA to microsatellite markers on chromosome 16q24.3. Strong evidence of allelic association with the disease was detected with the marker D16S303 in the Afrikaner population of South Africa, indicating the presence of a founder effect.
Phylogenetic reconstruction using molecular data is often subject to homoplasy, leading to inaccurate conclusions about phylogenetic relationships among operational taxonomic units. Compared with ...other molecular markers, single-nucleotide polymorphisms (SNPs) exhibit extremely low mutation rates, making them rare in recently emerged pathogens, but they are less prone to homoplasy and thus extremely valuable for phylogenetic analyses. Despite their phylogenetic potential, ascertainment bias occurs when SNP characters are discovered through biased taxonomic sampling; by using whole-genome comparisons of five diverse strains of Bacillus anthracis to facilitate SNP discovery, we show that only polymorphisms lying along the evolutionary pathway between reference strains will be observed. We illustrate this in theoretical and simulated data sets in which complex phylogenetic topologies are reduced to linear evolutionary models. Using a set of 990 SNP markers, we also show how divergent branches in our topologies collapse to single points but provide accurate information on internodal distances and points of origin for ancestral clades. These data allowed us to determine the ancestral root of B. anthracis, showing that it lies closer to a newly described "C" branch than to either of two previously described "A" or "B" branches. In addition, subclade rooting of the C branch revealed unequal evolutionary rates that seem to be correlated with ecological parameters and strain attributes. Our use of nonhomoplastic whole-genome SNP characters allows branch points and clade membership to be estimated with great precision, providing greater insight into epidemiological, ecological, and forensic questions.
Satellite tobacco necrosis virus RNA (STNV RNA) is a naturally uncapped viral RNA that contains 1239 nucleotides: 29 in the 5' untranslated region (UTR), 591 in the coding region and 619 in the 3' ...UTR. Mutations were made in the 5' and 3' UTRs, and the effects of these mutations on translational efficiency and cap independence were measured in an in vitro translation system from wheat germ. Removal of the first 12 nucleotides or 10 changes in the nucleotide sequence of the 5' UTR reduced translational efficiency approximately 3-fold; capping of these 5' mutant mRNAs restored their translational efficiencies. Truncation of the 3' UTR to nucleotide 627 or 700, or deletion of nucleotides 627-737, reduced translational efficiency more than 20-fold; capping of these 3' mutant mRNAs restored their translational efficiencies. These modifications in the 3' UTR increased the concentration of initiation factor 4F required for translation. Chimeric mRNAs were constructed which contained the coding region of rabbit alpha-globin mRNA and either the 5' UTR, 3' UTR, or both the 5' and 3' UTRs of STNV RNA. Both the 5' and 3' UTRs of STNV RNA were necessary to obtain cap-independent translation. These findings indicate that interaction between 5' UTR and the region between nucleotides 627 and 737 in the 3' UTR are required for cap-independent translation
Aims:
Physiological responses of marine luminous bacteria, Vibrio harveyi (ATCC 14216) and V. fischeri (UM1373) to nutrient‐limited normal strength (35 ppt iso‐osmolarity) and low (10 ppt ...hypo‐osmolarity) salinity conditions were determined.
Methods and Results:
Plate counts, direct viable counts, actively respiring cell counts, nucleoid‐containing cell counts, and total counts were determined. Vibrio harveyi incubated at 22°C in nutrient‐limited artificial seawater (ASW) became nonculturable after approximately 62 and 45 d in microcosms of 35 ppt and 10 ppt ASW, respectively. In contrast, V. fischeri became nonculturable at approximately 55 and 31 d in similar microcosms. Recovery of both culturability and luminescence of cells in the viable but nonculturable state was achieved by addition of nutrient broth or nutrient broth supplemented with a carbon source, including luminescence‐stimulating compounds. Temperature upshift from 22°C to 30°C or 37°C did not result in recovery from nonculturability.
Conclusions:
The study confirms entry of V. harveyi and V. fischeri into the viable but nonculturable state under low‐nutrient conditions and demonstrates nutrient‐dependent resuscitation from this state.
