Faecal metaproteomics analysis reveals a high cardiovascular risk profile across healthy individuals and heart failure patients.

The gut microbiota is a crucial link between diet and cardiovascular disease (CVD). Using fecal metaproteomics, a method that concurrently captures human gut and microbiome proteins, we determined the crosstalk between gut microbiome, diet, gut health, and CVD. Traditional CVD risk factors (age, BMI, sex, blood pressure) explained < 10% of the proteome variance.

Dynamic interplay of Sp1, YY1, and DUX4 in regulating FRG1 transcription with intricate balance.

Maintaining precise levels of FRG1 is vital. It's over-expression is tied to muscular dystrophy, while reduced levels are linked to tumorigenesis. Despite extensive efforts to characterize FRG1 expression and downstream molecular signaling, a comprehensive understanding of its regulation has remained elusive.

Clinical importance of patient-reported outcome measures in severe asthma: results from U-BIOPRED.

Rationale: Knowledge about the clinical importance of patient-reported outcome measures (PROMs) in severe asthma is limited.

Objectives: To assess whether and to what extent asthma exacerbations affect changes in PROMS over time and asthma-specific PROMs can predict exacerbations in adult patients with severe asthma in usual care.

Methods: Data of 421 patients with severe asthma (62% female; mean age 51.

Climatic forcing of the Southern Ocean deep-sea ecosystem.

The deep-time development of the Southern Ocean's deep-sea ecosystem remains poorly understood, despite being a key region in global ecological, climatological, and oceanographic systems, where deep water forms and biodiversity is unexpectedly high. Here, we present an ∼500,000-year fossil record of the deep-sea Southern Ocean ecosystem in the subantarctic zone. The results indicate that changes in surface productivity and the resulting food supply to the deep sea, driven by eolian dust input and iron fertilization, along with changes in bottom-water temperature influenced by deep-water circulation, have controlled the deep-sea ecosystem in the Southern Ocean on orbital (10-10 years) timescales following the Mid-Brunhes event (MBE), a major climatic transition ∼430,000 years ago.

Cisnormative Language and Erasure of Trans* and Genderqueer Student Representation in Biology Education Research.

Trans* and genderqueer student retention and liberation is integral for equity in undergraduate education. While STEM leadership calls for data-supported systemic change, the erasure and othering of trans* and genderqueer identities in STEM research perpetuates cisnormative narratives. We sought to characterize how sex and gender data are collected, analyzed, and described in biology education research.

An Asynchronous Chemistry-in-biology Intervention Improves Student Content Knowledge and Performance in Introductory Biology.

Introductory biology is a gateway course for majors and other science, technology, engineering, and mathematics (STEM) disciplines. Despite the importance of chemistry content knowledge for understanding biology, the relationship between chemistry knowledge and prior coursework and biology course performance is understudied. We used an opportunity gap framework to investigate the extent to which there were opportunity gaps in prior chemistry coursework and knowledge and associated these gaps with subsequent equity gaps in student performance on introductory biology assessments.

Role of forelimb morphology in muscle sensorimotor functions during locomotion in the cat.

Previous studies established strong links between morphological characteristics of mammalian hindlimb muscles and their sensorimotor functions during locomotion. Less is known about the role of forelimb morphology in motor outputs and generation of sensory signals. Here, we measured morphological characteristics of 46 forelimb muscles from six cats.

Identification of Cysteine Metabolism Regulator (CymR)-Derived Pentapeptides as Nanomolar Inhibitors of -Acetyl-l-serine Sulfhydrylase (CysK).

The pathway of bacterial cysteine biosynthesis is gaining traction for the development of antibiotic adjuvants. Bacterial cysteine biosynthesis is generally facilitated by two enzymes possessing -acetyl-l-serine sulfhydrylases (OASS), CysK and CysM. In , there exists a single OASS homologue, CysK.

Phase separation of MYB73 regulates seed oil biosynthesis in Arabidopsis.

