Search Results (43,030)

The regulation of vital plant activities by hormones is governed by a family of macromolecular peptides referred to as GH3 genes. This work analyzed the expression patterns of GH3 family genes in pear tissues using transcriptome data and bioinformatics analysis. In the Bai Li pear genome, a total of 18 PbGH3 genes were identified. Comparative evolutionary studies have shown a strong association between PbGH3 and AtGH3 class I and class II proteins. The role of PbGH3 genes in growth activities and hormone regulation was revealed using gene ontology (GO) and promoter region analysis. In addition, although certain PbGH3 genes exhibited tissue-specific expression in sepals, the majority had a ubiquitous expression across all tissues. Bioinformatics and expression studies suggest that the GH3 gene family in pears may have a role in controlling the abscission of the fruit’s sepals. This work sheds light on the pear fruit sepal shedding process and may inspire further research. Full article

Background: The presence of mitochondrial sequences in the nuclear genome (Numts) confounds analyses of mitochondrial sequence variation, and is a potential source of false positives in disease studies. To improve the analysis of mitochondrial variation in canines, we completed a systematic assessment of Numt content across genome assemblies, canine populations and the carnivore lineage. Results: Centering our analysis on the UU_Cfam_GSD_1.0/canFam4/Mischka assembly, a commonly used reference in dog genetic variation studies, we found a total of 321 Numts located throughout the nuclear genome and encompassing the entire sequence of the mitochondria. A comparison with 14 canine genome assemblies identified 63 Numts with presence–absence dimorphism among dogs, wolves, and a coyote. Furthermore, a subset of Numts were maintained across carnivore evolutionary time (arctic fox, polar bear, cat), with eight sequences likely more than 10 million years old, and shared with the domestic cat. On a population level, using structural variant data from the Dog10K Consortium for 1879 dogs and wolves, we identified 11 Numts that are absent in at least one sample, as well as 53 Numts that are absent from the Mischka assembly. Conclusions: We highlight scenarios where the presence of Numts is a potentially confounding factor and provide an annotation of these sequences in canine genome assemblies. This resource will aid the identification and interpretation of polymorphisms in both somatic and germline mitochondrial studies in canines. Full article

Background/objectives: Pseudomonas aeruginosa can cause community-acquired infections affecting various body sites. The present retrospective study investigated the genetic diversity of 173 isolates (166 clinical, 7 environmental) of P. aeruginosa collected from clinical pathology laboratories in Abidjan, Côte d’Ivoire (2001–2011). Methods: Multiple-Locus Variable Number of Tandem Repeats (VNTR) Analysis (MLVA) using 13 loci was applied to all isolates and compared to published MLVA data. The antibiotics status of the isolates was compiled when available and compared to published profiles. Results: Among 95 isolates analyzed for their antibiotics status, 14 displayed concerning resistance profiles: five multidrug-resistant (MDR) and nine extensively drug-resistant (XDR). MLVA typing revealed a high genetic diversity (>130 genotypes), with many genotypes represented by a single strain. Notably, thirteen clusters (≥4 related isolates) were observed. Some clusters displayed close genetic relatedness to isolates from France, Korea, and well-studied strains (ST560, LES and PA14). Comparative analysis suggested the presence of international high-risk MDR clones (CC233, CC111) in Côte d’Ivoire. Importantly, MLVA clustering revealed a close relationship of CC235-MDR strains with a locally identified cluster (group 9). Conclusions: These findings support MLVA as a reliable and cost-effective tool for low-resource settings, allowing the selection of relevant strains for future whole genome sequence analyses. This approach can improve outbreak investigations and public health interventions aimed at curbing MDR P. aeruginosa transmission within hospitals and at the national level. Full article

Pancreatic neuroendocrine tumors (NETs) are rare well-differentiated neoplasms with limited therapeutic options and unknown cells of origin. The current classification of pancreatic neuroendocrine tumors is based on proliferative grading, and guides therapeutic strategies, however, tumors within grades exhibit profound heterogeneity in clinical manifestation and outcome. Manifold studies have highlighted intra-patient differences in tumors at the genetic and transcriptomic levels. Molecular classification might become an alternative or complementary basis for treatment decisions and reflect tumor biology, actionable cellular processes. Here, we provide a comprehensive review of genomic, transcriptomic, proteomic and epigenomic studies of pancreatic NETs to elucidate patterns shared between proposed subtypes that could form a foundation for new classification. We denote four NET subtypes with distinct molecular features, which were consistently reproduced using various omics technologies. Full article

