CsMPDB 1.0: An interactive web application for visualizing and exploring the microRNAs and phasiRNAs of tea plant (Camellia sinensis var. sinensis 'Shuchazao').

The microRNAs and phasiRNAs of plant are small non-coding RNAs with important functions through regulating gene expression at the post-transcriptional level. However, identifying miRNAs, phasiRNAs and their target genes from numerous sequencing raw data requires multiple software and command-line operations, which are time-consuming and labor-intensive for non-model plants. Therefore, we present CsMPDB (miRNAs and phasiRNAs database of Camellia sinensis), an interactive web application with multiple analysis modules developed to visualize and explore miRNA and phasiRNA in tea plants based on 259 sRNA-seq samples and 24 degradome-seq samples in NCBI.

A 280 bp SINE insertion within the pig PLA2G16 could potentially modify gene expression through integration with its transcript.

In our previous study, we identified a Short Interspersed Nuclear Element Retrotransposon Insertion Polymorphism (SINE-RIP) within the 3' untranslated region (3'UTR) of the Phospholipase A2 Group XVI (PLA2G16) gene, which is essential in lipid metabolism. In this study, we confirmed the presence of this 280 bp SINE insertion and examined its distribution across ten distinct pig breeds using PCR and sequencing. Subsequently, RT-PCR was employed to determine its potential for co-transcription.

Potential Health Risks from Heavy Metal in Green Mussels (Perna Viridis) From the Southeastern Part of the Bay of Bengal.

The Southeastern part of the Bay of Bengal is increasingly threatened by heavy metal pollution, posing significant risks to both aquatic life and human health. In this context, the contamination levels of six heavy metals-Cadmium (Cd), Lead (Pb), Zinc (Zn), Copper (Cu), Manganese (Mn), and Iron (Fe)-were assessed in the soft tissues of Green mussels (Perna viridis) from five key sites: Matamuhuri, Moheshkhali, Bakhkhali, Naf, and St. Martin.

Assessing environmental gradients in relation to dark CO fixation in estuarine wetland microbiomes.

Unlabelled: The rising atmospheric concentration of CO is a major concern to society due to its global warming potential. In soils, CO-fixing microorganisms are preventing some of the CO from entering the atmosphere. Yet, the controls of dark CO fixation are rarely studied .

Opposing roles for Bmp signalling during the development of electrosensory lateral line organs.

The lateral line system enables fishes and aquatic-stage amphibians to detect local water movement via mechanosensory hair cells in neuromasts, and many species to detect weak electric fields via electroreceptors (modified hair cells) in ampullary organs. Both neuromasts and ampullary organs develop from lateral line placodes, but the molecular mechanisms underpinning ampullary organ formation are understudied relative to neuromasts. This is because the ancestral lineages of zebrafish (teleosts) and (frogs) independently lost electroreception.

Impact of rumen-protected glucose on performance, milk composition, and selected blood metabolites of early lactating Holstein Friesian cows.

Introduction: High-producing dairy cows often face calving stress and reduced feed intake during the transition period, leading to body fat mobilization to meet production demands. Supplementing rations with energy-dense sources like rumen-protected glucose (RPG) may enhance production performance in early lactation.

Methods: This study evaluated the effects of RPG supplementation on feed intake, body condition score (BCS), production performance, and blood metabolites in 32 early-lactation Holstein Friesian cows (6 ± 1 DIM; milk yield: 30 ± 5 kg/day; body weight: 550 ± 50 kg; BCS: 3.

Molecular phylogeny, morphology, and ultrastructure of a Mesomycetozoea member, Sphaeroforma nootkatensis isolated from Pacific oyster, Crassostrea gigas, on the Southern coast of Korea.

This study discovered the first Asian population of Sphaeroforma nootkatensis (SphX), a member of Mesomycetozoea, in the southern coastal region of South Korea. Although investigating parasites in Pacific oysters (Crassostrea gigas), a single-cell microorganism was isolated from gill tissues. Comprehensive phylogenetic analysis of its 18S rDNA revealed its placement within the order Ichthyophonida, class Mesomycetozoea.

Whole Genome Sequencing Reveals Substantial Genetic Structure and Evidence of Local Adaptation in Alaskan Red King Crab.

