Characterization of DNA methylation reader proteins in .

In plants, cytosine DNA methylation (mC) is largely associated with transcriptional repression of transposable elements, but it can also be found in the body of expressed genes, referred to as gene body methylation (gbM). gbM is correlated with ubiquitously expressed genes; however, its function, or absence thereof, is highly debated. The different outputs that mC can have raise questions as to how it is interpreted-or read-differently in these sequence and genomic contexts.

Proteomic and -glycomic comparison of synthetic and bovine whey proteins and their effect on human gut microbiomes.

Advances in food production systems and customer acceptance have led to the commercial launch of dietary proteins produced via modern biotechnological approaches as alternatives to traditional agricultural sources. At the same time, a deeper understanding of how dietary components interact with the gut microbiome has highlighted the importance of understanding the nuances underpinning diet-microbiome interactions. Novel food proteins with distinct post-translational modifications resulting from their respective production systems have not been characterized, nor how they may differ from their traditionally produced counterparts.

The cellular paraspeckle component SFPQ associates with the viral processivity factor ORF59 during lytic replication of Kaposi's Sarcoma-associated herpesvirus (KSHV).

Kaposi's sarcoma-associated herpesvirus (KSHV) relies on many cellular proteins to complete replication and generate new virions. Paraspeckle nuclear bodies consisting of core ribonucleoproteins splicing factor proline/glutamine-rich (SFPQ), Non-POU domain-containing octamer-binding protein (NONO), and paraspeckle protein component 1 (PSPC1) along with the long non-coding RNA NEAT1, form a complex that has been speculated to play an important role in viral replication. Paraspeckle bodies are multifunctional and involved in various processes including gene expression, mRNA splicing, and anti-viral defenses.

Temporal Transcriptomic Profiling of the Developing Eye.

Retinal progenitor cells (RPCs) are a multipotent and highly proliferative population that give rise to all retinal cell types during organogenesis. Defining their molecular signature is a key step towards identifying suitable approaches to treat visual impairments. Here, we performed RNA sequencing of whole eyes from at three embryonic stages and used differential expression analysis to define the transcriptomic profiles of optic tissues containing proliferating and differentiating RPCs during retinogenesis.

Temporal Transcriptomic Profiling of the Developing Eye.

Retinal progenitor cells (RPCs) are a multipotent and highly proliferative population that give rise to all retinal cell types during organogenesis. Defining their molecular signature is a key step towards identifying suitable approaches to treat visual impairments. Here, we performed RNA-sequencing of whole eyes from at three embryonic stages and used differential expression analysis to define the transcriptomic profiles of optic tissues containing proliferating and differentiating RPCs during retinogenesis.

Quantitative proteomics unveils known and previously unrecognized alterations in neuropathic nerves.

Charcot-Marie-Tooth disease type 1E (CMT1E) is an inherited autosomal dominant peripheral neuropathy caused by mutations in the peripheral myelin protein 22 (PMP22) gene. The identical leucine-to-proline (L16P) amino acid substitution in PMP22 is carried by the Trembler J (TrJ) mouse and is found in CMT1E patients presenting with early-onset disease. Peripheral nerves of patients diagnosed with CMT1E display a complex and varied histopathology, including Schwann cell hyperproliferation, abnormally thin myelin, axonal degeneration, and subaxonal morphological changes.

CCPA: cloud-based, self-learning modules for consensus pathway analysis using GO, KEGG and Reactome.

This manuscript describes the development of a resource module that is part of a learning platform named 'NIGMS Sandbox for Cloud-based Learning' (https://github.com/NIGMS/NIGMS-Sandbox). The module delivers learning materials on Cloud-based Consensus Pathway Analysis in an interactive format that uses appropriate cloud resources for data access and analyses.

Starvation-Induced Changes to the Midgut Proteome and Neuropeptides in .

Starvation is a complex physiological state that induces changes in protein expression to ensure survival. The insect midgut is sensitive to changes in dietary content as it is at the forefront of communicating information about incoming nutrients to the body via hormones. Therefore, a DIA proteomics approach was used to examine starvation physiology and, specifically, the role of midgut neuropeptide hormones in a representative lepidopteran, .

