Potential Networks Regulated by MSCs in Acute-On-Chronic Liver Failure: Exosomal miRNAs and Intracellular Target Genes
This study investigated the hepatocyte exosomal miRNAs which are regulated by MSCs and the target genes which have potential in the treatment of liver failure. Briefly, ACLF was induced in mice using carbon tetrachloride and primary hepatocytes were isolated and co-cultured (or not) with MSCs under serum-free conditions. Exosomes were then collected, and the expression of exosomal miRNAs was assessed using next-generation sequencing; a comparison was performed between liver cells from healthy versus ACLF animals. Additionally, to identify the intracellular targets of exosomal miRNAs in humans, we focused on previously publ...
Source: Frontiers in Genetics - April 23, 2021 Category: Genetics & Stem Cells Source Type: research

A Population-Specific Major Allele Reference Genome From The United Arab Emirates Population
The ethnic composition of the population of a country contributes to the uniqueness of each national DNA sequencing project and, ideally, individual reference genomes are required to reduce the confounding nature of ethnic bias. This work represents a representative Whole Genome Sequencing effort of an understudied population. Specifically, high coverage consensus sequences from 120 whole genomes and 33 whole exomes were used to construct the first ever population specific major allele reference genome for the United Arab Emirates (UAE). When this was applied and compared to the archetype hg19 reference, assembly of local ...
Source: Frontiers in Genetics - April 23, 2021 Category: Genetics & Stem Cells Source Type: research

Gene Targeting in Disease Networks
Profiling of whole transcriptomes has become a cornerstone of molecular biology and an invaluable tool for the characterization of clinical phenotypes and the identification of disease subtypes. Analyses of these data are becoming ever more sophisticated as we move beyond simple comparisons to consider networks of higher-order interactions and associations. Gene regulatory networks (GRNs) model the regulatory relationships of transcription factors and genes and have allowed the identification of differentially regulated processes in disease systems. In this perspective, we discuss gene targeting scores, which measure chang...
Source: Frontiers in Genetics - April 23, 2021 Category: Genetics & Stem Cells Source Type: research

CBP-JMF: An Improved Joint Matrix Tri-Factorization Method for Characterizing Complex Biological Processes of Diseases
Multi-omics molecules regulate complex biological processes (CBPs), which reflect the activities of various molecules in living organisms. Meanwhile, the applications to represent disease subtypes and cell types have created an urgent need for sample grouping and associated CBP-inferring tools. In this paper, we present CBP-JMF, a practical tool primarily for discovering CBPs, which underlie sample groups as disease subtypes in applications. Differently from existing methods, CBP-JMF is based on a joint non-negative matrix tri-factorization framework and is implemented in Python. As a pragmatic application, we apply CBP-JM...
Source: Frontiers in Genetics - April 23, 2021 Category: Genetics & Stem Cells Source Type: research

The Molecular Functions of MeCP2 in Rett Syndrome Pathology
MeCP2 protein, encoded by the MECP2 gene, binds to DNA and affects transcription. Outside of this activity the true range of MeCP2 function is still not entirely clear. As MECP2 gene mutations cause the neurodevelopmental disorder Rett syndrome in 1 in 10,000 female births, much of what is known about the biologic function of MeCP2 comes from studying human cell culture models and rodent models with Mecp2 gene mutations. In this review, the full scope of MeCP2 research available in the NIH Pubmed (https://pubmed.ncbi.nlm.nih.gov/) data base to date is considered. While not all original research can be mentioned due to spac...
Source: Frontiers in Genetics - April 23, 2021 Category: Genetics & Stem Cells Source Type: research

Exploration of Prognostic Biomarkers for Lung Adenocarcinoma Through Bioinformatics Analysis
This study firstly used several gene datasets from GEO database to mine differentially expressed genes (DEGs) in LUAD tissue and healthy tissue via joint analysis. Later, enrichment analysis for the DEGs was performed, and it was found that the DEGs were mainly activated in pathways involved in extracellular matrix, cell adhesion, and leukocyte migration. Afterward, a TCGA cohort was used to perform univariate Cox, least absolute shrinkage and selection operator method, and multivariate Cox regression analyses for the DEGs, and a prognostic model consisting of eight genes (GPX3, TCN1, ASPM, PCP4, CAV2, S100P, COL1A1, and S...
Source: Frontiers in Genetics - April 22, 2021 Category: Genetics & Stem Cells Source Type: research

