Effect of a probiotic and an antibiotic on the mobilome of the porcine microbiota
Conclusion: There is no positive effect of adding probiotics to an antibiotic treatment when these treatments are administered simultaneously. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - March 28, 2024 Category: Genetics & Stem Cells Source Type: research

Evaluating cardiovascular disease risk stratification using multiple-polygenic risk scores and pooled cohort equations: insights from a 17-year longitudinal Korean cohort study
This study aimed to evaluate the combined efficacy of multi-polygenic risk scores and pooled cohort equations (PCE) for predicting future CVD risks in the Korean population. In this longitudinal study, 7,612 individuals from the Ansan and Ansung cohorts were analyzed over a 17-year follow-up period. The participants were genotyped using the Korea Biobank Array, and quality-controlled genetic data were subjected to imputation analysis. The weighted sum of the PRSs (wPRSsum) was calculated using PRS-CS with summary statistics from myocardial infarction, ischemic stroke, coronary artery disease, and hypertension genome-wide a...
Source: Frontiers in Genetics - March 28, 2024 Category: Genetics & Stem Cells Source Type: research

Review of childhood genetic nephrolithiasis and nephrocalcinosis
Nephrolithiasis (NL) is a common condition worldwide. The incidence of NL and nephrocalcinosis (NC) has been increasing, along with their associated morbidity and economic burden. The etiology of NL and NC is multifactorial and includes both environmental components and genetic components, with multiple studies showing high heritability. Causative gene variants have been detected in up to 32% of children with NL and NC. Children with NL and NC are genotypically heterogenous, but often phenotypically relatively homogenous, and there are subsequently little data on the predictors of genetic childhood NL and NC. Most genetic ...
Source: Frontiers in Genetics - March 28, 2024 Category: Genetics & Stem Cells Source Type: research

Endogenous retroviral solo-LTRs in human genome
Human endogenous retroviruses (HERVs) are derived from the infection and integration of exogenetic retroviruses. HERVs account for 8% of human genome, and the majority of HERVs are solitary LTRs (solo-LTRs) due to homologous recombination. Multiple findings have showed that solo-LTRs could provide an enormous reservoir of transcriptional regulatory sequences involved in diverse biological processes, especially carcinogenesis and cancer development. The link between solo-LTRs and human diseases still remains poorly understood. This review focuses on the regulatory modules of solo-LTRs, which contribute greatly to the divers...
Source: Frontiers in Genetics - March 28, 2024 Category: Genetics & Stem Cells Source Type: research

The prognostic significance of LncRNA BLACAT1 overexpression in various tumors: a meta-analysis
Conclusion:The findings highlight that high LncRNA BLACAT1 expression might be detrimental and induce a worse prognosis for cancer patients. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - March 27, 2024 Category: Genetics & Stem Cells Source Type: research

Causal association of gastroesophageal reflux disease on irritable bowel syndrome: a two-sample Mendelian randomization study
Conclusion:This study provides evidence that the presence of GERD increases the risk of developing IBS, and it is observed from the reverse MR results that IBS did not increase the risk of GERD. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - March 27, 2024 Category: Genetics & Stem Cells Source Type: research

Functional analysis of RRAS2 pathogenic variants with a Noonan-like phenotype
Discussion: Recurrent and novel RRAS2 variants that we reported showed increased in vitro or in vivo RAS signaling pathway activity because of gain-of-function RRAS2 variants. Clinical features are similar to those previously reported, suggesting that RRAS2 gain-of-function variants cause this disease in patients. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - March 27, 2024 Category: Genetics & Stem Cells Source Type: research

The genetic architecture of complete blood counts in lactating Holstein dairy cows
The objective of this study is to determine the heritability of CBC traits and identify genomic regions that are associated with CBC measurements in lactating Holstein dairy cattle. The heritability of CBCs was estimated using a Bayes C0 model. The study population consisted of 388 cows with genotypes at roughly 75,000 markers and 16 different CBC phenotypes taken at one to three time points (n = 33, 131, and 224 for 1, 2, and 3 time points, respectively). Heritabilities ranged from 0.00 ± 0.00 (red cell distribution width) to 0.68 ± 0.06 (lymphocytes). A total of 96 different 1-Mb windows were identified that explained ...
Source: Frontiers in Genetics - March 27, 2024 Category: Genetics & Stem Cells Source Type: research

Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden)
Eucalyptus dunnii is one of the most important Eucalyptus species for short-fiber pulp production in regions where other species of the genus are affected by poor soil and climatic conditions. In this context, E. dunnii holds promise as a resource to address and adapt to the challenges of climate change. Despite its rapid growth and favorable wood properties for solid wood products, the advancement of its improvement remains in its early stages. In this work, we evaluated the performance of two single nucleotide polymorphism, (SNP), genotyping methods for population genetics analysis and Genomic Selection in E. dunnii. Dou...
Source: Frontiers in Genetics - March 26, 2024 Category: Genetics & Stem Cells Source Type: research

Causal relationships between mitochondrial proteins and different pathological types of lung cancer: a bidirectional mendelian randomization study
An increasing number of studies point to an association between mitochondrial proteins (MPs) and lung cancer (LC). However, the causal relationship between MPs and LC remains unclear. Consequently, our study employed a bidirectional Mendelian randomization (MR) analysis to explore the causal association between MPs and different pathological types of LC. A two-sample MR study was performed using the genome-wide association study (GWAS) data publicly available. We applied the primary inverse variance weighted (IVW) method along with additional MR methods to validate the causality between MPs and different pathological types...
Source: Frontiers in Genetics - March 26, 2024 Category: Genetics & Stem Cells Source Type: research

Unveiling the role of tRNA-derived small RNAs in MAPK signaling pathway: implications for cancer and beyond
tRNA-derived small RNAs (tsRNAs) are novel small non-coding RNAs originating from mature or precursor tRNAs (pre-tRNA), typically spanning 14 to 30 nt. The Mitogen-activated protein kinases (MAPK) pathway orchestrates cellular responses, influencing proliferation, differentiation, apoptosis, and transformation. tsRNAs influence the expression of the MAPK signaling pathway by targeting specific proteins within the pathway. Presently, four MAPK-linked tsRNAs have implications in gastric cancer (GC) and high-grade serous ovarian cancer (HGSOC). Notably, tRF-Glu-TTC-027 and tRF-Val-CAC-016 modulate MAPK-related protein expres...
Source: Frontiers in Genetics - March 26, 2024 Category: Genetics & Stem Cells Source Type: research

Mutation analysis and clinical profile of South African patients with Neurofibromatosis type 1 (NF1) phenotype
Neurofibromatosis type 1 (NF1) is an autosomal dominant genetic condition with complete age-dependent penetrance, variable expressivity and a global prevalence of ∼1/3,000. It is characteriszed by numerous café-au-lait macules, skin freckling in the inguinal or axillary regions, Lisch nodules of the iris, optic gliomas, neurofibromas, and tumour predisposition. The diagnostic testing strategy for NF1 includes testing for DNA single nucleotide variants (SNVs), copy number variants (CNVs) as well as RNA analysis for deep intronic and splice variants, which can cumulatively identify the causative variant in 95% of patients...
Source: Frontiers in Genetics - March 26, 2024 Category: Genetics & Stem Cells Source Type: research

The complex landscape of DMD mutations: moving towards personalized medicine
Duchenne muscular dystrophy (DMD) is a severe genetic disorder characterized by progressive muscle degeneration, with respiratory and cardiac complications, caused by mutations in the DMD gene, encoding the protein dystrophin. Various DMD mutations result in different phenotypes and disease severity. Understanding genotype/phenotype correlations is essential to optimize clinical care, as mutation-specific therapies and innovative therapeutic approaches are becoming available. Disease modifier genes, trans-active variants influencing disease severity and phenotypic expressivity, may modulate the response to therapy, and bec...
Source: Frontiers in Genetics - March 26, 2024 Category: Genetics & Stem Cells Source Type: research

Hi-C, a chromatin 3D structure technique advancing the functional genomics of immune cells
The functional performance of immune cells relies on a complex transcriptional regulatory network. The three-dimensional structure of chromatin can affect chromatin status and gene expression patterns, and plays an important regulatory role in gene transcription. Currently available techniques for studying chromatin spatial structure include chromatin conformation capture techniques and their derivatives, chromatin accessibility sequencing techniques, and others. Additionally, the recently emerged deep learning technology can be utilized as a tool to enhance the analysis of data. In this review, we elucidate the definition...
Source: Frontiers in Genetics - March 22, 2024 Category: Genetics & Stem Cells Source Type: research

Identification of potential biomarkers for idiopathic pulmonary arterial hypertension using single-cell and bulk RNA sequencing analysis
In conclusion, our findings shed light on the pivotal role of arterial endothelial cells in the development of IPAH. Furthermore, the integration of single-cell and bulk RNA sequencing datasets allowed us to pinpoint novel candidate biomarkers for the diagnosis of IPAH. This work opens up new avenues for research and potential therapeutic interventions in IPAH management. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - March 22, 2024 Category: Genetics & Stem Cells Source Type: research