Glaucoma is a group of optic neuropathies characterized by the degeneration of retinal ganglion cells and the loss of their axons in the optic nerve. The only approved therapies for the treatment of glaucoma are topical medications and surgical procedures aimed at lowering intraocular pressure. Gene therapy involves the insertion, removal, or modification of genetic material within cells to repair or compensate for the loss of a gene’s function. It describes a process or technology that enables the genetic modification of cells to produce a therapeutic effect. However, changing the genetic material alone does not extend the duration of overexpression of proteins that combat disease, nor does it facilitate the production of new proteins for this purpose. We reviewed the literature concerning the use of gene therapy in the treatment of glaucoma and explored the future directions that this innovation may offer. Three genes associated with glaucoma have been identified within these loci: myocilin/trabecular meshwork glucocorticoid response (TIGR) (GLC1A), optineurin (GLC1E), and WDR36 (GLC1G). Among these, the most extensively studied glaucoma gene is myocilin (a TM-inducible glucocorticoid response gene). Building on previous successes, researchers have begun to apply genetic therapeutic approaches to alleviate or reduce symptoms associated with ocular hypertension (OHT) and glaucoma-like optic neuropathy (GON). It is evident that several therapeutic strategies exist that modulate aqueous humor production and flow, thereby regulating intraocular pressure (IOP) and protecting retinal ganglion cells (RGCs) from apoptosis. With the emergence of gene therapy as a potentially viable approach to preserving vision, new methods for managing glaucoma may soon become available. Genomic therapy is a promising treatment option for glaucoma patients and has significant potential for widespread clinical application. Full article

Since the first reported case of COVID-19 in December 2019, several SARS-CoV-2 variants have evolved, and some of them have shown higher transmissibility, becoming the prevalent strains. Genomic epidemiological investigations into strains from different time points, including the early stages of the pandemic, are very crucial for understanding the evolution and transmission patterns. Using whole-genome sequences, our study describes the early landscape of SARS-CoV-2 variants in central India retrospectively (including the first known occurrence of SARS-CoV-2 in Madhya Pradesh). We performed amplicon-based whole-genome sequencing of randomly selected SARS-CoV-2 isolates (n = 38) collected between 2020 and 2022 at state level VRDL, ICMR-NIRTH, Jabalpur, from 11899 RT-qPCR-positive samples. We observed the presence of five lineages, namely B.1, B.1.1, B.1.36.8, B.1.195, and B.6, in 19 genomes from the first wave cases and variants of concern (VOCs) lineages, i.e., B.1.617.2 (Delta) and BA.2.10 (Omicron) in the second wave cases. There was a shift in mutational pattern in the spike protein coding region of SRAS-CoV-2 strains from the second wave in contrast to the first wave. In the first wave of infections, we observed variations in the ORF1Ab region, and with the emergence of Delta lineages, the D614G mutation associated with an increase in infectivity became a prominent change. We have identified five immune escape variants in the S gene, P681R, P681H, L452R, Q57H, and N501Y, in the isolates collected during the second wave. Furthermore, these genomes were compared with 2160 complete genome sequences reported from central India that encompass 109 different SARS-CoV-2 lineages. Among them, VOC lineages Delta (28.93%) and Omicron (56.11%) were circulating predominantly in this region. This study provides useful insights into the genetic diversity of SARS-CoV-2 strains over the initial course of the COVID-19 pandemic in central India. Full article

The androgen receptor (AR), a member of the nuclear steroid hormone receptor family of transcription factors, plays a crucial role not only in the development of the male phenotype but also in the development and growth of prostate cancer. While AR structure and AR interactions with coregulators and chromatin have been studied in detail, improving our understanding of AR function in gene transcription regulation, the spatio-temporal organization and the role of microscopically discernible AR foci in the nucleus are still underexplored. This review delves into the molecular mechanisms underlying AR foci formation, focusing on liquid–liquid phase separation and its role in spatially organizing ARs and their binding partners within the nucleus at transcription sites, as well as the influence of 3D-genome organizations on AR-mediated gene transcriptions. Full article