MYB family transcription factors (TFs) play crucial roles in plant development, metabolism, and responses to various stresses. However, whether MYB TFs are involved in regulating fatty acid biosynthesis in seeds remains largely elusive. Here, we demonstrated that transgenic Arabidopsis (Arabidopsis thaliana) plants overexpressing MYB73 exhibit altered FATTY ACID ELONGATION1 (FAE1) expression, seed oil content, and seed fatty acid composition.

The interplay of the translocase activity and protein recruitment function of PICH in ultrafine anaphase bridge resolution and genomic stability.

Incomplete sister centromere decatenation results in centromeric ultrafine anaphase bridges (UFBs). PICH (PLK1-interacting checkpoint helicase), a DNA translocase, plays a crucial role in UFB resolution by recruiting UFB-binding proteins and stimulating topoisomerase IIα. However, the involvement of distinct PICH functions in UFB resolution remains ambiguous.

A 16-week progressive exercise training intervention in treatment-naïve chronic lymphocytic leukaemia: a randomised-controlled pilot study.

Background: Chronic lymphocytic leukaemia (CLL) typically presents with asymptomatic, early-stage disease that is monitored until disease progression ('treatment-naïve' CLL). The objective of this pilot study was to assess the feasibility and preliminary safety of an exercise program in treatment-naïve CLL. We also sought to preliminarily assess the impact of the exercise program on disease activity, as it has been proposed that exercise training may reduce disease outgrowth in treatment-naïve CLL.

SARTAB, a scalable system for automated real-time behavior detection based on animal tracking and Region Of Interest analysis: validation on fish courtship behavior.

Methods from Machine Learning (ML) and Computer Vision (CV) have proven powerful tools for quickly and accurately analyzing behavioral recordings. The computational complexity of these techniques, however, often precludes applications that require real-time analysis: for example, experiments where a stimulus must be applied in response to a particular behavior or samples must be collected soon after the behavior occurs. Here, we describe SARTAB (Scalable Automated Real-Time Analysis of Behavior), a system that achieves automated real-time behavior detection by continuously monitoring animal positions relative to behaviorally relevant Regions Of Interest (ROIs).

Approximate nearest neighbor graph provides fast and efficient embedding with applications for large-scale biological data.

Dimension reduction (DR or embedding) algorithms such as t-SNE and UMAP have many applications in big data visualization but remain slow for large datasets. Here, we further improve the UMAP-like algorithms by (i) combining several aspects of t-SNE and UMAP to create a new DR algorithm; (ii) replacing its rate-limiting step, the K-nearest neighbor graph (K-NNG), with a Hierarchical Navigable Small World (HNSW) graph; and (iii) extending the functionality to DNA/RNA sequence data by combining HNSW with locality sensitive hashing algorithms (e.g.

Skinks on a Plane: Does Human-Mediated Transportation Impact the Behaviour of an Invasive Lizard?

The human-mediated transportation of stowaway individuals to non-native regions is a major driver of new biological invasions, and the post-establishment spread of the invader in its introduced range. In order for the stowaway individuals to successfully establish in the non-native region, they must survive the harsh conditions during the journey (e.g.

Oxylipin Receptors and Their Role in Inter-Partner Signalling in a Model Cnidarian-Dinoflagellate Symbiosis.

Oxylipin signalling is central in biology, mediating processes such as cellular homeostasis, inflammation and molecular signalling. It may also facilitate inter-partner communication in the cnidarian-dinoflagellate symbiosis, though this aspect remains understudied. In this study, four oxylipin receptors were characterised using immunohistochemistry and immunoblotting in the sea anemone Exaiptasia diaphana ('Aiptasia'): Prostaglandin E2 receptor 2 (EP2) and 4 (EP4), Transient Receptor Potential cation channel A1 (TRPA1) and Glutamate Receptor Ionotropic, Kainate 2 (GRIK2).

Genomic, transcriptomic, and metabolomic analyses reveal convergent evolution of oxime biosynthesis in Darwin's orchid.

Angraecum sesquipedale, also known as Darwin's orchid, possesses an exceptionally long nectar spur. Charles Darwin predicted the orchid to be pollinated by a hawkmoth with a correspondingly long proboscis, later identified as Xanthopan praedicta. In this plant-pollinator interaction, the A.