High-latitude ocean basins are the most productive on earth, supporting high diversity and biomass of economically and socially important species. A long tradition of responsible fisheries management has sustained these species for generations, but modern threats from climate change, habitat loss, and new fishing technologies threaten their ecosystems and the human communities that depend on them. Among these species, Alaska's most charismatic megafaunal invertebrate, the red king crab, faces all three of these threats and has declined substantially in many parts of its distribution.

Conference 2024: Building an innovative scientific research ecosystem for microbiome and One Health.

The Conference 2024 provides a platform to promote the development of an innovative scientific research ecosystem for microbiome and One Health. The four key components - Technology, Research (Biology), Academic journals, and Social media - form a synergistic ecosystem. Advanced technologies drive biological research, which generates novel insights that are disseminated through academic journals.

Novel Stepped Combined Constructed Wetland For Surface Water Removal: Enhancing the Performance and Responses of Microbial Communities.

Micro-polluted surface waters (MPSWs) draw increased concern for environmental protection. However, traditional treatment methods such as activated sludge, ozone activated carbon, and membrane filtration suffer from high cost and susceptibility to secondary pollution and are rarely used to address MPSWs. Herein, a new stepped combined constructed wetland planted with without additional inputs was developed.

Interpretation of machine learning-based prediction models and functional metagenomic approach to identify critical genes in HBCD degradation.

Hexabromocyclododecane (HBCD) poses significant environmental risks, and identifying HBCD-degrading microbes and their enzymatic mechanisms is challenging due to the complexity of microbial interactions and metabolic pathways. This study aimed to identify critical genes involved in HBCD biodegradation through two approaches: functional annotation of metagenomes and the interpretation of machine learning-based prediction models. Our functional analysis revealed a rich metabolic potential in Chiang Chun soil (CCS) metagenomes, particularly in carbohydrate metabolism.

Comparing methods for catching and crating broiler chicken flocks: A trade-off between animal welfare, ergonomics and economics.

Catching, carrying, and loading of broilers before transport to the slaughterhouse causes stress. In this study three catching methods (two manual (inverted, upright) and one mechanical) were compared using a cost-benefit analysis of animal welfare, ergonomics and economic analysis. Depopulation of approximately 5,000 broilers per catching method per flock (upright vs.

Predicting the abundance of Lepeophtheirus salmonis in the Bay of Fundy, New Brunswick.

Objective: The primary objective was to construct a time series model for the abundance of the adult female (AF) sea lice Lepeophtheirus salmonis in Atlantic Salmon Salmo salar farms in the Bay of Fundy, New Brunswick, Canada, for the period 2016-2021 and to illustrate its short-term predictive capabilities.

Methods: Sea lice are routinely counted for monitoring purposes, and these data are recorded in the Fish-iTrends database. A multivariable autoregressive linear mixed-effects model (second-order autoregressive structure) was generated with the outcome of the abundance of AF sea lice and included treatments, infestation pressures (a measure that represents the dose of exposure of sea louse parasitic stages to potential fish hosts) within sites (internal) and among sites (external), and other predictors.

Assessing how restoration can facilitate 30×30 goals for climate-resilient coastal ecosystems in the United States.

Ecosystems globally have reached critical tipping points because of climate change, urbanization, unsustainable resource consumption, and pollution. In response, international agreements have set targets for conserving 30% of global ecosystems and restoring 30% of degraded lands and waters by 2030 (30×30). In 2021, the United States set a target to jointly conserve and restore 30% of US lands and waters by 2030, with a specific goal to restore coastal ecosystems, namely wetlands, seagrasses, coral and oyster reefs, and mangrove and kelp forests, to increase resilience to climate change.

Coefficients in Taylor's law increase with the time scale of water clarity measurements in a global suite of lakes.

Identifying the scaling rules describing ecological patterns across time and space is a central challenge in ecology. Taylor's law of fluctuation scaling, which states that the variance of a population's size or density is proportional to a positive power of the mean size or density, has been widely observed in population dynamics and characterizes variability in multiple scientific domains. However, it is unclear if this phenomenon accurately describes ecological patterns across many orders of magnitude in time, and therefore links otherwise disparate observations.

Biotechnological advances in plant growth-promoting rhizobacteria for sustainable agriculture.