Phoenix barb (Spinibarbus denticulatus denticulatus) is a notable fish species in South China and is valued for its ecological and economic importance. To elucidate the molecular basis underlying its growth, we collected transcriptome profiles from the brains and livers of individual fish with different growth rates and compared differentially expressed genes (DEGs) at 3 and 9 months after hatching (MAH). Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the pathways associated with growth were predominantly enriched in fatty acid biosynthesis, AMPK signaling, PI3K-Akt signaling, estrogen signaling, and protein metabolism. Notably, a greater number of DEGs from the fast-growing group were associated with these pathways at the early growth stage (3 MAH) than at the later stage (9 MAH). Real-time quantitative PCR results further validated that the genes involved in these pathways exhibited higher expression levels in fast-growing samples. This study enhances our understanding of the genetic mechanisms underlying growth rate differences and provides valuable genetic resources for future growth-related molecular breeding programs of phoenix barbs. Full article

Drought stress during sorghum emergence significantly affects seedling establishment, adversely affecting both emergence and population growth. This study investigates drought tolerance mechanisms during sorghum germination by analyzing physiological changes and transcriptomic data from two lines: W069 (drought tolerant) and W040 (drought sensitive). Under drought conditions, a phenotypic analysis revealed that W069 exhibited longer shoots and roots than W040. Additionally, physiological data indicated higher osmotic substance and lower malondialdehyde levels in W069. Using Kyoto Encyclopedia of Genes and Genome analyses, we identified three key pathways (starch and sucrose metabolism, phenylpropanoid biosynthesis, and phytohormone signaling) as pivotal in the drought response during seed germination in sorghum plants. Expression profiling revealed that most drought tolerance-related genes in the three key pathways were expressed at higher levels in the drought-tolerant cultivar W069, possibly explaining its greater stress tolerance. These findings enhance our understanding of drought-responsive gene networks in sorghum seed germination, offering potential target genes and strategies for enhancing drought tolerance in this crop. Full article

Reporter alleles are essential for advancing research with human induced pluripotent stem cells (hiPSCs), notably in developmental biology and disease modeling. This study investigates the state-of-the-art gene-editing techniques tailored for generating reporter alleles in hiPSCs, emphasizing their effectiveness in investigating cellular dynamics and disease mechanisms. Various methodologies, including the application of CRISPR/Cas9 technology, are discussed for accurately integrating reporter genes into the specific genomic loci. The synthesis of findings from the studies utilizing these reporter alleles reveals insights into developmental processes, genetic disorder modeling, and therapeutic screening, consolidating the existing knowledge. These hiPSC-derived models demonstrate remarkable versatility in replicating human diseases and evaluating drug efficacy, thereby accelerating translational research. Furthermore, this review addresses challenges and future directions in refining the reporter allele design and application to bolster their reliability and relevance in biomedical research. Overall, this investigation offers a comprehensive perspective on the methodologies, applications, and implications of reporter alleles in hiPSC-based studies, underscoring their essential role in advancing both fundamental scientific understanding and clinical practice. Full article

This study explores the integration of genome sequencing and digital droplet polymerase chain reaction (ddPCR)-based methods for tracking the diversity of COVID-19 variants in wastewater. The research focuses on monitoring various Omicron subvariants during a period of significant viral evolution. Genome sequencing, particularly using Oxford Nanopore Technology (ONT), provides a detailed view of emerging variants, surpassing the limitations of PCR-based detection kits that rely on known sequences. Of the 43 samples analyzed, 39.5% showed matching results between the GT Molecular ddPCR kits and sequencing, though only 4% were exact matches. Some mismatches occurred due to newer subvariants like XBB and BQ.1, which the ddPCR kits could not detect. This emphasized the limitations of ddPCR kits, which rely on known variant sequences, while sequencing provides real-time data on emerging variants, offering a more comprehensive view of circulating strains. This study highlights the effectiveness of combining these methodologies to enhance early detection and inform public health strategies, especially in regions with limited clinical sequencing capabilities. Full article

Retroviruses perpetuate their survival by incorporating a copy of their genome into the host cell, a critical step catalyzed by the virally encoded integrase. The viral capsid plays an important role during the viral life cycle, including nuclear importation in the case of lentiviruses and integration targeting events; hence, targeting the integrase and the viral capsid is a favorable therapeutic strategy. While integrase strand transfer inhibitors (INSTIs) are recommended as first-line regimens given their high efficacy and tolerability, lenacapavir is the first capsid inhibitor and the newest addition to the HIV treatment arsenal. These inhibitors are however designed for treatment of HIV-1 infection, and their efficacy against HIV-2 remains widely understudied and inconclusive, supported only by a few limited phenotypic susceptibility studies. We therefore carried out inhibition profiling of a panel of second-generation INSTIs and lenacapavir against HIV-2 in cell culture, utilizing pseudovirion inhibition profiling assays. Our results show that the tested INSTIs and lenacapavir exerted excellent efficacy against ROD-based HIV-2 integrase. We further evaluated the efficacy of raltegravir and other INSTIs against different variants of SARS-CoV-2; however, contrary to previous in silico findings, the inhibitors did not demonstrate significant antiviral activity. Full article

