Draft genome sequence of soil isolate DVD-1301.

Some strains of possess high sterol-oxidizing activity and are used in the pharmaceutical industry for the production of steroid precursors. Herein, we report a draft genome sequence of the soil-dwelling DVD-1301 isolated in the floodplain of the river Oka. The genome contains a full set of steroid catabolic genes.

Machine-Learning Model for Prediction of Cefepime Susceptibility in Escherichia coli from Whole-Genome Sequencing Data.

The declining cost of performing bacterial whole-genome sequencing (WGS) coupled with the availability of large libraries of sequence data for well-characterized isolates have enabled the application of machine-learning (ML) methods to the development of nonlinear sequence-based predictive models. We tested the ML-based model developed by Next Gen Diagnostics for prediction of cefepime phenotypic susceptibility results in Escherichia coli. A cohort of 100 isolates of E.

Draft Genome Sequence of Mycolicibacterium smegmatis VKM Ac-1171 Contains Full Set of Sterol Catabolic Genes.

VKM Ac-1171 is a saprotrophic bacterium that was isolated several decades ago and is deposited in microbial collections around the world. We report here a draft genome sequence of the strain. Annotation of the genome revealed the presence of a complete set of genes related to the sterol catabolic pathway.

Large-Scale Evaluation of a Rapid Fully Automated Analysis Platform to Detect and Refute Outbreaks Based on MRSA Genome Comparisons.

Genomic epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) could transform outbreak investigations, but its clinical introduction is hampered by the lack of automated data analysis tools to rapidly and accurately define transmission based on sequence relatedness. We aimed to evaluate a fully automated bioinformatics system for MRSA genome analysis versus a bespoke researcher-led manual informatics pipeline. We analyzed 781 MRSA genomes from 777 consecutive patients identified over a 9-month period in a clinical microbiology laboratory in the United Kingdom.

Recombinant Extracellular Cholesterol Oxidase from Nocardioides simplex.

Cholesterol oxidase is a highly demanded enzyme used in medicine, pharmacy, agriculture, chemistry, and biotechnology. It catalyzes oxidation of 3β-hydroxy-5-ene- to 3-keto-4-ene- steroids with the formation of hydrogen peroxide. Here, we expressed 6xHis-tagged mature form of the extracellular cholesterol oxidase (ChO) from the actinobacterium Nocardioides simplex VKM Ac-2033D (55.

The Incidence Risk for Primary Glaucoma and Its Subtypes following Chronic Exposure to Ionizing Radiation in the Russian Cohort of Mayak Nuclear Workers.

Secondary glaucoma is a typical normal tissue complication following radiation therapy involving ocular radiation exposure at high fractionated dose (several tens of Gy). In contrast, recent studies in acutely exposed Japanese atomic bomb survivors showed a significantly increased risk for normal-tension glaucoma (NTG, a subtype of primary open-angle glaucoma) at much lower dose, but such information is not available in any other cohorts. We therefore set out to evaluate the incidence of risk for primary glaucoma and its subtypes in a Russian cohort of Mayak Production Association nuclear workers who received chronic radiation exposure over many years.

Steroid Metabolism in Thermophilic Actinobacterium VKM Ac-666.

The application of thermophilic microorganisms opens new prospects in steroid biotechnology, but little is known to date on steroid catabolism by thermophilic strains. The thermophilic strain VKM Ac-666 has been shown to convert various steroids and to fully degrade cholesterol. Cholest-4-en-3-one, cholesta-1,4-dien-3-one, 26-hydroxycholest-4-en-3-one, 3-oxo-cholest-4-en-26-oic acid, 3-oxo-cholesta-1,4-dien-26-oic acid, 26-hydroxycholesterol, 3β-hydroxy-cholest-5-en-26-oic acid were identified as intermediates in cholesterol oxidation.

Different genome-wide transcriptome responses of Nocardioides simplex VKM Ac-2033D to phytosterol and cortisone 21-acetate.