The rhizosphere, the soil zone surrounding plant roots, serves as a reservoir for numerous beneficial microorganisms that enhance plant productivity and crop yield, with substantial potential for application as biofertilizers. These microbes play critical roles in ecological processes such as nutrient recycling, organic matter decomposition, and mineralization. Plant growth-promoting rhizobacteria (PGPR) represent a promising tool for sustainable agriculture, enabling green management of crop health and growth, being eco-friendly alternatives to replace chemical fertilizers and pesticides.

Plasticity syndromes in wild vertebrates: Patterns and consequences of individual variation in plasticity across multiple behaviours.

Behavioural plasticity is an important mechanism allowing animals to cope with changing environments. Theory has hypothesized the existence of 'plasticity syndromes'-positive correlations in plasticity across multiple behaviours within an individual-affording a generalized ability to respond to environmental change. However, the occurrence of correlated plasticities and their potential fitness consequences in natural populations remain untested.

Edibility of cultivated green seaweed Ulva intestinalis from Monkhali Beach, Cox's Bazar coast of Bangladesh: bio-toxicity and heavy metal contents.

Ulva intestinalis (UI) is widely available edible seaweed and has potential to be introduced as functional food items in Bangladesh. However, potential health hazards of this seaweed with biotoxicity assays and its relation to heavy metal contents were not evaluated previously. With these objectives, toxic effects of UI collected from floating raft culture in Monkhali Beach was evaluated using various organisms such as Chlorella vulgaris, Artemia salina, Daphnia magna, and Lactuca sativa.

Increase maximum economic yield in a patchy environment.

In this work, we study the model of a fish species growing logistically exploited by a fishing fleet in a heterogeneous environment. The environment is made up of a network of fishing patches connected by fish migrations taking place on a fast time scale. We are interested in the maximum economic yield (MEY) which corresponds to the maximum profit made by the fishing fleet.

Spatiotemporal patterns of mortality events in farmed Atlantic salmon in British Columbia, Canada, using publicly available data.

Monitoring mortality is an essential strategy for fish health management. Commercial marine finfish sites in British Columbia, Canada, are required to report mortality events (MEs) to Fisheries and Oceans Canada (DFO), which makes these data publicly available. This study aimed to analyze the spatial and temporal patterns of ME composition and total MEs.

Globisporangium tabrizense sp. nov., Globisporangium mahabadense sp. nov., and Pythium bostanabadense sp. nov. (Oomycota), three new species from Iranian aquatic environments.

During a survey on the biodiversity of oomycetes in aquatic environments in northwest Iran (East Azarbaijan and West Azarbaijan provinces), three Pythium and four Globisporangium isolates were recovered from agricultural water pools and irrigation canals, respectively. Through a polyphasic approach combining morphology and phylogenetic analysis using the nuclear rDNA ITS1-5.8 S-ITS2 (ITS) and partial sequences of the cytochrome c oxidase subunit I and II (COX1 and COX2), three novel species were identified namely Globisporangium tabrizense sp.

Evaluation of hydro-chemical facies and surface water quality dynamics using multivariate statistical approaches in Southern Nigeria.

The geochemical and chemical constituents of river water quality could be influenced by human activities and organic processes like water interacting with the lithogenic structure that the river flows through. Evaluating evidence based primary root of the predominant pollutant ions, their interactions as well as the factors controlling their dominance is crucial in studies regarding water environment and hydrology especially as most studies focus on theoretical methods. In order to understand the water cycle, safeguard surface water resources, and preserve the human environment, this study evaluated surface water hydro-chemical facies, quality dynamics, and portability in southern Nigeria using multivariate statistical approaches by analyzing selected hydro-chemical characteristics as indicators of pollution along the river during wet and dry seasons.

Molecular characterization of the sea lamprey retina illuminates the evolutionary origin of retinal cell types.

The lamprey, a primitive jawless vertebrate whose ancestors diverged from all other vertebrates over 500 million years ago, offers a unique window into the ancient formation of the retina. Using single-cell RNA-sequencing, we characterize retinal cell types in the lamprey and compare them to those in mouse, chicken, and zebrafish. We find six cell classes and 74 distinct cell types, many shared with other vertebrate species.