Interspecific hybridization between two different Brassicaceae species, namely Brassica rapa ssp. pekinensis (♀) (AA, 2n = 2x = 20) and genetically modified Brassica napus (♂) (AACC, 2n = 4x = 38), was performed to study the transmission of a herbicide resistance gene from a tetraploid to a diploid Brassica species. Initially, four different GM B. napus lines were used for hybridization with B. rapa via hand pollination. Among the F1 hybrids, the cross involving the B. rapa (♀) × GM B. napus (♂) TG#39 line exhibited the highest recorded crossability index of 14.7 ± 5.7. However, subsequent backcross progenies (BC1, BC2, and BC3) displayed notably lower crossability indices. The F1 plants displayed morphological characteristics more aligned with the male parent B. napus, with significant segregation observed in the BC1 generation upon backcrossing with the recurrent parent B. rapa. By the BC2 and BC3 generations, the progeny stabilized, manifesting traits from both parents to varying degrees. Cytogenetic analysis revealed a substantial reduction in chromosome numbers, particularly in backcrossing progenies. BC1 plants typically exhibited 21–25 chromosomes, while BC2 progenies showed 21–22 chromosomes, and by the BC3 generation, stability was achieved with an average of 20 chromosomes. SSR marker analysis confirmed the progressive reduction of C-genome regions, retaining minimal C-genome-specific bands throughout successive backcrossing. Despite the extensive elimination of C-genome-specific genomic regions, the glyphosate resistance gene from the male parent B. napus was introgressed into BC3 progenies, suggesting that the glyphosate resistance gene located and introgressed in A-chromosome/genome regions of the Brassica plants. Full article

Peanut (Arachis hypogaea L.) is one of the most important oil and food legume crops worldwide. ASR (abscisic acid, stress, ripening) plays extremely important roles in plant growth and development, fruit ripening, pollen development, and stress. Here, six ASR genes were identified in peanut. Structural and conserved motif analyses were performed to identify common ABA/WDS structural domains. The vast majority of ASR genes encoded acidic proteins, all of which are hydrophilic proteins and localized on mitochondria and nucleus, respectively. The cis-element analysis revealed that some cis-regulatory elements were related to peanut growth and development, hormone, and stress response. Under normal growth conditions, AhASR4 and AhASR5 were expressed in all tissues of peanut plants. Quantitative real-time PCR (qRT-PCR) results indicated that peanut ASR genes exhibited complex expression patterns in response to abiotic stress. Notably, under drought and cadmium (Cd) stress, the expression levels of AhASR4 and AhASR5 were significantly upregulated, suggesting that these genes may play a crucial role in the peanut plant’s resistance to such stressors. These results provide a theoretical basis for studying the evolution, expression, and function of the peanut ASR gene family and will provide valuable information in the identification and screening of genes for peanut stress tolerance breeding. Full article

This study explores the phylogeny of Korean native black goats through analysis of their complete mitochondrial DNA. The National Institute of Animal Science has gathered genetic material on purebred goats from isolated regions such as Tongyeong, Dangjin, and Jangsu, and is actively breeding them on a national level. These populations, however, are small and exhibit high inbreeding rates, highlighting the urgent need to preserve genetic diversity. The haplotype diversity within this native group is 0.659, with 39 haplotypes identified. By contrast, including international breeds in the analysis increases the overall haplotype diversity to 0.925 with 203 haplotypes identified, highlighting the limited genetic diversity among native black goats. For phylogenetic assessment, a neighbor-joining tree and median-joining network were constructed using identified haplogroups (A, B, C, D, G, and F) from prior studies. The results pinpoint the native black goats as closely related to, but distinct from, Haplogroup A with a bootstrap value of 98, establishing them as a separate clade (A’). This supports the notion of a shared ancestry with various global populations. This research provides essential data on the origins and evolutionary history of Korean native black goats, supporting conservation and breeding efforts aimed at enhancing genetic diversity. Full article