SARS-CoV-2 superinfection in CD14 monocytes with latent human cytomegalovirus (HCMV) promotes inflammatory cascade.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of coronavirus disease 2019 (COVID-19), has posed significant challenges to global health. While much attention has been directed towards understanding the primary mechanisms of SARS-CoV-2 infection, emerging evidence suggests co-infections or superinfections with other viruses may contribute to increased morbidity and mortality, particularly in severe cases of COVID-19. Among viruses that have been reported in patients with SARS-CoV-2, seropositivity for Human cytomegalovirus (HCMV) is associated with increased COVID-19 risk and hospitalization.

Circadian rhythm in turbot (Scophthalmus maximus): daily variation of blood metabolites in recirculating aquaculture systems.

Introduction: Animal welfare in aquaculture is becoming increasingly important, and detailed knowledge of the species concerned is essential for further optimization on farms. Every organism is controlled by an internal clock, the circadian rhythm, which is crucial for metabolic processes and is partially influenced by abiotic factors, making it important for aquaculture practices.

Objective: In order to determine the circadian rhythm of adult turbot (Scophthalmus maximus), blood samples were collected over a 24-h period and plasma metabolite profiles were analyzed by H-NMR spectroscopy.

DNABERT-based explainable lncRNA identification in plant genome assemblies.

Long non-coding ribonucleic acids (lncRNAs) have been shown to play an important role in plant gene regulation, involving both epigenetic and transcript regulation. LncRNAs are transcripts longer than 200 nucleotides that are not translated into functional proteins but can be translated into small peptides. Machine learning models have predominantly used transcriptome data with manually defined features to detect lncRNAs, however, they often underrepresent the abundance of lncRNAs and can be biased in their detection.

Localizing unmapped sequences with families to validate the Telomere-to-Telomere assembly and identify new hotspots for genetic diversity.

Although it is ubiquitous in genomics, the current human reference genome (GRCh38) is incomplete: It is missing large sections of heterochromatic sequence, and as a singular, linear reference genome, it does not represent the full spectrum of human genetic diversity. To characterize gaps in GRCh38 and human genetic diversity, we developed an algorithm for sequence location approximation using nuclear families (ASLAN) to identify the region of origin of reads that do not align to GRCh38. Using unmapped reads and variant calls from whole-genome sequences (WGSs), ASLAN uses a maximum likelihood model to identify the most likely region of the genome that a subsequence belongs to given the distribution of the subsequence in the unmapped reads and phasings of families.

Crush Injury and Simulated Flight Effects on Muscle Gene Expression in Female Mice.

Background: Aeromedical evacuation provides critical care during long-distance transport of injured victims between medical facilities. Often, these victims sustain muscle trauma related to mechanical insults, such as crush. Understanding the effects of flight on injured muscle is important because the aircraft cabin represents an external environment with mild hypoxia-the cabin's altitude is 2,438 m instead of sea level.

crosshap: R package for local haplotype visualization for trait association analysis.

Summary: Genome-wide association studies (GWAS) excels at harnessing dense genomic variant datasets to identify candidate regions responsible for producing a given phenotype. However, GWAS and traditional fine-mapping methods do not provide insight into the complex local landscape of linkage that contains and has been shaped by the causal variant(s). Here, we present crosshap, an R package that performs robust density-based clustering of variants based on their linkage profiles to capture haplotype structures in a local genomic region of interest.

The conservation of gene models can support genome annotation.

Many genome annotations include false-positive gene models, leading to errors in phylogenetic and comparative studies. Here, we propose a method to support gene model prediction based on evolutionary conservation and use it to identify potentially erroneous annotations. Using this method, we developed a set of 15,345 representative gene models from 12 legume assemblies that can be used to support genome annotations for other legumes.

Class I HDAC inhibitors attenuate dexamethasone-induced muscle atrophy via increased protein kinase C (PKC) delta phosphorylation.

Skeletal muscle atrophy is defined by wasting or decrease in muscle mass owing to injury, aging, malnutrition, chronic disuse, or physical consequences of chronic illness. Under normal physiological conditions, a network of signal transduction pathways serves to balance muscle protein synthesis and proteolysis; however, metabolic shifts occur from protein synthesis to protein degradation that leads to a reduction in cross-sectional myofibers and can result in loss of skeletal muscle mass (atrophy) over time. Recent evidence highlights posttranslational modifications (PTMs) such as acetylation and phosphorylation in contractile dysfunction and muscle wasting.