Background: Bacterial degradation/transformation of steroids is widely investigated to create biotechnologically relevant strains for industrial application. The strain of Nocardioides simplex VKM Ac-2033D is well known mainly for its superior 3-ketosteroid Δ-dehydrogenase activity towards various 3-oxosteroids and other important reactions of sterol degradation. However, its biocatalytic capacities and the molecular fundamentals of its activity towards natural sterols and synthetic steroids were not fully understood.

Genome-Wide Transcriptome Profiling Provides Insight on Cholesterol and Lithocholate Degradation Mechanisms in VKM Ac-2033D.

Steroid microbial degradation plays a significant ecological role for biomass decomposition and removal/detoxification of steroid pollutants. In this study, the initial steps of cholesterol degradation and lithocholate bioconversion by a strain with enhanced 3-ketosteroid dehydrogenase (3-KSD) activity, VKM Ac-2033D, were studied. Biochemical, transcriptomic, and bioinformatic approaches were used.

Defining metrics for whole-genome sequence analysis of MRSA in clinical practice.

Bacterial sequencing will become increasingly adopted in routine microbiology laboratories. Here, we report the findings of a technical evaluation of almost 800 clinical methicillin-resistant (MRSA) isolates, in which we sought to define key quality metrics to support MRSA sequencing in clinical practice. We evaluated the accuracy of mapping to a generic reference versus clonal complex (CC)-specific mapping, which is more computationally challenging.

CRAMER: a lightweight, highly customizable web-based genome browser supporting multiple visualization instances.

Summary: In recent years, the ability to generate genomic data has increased dramatically along with the demand for easily personalized and customizable genome browsers for effective visualization of diverse types of data. Despite the large number of web-based genome browsers available nowadays, none of the existing tools provides means for creating multiple visualization instances without manual set up on the deployment server side. The Cranfield Genome Browser (CRAMER) is an open-source, lightweight and highly customizable web application for interactive visualization of genomic data.

Evaluation of a fully automated bioinformatics tool to predict antibiotic resistance from MRSA genomes.

Objectives: The genetic prediction of phenotypic antibiotic resistance based on analysis of WGS data is becoming increasingly feasible, but a major barrier to its introduction into routine use is the lack of fully automated interpretation tools. Here, we report the findings of a large evaluation of the Next Gen Diagnostics (NGD) automated bioinformatics analysis tool to predict the phenotypic resistance of MRSA.

Methods: MRSA-positive patients were identified in a clinical microbiology laboratory in England between January and November 2018.

Draft Genome Sequence of the Moderately Thermophilic Actinobacterial Steroid-Transforming Saccharopolyspora hirsuta subsp. Strain VKM Ac-666.

The draft genome sequence of the type strain subsp. VKM Ac-666 was sequenced. This moderately thermophilic actinobacterial strain of sugarcane bagasse origin is able to transform different steroid substrates.

Glaucoma incidence risk in a cohort of Mayak PA workers occupationally exposed to ionizing radiation.

Glaucoma is a major cause of visual impairment, and secondary glaucoma manifested as neovascular glaucoma has long been known to occur following high-dose fractionated radiation therapy. In contrast, little is known as to whether ionizing radiation exposure causes primary glaucoma, except that a single study in Japanese atomic bomb survivors has reported a significantly increase risk. Therefore, the effect of lower dose and lower dose rate remains unclear.

Pilot Evaluation of a Fully Automated Bioinformatics System for Analysis of Methicillin-Resistant Staphylococcus aureus Genomes and Detection of Outbreaks.

Genomic surveillance that combines bacterial sequencing and epidemiological information will become the gold standard for outbreak detection, but its clinical translation is hampered by the lack of automated interpretation tools. We performed a prospective pilot study to evaluate the analysis of methicillin-resistant (MRSA) genomes using the Next Gen Diagnostics (NGD) automated bioinformatics system. Seventeen unselected MRSA-positive patients were identified in a clinical microbiology laboratory in England over a period of 2 weeks in 2018, and 1 MRSA isolate per case was sequenced on the Illumina MiniSeq instrument.

