Результаты поиска

Comparative genomics clarifies phylogenetic relationships and genome evolution in Hippophae from the Qinghai-Tibet plateau.

The uplift of the Qinghai-Tibet Plateau (QTP) and associated climatic oscillations have shaped plant evolution, yet how adaptive strategies diversify along elevational, moisture, and latitudinal gradients within a single clade remains poorly understood. Hippophae (Elaeagnaceae) is distributed along these gradients, with all members sharing Frankia-mediated nitrogen-fixing symbiosis and dioecy. Here, we assembled chromosome-level genomes of H. neurocarpa, H. rhamnoides subsp. yunnanensis, and H. rhamnoides subsp. turkestanica, integrated them with four published assemblies, covering seven taxa

Large-scale phenotyping and comparative genomics reveal genetic features of Listeria persistence in epithelial cells.

During infection in epithelial cells, after invading the cytosol, multiplying, and spreading, Listeria monocytogenes (Lm) ceases to produce ActA and becomes trapped in Listeria-containing vacuoles (LisCVs). These persistence acidic vacuoles harbor bacterial subpopulations that resist to stress in a metabolically dormant state. Although LisCVs have been proposed as a hallmark of Lm persistence in epithelial cells, their prevalence across strains and the bacterial factors underlying their formation remain uncharacterized. Given the significant genetic diversity within the species, it is importan

Genomics and social practices at Mogou and other Gansu sites during prehistoric trans-Eurasian exchange.

Beginning approximately 4,000 years ago, southwest-Asian-originating domesticated crops and livestock began appearing in Gansu, a key crossroads in northwestern China, yet the population dynamics and social practices underlying these historically transformative events in the region have not been fully explored. Despite the adoption of western domesticates, genome sequences of 149 individuals from the large Mogou cemetery and ten other sites in Gansu, dating between 4,700 and 3,000 years ago, revealed migrations within East Asian regions but no detectable evidence of genetic influence from west

Global functional genomics reveals GRK5 as a cystic fibrosis therapeutic target synergistic with current modulators.

Cystic fibrosis (CF) is a life-shortening disease affecting >160,000 individuals worldwide predominantly with respiratory symptoms. About 80% of individuals with CF have the p.Phe508del variant that causes the CF transmembrane conductance regulator (CFTR) protein to misfold and be targeted for premature degradation by the endoplasmic reticulum (ER) quality control (ERQC), thus preventing its plasma membrane (PM) traffic. Despite the recent approval of a "highly effective" drug rescuing p.Phe508del-CFTR, maximal lung function improvement is ∼14%. To identify global modulators of p.Phe508del tra

Bibliometric Analysis: Insights Into the Podiatric Medicine Landscape of Diabetic Sensory Peripheral Neuropathy and Genomics.

BACKGROUND AND AIMS: Research into diabetic foot complications is extensive; it remains challenging to identify critical literature. Evolving interprofessional boundaries, alongside advances in molecular medicine and pathophysiological understanding, necessitates mapping of the scientific literature (corpus). Impact of these advances on podiatric medicine remains unclear. This study explores topics, research performance, and evolution across the literature and disciplines to understand the corpus in its current state. METHOD: A retrospective-observational bibliometric analysis examined Web of

Integrative Proteomics and Genomics Identify Novel Biomarkers and Therapeutic Targets in Vitiligo via Mendelian Randomization.

INTRODUCTION: Given that the proteome is a major source of therapeutic targets, we conducted a proteome-wide Mendelian randomization (MR) combined with transcriptome sequencing analysis to identify candidate protein markers and therapeutic targets for vitiligo. METHODS: Based on protein quantitative trait loci (pQTLs) and genetic associations with vitiligo obtained from the European Bioinformatics Institute (EBI) database (60 vitiligo cases and 402,672 controls), and the UK Biobank (95 vitiligo cases and 337,064 controls), bidirectional MR and colocalization analyses identified genetically pr

Artificial Intelligence in the Management of Hereditary and Acquired Hemophilia: From Genomics to Treatment Optimization.

