Concurrent stimulation of diflufenican biodegradation and changes in the active microbiome in gravel revealed by Total RNA.

The use of slowly degraded pesticides poses a particular problem when these are applied to urban areas such as gravel paths. The urban gravel provides an environment very different from agricultural soils; i.e.

NetMHCpan-4.2: improved prediction of CD8+ epitopes by use of transfer learning and structural features.

Introduction: Identification of CD8+ T cell epitopes is crucial for advancing vaccine development and immunotherapy strategies. Traditional methods for predicting T cell epitopes primarily focus on MHC presentation, leveraging immunopeptidome data. Recent advancements however suggest significant performance improvements through transfer learning and refinement using epitope data.

In Situ Structural Evolution and Activity Descriptor of Atomically Dispersed Catalysts During Nitrate Electroreduction.

Single-Atom Catalysts (SAC) have emerged as a promising class of materials for various catalytic applications, including the electrochemical nitrate reduction reaction (eNORR) and consequently ammonia production. While the efficiency and selectivity of these materials have been extensively highlighted for the eNORR, the in situ evolution to their structure and composition during electrocatalysis is largely unexplored and lacks catalyst design principles. To solve this, we investigated a series of high utilization metal-nitrogen-carbon (MNC) SACs (M = Cr, Fe, Co, Ni, and Cu) for eNORR.

Change in pulmonary pathogens three years after elexacaftor/tezacaftor/ivacaftor: an observational study in the Danish cystic fibrosis cohort.

Objectives: Cystic fibrosis (CF) is a severe autosomal recessive disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. The resulting dysfunction of the CFTR chloride channel leads to dehydrated mucus, reduced mucociliary clearance, and pulmonary infections. Introduction of the CFTR modulator elexacaftor/tezacaftor/ivacaftor (ETI) has revolutionized treatment of people with CF (pwCF).

Pan-reactome analysis of Streptomyces strains reveals association and disconnection between primary and secondary metabolism.

Secondary metabolites have crucial medicinal and industrial applications, but their alignment with primary metabolism remains unclear. As secondary metabolism depends on primary metabolism for precursor supply, we present a pan-reactome analysis of 242 Streptomyces strains to investigate their association and disconnection. This analysis includes phylogenetic grouping of the strains using genome data, and uniform manifold approximation and projection (UMAP) analysis of their genome-scale metabolic models (GEMs) and biosynthetic gene cluster (BGC) data, which represent biochemical reactions in primary and secondary metabolism.

Characterization of neurite and soma organization in the brain and spinal cord with diffusion MRI.

The central nervous system (CNS), comprising both the brain and spinal cord, is a complex network of white and gray matter responsible for sensory, motor, and cognitive functions. Advanced diffusion MRI (dMRI) techniques offer a promising mechanism to non-invasively characterize CNS architecture, however, most studies focus on the brain or spinal cord in isolation. Here, we implemented a clinically feasible dMRI protocol on a 3T scanner to simultaneously characterize neurite and soma microstructure of both the brain and spinal cord.

Dual-site beta transcranial alternating current stimulation during a bimanual coordination task modulates functional connectivity between motor areas.

Background: Communication within brain networks depends on functional connectivity. One promising approach to modulate such connectivity between cortical areas is dual-site transcranial alternating current stimulation (tACS), which non-invasively applies weak alternating currents to two brain areas.

Objectives: In the current study, we aimed to modulate inter-regional functional connectivity with dual-site tACS to bilateral primary motor cortices (M1s) during bimanual coordination and, in turn, alter behaviour.

Preference and similarity of combined noise reduction and dynamic range compression in hearing-impaired listeners.

Single-channel noise reduction (SCNR) and wide dynamic range compression (WDRC) are used in hearing aids to suppress background noise and enhance speech audibility. However, these processing stages can have opposing effects as SCNR may unintentionally reduce soft speech components, whereas WDRC can amplify SCNR artifacts and reduce signal-to-noise ratio. This study presents a behavioral evaluation of WDRC configurations with and without a deep neural network (DNN)-based SCNR.

Mapping early human blood cell differentiation using single-cell proteomics and transcriptomics.

Single-cell transcriptomics (scRNA-seq) has facilitated the characterization of cell state heterogeneity and recapitulation of differentiation trajectories. However, the exclusive use of mRNA measurements comes at the risk of missing important biological information. Here we leveraged recent technological advances in single-cell proteomics by Mass Spectrometry (scp-MS) to generate an scp-MS dataset of an in vivo differentiation hierarchy encompassing over 2500 human CD34+ hematopoietic stem and progenitor cells.

Influence of Polymerization Conditions and Postdeposition Oxidation on Polydopamine Film Characteristics.

Polydopamine (PDA) is widely used as a universal surface modification layer due to its strong adhesion and chemical versatility. However, the properties of PDA films can vary significantly depending on polymerization conditions and postdeposition handling. In this study, we hypothesize that oxygen availability during deposition and subsequent exposure to air after film formation critically influence the physical structure and chemical reactivity of PDA coatings.

Engineered yeast provides rare but essential pollen sterols for honeybees.

Honeybees are important crop pollinators, but they increasingly face pollen starvation as a result of agricultural intensification and climate change. Frequent flowering dearth periods and high-density rearing conditions weaken colonies, which often leads to their demise. Beekeepers provide colonies with pollen substitutes, but these feeds do not sustain brood production because they lack essential sterols found in pollen.

Decoding phospho-regulation and flanking regions in autophagy-associated short linear motifs.

Short Linear Motifs (SLiMs) play a pivotal role in the interactions between intrinsically disordered proteins and their binding partners. SLiMs can undergo regulation through post-translational modifications, including phosphorylation. The flanking regions surrounding the core motifs also exert a crucial role for the interaction.