A Novel Signature for Predicting Prognosis of Smoking-Related Squamous Cell Carcinoma
Tobacco smoking is an established risk factor for squamous cell carcinoma (SCC). We obtained smoking-related SCC, including cervical SCC (CSCC), esophageal SCC (ESCC), head and neck SCC (HNSC), and lung SCC (LUSC), from The Cancer Genome Atlas (TCGA) database to investigate the association between smoking status (reformed and current smoking) and prognosis. We found that reformed smokers had a better prognosis than current smokers in CSCC (p = 0.003), HNSC (p = 0.019), and LUSC (p
Source: Frontiers in Genetics - April 22, 2021 Category: Genetics & Stem Cells Source Type: research

NEM-Tar: A Probabilistic Graphical Model for Cancer Regulatory Network Inference and Prioritization of Potential Therapeutic Targets From Multi-Omics Data
In this study, we developed NEM-Tar, which extends the original NEMs to predict drug targets by incorporating causal information of (epi)genetic aberrations for signaling pathway inference. An information theory-based score, weighted information gain (WIG), was proposed to assess the impact of signaling genes on a specific downstream biological process of interest. Subsequently, we conducted simulation studies to compare three inference methods and found that the greedy hill-climbing algorithm demonstrated the highest accuracy and robustness to noise. Furthermore, two case studies were conducted using multi-omics data for ...
Source: Frontiers in Genetics - April 22, 2021 Category: Genetics & Stem Cells Source Type: research

Elucidation of the Host Bronchial Lymph Node miRNA Transcriptome Response to Bovine Respiratory Syncytial Virus
The objective of the present study was to elucidate the changes in the bovine bronchial lymph node miRNA transcriptome in response to BRSV following an experimental viral challenge. Holstein-Friesian calves were either administered a challenge dose of BRSV (103.5 TCID50/ml × 15 ml) (n = 12) or were mock inoculated with sterile phosphate buffered saline (n = 6). Daily scoring of clinical signs was performed and calves were euthanized at day 7 post-challenge. Bronchial lymph nodes were collected for subsequent RNA extraction and sequencing (75 bp). Read counts for known miRNAs were generated using the miRDeep2 package ...
Source: Frontiers in Genetics - April 22, 2021 Category: Genetics & Stem Cells Source Type: research

Combined Analysis of Volatile Terpenoid Metabolism and Transcriptome Reveals Transcription Factors Related to Terpene Synthase in Two Cultivars of Dendrobium officinale Flowers
Dendrobium officinale is a kind of traditional Chinese herbal medicine. Its flowers could be used as health care tea for its aroma flavor and medicinal value. Most recent studies demonstrated that terpenoids are the main components of the aromatic compounds in the flowers, but the biosynthesis of terpenoids is poorly understood in D. officinale. In the experiment, the flowers from two cultivars of D. officinale with different smells were collected. The transcriptome analysis and combined volatile terpenoids determination were performed to identify the genes related to the biosynthesis of the terpenoids. The results showed ...
Source: Frontiers in Genetics - April 22, 2021 Category: Genetics & Stem Cells Source Type: research

Identification of a Potentially Functional circRNA-miRNA-mRNA Regulatory Network in Melanocytes for Investigating Pathogenesis of Vitiligo
CircRNAs have been reported to play essential roles in regulating immunity and inflammation, which may be an important regulatory factor in the development of vitiligo. However, the expression profile of circRNAs and their potential biological functions in vitiligo have not been reported so far. In our study we found there are 64 dysregulated circRNAs and 14 dysregulated miRNAs in the patients with vitiligo. Through the correlation analysis, we obtained 12 dysregulated circRNAs and 5 dysregulated miRNAs, forming 48 relationships in the circRNA-miRNA-mRNA regulatory network. Gene Ontology analysis indicated dysregulated cir...
Source: Frontiers in Genetics - April 21, 2021 Category: Genetics & Stem Cells Source Type: research