Hemophilia, an X-linked bleeding disorder, is characterized by a deficiency in coagulation factors. It manifests as spontaneous bleeding, leading to severe complications if not properly managed. In contrast, acquired hemophilia is an autoimmune condition marked by the development of inhibitory antibodies against coagulation factors. Both forms present significant diagnostic and therapeutic challenges, highlighting the need for advanced genetic, molecular, laboratory, and clinical assessments. Recent advances in artificial intelligence have opened new avenues for the management of hemophilia. M

Совпадение в полном тексте источника
… The research was confined to the PubMed database, selecting publications that mentioned at least one of the following terms: “genetics,” “genomics,” “genetic,” “mutation(s),” “polymorphism(s),” or “genetic variation.” … In related hematologic conditions such as multiple myeloma and amyloidosis, ML models can integrate genomic, clinical, and imaging data to recommend treatment regimens likely to result in better outcomes [ 60 , 61 ]. …

Harnessing AI for precision medicine and its applications in genomics, systems pharmacology, and drug discovery.

Artificial intelligence and machine learning are revolutionizing pharmaceutical research by enabling the rapid analysis of complex datasets and automating critical tasks throughout the drug-development process. In this review, we surveyed how artificial intelligence accelerated target identification, guided lead-compound design and enhanced safety and efficacy profiling through predictive ADMET modeling and PK/PD simulations. We also explored downstream applications, including modelling complex biological interactions and leveraging real-world clinical data, while emphasizing the essential req

Orthogonal chemical genomics approaches reveal genomic targets for increasing anaerobic chemical tolerance in Zymomonas mobilis.

Genetically engineered microbes have the potential to increase efficiency in the bioeconomy by overcoming growth-limiting production stress. Screens of gene perturbation libraries against production stressors can identify high-value engineering targets, but follow-up experiments needed to guard against false positives are slow and resource-intensive. In principle, the use of orthogonal gene perturbation approaches could increase recovery of true positives over false positives because the strengths of one technique compensate for the weaknesses of the other, but, in practice, two parallel scree

Unveiling novel features and phylogenomic assessment of indigenous Priestia megaterium AB-S79 using comparative genomics.

UNLABELLED: Priestia megaterium strain AB-S79 isolated from active gold mine soil previously expressed in vitro heavy metal resistance and has a 5.7 Mb genome useful for biotechnological exploitation. This study used web-based bioinformatic resources to analyze P. megaterium AB-S79 genomic relatedness, decipher its secondary metabolite biosynthetic gene clusters (BGCs), and better comprehend its taxa. Genes were highly conserved across the 14 P. megaterium genomes examined here. The pangenome reflected a total of 61,397 protein-coding genes, 59,745 homolog protein family hits, and 1,652 single

Comparative genomics of Brucella species reveals key determinants of secondary metabolism, antimicrobial resistance, and virulence.

The genomes of 40 Brucella strains were retrieved from the NCBI database to investigate Brucellosis at the genomic level, focusing on secondary metabolites, resistance genes, and virulence factors. Genome analysis software, secondary metabolite mining tools, and relevant gene databases were employed for detailed analysis. The genome sizes of these strains range from 4.88 to 6.00 MB, with G+C content between 53.5 and 60.5%. Phylogenetic analysis classified the strains into three distinct clades: Brucella anthropi CCUG 34461, Brucella sp. NBRC 13694, and Brucella anthropi MAG47. Pan-genome analy

Impact of Genetic Ancestry on Genomics and Survival Outcomes in T-cell Acute Lymphoblastic Leukemia.

The influence of genetic ancestry on genomics in T-cell Acute Lymphoblastic Leukemia (T-ALL) has not been fully explored. We examined the impact of genetic ancestry on multi-omic alterations, survival outcomes, and risk stratification. Among 1309 children and young adults with T-ALL treated on the Children's Oncology Group trial AALL0434, the prognostic value of five commonly altered T-ALL genes varied by ancestry-including NOTCH1, which was associated with superior overall survival for patients of European ancestry but non-prognostic among patients of African ancestry. Integrating genetic anc…

Integrated subtractive genomics and inhibitor identification of novel FAD-dependent monooxygenase in Nocardia farcinica JJSBBCNF_01.

Nocardia farcinica is among the most common Nocardia species responsible for human nocardiosis. This study aims to identify potential drug targets involved in unique metabolic pathways of N. farcinica using a subtractive genomics approach and to prioritize potential inhibitors through structural bioinformatics. Compared to previous studies, this work integrates a subtractive genomics pipeline with diverse compound libraries and comprehensive molecular simulations, offering a more targeted and robust approach to drug discovery. The subtractive approach was applied to the pathogen's whole genome…

Comparative genomics of Mycobacterium avium subsp. hominissuis strains within a group of captive lowland tapirs.

