Search Results (4,016)

Citrus nematode (Tylenchulus semipenetrans) is one of the dominant plant-parasitic nematodes in citrus-growing regions, resulting in an average yield loss between 10 and 30%. Tylenchulus semipenetrans is a sedentary semi-endoparasitic nematode that infects the roots of citrus trees, causing stunted growth, reduced fruit yield, and poor fruit quality; collectively this pathology and thus the disease caused is referred to as the slow decline of citrus. Despite its huge importance, the citrus nematode is regarded as a neglected parasite, and most research focuses on biological control and integrated pest management. Advancements in understanding the molecular mechanisms of other plant-parasitic nematodes, such as sedentary endoparasites with biological similarities to citrus nematodes, can be leveraged to gain deeper insights into the molecular mechanisms of citrus nematodes. In this review, we examine the biology, and integrated pest management of citrus nematodes, and explore future research directions toward understanding the role of genomics, gene-editing tools, and the molecular mechanisms of host-seeking and effectors used by other plant-parasitic nematodes to cause infection, which can serve as a foundation for future work in citrus nematode management. Full article

Peanut is a key cash crop worldwide, yet the limited availability of functional genes and markers for breeding hinders further progress, largely due to the lack of an efficient and user-friendly transformation system. This study aimed to comprehensively evaluate the effectiveness of nodal agroinjection, a novel transformation technique we developed for peanut, by introducing the soybean cold-tolerance gene SCTF-1. Putative transgenic seeds and seedlings were screened using genomic DNA PCR, while transgene expression was analyzed via qRT-PCR and phenotypic assessments. Southern blotting confirmed the stable integration of SCTF-1. The transgenic seedlings displayed enhanced chilling tolerance, characterized by increased proline accumulation, reduced malondialdehyde (MDA), and elevated peroxidase (POD) activity. These findings demonstrate that nodal agroinjection is an efficient and reliable approach for generating transgenic peanut and analyzing gene function. This method offers a promising alternative to conventional tissue culture-based transformation strategies. Full article

Background/Objectives: Despite decades of extensive vaccinations against avian infectious bronchitis virus (IBV) infection, outbreaks caused by constantly emerging variants due to genome recombination between different viral strains, including vaccine strains, occur annually worldwide. The development of novel vaccines with favorable safety and effectiveness is required but is hindered by a limited understanding of vaccination against IBV. Methods: Here, we performed a comprehensive analysis of the in vivo dynamics of peripheral blood mononuclear cells (PBMCs) in specific pathogen-free chickens inoculated with the widely used live attenuated IBV vaccine strain H120 at single-cell level, using high-throughput single-cell transcriptome sequencing (scRNA-seq). Results: High-quality sequencing dataset for four scRNA-seq data containing the transcriptomes of 29,846 individual chicken PBMCs were obtained, defining 22 populations and 7 cell types based on distinct molecular signatures and known markers. Further integrative analysis constructed the time series dynamic cell transition and immune response landscapes within the two weeks post-prime vaccination against IBV. Enhanced crosstalk between antigen-presenting cells and T lymphocytes was revealed as early as four days post-vaccination. The specific immune cell populations and their comprehensive cellular and molecular networks involved in the initiation phase of antiviral adaptive immune responses were elucidated in details. Conclusions: Our study provides a comprehensive view of the dynamic initiation of immune responses in chickens against IBV infection at the cellular and molecular levels, which provides theoretical support and potential solutions for the future rational design of safe and effective vaccines, the augmentation of the efficacy of current vaccines, and the optimization of immune programs. Full article

Fasciola hepatica is a parasitic trematode responsible for fascioliasis, a significant zoonotic disease affecting livestock worldwide, as well as humans. This study identifies peptides with potential for use in vaccines against Fasciola hepatica and validates multi-epitope constructs from those peptides in vitro. Putative protein sequences derived from the genome of F. hepatica were integrated with phase-specific transcriptomic data to prioritize highly expressed proteins. Among these, extracellular proteins were selected using DeepLoc 2.0 and strong binding affinities across diverse human and murine alleles were predicted with the IEDB MHC II tool. Peptides were further selected based on their toxicity, immunogenicity, and allergenicity. Finally, 55 high-priority candidates were obtained. To express these candidates, mRNA constructs encoding various combinations of these peptides were designed, synthesized using in vitro transcription with T7 or SP6 RNA polymerases, and transfected into cells for expression analysis. SP6 polymerase produced proper capping using CleanCapAG and was far superior in transcribing peptide constructs. Peptides fused in frame with eGFP were expressed efficiently, particularly when peptides were positioned at the 3′ terminus, opening a new field of peptide vaccines created using mRNA technology. Full article

