High-resolution mapping of cell cycle dynamics during steady-state T cell development and regeneration in vivo.

Control of cell proliferation is critical for the lymphocyte life cycle. However, little is known about how stage-specific alterations in cell cycle behavior drive proliferation dynamics during T cell development. Here, we employed in vivo dual-nucleoside pulse labeling combined with the determination of DNA replication over time as well as fluorescent ubiquitination-based cell cycle indicator mice to establish a quantitative high-resolution map of cell cycle kinetics of thymocytes.

Correction: Muñoz-Villagrán et al. The Thioredoxin Fold Protein (TFP2) from Extreme Acidophilic sp. CF-1 Is a Chaperedoxin-like Protein That Prevents the Aggregation of Proteins under Oxidative Stress. 2024, , 6905.

Susanne Sievers and Daniela Zühlke were not included as authors in the original publication [...

sp. nov., a member of the isolated from badland surfaces in the Red Desert, Wyoming, USA.

A novel Gram-stain-positive, black-pigmented bacterium, designated as WL48A , was isolated from the surface of badland sedimentary rock in the Red Desert of Wyoming and characterized using a polyphasic taxonomic approach. Good growth occurred at 28-32 °C, pH 7-9, and NaCl less than 1% (w/v). Colonies, growing well on International Streptomyces Project media (ISP) 3 and ISP 7, were black and adhering to the agar.

Modelling and stability analysis of the dynamics of measles with application to Ethiopian data.

Measles, a highly contagious airborne disease, remains endemic in many developing countries with low vaccination coverage. In this paper, we present a deterministic mathematical compartmental model to analyze the dynamics of measles. We establish global stability conditions for both disease-free and endemic equilibria using the Lyapunov functional stability method.

MeTEor: an R Shiny app for exploring longitudinal metabolomics data.

Motivation: The availability of longitudinal omics data is increasing in metabolomics research. Viewing metabolomics data over time provides detailed insight into biological processes and fosters understanding of how systems react over time. However, the analysis of longitudinal metabolomics data poses various challenges, both in terms of statistical evaluation and visualization.

Succession of Bacteria and Archaea Within the Soil Micro-Food Web Shifts Soil Respiration Dynamics.

Bacterivorous nematodes are important grazers in the soil micro-food web. Their trophic regulation shapes the composition and ecosystem services of the soil microbiome, but the underlying population dynamics of bacteria and archaea are poorly understood. We followed soil respiration and 221 dominant bacterial and archaeal 16S rRNA gene amplicon sequencing variants (ASVs) in response to top-down control by a common bacterivorous soil nematode, Acrobeloides buetschlii, bottom-up control by maize litter amendment and their combination over 32 days.

Biotechnological and pharmaceutical potential of twenty-eight novel type strains of from different environments worldwide.

Actinomycetes are a prolific source of bioactive natural compounds many of which are used as antibiotics or other drugs. In this study we investigated the genomic and biochemical diversity of 32 actinobacterial strains that had been deposited at the DSMZ-German Collection of Microorganisms and Cell Cultures decades ago. Genome-based phylogeny and DNA-DNA hybridization supported the assignment of these strains to 26 novel species and two novel subspecies and a reclassification of a species.

Scar/WAVE drives actin protrusions independently of its VCA domain using proline-rich domains.

Cell migration requires the constant modification of cellular shape by reorganization of the actin cytoskeleton. Fine-tuning of this process is critical to ensure new actin filaments are formed only at specific times and in defined regions of the cell. The Scar/WAVE complex is the main catalyst of pseudopod and lamellipodium formation during cell migration.

Multifaceted metabolic role of infections in the tumor microenvironment.

The impact of bacteria and viruses on tumor growth has long been recognized. In recent decades, interest in the role of microorganisms in the tumor microenvironment (TME) has expanded. Infections induce metabolic reprogramming and influence immune responses within the TME that may either support proliferation and metastasis or limit tumor growth.

sp. nov., a new acidophilic representative of the isolated from fen soils.

Two new strains JP48 and JP55 affiliated with the acidobacterial class have been isolated from fen soil sampled in the Fichtelgebirge Mountains near Bayreuth, Germany. Both strains were Gram-stain-negative, non-motile, non-spore-forming rods that divide by binary fission, segregate exopolysaccharide-like material and form capsules. Strains JP48 and JP55 grew at 4-36 °C (optimum at 27 °C), pH 3.