Elevated Heterozygosity in Adults Relative to Juveniles Provides Evidence of Viability Selection on Eagles and Falcons.

Viability selection yields adult populations that are more genetically variable than those of juveniles, producing a positive correlation between heterozygosity and survival. Viability selection could be the result of decreased heterozygosity across many loci in inbred individuals and a subsequent decrease in survivorship resulting from the expression of the deleterious alleles. Alternatively, locus-specific differences in genetic variability between adults and juveniles may be driven by forms of balancing selection, including heterozygote advantage, frequency-dependent selection, or selection across temporal and spatial scales.

Genome-wide response on phytosterol in 9-hydroxyandrostenedione-producing strain of Mycobacterium sp. VKM Ac-1817D.

Background: Aerobic side chain degradation of phytosterols by actinobacteria is the basis for the industrial production of androstane steroids which are the starting materials for the synthesis of steroid hormones. A native strain of Mycobacterium sp. VKM Ac-1817D effectively produces 9α-hydroxyandrost-4-ene-3,17-dione (9-OH-AD) from phytosterol, but also is capable of slow steroid core degradation.

Registry for chronic radiation syndrome in a worker cohort of the Russian nuclear enterprise, Mayak Production Association.

A registry for chronic radiation syndrome (CRS), a deterministic effect of chronic exposure to external and/or internal radiation at doses and dose rates exceeding thresholds for tissue reactions, was established within a medical and dosimetry database known as 'Clinics', of the Southern Urals Biophysics Institute at the Federal Medical and Biological Agency of Russia. It includes 2068 CRS cases: 1517 (73.4%) in males and 551 (26.

Draft Genome Sequence of FK506-Producing Strain VKM Ac-2618D.

The 23-membered macrolide tacrolimus (FK506) is an important immunosuppressant that is widely used in the prevention of graft rejection and in the treatment of inflammatory skin diseases and immune diseases. We report here the draft genome sequence of the FK506 producer VKM Ac-2618D.

Risk of cataract removal surgery in Mayak PA workers occupationally exposed to ionizing radiation over prolonged periods.

In this study, the risk of cataract removal surgery was assessed in a cohort of workers occupationally exposed to ionizing radiation over a prolonged period. The study cohort includes 22,377 workers of the Mayak Production Association (about 25% of whom are females) first employed at one of the main facilities in 1948-1982, who were followed up to the end of 2008. Dose estimates used in the study are provided by the Mayak Worker Dosimetry System 2008.

Risk of various types of cataracts in a cohort of Mayak workers following chronic occupational exposure to ionizing radiation.

This study is the first to report cataract type specific risks in a cohort of Russian Mayak Production Association workers following chronic occupational exposure to ionizing radiation. In this retrospective cohort study, 22,377 workers (females 25.4%) first employed in 1948-1982 were followed up till the end of 2008.

[Risk of senile cataract among nuclear industry workers].

Aim: to assess the relative risk (RR) of senile cataract in a cohort of workers occupationally exposed to external gamma-rays over a long time period.

Material And Methods: The RR of cataract development was studied in a cohort of nuclear workers that were first employed in 1948-1982 and followed up till the end of 2008 (n=22,377; females, 25.4%).

Effect of methyl-β-cyclodextrin on gene expression in microbial conversion of phytosterol.

Modified β-cyclodextrins are widely used for the enhancement of microbial conversions of lipophilic compounds such as steroids. Multiple mechanisms of cyclodextrin-mediated enhancement of phytosterol bioconversion by mycobacteria had previously been shown to include steroid solubilization, alterations in the cell wall permeability for both steroids and nutrients, facilitation of protein leaking, and activity suppression of some steroid-transforming enzymes.In this work, we studied whether cyclodextrins might affect expression of the genes involved in the steroid catabolic pathway.