Transmembrane serine protease 2 Polymorphisms and Susceptibility to Severe Acute Respiratory Syndrome Coronavirus Type 2 Infection: A German Case-Control Study
The transmembrane serine protease 2 (TMPRSS2) is the major host protease that enables entry of the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) into host cells by spike (S) protein priming. Single nucleotide polymorphisms (SNPs) in the gene TMPRSS2 have been associated with susceptibility to and severity of H1N1 or H1N9 influenza A virus infections. Functional variants may influence SARS-CoV-2 infection risk and severity of Coronavirus disease 2019 (COVID-19) as well. Therefore, we analyzed the role of SNPs in the gene TMPRSS2 in a German case-control study. We performed genotyping of the SNPs rs207078...
Source: Frontiers in Genetics - April 21, 2021 Category: Genetics & Stem Cells Source Type: research

Cryopreservation Preserves Cell-Type Composition and Gene Expression Profiles in Bone Marrow Aspirates From Multiple Myeloma Patients
Single-cell RNA sequencing reveals gene expression differences between individual cells and also identifies different cell populations that are present in the bulk starting material. To obtain an accurate assessment of patient samples, single-cell suspensions need to be generated as soon as possible once the tissue or sample has been collected. However, this requirement poses logistical challenges for experimental designs involving multiple samples from the same subject since these samples would ideally be processed at the same time to minimize technical variation in data analysis. Although cryopreservation has been shown ...
Source: Frontiers in Genetics - April 21, 2021 Category: Genetics & Stem Cells Source Type: research

Editorial: Computational Methods in Predicting Complex Disease Associated Genes and Environmental Factors
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - April 21, 2021 Category: Genetics & Stem Cells Source Type: research

Community Detection in Large-Scale Bipartite Biological Networks
Networks are useful tools to represent and analyze interactions on a large, or genome-wide scale and have therefore been widely used in biology. Many biological networks—such as those that represent regulatory interactions, drug-gene, or gene-disease associations—are of a bipartite nature, meaning they consist of two different types of nodes, with connections only forming between the different node sets. Analysis of such networks requires methodologies that are specifically designed to handle their bipartite nature. Community structure detection is a method used to identify clusters of nodes in a network. This ...
Source: Frontiers in Genetics - April 21, 2021 Category: Genetics & Stem Cells Source Type: research

Governing Personalized Health: A Scoping Review
Genetic research is advancing rapidly. One important area for the application of the results from this work is personalized health. These are treatments and preventive interventions tailored to the genetic profile of specific groups or individuals. The inclusion of personalized health in existing health systems is a challenge for policymakers. In this article, we present the results of a thematic scoping review of the literature dealing with governance and policy of personalized health. Our analysis points to four governance challenges that decisionmakers face against the background of personalized health. First, researche...
Source: Frontiers in Genetics - April 21, 2021 Category: Genetics & Stem Cells Source Type: research

Construction and Comparison of ceRNA Regulatory Network for Different Age Female Breast Cancer
In this study, expression profiles of female breast cancer (BRCA) associated mRNAs, lncRNAs and miRNAs were downloaded from the TCGA database. The sample were manually classified into three groups according to their age at initial pathological diagnosis: young (age ≤ 39 years), elderly (age ≥ 65 years), and intermediate (age 40–64 years). lncRNA-miRNA-mRNA competitive endogenous RNA (ceRNA) network was respectively constructed for different age BRCA. Then, the biological functions of differentially expressed mRNAs (DEmRNAs) in ceRNA network were further investigated by Gene Ontology (GO) and Kyoto Encyclopedia ...
Source: Frontiers in Genetics - April 21, 2021 Category: Genetics & Stem Cells Source Type: research

