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Precision Nutritional Genomics, Gut Microbiota and Artificial Intelligence in Chronic Kidney Disease.

Chronic kidney disease (CKD) is a prevalent global health issue, and nutritional management of CKD is an integral component through all stages of the disease. However, response to dietary interventions varies, potentially due to genetic variations influencing metabolic pathways. This review highlights key gene-diet interactions relevant to CKD management, including risk factors and comorbidities such as hypertension, diabetes, and proteinuria. Variants in the ACE gene influence salt sensitivity and blood pressure responses, while TCF7L2 polymorphisms affect the relationship between dietary gly

Genomics guiding personalized first-line immunotherapy response in lung and bladder tumors.

BACKGROUND: Immune checkpoint inhibitors (ICI) have revolutionized cancer treatment, particularly in advanced non-small cell lung cancer (NSCLC) and muscle-invasive bladder cancer (MIBC). However, identifying reliable predictive biomarkers for ICI response remains a significant challenge. In this study, we analyzed real-world cohorts of advanced NSCLC and MIBC patients treated with ICI as first-line therapy. METHODS: Tumor samples underwent Whole Genome Sequencing (WGS) to identify specific somatic variants and assess tumor mutational burden (TMB). Additionally, mutational signature extractio

Identifying potential novel biomarkers for varicocele: A bioinformatics approach to genomics analysis.

Introduction: Varicocele, characterized by the enlargement of scrotal veins, is a common contributor to male infertility, but its genetic underpinnings remain largely unknown. Aim: The goal of this study is to identify potential biomarkers associated with varicocele in order to better understand its molecular mechanisms. Materials and methods: Using the three primary databases, NCBI, DisGeNET, and OpenTarget, we analyzed gene variants and found 79 pertinent genes associated with varicocele. Protein-protein interaction analysis was performed using STRING and visualized with Cytoscape. Molecular

Phylogeny, population structure, and conservation genomics of Galapagos vermilion flycatchers (genus Pyrocephalus).

The Galapagos archipelago in the Eastern Tropical Pacific is known for its isolation, island endemism, and rapid diversification. Despite considerable scientific research many groups remain poorly studied. One of these groups is the genus Pyrocephalus, a group of brightly-colored and charismatic flycatchers whose populations have declined significantly in recent decades. To study the evolution and diversification of Pyrocephalus, we used samples from 53 individuals across 11 Galapagos Islands (Pyrocephalus dubius and P. nanus) and a continental outgroup (P. obscurus) and reconstructed a phylog

Comparative single-cell genomics of two uncultivated Naegleria species harboring Legionella cobionts.

Amoeboflagellates of the genus Naegleria are free-living protists ubiquitously found in soil and freshwater habitats worldwide. They include … ecies as close relatives of Naegleria fultoni and Naegleria pagei. Exploring Naegleria evolutionary genomics, we identified gene families encoding antistasin-like domains, which have been characterized as factors that inhibit coagulation in blood-feeding leeches. Antistasin-like domains were identified in all sequenced Naegleria species and their close rel …

Cancer cytogenetics in a genomics world: Wedding the old with the new.

Since the discovery of the Philadelphia chromosome in 1960, cytogenetic studies have been instrumental in detecting chromosomal abnormalities that can inform cancer diagnosis, treatment, and risk assessment efforts. The initial expansion of cancer cytogenetics was with fluorescence in situ hybridization (FISH) to assess submicroscopic alterations in dividing or non-dividing cells and has grown into the incorporation of chromosomal microarrays (CMA), and next generation sequencing (NGS). These molecular technologies add additional dimensions to the genomic assessment of cancers by uncovering cy

Exploring Synaptic Pathways in Traumatic Brain Injury: A Cross-Phenotype Genomics Approach.

