QTL mapping provides new insights into emamectin benzoate resistance in salmon lice, Lepeophtheirus salmonis.

Background: The salmon louse (Lepeophtheirus salmonis) is a parasite of wild and farmed salmonid fish, causing huge economic damage to the commercial farming of Atlantic salmon (Salmo salar) in the northern hemisphere. The avermectin emamectin benzoate (EMB) is widely used for salmon delousing. While resistance to EMB is widespread in Atlantic populations of L.

Chromosome-scale genome assembly and de novo annotation of Alopecurus aequalis.

Alopecurus aequalis is a winter annual or short-lived perennial bunchgrass which has in recent years emerged as the dominant agricultural weed of barley and wheat in certain regions of China and Japan, causing significant yield losses. Its robust tillering capacity and high fecundity, combined with the development of both target and non-target-site resistance to herbicides means it is a formidable challenge to food security. Here we report on a chromosome-scale assembly of A.

Multiple independent genetic code reassignments of the UAG stop codon in phyllopharyngean ciliates.

The translation of nucleotide sequences into amino acid sequences, governed by the genetic code, is one of the most conserved features of molecular biology. The standard genetic code, which uses 61 sense codons to encode one of the 20 standard amino acids and 3 stop codons (UAA, UAG, and UGA) to terminate translation, is used by most extant organisms. The protistan phylum Ciliophora (the 'ciliates') are the most prominent exception to this norm, exhibiting the grfeatest diversity of nuclear genetic code variants and evidence of repeated changes in the code.

Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research.

Introduction: The agriculture genomics community has numerous data submission standards available, but the standards for describing and storing single-cell (SC, e.g., scRNA- seq) data are comparatively underdeveloped.

Identification and characterization of human KALRN mRNA and Kalirin protein isoforms.

Kalirin is a multidomain protein with important roles in neurite outgrowth, and synaptic spine formation and remodeling. Genetic and pathophysiological links with various neuropsychiatric disorders associated with synaptic dysfunction and cognitive impairment have sparked interest in its potential as a pharmacological target. Multiple Kalirin proteoforms are detected in the adult human brain, yet we know little about the diversity of the transcripts that encode them or their tissue profiles.

One Year of Gluten Free Diet Impacts Gut Function and Microbiome in Celiac Disease.

Background & Aims: Currently, the main treatment for celiac disease (CD) is gluten free diet (GFD). This observational cohort study investigated the impact of CD and 1 year of GFD on gut function and microbiome.

Methods: 36 newly diagnosed patients and 36 healthy volunteers (HVs) were studied at baseline and at 12 months follow up.

The genome sequence of the Golden-tabbed robberfly, (Meigen, 1820).

We present a genome assembly from an individual female Golden-tabbed robberfly, (Arthropoda; Insecta; Diptera; Asilidae). The genome sequence has a total length of 285.90 megabases.

AutoXAI4Omics: an automated explainable AI tool for omics and tabular data.

Machine learning (ML) methods offer opportunities for gaining insights into the intricate workings of complex biological systems, and their applications are increasingly prominent in the analysis of omics data to facilitate tasks, such as the identification of novel biomarkers and predictive modeling of phenotypes. For scientists and domain experts, leveraging user-friendly ML pipelines can be incredibly valuable, enabling them to run sophisticated, robust, and interpretable models without requiring in-depth expertise in coding or algorithmic optimization. By streamlining the process of model development and training, researchers can devote their time and energies to the critical tasks of biological interpretation and validation, thereby maximizing the scientific impact of ML-driven insights.

Traits Underlying Experimentally Evolved Dispersal Behavior in .

Unlabelled: Dispersal is an important behavior in many animals, with profound effects on individual fitness and the evolutionary trajectories of populations. This is especially true within taxa with particular life-history strategies, for example those that exploit ephemeral habitat. Further, dispersal is commonly seen to be part of behavioral syndromes - suites of traits that covary across behavioral contexts.

From synthetic communities to synthetic ecosystems: exploring causalities in plant-microbe-environment interactions.