Toward Genome-Based Selection in Asian Seabass: What Can We Learn From Other Food Fishes and Farm Animals?
We describe the practices of wet lab, farm and lab in detail by focusing onto the foundations and achievements of the program. In addition to the approaches used for selection, our review also provides an inventory of genetic/genomic platforms and technologies developed to (i) provide current and future support for the selection process; and (ii) improve our understanding of the biology of the species. Approaches used for the improvement of terrestrial farm animals are used as examples and references, as those processes are far ahead of the ones used in aquaculture and thus they might help those working on fish to select t...
Source: Frontiers in Genetics - April 21, 2021 Category: Genetics & Stem Cells Source Type: research

Inter-Individual Diversity Scaling Analysis of the Human Virome With Classic Diversity-Area Relationship (DAR) Modeling
The human virome is a critical component of the human microbiome, and it is believed to hold the richest diversity within human microbiomes. Yet, the inter-individual scaling (changes) of the human virome has not been formally investigated to the best of our knowledge. Here we fill the gap by applying diversity-area relationship (DAR) modeling (a recent extension to the classic species-area law in biodiversity and biogeography research) for analyzing four large datasets of the human virome with three DAR profiles: DAR scaling (z)—measuring the inter-individual heterogeneity in virome diversity, MAD (maximal accrual d...
Source: Frontiers in Genetics - April 20, 2021 Category: Genetics & Stem Cells Source Type: research

Genetic Characterization of Mutations Related to Conidiophore Stalk Length Development in Aspergillus niger Laboratory Strain N402
Aspergillus niger is an important filamentous fungus in industrial biotechnology for the production of citric acid and enzymes. In the late 1980s, the A. niger N400/NRRL3 strain was selected for both fundamental and applied studies in relation to several processes including gluconic acid and protein production. To facilitate handling of A. niger, the N400 wild-type strain was UV mutagenized in two consecutive rounds to generate N401 and N402. N402 was used as a reference laboratory strain and exhibits the phenotypes with reduced conidiophore stalk length and reduced radial growth. The conidiophore stalk length and radial g...
Source: Frontiers in Genetics - April 20, 2021 Category: Genetics & Stem Cells Source Type: research

Amino Acid Reduction Can Help to Improve the Identification of Antimicrobial Peptides and Their Functional Activities
This article goes into details about evaluating the performances of more than 5,000 amino acid reduced descriptors generated from 74 types of amino acid reduced alphabet in the first stage and the second stage to construct an excellent two-stage classifier, Identification of Antimicrobial Peptides by Reduced Amino Acid Cluster (iAMP-RAAC), for identifying AMPs and their functional activities, respectively. The results show that the first stage AMP classifier is able to achieve the accuracy of 97.21 and 97.11% for the training data set and independent test dataset. In the second stage, our classifier still shows good perfor...
Source: Frontiers in Genetics - April 20, 2021 Category: Genetics & Stem Cells Source Type: research

A Prognostic Model Based on the Immune-Related lncRNAs in Colorectal Cancer
In this study, bioinformatics methods were used to screen the prognostic immune-related lncRNAs of CRC, and a prognostic risk scoring model based on immune-related lncRNAs signatures were constructed to provide a basis for prognostic evaluation and immunotherapy of CRC patients.MethodsThe clinical information and RNA-seq data of CRC patients were obtained from The Cancer Genome Atlas (TCGA) database. The information of immune-related lncRNA was downloaded from the immunology database and analysis portal. The differentially expressed immune-related lncRNAs (IRLs) were screened by the edgeR package of R software. The prognos...
Source: Frontiers in Genetics - April 20, 2021 Category: Genetics & Stem Cells Source Type: research

Acute Toxicity and DNA Instability Induced by Exposure to Low Doses of Triclosan and Phthalate DEHP, and Their Combinations, in vitro
Triclosan (TCS) is an antimicrobial agent widely used in personal care products (PCP) and the di-(2-ethyl hydroxy-phthalate) (DEHP) is a chemical compound derived from phthalic acid, used in medical devices and plastic products with polyvinyl chloride (PVCs). As result of their extensive use, TCS and DEHP have been found in the environment and previous studies demonstrated the association between their exposure and toxic effects, mostly in aquatic organisms, but there is a shortage in the literature concerning the exposure of TCS and DEHP in human cells. The aim of the present study was to assess the impact of exposure to ...
Source: Frontiers in Genetics - April 20, 2021 Category: Genetics & Stem Cells Source Type: research

