Complete Genome Sequence of a Novel Strain TA Isolated from Western Siberia Chernevaya Taiga Soil.

A whole genome sequence of a new strain of the nitrogen-fixing bacterium known for its diverse plant growth-promoting bacteria (PGPB), was obtained for the first time. The strain, designated e AT, was isolated during a soil analysis in the Chernevaya taiga of Western Siberia, a unique and fertile forest ecosystem known for its diverse plant growth-promoting bacteria (PGPB). The genome under study is fully assembled into seven circular molecules, none of which are unequivocally plasmids, with a total length of 6.

Creation of Cellulolytic Communities of Soil Microorganisms-A Search for Optimal Approaches.

For the targeted selection of microbial communities that provide cellulose degradation, soil samples containing cellulolytic microorganisms and specific plant residues as a substrate can be used. The details of this process have not been studied: in particular, whether the use of different soils determines the varying efficiency of communities; whether these established cellulolytic communities will have substrate specificity, and other factors. To answer these questions, four soil microbial communities with different cellulolytic activity (Podzol and the soil of Chernevaya taiga) and substrates (oat straw and hemp shives) with different levels of cellulose availability were used, followed by trained communities that were tested on botrooth substrates (in all possible combinations).

Herpes zoster in patients with glioma treated with temozolomide.

Background: The risk of herpes zoster in patients treated with temozolomide is poorly defined in the literature. We aimed to evaluate the incidence of and risk factors for herpes zoster in individuals receiving temozolomide for glioma.

Methods: A retrospective observational study was conducted on a series of patients treated with temozolomide for glioma at a single centre between 1 October 2018 and 30 September 2023.

Topical Calcipotriol Plus 5-Fluorouracil in the Treatment of Actinic Keratosis, Bowen's Disease, and Squamous Cell Carcinoma: A Systematic Review.

Background/objectives: Actinic keratoses (AK) are premalignant skin lesions caused by chronic sun exposure, topically managed by 5-fluorouracil (5-FU), diclofenac 3% gel, and imiquimod. Despite their effectiveness, long treatment duration and severe adverse local skin reactions have limited patient concordance. Calcipotriol has recently been used as a combination agent for existing topical AK treatments.

A systematic review of the impact of brain tumours on risk of motor vehicle crashes.

Purpose: Brain tumours are associated with neurocognitive impairments that are important for safe driving. Driving is vital to maintaining patient autonomy, despite this there is limited research on driving capacity amongst patients with brain tumours. The purpose of this review is to examine MVC risk in patients with brain tumours to inform development of clearer driving guidelines.

Analysis of rhizosphere fungal community of agricultural crops cultivated in laboratory experiments on Chernevaya taiga soil.

Chernevaya taiga of Western Siberia, Russia, is a unique ecosystem characterized by fertile soil, exceptionally large herbaceous plant sizes, and extraordinarily rapid rates of plant residue degradation. We expected that growing crops on soil collected from Chernevaya taiga, which has never been used for agricultural purposes before, would result in a distinct rhizospheric fungal community. This community could potentially yield novel, potent biostimulators and biocontrol fungi for modern agriculture.

Protocol for refining metagenomic binning with BinSPreader.

The analysis of metagenomic data obtained via high-throughput DNA sequencing is primarily carried out by a dedicated binning process involving clustering contigs, presumably belonging to the same species. Here, we present a protocol for improving the quality of binning using BinSPreader. We describe steps for typical metagenome assembly and binning workflow.

Medical student intentions to practice internal medicine in underserved areas associated with debt, identity and extracurricular participation.

Background: Currently, Internal Medicine (IM) physicians do not reflect the ethno-racial diversity of the US population. Moreover, there is a shortage of IM physicians in Medically Underserved Areas (MUAs) in the US. The purpose of this study was to determine factors that influence medical students' intent to practice IM in MUAs.

An Engineering Method of Analyzing the Dynamics of Mass Transfer during Concrete Corrosion Processes in Offshore Structures.

The environment of an underground structure is much more complex than the above-ground environment. Erosion processes are underway in soil and groundwater; groundwater seepage and soil pressure are also typical for underground environments. Alternating layers of dry and wet soil have a strong effect on concrete, and they reduce its durability.

Accurate isoform discovery with IsoQuant using long reads.

Annotating newly sequenced genomes and determining alternative isoforms from long-read RNA data are complex and incompletely solved problems. Here we present IsoQuant-a computational tool using intron graphs that accurately reconstructs transcripts both with and without reference genome annotation. For novel transcript discovery, IsoQuant reduces the false-positive rate fivefold and 2.

MetaGT: A pipeline for assembly of metatranscriptomes with the aid of metagenomic data.