This study investigates the genetic architecture of the Kazakh Whiteheaded (KWH) cattle, applying population genetics approaches to resequenced genomes. F_ST analysis of 66 cattle breeds identified breeds for admixture analysis. At K = 19, the composite KWH breed showed contributions from Hereford, Altai, and Kalmyk cattle. Principal component analysis and ancestry inference confirmed these patterns, with KWH genomes comprising 45% Hereford, 30% Altai, and 25% Kalmyk ancestries. Haplotype analysis revealed 73 regions under putative selection in KWH, some shared with Hereford (e.g., with the gene DCUN1D4) and some KWH-specific (e.g., with the gene SCMH1). F_ST analysis identified 105 putative intervals under selection, with key genes (KITLG, SLC9C1, and SCMH1) involved in coat colour and physiological adaptations. Functional enrichment using The Database for Annotation, Visualization, and Integrated Discovery (DAVID) in selected regions highlighted clusters associated with developmental processes, ubiquitination, and fatty acid metabolism. Point F_ST identified 42 missense variants in genes enriched in functions related to economically important traits. Local ancestry inference revealed genomic intervals with predominantly non-Hereford ancestry, including high Altai (e.g., SCAPER) and Kalmyk (e.g., SRD5A2) contributions, while Hereford-dominated regions included genes ENO1 and RERE. This work elucidates the genomic contributions and adaptive signatures of selection shaping the KWH breed, providing candidate genetic variants for breeding program improvement and enhanced genome predictions. Full article

Genome editing-mediated haploid inducer systems (HISs) present a promising strategy for enhancing breeding efficiency in legume crops, which are vital for sustainable agriculture due to their nutritional benefits and ability to fix nitrogen. Traditional legume breeding is often slow and complicated by the complexity of legumes’ genomes and the challenges associated with tissue culture. Recent advancements have broadened the applicability of HISs in legume crops, facilitating a reduction in the duration of the breeding cycle. By integrating genome editing technology with haploid breeding systems, researchers can achieve precise genetic modifications and rapidly produce homozygous lines, thereby significantly accelerating the development of desired traits. This review explores the current status and future prospects of genome editing-mediated HISs in legumes, emphasizing the mechanisms of haploid induction; recent breakthroughs; and existing technical challenges. Furthermore, we highlight the necessity for additional research to optimize these systems across various legume species, which has the potential to greatly enhance breeding efficiency and contribute to the sustainability of legume production. Full article

The Harnischia generic complex, a significant assemblage within the tribe Chi-ronomini, extensive global sampling and the integration of multi-characteristic data for comprehensive analysis are essential to elucidate the phylogenetic relationships within the Harnischia generic complex. We sequenced, assembled, and annotated the mitochondrial genomes of a single species each from the genera Parachironomus Lenz, Robackia Saether and Saetheria Jackson. Additionally, we incorporated 26 previously published mitogenomes into our analysis to delve deeper into the characteristics of these mitogenomes. Our findings indicate the close affinity between (Cryptochironomus + Demicryptochironomus) and (Harnischia + Microchironomus), aligning consistently with previous research outcomes showing that the Harnischia generic complex and Chironomus are phylogenetically close, and their clade forms a sister group with the Polypedilum generic complex. Based on mitochondrial genome data, Robackia is identified as the basal taxon being relatively primitive, with Parachironomus and Saetheria also appearing as primitive within the complex. Full article

Climate change heightens the threat of infectious diseases in Europe, necessitating innovative surveillance methods. Based on 390 scientific papers, for the first time, this review associates climate-related pathogens, data related to their presence in wastewater, and associated available genomic detection methods. This deep analysis reveals a wide range of pathogens that can be tracked through methods such as quantitative and digital PCR, as well as genomic pathogen enrichment in combination with sequencing and metagenomics. Nevertheless, significant gaps remain in the development of methods, particularly for vector-borne pathogens, and in their general harmonization relating to performance criteria. By offering an overview of recent advancements while identifying critical gaps, we advocate for collaborative research and validation to integrate detection techniques into surveillance frameworks. This will enhance public health resilience against emerging infectious diseases driven by climate change. Full article