Intraspecific differences in the effects of salinity and light on growth and prymnesin cell quota in Prymnesium parvum.

The haptophyte Prymnesium parvum produces large polyether compounds (prymnesins) with lytic properties that accumulate in the cell or may be released into the surrounding environment. At high cell abundances the prymnesins cause devastating damage to ecosystems. Blooms of P.

Predator-induced defense reduces growth rate and carrying capacity in a toxic diatom, Pseudo-nitzschia seriata.

Phytoplankton employ a wide variety of defenses to reduce mortality from zooplankton grazing. Many such defenses are inducible, that is, they are upregulated in the event of increased predation. Thus, theory predicts that they should come at a cost to the organism.

Cut-Enabled Mechanical Metamaterials for Multimodal and Reprogrammable Static Nonreciprocity.

Static nonreciprocity offers distinct outputs when switching the positions of action and reaction, which is of great interest for designing mechanical logic elements or soft robots. Existing mechanical metamaterials can present specific static nonreciprocal responses, but it remains challenging to obtain multiple and reprogrammable static nonreciprocal modes in a single microstructural topology. Here, a design method of cellular metamaterials is demonstrated via leaving cuts inside metacells, whose contact nonlinearity in the single metacell can offer orthogonal, uniaxial, shear (displacement and Poynting effect) static nonreciprocal modes.

Accelerating Biomolecular Modeling with AtomWorks and RF3.

Deep learning methods trained on protein structure databases have revolutionized biomolecular structure prediction, but developing and training new models remains a considerable challenge. To facilitate the development of new models, we present AtomWorks: a broadly applicable data framework for developing state-of-the-art biomolecular foundation models spanning diverse tasks, including structure prediction, generative protein design, and fixed backbone sequence design. We use AtomWorks to train RosettaFold-3 (RF3), a structure prediction network capable of predicting arbitrary biomolecular complexes with an improved treatment of chirality that narrows the performance gap between closed-source AlphaFold3 (AF3) and existing open-source implementations.

NetStart 2.0: prediction of eukaryotic translation initiation sites using a protein language model.

Background: Accurate identification of translation initiation sites is essential for the proper translation of mRNA into functional proteins. In eukaryotes, the choice of the translation initiation site is influenced by multiple factors, including its proximity to the 5[Formula: see text] end and the local start codon context. Translation initiation sites mark the transition from non-coding to coding regions.

MiFoDB, a workflow for microbial food metagenomic characterization, enables high-resolution analysis of fermented food microbial dynamics.

Fermented foods, which contain a diversity of microbes and microbial metabolites, have been used for millennia to increase food security, flavor, and nutritional content; more recently, they have been recognized as potential mediators of human health. Metagenomics is a powerful approach to characterize microbes in fermented foods, providing high taxonomic resolution and functional insights. Here, we introduce the Microbial Food DataBase, a metagenomics-based approach designed for the identification of fermentation-associated microbes.

Sex-Specific Long-Term Effects of Perinatal Limosilactobacillus reuteri on Social Cognition, Gene Expression, and Gut Microbiota.

Recent research highlights the potential of early-life probiotic interventions to promote brain health later in life. In this study, we investigated the long-term effects of Limosilactobacillus reuteri (L. reuteri) supplementation during a critical perinatal window (gestational Day 6 to postnatal Day 7) on behavioral, molecular, and gut microbiota outcomes in adult male and female BALB/c mice.

Imogolite nanotube modifications impact pulmonary toxicity in mice: implications for safe and sustainable by design (SSbD).

Background: Imogolite is a naturally occurring hollow aluminosilicate nanotube with potential for engineered applications due to its high aspect ratio, hydrophilicity, and polarization. However, these same features raise concerns about potential adverse health effects. These concerns parallel those associated with multi-walled carbon nanotubes (MWCNTs), which are known to cause inflammation, fibrosis, and cardiovascular effects.

Lysogenic control of Bacillus subtilis morphology and fitness by Spbetavirus phi3T.

In lysogenic conversion, temperate phages can profoundly alter the phenotypes of their bacterial hosts. When studying the effects of SPbeta-like viruses on a Bacillus subtilis soil isolate, we observed that phage phi3T induced a stable and heritable acquisition of a spherical cell morphology, departing from the typical rod shape of its ancestor. Although time-lapse imaging revealed that the lysogen retained cell wall integrity and symmetric division, it exhibited reduced fitness and increased susceptibility to cell wall-targeting antimicrobials.

Environmentally sustainable health care: the opportunities and challenges of life cycle assessments.

The health-care sector is a substantial contributor to climate change. To address this global issue, more than 120 countries committed to creating environmentally sustainable health systems at the COP28 UN Climate Change Conference held in November, 2023. Sustainability is thus becoming increasingly important for clinical practice.

Investigation of mobile genetic elements and their association with antibiotic resistance genes in clinical pathogens worldwide.

Objectives: Antimicrobial-resistant bacteria are a major global health threat. Mobile genetic elements (MGEs) have been crucial for spreading resistance to new bacterial species, including human pathogens. Understanding how MGEs promote resistance could be essential for prevention.

Synthetic C metabolism in enables strict formatotrophy and methylotrophy via the reductive glycine pathway.

Formate and methanol are promising alternatives to sugar-based feedstocks for biotechnological applications. These one-carbon (C) substrates can be sustainably produced from CO and renewable electricity and assimilated by both native and engineered microbial systems. However, their broader adoption is limited by the narrow range of bacterial hosts capable of efficient methanol and formate utilization.