Network medicine-based epistasis detection in complex diseases: ready for quantum computing.

Most heritable diseases are polygenic. To comprehend the underlying genetic architecture, it is crucial to discover the clinically relevant epistatic interactions (EIs) between genomic single nucleotide polymorphisms (SNPs) (1-3). Existing statistical computational methods for EI detection are mostly limited to pairs of SNPs due to the combinatorial explosion of higher-order EIs.

The potential therapeutic role of itaconate and mesaconate on the detrimental effects of LPS-induced neuroinflammation in the brain.

Despite advances in antimicrobial and anti-inflammatory treatment, inflammation and its consequences remain a major challenge in the field of medicine. Inflammatory reactions can lead to life-threatening conditions such as septic shock, while chronic inflammation has the potential to worsen the condition of body tissues and ultimately lead to significant impairment of their functionality. Although the central nervous system has long been considered immune privileged to peripheral immune responses, recent research has shown that strong immune responses in the periphery also affect the brain, leading to reactive microglia, which belong to the innate immune system and reside in the brain, and neuroinflammation.

The Thioredoxin Fold Protein (TFP2) from Extreme Acidophilic sp. CF-1 Is a Chaperedoxin-like Protein That Prevents the Aggregation of Proteins under Oxidative Stress.

Extreme acidophilic bacteria like sp. require an efficient enzyme system to counteract strong oxygen stress conditions in their natural habitat. The genome of sp.

Importations of SARS-CoV-2 lineages decline after nonpharmaceutical interventions in phylogeographic analyses.

During the early stages of the SARS-CoV-2 pandemic, before vaccines were available, nonpharmaceutical interventions (NPIs) such as reducing contacts or antigenic testing were used to control viral spread. Quantifying their success is therefore key for future pandemic preparedness. Using 1.

Metabolic adaptation in epithelial ovarian cancer metastasis.

Epithelial ovarian cancer (EOC) is highly lethal due to its unique metastatic characteristics. EOC spheroids enter a non-proliferative state, with hypoxic cores and reduced oncogenic signaling, all of which contribute to tumour dormancy during metastasis. We investigated the metabolomic states of EOC cells progressing through the three steps to metastasis.

Differential cell type-specific function of the aryl hydrocarbon receptor and its repressor in diet-induced obesity and fibrosis.

Objective: The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor regulating xenobiotic responses as well as physiological metabolism. Dietary AhR ligands activate the AhR signaling axis, whereas AhR activation is negatively regulated by the AhR repressor (AhRR). While AhR-deficient mice are known to be resistant to diet-induced obesity (DIO), the influence of the AhRR on DIO has not been assessed so far.

Genome sequence of the bialaphos producer Streptomyces sp. DSM 41527 and two putative phosphonate antibiotic producers Streptomyces sp. DSM 41014 and DSM 41981 from the DSMZ strain collection.

sp. DSM 41014, DSM 41527, and DSM 41981 are three strains from the DSMZ strain collection. Here, we present the draft genome sequences of DSM 41014, DSM 41527, and DSM 41981 with a size of 9.

Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes.

The advent of rapid whole-genome sequencing has created new opportunities for computational prediction of antimicrobial resistance (AMR) phenotypes from genomic data. Both rule-based and machine learning (ML) approaches have been explored for this task, but systematic benchmarking is still needed. Here, we evaluated four state-of-the-art ML methods (Kover, PhenotypeSeeker, Seq2Geno2Pheno and Aytan-Aktug), an ML baseline and the rule-based ResFinder by training and testing each of them across 78 species-antibiotic datasets, using a rigorous benchmarking workflow that integrates three evaluation approaches, each paired with three distinct sample splitting methods.

Inference of differential gene regulatory networks using boosted differential trees.

Summary: Diseases can be caused by molecular perturbations that induce specific changes in regulatory interactions and their coordinated expression, also referred to as network rewiring. However, the detection of complex changes in regulatory connections remains a challenging task and would benefit from the development of novel nonparametric approaches. We develop a new ensemble method called BoostDiff (boosted differential regression trees) to infer a differential network discriminating between two conditions.