The plant microbiota research field has rapidly shifted from efforts aimed at gaining a descriptive understanding of microbiota composition to a focus on acquiring mechanistic insights into microbiota functions and assembly rules. This evolution was driven by our ability to establish comprehensive collections of plant-associated microbes and to reconstruct meaningful microbial synthetic communities (SynComs). We argue that this powerful deconstruction-reconstruction strategy can be used to reconstitute increasingly complex synthetic ecosystems (SynEcos) and mechanistically understand high-level biological organization.

CTLA-4 expressing innate lymphoid cells modulate mucosal homeostasis in a microbiota dependent manner.

The maintenance of intestinal homeostasis is a fundamental process critical for organismal integrity. Sitting at the interface of the gut microbiome and mucosal immunity, adaptive and innate lymphoid populations regulate the balance between commensal micro-organisms and pathogens. Checkpoint inhibitors, particularly those targeting the CTLA-4 pathway, disrupt this fine balance and can lead to inflammatory bowel disease and immune checkpoint colitis.

Community standards and future opportunities for synthetic communities in plant-microbiota research.

Harnessing beneficial microorganisms is seen as a promising approach to enhance sustainable agriculture production. Synthetic communities (SynComs) are increasingly being used to study relevant microbial activities and interactions with the plant host. Yet, the lack of community standards limits the efficiency and progress in this important area of research.

A history-dependent integrase recorder of plant gene expression with single-cell resolution.

During development, most cells experience a progressive restriction of fate that ultimately results in a fully differentiated mature state. Understanding more about the gene expression patterns that underlie developmental programs can inform engineering efforts for new or optimized forms. Here, we present a four-state integrase-based recorder of gene expression history and demonstrate its use in tracking gene expression events in Arabidopsis thaliana in two developmental contexts: lateral root initiation and stomatal differentiation.

Microbial composition and dynamics in environmental samples from a ready-to-eat food production facility with a long-term colonization of Listeria monocytogenes.

Listeria monocytogenes is a foodborne pathogen of significant concern for the food industry due to its remarkable ability to persist through safety control efforts, posing a subsequent health threat to consumers. Understanding the microbial communities coexisting with L. monocytogenes in food processing environments provides insights into its persistence mechanisms.

Building pangenome graphs.

Pangenome graphs can represent all variation between multiple reference genomes, but current approaches to build them exclude complex sequences or are based upon a single reference. In response, we developed the PanGenome Graph Builder, a pipeline for constructing pangenome graphs without bias or exclusion. The PanGenome Graph Builder uses all-to-all alignments to build a variation graph in which we can identify variation, measure conservation, detect recombination events and infer phylogenetic relationships.

mulea: An R package for enrichment analysis using multiple ontologies and empirical false discovery rate.

Traditional gene set enrichment analyses are typically limited to a few ontologies and do not account for the interdependence of gene sets or terms, resulting in overcorrected p-values. To address these challenges, we introduce mulea, an R package offering comprehensive overrepresentation and functional enrichment analysis. mulea employs a progressive empirical false discovery rate (eFDR) method, specifically designed for interconnected biological data, to accurately identify significant terms within diverse ontologies.

Single-cell RNA sequencing offers opportunities to explore the depth of physiology, adaptation, and biochemistry in non-model organisms exposed to pollution.

Single-cell Sequencing technology (scSeq) has revolutionized our understanding of individual cells, uncovering unprecedented heterogeneity within tissues and cell populations, principality through single-cell RNA Sequencing (scRNA-Seq). This short review highlights the pivotal role of scRNA-Seq in elucidating genotype-phenotype relationships, particularly in biological systems. Based on published articles, our analysis involved manual curation and automated Scopus tools to illustrate recent advances in the application of scRNA-Seq.

Regulation of intestinal senescence during cholestatic liver disease modulates barrier function and liver disease progression.

Background & Aims: Senescence has been reported to have differential functions in cholangiocytes and hepatic stellate cells (HSCs) during human and murine cholestatic disease, being detrimental in biliary cells and anti-fibrotic in HSCs. Cholestatic liver disease is associated with loss of intestinal barrier function and changes in the microbiome, the mechanistic cause of which is undetermined.

Methods: Intestinal samples were analysed from controls and patients with primary sclerosing cholangitis, as well as wild-type (WT) and p16-3MR transgenic mice.