Traumatic brain injury (TBI), a global leading cause of mortality and disability, lacks effective treatments to enhance recovery. Synaptic remodeling has been postulated as one mechanism that influences outcomes after TBI. We sought to investigate whether common mechanisms affecting synapse maintenance are shared between TBI and other neuropsychiatric conditions using pathway enrichment tools and genome-wide genotype data, with the goal of highlighting novel treatment targets. We leveraged an integrative approach, combining data from genome-wide association studies with pathway and gene-set en

Revolutionizing soybean genomics: How CRISPR and advanced sequencing are unlocking new potential.

Soybean Glycine max L., paleopolyploid genome, poses challenges to its genetic improvement. However, the development of reference genome assemblies and genome sequencing has completely changed the field of soybean genomics, allowing for more accurate and successful breeding techniques as well as research. During the single-cell revolution, one of the most advanced sequencing tools for examining the transcriptome landscape is single-cell RNA sequencing (scRNA-seq). Comprehensive resources for genetic improvement of soybeans may be found in the SoyBase and other genomics databases. CRISPR-Cas9 g…

Functional genomics of human skeletal development and the patterning of height heritability.

Underlying variation in height are regulatory changes to chondrocytes, cartilage cells comprising long-bone growth plates. Currently, we lack knowledge on epigenetic regulation and gene expression of chondrocytes sampled across the human skeleton, and therefore we cannot understand basic regulatory mechanisms controlling height biology. We first rectify this issue by generating extensive epigenetic and transcriptomic maps from chondrocytes sampled from different growth plates across developing human skeletons, discovering novel regulatory networks shaping human bone/joint development. Next, us

Phylogenetic and Comparative Genomics Study of Cephalopina titillator Based on Mitochondrial Genomes.

Camel bot fly (Cephalopina titillator) larvae cause myiasis in domesticated and wild camels, resulting in significant economic losses to the camel industry and posing a serious global public health concern. To date, only one mitochondrial genome (mitogenome) of C. titillator isolated from the Alxa Bactrian camel has been reported. Herein, C. titillator was isolated from the Junggar Bactrian camel to assemble a complete circular mitogenome with a length of 16,552 bp encoding 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. The mitogenome showed a high A + T content (73.31%), positive

Сравнительная геномика и эволюционный анализ штаммов вируса денге, циркулирующих в Пакистане.

Вирус лихорадки денге (ДЕНВ) представляет серьезную угрозу для здоровья населения в тропических и субтропических регионах мира. Несмотря на то, что вирус лихорадки денге (ДЕНВ) обладает значительным генетическим разнообразием и потенциалом развития, в Пакистане отсутствуют всеобъемлющие исследования относительно сравнительной геномики и эволюционной динамики этого вируса. Филиогенетический анализ показал циркуляцию всех четырех серотипов вируса денге (DENV-1, - 2, - 3 и - 4) с преобладающими генотипами III и V в рамках DENV-1, космополитического генотипа в рамках DENV-2, генотипа III в рамках

Совпадение в аннотации оригинала
Dengue fever virus (DENV) poses a significant public health risk in tropical and subtropical regions across the world. Although the dengue fever virus (DENV) exhibits significant genetic diversity and has the potential to evolve, there is a lack of comprehensive research on the comparative genomics and evolutionary dynamics of the virus in Pakistan. Phylogen…

High performance Legionella pneumophila source attribution using genomics-based machine learning classification.

Fundamental to effective Legionnaires' disease outbreak control is the ability to rapidly identify the environmental source(s) of the causative agent, Legionella pneumophila. Genomics has revolutionized pathogen surveillance, but L. pneumophila has a complex ecology and population structure that can limit source inference based on standard core genome phylogenetics. Here, we present a powerful machine learning approach that assigns the geographical source of Legionnaires' disease outbreaks more accurately than current core genome comparisons. Models were developed upon 534 L. pneumophila genom…

The genomics of visuospatial neurocognition in obsessive-compulsive disorder: A preliminary GWAS.