While metagenome sequencing may provide insights on the genome sequences and composition of microbial communities, metatranscriptome analysis can be useful for studying the functional activity of a microbiome. RNA-Seq data provides the possibility to determine active genes in the community and how their expression levels depend on external conditions. Although the field of metatranscriptomics is relatively young, the number of projects related to metatranscriptome analysis increases every year and the scope of its applications expands.

Agricultural Crops Grown in Laboratory Conditions on Chernevaya Taiga Soil Demonstrate Unique Composition of the Rhizosphere Microbiota.

Chernevaya taiga in West Siberia is a unique environment, with gigantism of grasses and shrubs. Exceptionally high productivity of plants is determined by the synergistic interaction of various factors, with a special role belonging to microorganisms colonizing the plant roots. This research explored whether agricultural plants can recruit specific microorganisms from within virgin Chernevaya Umbrisol and thus increase their productivity.

Deferred Action for Childhood Arrivals (DACA): Maximizing Impacts in Medical Education and Health Care.

Introduction: Deferred Action for Childhood Arrivals (DACA) provides a path for individuals who are undocumented to join the physician workforce. Indeed, recipients of DACA can play an important role in addressing health inequities in medicine. Although DACA has been in place since 2012, many medical schools remain unaware of it or are hesitant to consider recipients for admission.

Neuroimaging findings in immune effector cell associated neurotoxicity syndrome after chimeric antigen receptor T-cell therapy.

Chimeric antigen receptor T-cell (CAR-T) therapy is a promising immunotherapy approved for hematological malignancies. Despite its effectiveness, clinically significant rates of toxicity, including immune effector cell associated neurotoxicity syndrome (ICANS), limit its widespread use. In certain contexts, ICANS may occur in up to one-third of patients using commercially available CAR-T therapies.

Fungal Metagenome of Chernevaya Taiga Soils: Taxonomic Composition, Differential Abundance and Factors Related to Plant Gigantism.

The Chernevaya taiga of Western Siberia is a unique and complex ecosystem, distinguished by the unusually large sizes of herbaceous plants, the reasons for which are poorly understood. Here, we explored the fungal diversity of the Chernevaya taiga soils in the Tomsk regions of Western Siberia in comparison with other soil types. The soil biomes of Chernevaya taiga and the control regions were investigated using Illumina ITS rRNA sequencing, and taxonomic analysis revealed a predominance of fungal phyla in the different soils.

Metagenomic Data Assembly - The Way of Decoding Unknown Microorganisms.

Metagenomics is a segment of conventional microbial genomics dedicated to the sequencing and analysis of combined genomic DNA of entire environmental samples. The most critical step of the metagenomic data analysis is the reconstruction of individual genes and genomes of the microorganisms in the communities using metagenomic assemblers - computational programs that put together small fragments of sequenced DNA generated by sequencing instruments. Here, we describe the challenges of metagenomic assembly, a wide spectrum of applications in which metagenomic assemblies were used to better understand the ecology and evolution of microbial ecosystems, and present one of the most efficient microbial assemblers, SPAdes that was upgraded to become applicable for metagenomics.

Draft Genome Sequence of sp. Strain FB-8, Isolated from a Former Uranium Mining Area in Germany.

Here, we present the draft genome sequence of sp. strain FB-8, a mixotrophic iron-oxidizing bacterium isolated from creek sediment in the former uranium-mining district of Ronneburg, Germany. To date, iron oxidation has not been reported in species, indicating that FB-8 may be an environmentally important sp.

Mixotrophic Iron-Oxidizing Isolates from an Acid Mine Drainage-Affected Creek.

Natural attenuation of heavy metals occurs via coupled microbial iron cycling and metal precipitation in creeks impacted by acid mine drainage (AMD). Here, we describe the isolation, characterization, and genomic sequencing of two iron-oxidizing bacteria (FeOB) species: FB-6 and FB-Cd, isolated from slightly acidic (pH 6.3), Fe-rich, AMD-impacted creek sediments.

Correction to: CDSnake: Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT utilities.

An amendment to this paper has been published and can be accessed via the original article.

CDSnake: Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT utilities.

Background: Illumina paired-end reads are often used for 16S analysis in metagenomic studies. Since DNA fragment size is usually smaller than the sum of lengths of paired reads, reads can be merged for downstream analysis. In spite of development of several tools for merging of paired-end reads, poor quality at the 3' ends within the overlapping region prevents the accurate combining of significant portion of read pairs.

Extending rnaSPAdes functionality for hybrid transcriptome assembly.

Background: De novo RNA-Seq assembly is a powerful method for analysing transcriptomes when the reference genome is not available or poorly annotated. However, due to the short length of Illumina reads it is usually impossible to reconstruct complete sequences of complex genes and alternative isoforms. Recently emerged possibility to generate long RNA reads, such as PacBio and Oxford Nanopores, may dramatically improve the assembly quality, and thus the consecutive analysis.