Taiwan Country chickens are integral to Taiwanese culture and the poultry industry. By establishing a crossbreeding system, breeders must consider the growth-related traits of the dam line to achieve acceptable traits in commercial meat-type chickens. This study compared the accuracy of genomic estimated breeding values (GEBVs) predicted using the pedigree-based best linear unbiased prediction (PBLUP) model and the single-step genomic BLUP (ssGBLUP) model. Additionally, we conducted a genome-wide association study (GWAS) to identify single-nucleotide polymorphisms (SNPs) associated with growth, shank, and body conformation traits to support marker-assisted selection (MAS). The results showed that the ssGBLUP model achieved 4.3% to 16.4% higher prediction accuracy than the PBLUP model. GWAS identified four missense SNPs and four significant SNPs associated with body weight, shank length, and shank width at 12 weeks. These findings highlight the potential of integrating the ssGBLUP model with identified SNPs to improve genetic gain and breeding efficiency and provide preliminary results to assess the feasibility of genomic prediction and MAS in Taiwan Country chicken breeding programs. Further research is necessary to validate these findings and explore their mechanisms and broader application across different breeding programs, particularly for the NCHU-G101 breed of Taiwan Country chickens. Full article

Objective: To investigate the preclinical efficacy and identify predictive biomarkers of polo-like kinase 1 (PLK1) inhibitors in small cell lung cancer (SCLC) models. Methods: We tested the cytotoxicity of selective PLK1 inhibitors (rigosertib, volasertib, and onvansertib) in a panel of SCLC cell lines. We confirmed the therapeutic efficacy of subcutaneous xenografts of representative cell lines and in four patient-derived xenograft models generated from patients with platinum-sensitive and platinum-resistant SCLC. We employed an integrated analysis of genomic and transcriptomic sequencing data to identify potential biomarkers of the activity and mechanisms of resistance in laboratory-derived resistance models. Results: Volasertib, rigosertib, and onvansertib showed strong in vitro cytotoxicity at nanomolar concentrations in human SCLC cell lines. Rigosertib, volasertib, and onvansertib showed equivalent efficacy to that of standard care agents (irinotecan and cisplatin) in vivo with significant growth inhibition superior to cisplatin in PDX models of platinum-sensitive and platinum-resistant SCLC. There was an association between YAP1 expression and disruptive or inactivation TP53 gene mutations, with greater efficacy of PLK1 inhibitors. Comparison of lab-derived onvansertib-resistant H526 cells to parental cells revealed differential gene expression with upregulation of NAP1L3, CYP7B1, AKAP7, and FOXG1 and downregulation of RPS4Y1, KDM5D, USP9Y, and EIF1AY highlighting the potential mechanisms of resistance in the clinical setting. Conclusions: We established the efficacy of PLK1 inhibitors in vitro and in vivo using PDX models of platinum-sensitive and resistant relapsed SCLC. An ongoing phase II trial is currently testing the efficacy of onvansertib in patients with SCLC (NCT05450965). Full article

Background: Buffaloes are considered an indispensable genetic resource for dairy production. However, improvements in lactation performance have been relatively limited. Advances in sequencing technology, combined with genome-wide association studies, have facilitated the breeding of high-quality buffalo. Methods: We conducted an integrated analysis of genomic sequencing data from 120 water buffalo, the high-quality water buffalo genome assembly designated as UOA_WB_1, and milk production traits, including 305-day milk yield (MY), peak milk yield (PM), total protein yield (PY), protein percentage (PP), fat percentage (FP), and total milk fat yield (FY). Results: The results identified 56 significant SNPs, and based on these markers, 54 candidate genes were selected. These candidate genes were significantly enriched in lactation-related pathways, such as the cAMP signaling pathway (ABCC4), TGF-β signaling pathway (LEFTY2), Wnt signaling pathway (CAMK2D), and metabolic pathways (DGAT1). Conclusions: These candidate genes (e.g., ABCC4, LEFTY2, CAMK2D, DGAT1) provide a substantial theoretical foundation for molecular breeding to enhance milk production in buffaloes. Full article

The landscape of psychiatric care is poised for transformation through the integration of pharmaco-multiomics, encompassing genomics, proteomics, metabolomics, transcriptomics, epigenomics, and microbiomics. This review discusses how these approaches can revolutionize personalized treatment strategies in psychiatry by providing a nuanced understanding of the molecular bases of psychiatric disorders and individual pharmacotherapy responses. With nearly one billion affected individuals globally, the shortcomings of traditional treatments, characterized by inconsistent efficacy and frequent adverse effects, are increasingly evident. Advanced computational technologies such as artificial intelligence (AI) and machine learning (ML) play crucial roles in processing and integrating complex omics data, enhancing predictive accuracy, and creating tailored therapeutic strategies. To effectively harness the potential of pharmaco-multiomics approaches in psychiatry, it is crucial to address challenges such as high costs, technological demands, and disparate healthcare systems. Additionally, navigating stringent ethical considerations, including data security, potential discrimination, and ensuring equitable access, is essential for the full realization of this approach. This process requires ongoing validation and comprehensive integration efforts. By analyzing recent advances and elucidating how different omic dimensions contribute to therapeutic customization, this review aims to highlight the promising role of pharmaco-multiomics in enhancing patient outcomes and shifting psychiatric treatments from a one-size-fits-all approach towards a more precise and patient-centered model of care. Full article