Within a group of three captive lowland tapirs (Tapirus terrestris) suffering from clinically apparent mycobacteriosis, non-tuberculous Mycobacterium avium subsp. hominissuis (MAH) strains were isolated from the animals and the tapir's enclosure. Based on MIRU-VNTR findings, which identified two closely related INMV profiles (124 and 246), a micro-evolutionary event was assumed, and four available MAH strains were submitted to whole genome sequencing (short- and long-read technologies). Surprisingly, the differences based on single nucleotide polymorphisms (SNPs) were exceptionally high betwee

Inhibiting multidrug resistant Shigella flexneri using comparative genomics guided In vitro and In silico screening.

ETHNOPHARMACOLOGICAL RELEVANCE: The Gram-negative bacterium Shigella is the most widely documented etiologic factor for diarrheal mortality in infants, contributing to 13.2 % of diarrheal episodes across the globe. The present surge in antibiotic resistance, increasing numbers of non-typeable strains, and the disparate regional distribution of multiple Shigella variants has rendered it obvious that novel therapeutic alternatives are desperately sought after to address the growing threat of shigellosis. AIM OF THE STUDY: In the present investigation, we have assessed the antibacterial properti

Comparative genomics of monotremes provides insights into the early evolution of mammalian epidermal differentiation genes.

The function of the skin as a barrier against the environment depends on the differentiation of epidermal keratinocytes into highly resilient corneocytes that form the outermost skin layer. Many genes encoding structural components of corneocytes are clustered in the epidermal differentiation complex (EDC), which has been described in placental and marsupial mammals as well as non-mammalian tetrapods. Here, we analyzed the genomes of the platypus (Ornithorhynchus anatinus) and the echidna (Tachyglossus aculeatus) to determine the gene composition of the EDC in the basal clade of mammals, the m

Genomics and tumor microenvironment of breast mucoepidermoid carcinoma based on whole-exome and RNA sequencing.

Mammary mucoepidermoid carcinoma (MEC) is a rare entity. The molecular characteristics of breast MEC have not been fully investigated due to … ry gland MEC, whose plasma cells were in the low infiltration group. Overall, we first analyzed the genomics and tumor microenvironment of breast mucoepidermoid carcinoma and proposed our hypothesis that although MECs arising in the breast resemble their salivary gland counterparts phenotypically, our findings indicate that breast MECs probably resemble in …

Big data analytics for MerTK genomics reveals its double-edged sword functions in human diseases.

RATIONALE: MER proto-oncogene tyrosine kinase (MerTK) is a key receptor for the clearance of apoptotic cells (efferocytosis) and plays important roles in redox-related human diseases. We will explore MerTK biology in human cells, tissues, and diseases based on big data analytics. METHODS: The human RNA-seq and scRNA-seq data about 42,700 samples were from NCBI Gene Expression Omnibus and analyzed by QIAGEN Ingenuity Pathway Analysis (IPA) with about 170,000 crossover analysis. MerTK expression was quantified as Log2 (FPKM + 0.1). RESULTS: We found that, in human cells, MerTK is highly expres

Comparative genomics reveals insights into the potential of Lysinibacillus irui as a plant growth promoter.

Members of the genus Lysinibacillus attract attention for their mosquitocidal, bioremediation, and plant growth-promoting abilities. Despite … s. KEY POINTS: • Pioneer study in elucidating plant growth promoting in L. irui through comparative genomics. • Genome mining identified biosynthetic pathways of putative novel bacteriocins. • Future research directions to develop L. irui-based biofertilizers for sustainable agriculture.

Comparative genomics of IncQ1 plasmids carrying blaGES variants from clinical and environmental sources in Brazil.

IncQ-type plasmids have become important vectors in the dissemination of blaGES among different bacterial genera and species from different environments around the world, and studies estimating the occurrence of Guiana extended-spectrum (GES)-type β-lactamases are gaining prominence. We analyzed the genetic aspects of two IncQ1 plasmids harboring different blaGES variants from human and environmental sources. The blaGES variants were identified using polymerase chain reaction (PCR) in Aeromonas veronii isolated from hospital effluent and Klebsiella variicola isolated from a rectal swab of a pa