Insights into the divergence of the photosynthetic LH1 complex obtained from structural analysis of the unusual photocomplexes of Roseospirillum parvum.

Purple phototrophic bacteria produce two kinds of light-harvesting complexes that function to capture and transmit solar energy: the core antenna (LH1) and the peripheral antenna (LH2). The apoproteins of these antennas, encoded respectively by the genes pufBA and pucBA within and outside the photosynthetic gene cluster, respectively, exhibit conserved amino acid sequences and structural topologies suggesting they were derived from a shared ancestor. Here we present the structures of two photosynthetic complexes from Roseospirillum (Rss.

Root carbon inputs outweigh litter in shaping grassland soil microbiomes and ecosystem multifunctionality.

Global change has the potential to alter soil carbon (C) inputs from above- and below-ground sources, with subsequent influences on soil microbial communities and ecological functions. Using data from a 13-year field experiment in a semi-arid grassland, we investigated the effects of litter manipulations and plant removal on soil microbiomes and ecosystem multifunctionality (EMF). Litter addition did not affect soil microbial α-diversity whereas litter removal reduced bacterial and fungal α-diversity due to decreased C substrate supply and soil moisture.

The biogenesis and regulation of animal microRNAs.

MicroRNAs (miRNAs) are small, yet profoundly influential, non-coding RNAs that base-pair with mRNAs to induce RNA silencing. Although the basic principles of miRNA biogenesis and function have been established, recent breakthroughs have yielded important new insights into the molecular mechanisms of miRNA biogenesis. In this Review, we discuss the metazoan miRNA biogenesis pathway step-by-step, focusing on the key biogenesis machinery, including the Drosha-DGCR8 complex (Microprocessor), exportin-5, Dicer and Argonaute.

SARS-CoV-2 introductions to the island of Ireland: a phylogenetic and geospatiotemporal study of infection dynamics.

Background: Ireland's COVID-19 response combined extensive SARS-CoV-2 testing to estimate incidence, with whole genome sequencing (WGS) for genome surveillance. As an island with two political jurisdictions-Northern Ireland (NI) and Republic of Ireland (RoI)-and access to detailed passenger travel data, Ireland provides a unique setting to study virus introductions and evaluate public health measures. Using a substantial Irish genomic dataset alongside global data from GISAID, this study aimed to trace the introduction and spread of SARS-CoV-2 across the island.

Exploitation of phylum-spanning omics resources reveals complexity in the nematode FLP signalling system and provides insights into flp-gene evolution.

Background: Parasitic nematodes significantly undermine global human and animal health and productivity. Parasite control is reliant on anthelmintic administration however over-use of a limited number of drugs has resulted in escalating parasitic nematode resistance, threatening the sustainability of parasite control and underscoring an urgent need for the development of novel therapeutics. FMRFamide-like peptides (FLPs), the largest family of nematode neuropeptides, modulate nematode behaviours including those important for parasite survival, highlighting FLP receptors (FLP-GPCRs) as appealing putative novel anthelmintic targets.

Higher order interaction analysis quantifies coordination in the epigenome revealing novel biological relationships in Kabuki syndrome.

Complex direct and indirect relationships between multiple variables, termed higher order interactions (HOIs), are characteristics of all natural systems. Traditional differential and network analyses fail to account for the omic datasets richness and miss HOIs. We investigated peripheral blood DNA methylation data from Kabuki syndrome type 1 (KS1) and control individuals, identified 2,002 differentially methylated points (DMPs), and inferred 17 differentially methylated regions, which represent only 189 DMPs.

Methane production related to microbiota in dairy cattle feces.

Methane (CH) emission from livestock feces, led by ruminants, shows a profound impact on global warming. Despite this, we have almost no information on the syntrophy of the intact microbiome metabolisms, from carbohydrates to the one-carbon units, covering multiple stages of ruminant development. In this study, syntrophic effects of polysaccharide degradation and acetate-producing bacteria, and methanogenic archaea were revealed through metagenome-assembled genomes from water saturated dairy cattle feces.