Infection by gastrointestinal nematodes (GINs) in sheep is a significant health issue that affects animal welfare and leads to economic losses in the production sector. Genetic selection for parasite resistance has shown promise in improving animal health and productivity. This study aimed to determine if incorporating genomic data into genetic prediction models currently used in Uruguay could improve the accuracy of breeding value estimations for GIN resistance in the Australian Merino breed. This study compared the accuracy of breeding value predictions using the BLUP (Best Linear Unbiased Prediction) and ssGBLUP (single-step genomic BLUP) models on partial and complete data sets, including 32,713 phenotyped and 3238 genotyped animals. The quality of predictions was evaluated using a linear regression method, focusing on 145 rams. The inclusion of genomic data increased the average individual accuracies by 4% for genotyped and phenotyped animals. For animals with genomic and non-phenotyped data, the accuracy improvement reached 8%. Of these, one group of animals that benefited from an ssGBLUP evaluation came from a facility with a strong connection to the informative nucleus and showed an average increase of 20% in their individual accuracy. Additionally, ssGBLUP slightly outperformed BLUP in terms of prediction quality. These findings demonstrate the potential of genomic information to improve the accuracy of breeding value predictions for parasite resistance in sheep. The integration of genomic data, particularly in non-phenotyped animals, offers a promising tool for enhancing genetic selection in Australian Merino sheep to improve resistance to gastrointestinal parasites. Full article

Red-leaf lettuces, rich in bioactive compounds like anthocyanins and flavonoids, offer health benefits by reducing oxidative stress and boosting immunity. This article provides an extensive review of the genetic, epigenetic, environmental, and technological factors influencing anthocyanin biosynthesis and leaf coloration in red-leaf lettuce, emphasizing its significance in agriculture and nutrition. The genetics of anthocyanin biosynthesis, environmental influences, practical applications, agronomic insights, and future directions are the main areas covered. Anthocyanin accumulation is regulated by structural, regulatory, and transporter genes, as well as the MYB-bHLH-WD40 (MBW) complex. Mutations in these genes impact coloration and stress responses. Advances in genomic studies, such as GWAS and QTL mapping, have identified key genes and pathways involved in anthocyanin biosynthesis, aiding breeding programs for desirable traits. In addition, light intensity, stress conditions (e.g., drought, temperature), and phytohormones affect anthocyanin levels and photomorphogenesis in general. Controlled environments, like vertical farms, optimize these conditions to enhance pigmentation and phytochemical content. LED lighting and tailored cultivation techniques improve color intensity, antioxidant capacity, and yield in controlled settings. Sustainable production technologies for red-leaf lettuce in vertical farms are being developed to meet consumer demand and promote functional foods, integrating genetic, epigenetic, and environmental research into agronomy. This review highlights red-leaf lettuce’s aesthetic, nutritional, and functional value, advocating for innovative cultivation methods to enhance its market and health potential. Full article

Phyllodoce koreana was first described in 1985 in Gwangyang Bay, a semi-enclosed bay in Korea affected by significant organic input from the Seomjin River and dredging activities near the Gwangyang Port. Since then, this Korean endemic species has received limited attention in taxonomic and ecological studies. Phyllodoce koreana is known for its resilience to mild disturbances but is vulnerable to severe environmental changes. In this study, P. koreana specimens were collected from organically polluted Asian stalked tunicate aquaculture farms at eight sites in Jindong Bay, a location with environmental conditions similar to those of Gwangyang Bay, over the course of five sampling events from March to November. Both bays experience benthic hypoxia in summer due to elevated water temperatures and organic matter accumulation. Phyllodocid specimens were primarily collected in March and November 2023, non-hypoxic periods, suggesting potential seasonal adaptations to environmental fluctuations. The morphological features of the collected specimens were consistent with the original description of P. koreana, confirming their identification. Additionally, we reported previously overlooked morphological details, contributing to a more comprehensive taxonomic understanding of the species. We also present, for the first time, the complete mitochondrial genome of this species, comprising 15,559 bp, which provides essential genetic data for future taxonomic and phylogenetic studies. The phylogenetic analysis of protein-coding genes shows that, among 17 related polychaete species, P. koreana (family Phyllodocidae) is closely related to the family Goniadidae. Future research should expand our knowledge of polychaete taxonomy by integrating additional mitochondrial genomes and investigating the role of conserved gene synteny within Polychaeta. Full article