Significance and Impact of the Study:
This study confirms loss of luminescence of V. harveyi and V. fischeri on entry into the viable but nonculturable state and suggests that enumeration of luminescent cells in water samples may be a rapid method to deduce the nutrient status of a water sample.
Background: Specific cervicovaginal bacteria are associated with elevated inflammation in the female genital tract (FGT) and a number of poor reproductive outcomes, including HIV acquisition. These ...associations have been identified using bacterial 16S rRNA gene sequencing, which has limited resolution and often fails to achieve species-level taxonomic assignment. Genome sequencing of bacteria affords strain-level resolution, revealing that many species contain enough genes to make multiple independent genomes, reflecting a tremendous amount of diversity in potential phenotypes (virulence factors, antibiotic resistance, metabolic function, etc.). Few studies have used these methods to characterize the FGT microbiome, leaving much of the microbial diversity unexplored. Methods: We isolated 1400 bacteria using selective media and performed whole genome sequencing, applying cutting-edge methods for combining these data with assembled microbial genomes from over 1200 newly shotgun sequenced metagenomes from multiple geographic locations, to produce a comprehensive genome catalogue. Imposing species-level phylogenetic clustering on the resulting genomes allowed us to identify both known and previously unknown species. Mapping of shotgun metagenomic reads to these genomes allowed us to determine prevalence and amount of genetic diversity accounted for by these new species across multiple demographic factors (race, ethnicity, geography, pregnancy and menopause). Results: We identified 605 species in the female genital tract, 130 of which have not been previously described. Of these, 46 were only found in samples from African American and African women. Many of these new species were highly prevalent and co-occurred with known and previously unknown species in community assemblages. Furthermore, we significantly increased observable genetic diversity for known species associated with poor reproductive outcomes. One notable example is Prevotella bivia, a bacterium associated with increased HIV acquisition risk, was found to be different in both metabolic and antibiotic resistance gene content in South African isolates when compared to those from North America. Conclusions: We have massively expanded the observable genetic diversity in the FGT microbiome and identified both new species and previously unrecognized sub-species structures. This catalogue will contribute to developing novel approaches to modulate the vaginal microbiome and reduce poor reproductive outcomes, including HIV acquisition risk.
Abstract
Background
Women with a cervicovaginal microbiota dominated by
Lactobacillus
spp. are at reduced risk of acquiring sexually transmitted infections including HIV, but the biological ...mechanisms involved remain poorly defined. Here, we performed metaproteomics on vaginal swab samples from young South African women (
n
= 113) and transcriptomics analysis of cervicovaginal epithelial cell cultures to examine the ability of lactic acid, a metabolite produced by cervicovaginal lactobacilli, to modulate genital epithelial barrier function.
Results
Compared to women with
Lactobacillus
-depleted microbiota, women dominated by vaginal lactobacilli exhibit higher abundance of bacterial lactate dehydrogenase, a key enzyme responsible for lactic acid production, which is independently associated with an increased abundance of epithelial barrier proteins. Physiological concentrations of lactic acid enhance epithelial cell culture barrier integrity and increase intercellular junctional molecule expression.
Conclusions
These findings reveal a novel ability of vaginal lactic acid to enhance genital epithelial barrier integrity that may help prevent invasion by sexually transmitted pathogens.
Molecular karyotyping has revealed that microdeletions/duplications in the human genome are a major cause of multiple congenital anomalies associated with mental retardation (MCA/MR). The ...identification of a de novo chromosomal imbalance in a patient with MCA/MR is usually considered causal for the phenotype while a chromosomal imbalance inherited from a phenotypically normal parent is considered as a benign variation and not related to the disorder. Around 40% of imbalances in patients with MCA/MR in this series is inherited from a healthy parent and the majority of these appear to be (extremely) rare variants. As some of these contain known disease-causing genes and have also been found to be de novo in MCA/MR patients, this challenges the general view that such familial variants are innocent and of no major phenotypic consequence. Rather, we argue, that human genomes can be tolerant of genomic copy number variations depending on the genetic and environmental background and that different mechanisms play a role in determining whether these chromosomal imbalances manifest themselves.
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