BACKGROUND: The study of Obsessive-Compulsive Disorder (OCD) genomics has primarily been tackled by Genome-wide association studies (GWAS), which have encountered troubles in identifying replicable single nucleotide polymorphisms (SNPs). Endophenotypes have emerged as a promising avenue of study in trying to elucidate the genomic bases of complex traits such as OCD. METHODS: We analyzed the association of SNPs across the whole genome with the construction of visuospatial information and executive performance through four neurocognitive variables assessed by the Rey-Osterrieth Complex Figure T…

Safety assessment of Enterococcus lactis based on comparative genomics and phenotypic analysis.

Enterococcus faecium is sometimes used in food production; however, its acquisition of antibiotic resistance has become an alarming health concern. The E. lactis species is closely related to E. faecium and has good probiotic potential. This study aimed to investigate the antibiotic resistance of E. lactis. We analyzed the antibiotic resistance phenotype and whole-genome sequences of 60 E. lactis isolates (23, 29, and 8 isolates from dairy products, Rice wine Koji, and human feces, respectively). These isolates showed varying degree of resistance to 13 antibiotics, and were sensitive to ampici

Comparative genomics of Mycoplasma feriruminatoris, a fast-growing pathogen of wild Caprinae.

Mycoplasma feriruminatoris is a fast-growing Mycoplasma species isolated from wild Caprinae and first described in 2013. M. feriruminatoris isolates have been associated with arthritis, kerato conjunctivitis, pneumonia and septicemia, but were also recovered from apparently healthy animals. To better understand what defines this species, we performed a genomic survey on 14 strains collected from free-ranging or zoo-housed animals between 1987 and 2017, mostly in Europe. The average chromosome size of the M. feriruminatoris strains was 1,040±0,024 kbp, with 24 % G+C and 852±31 CDS. The core gen

Genomics and phenomics of body mass index reveals a complex disease network.

Elevated body mass index (BMI) is heritable and associated with many health conditions that impact morbidity and mortality. The study of the genetic association of BMI across a broad range of common disease conditions offers the opportunity to extend current knowledge regarding the breadth and depth of adiposity-related diseases. We identify 906 (364 novel) and 41 (6 novel) genome-wide significant loci for BMI among participants of European (N~1.1 million) and African (N~100,000) ancestry, respectively. Using a BMI genetic risk score including 2446 variants, 316 diagnoses are associated in the

Update on Biology and Genomics of Adrenocortical Carcinomas: Rationale for Emerging Therapies.

The adrenal glands are paired endocrine organs that produce steroid hormones and catecholamines required for life. Adrenocortical carcinoma (ACC) is a rare and often fatal cancer of the peripheral domain of the gland, the adrenal cortex. Recent research in adrenal development, homeostasis, and disease have refined our understanding of the cellular and molecular programs controlling cortical growth and renewal, uncovering crucial clues into how physiologic programs are hijacked in early and late stages of malignant neoplasia. Alongside these studies, genome-wide approaches to examine adrenocort

Diagnosis of the origin of an epibulbar melanocytic tumor with molecular genomics.

BACKGROUND: Uveal melanoma (UM) and conjunctival melanoma (CM) are distinct entities with different etiologies and genetic background. We present a case of an atypical subconjunctival melanoma arising from a blue nevus. PATIENTS AND METHODS: A 61-year-old female presented with a partially melanocytic epibulbar mass with surrounding episcleral pigmented spots. The lesion was detached from the overlying conjunctiva without an intraocular component. Excisional biopsy revealed a predominantly epithelioid melanoma, that was suggested to be metastasic, although there was no evidence of a primary me

Genomics and transcriptomics reveal new molecular mechanism of vibriosis resistance in fish.

Infectious diseases have caused dramatic production decline and economic loss for fish aquaculture. However, the poor understanding of fish disease resistance severely hampered disease prevention. Chinese tongue sole (Cynoglossus semilaevis) is an important economic flatfish suffering from vibriosis. Here we used genomic, transcriptomic and experimental approaches to investigate the molecular genetic mechanisms underlying fish vibriosis resistance. A genome-wide comparison revealed that the genes under selective sweeps were enriched for glycosaminoglycan (GAG) chondroitin sulfate (CS)/dermatan