Towards the generation of gnotobiotic larvae as a tool to investigate the influence of the microbiome on the development of the amphibian immune system.

The immune equilibrium model suggests that exposure to microbes during early life primes immune responses for pathogen exposure later in life. While recent studies using a range of gnotobiotic (germ-free) model organisms offer support for this theory, we currently lack a tractable model system for investigating the influence of the microbiome on immune system development. Here, we used an amphibian species () to investigate the importance of the microbiome in larval development and susceptibility to infectious disease later in life.

H-NMR-Based Metabolic Profiling in Muscle and Liver Tissue of Juvenile Turbot () Fed with Plant and Animal Protein Sources.

Circular economy driven feed ingredients and emerging protein sources, such as insects and microbial meals, has the potential to partially replace fishmeal in diets of high-trophic fish. Even though growth and feed performance are often unaffected at low inclusion levels, the metabolic effects are unknown. This study examined the metabolic response of juvenile turbot () to diets with graded fishmeal replacement with plant, animal, and emerging protein sources (PLANT, PAP, and MIX) in comparison to a commercial-like diet (CTRL).

Significance of wastewater surveillance in detecting the prevalence of SARS-CoV-2 variants and other respiratory viruses in the community - A multi-site evaluation.

Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral genome in wastewater has proven to be useful for tracking the trends of virus prevalence within the community. The surveillance also provides precise and early detection of any new and circulating variants, which aids in response to viral outbreaks. Site-specific monitoring of SARS-CoV-2 variants provides valuable information on the prevalence of new or emerging variants in the community.

Legume-wide comparative analysis of pod shatter locus PDH1 reveals phaseoloid specificity, high cowpea expression, and stress responsive genomic context.

Pod dehiscence is a major source of yield loss in legumes, which is exacerbated by aridity. Disruptive mutations in "Pod indehiscent 1" (PDH1), a pod sclerenchyma-specific lignin biosynthesis gene, has been linked to significant reductions in dehiscence in several legume species. We compared syntenic PDH1 regions across 12 legumes and two outgroups to uncover key historical evolutionary trends at this important locus.

Modeling Human Lung Cells Exposure to Wildfire Uncovers Aberrant lncRNAs Signature.

Emissions generated by wildfires are a growing threat to human health and are characterized by a unique chemical composition that is tightly dependent on geographic factors such as fuel type. Long noncoding RNAs (lncRNAs) are a class of RNA molecules proven to be critical to many biological processes, and their condition-specific expression patterns are emerging as prominent prognostic and diagnostic biomarkers for human disease. We utilized a new air-liquid interface (ALI) direct exposure system that we designed and validated in house to expose immortalized human tracheobronchial epithelial cells (AALE) to two unique wildfire smokes representative of geographic regions (Sierra Forest and Great Basin).

Country-specific food culture and scientific knowledge transfer events - Do they influence the purchasing behaviour of seafood products?

A positive perception of aquaculture products is essential to boost production by using more sustainable and eco-friendly solutions. However, consumer perception and resulting purchasing decisions remain poorly understood. In most European countries, the consumer perception tends to be rather negative, which is reinforced by knowledge gaps and misleading information from the media.

Copy Number Variation among Resistance Genes Analogues in .

Copy number variations (CNVs) are defined as deletions, duplications and insertions among individuals of a species. There is growing evidence that CNV is a major factor underlining various autoimmune disorders and diseases in humans; however, in plants, especially oilseed crops, the role of CNVs in disease resistance is not well studied. Here, we investigate the genome-wide diversity and genetic properties of CNVs in resistance gene analogues (RGAs) across eight lines.

Isolation and Sequencing of Chromosome Arm 7RS of Rye, .

Rye () is a climate-resilient cereal grown extensively as grain or forage crop in Northern and Eastern Europe. In addition to being an important crop, it has been used to improve wheat through introgression of genomic regions for improved yield and disease resistance. Understanding the genomic diversity of rye will assist both the improvement of this crop and facilitate the introgression of more valuable traits into wheat.