Metagenomic Geolocation Prediction Using an Adaptive Ensemble Classifier
Microbiome samples harvested from urban environments can be informative in predicting the geographic location of unknown samples. The idea that different cities may have geographically disparate microbial signatures can be utilized to predict the geographical location based on city-specific microbiome samples. We implemented this idea first; by utilizing standard bioinformatics procedures to pre-process the raw metagenomics samples provided by the CAMDA organizers. We trained several component classifiers and a robust ensemble classifier with data generated from taxonomy-dependent and taxonomy-free approaches. Also, we imp...
Source: Frontiers in Genetics - April 20, 2021 Category: Genetics & Stem Cells Source Type: research

Luminal A Breast Cancer Co-expression Network: Structural and Functional Alterations
Luminal A is the most common breast cancer molecular subtype in women worldwide. These tumors have characteristic yet heterogeneous alterations at the genomic and transcriptomic level. Gene co-expression networks (GCNs) have contributed to better characterize the cancerous phenotype. We have previously shown an imbalance in the proportion of intra-chromosomal (cis-) over inter-chromosomal (trans-) interactions when comparing cancer and healthy tissue GCNs. In particular, for breast cancer molecular subtypes (Luminal A included), the majority of high co-expression interactions connect gene-pairs in the same chromosome, a ph...
Source: Frontiers in Genetics - April 20, 2021 Category: Genetics & Stem Cells Source Type: research

The Links of Ghrelin to Incretins, Insulin, Glucagon, and Leptin After Bariatric Surgery
Type 2 diabetes mellitus (T2DM) is one of the most prominent and socially significant problems. The present study aimed to identify the mechanisms of interaction of critical regulators of carbohydrate metabolism using bioinformatics and experimental methods and to assess their influence on the development of T2DM. We conducted an in silico search for the relationship of hormones and adipokines and performed functional annotation of the receptors for ghrelin and incretins. Hormones and adipokines were assessed in the plasma of obese patients with and without T2DM as well as after laparoscopic sleeve gastrectomy (LSG) and Ro...
Source: Frontiers in Genetics - April 20, 2021 Category: Genetics & Stem Cells Source Type: research

Advances in Genome Editing and Application to the Generation of Genetically Modified Rat Models
The objective of this review is to provide a comprehensive description of the advantages and potential of rat models for addressing specific scientific questions and to characterize the best genome-engineering tools for developing new projects. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - April 20, 2021 Category: Genetics & Stem Cells Source Type: research

Digenic Inheritance and Gene-Environment Interaction in a Patient With Hypertriglyceridemia and Acute Pancreatitis
The etiology of hypertriglyceridemia (HTG) and acute pancreatitis (AP) is complex. Herein, we dissected the underlying etiology in a patient with HTG and AP. The patient had a 20-year history of heavy alcohol consumption and an 8-year history of mild HTG. He was hospitalized for alcohol-triggered AP, with a plasma triglyceride (TG) level up to 21.4 mmol/L. A temporary rise in post-heparin LPL concentration (1.5–2.5 times of controls) was noted during the early days of AP whilst LPL activity was consistently low (50∼70% of controls). His TG level rapidly decreased to normal in response to treatment, and remained n...
Source: Frontiers in Genetics - April 16, 2021 Category: Genetics & Stem Cells Source Type: research

Identification and Functional Prediction of Long Non-Coding RNAs in Dilated Cardiomyopathy by Bioinformatics Analysis
In conclusion, these findings identified eight candidate lncRNAs associated with DCM disease and revealed their potential involvement in DCM partly through ceRNA crosstalk. Our results facilitate the discovery of therapeutic targets and enhance the understanding of DCM pathogenesis. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - April 16, 2021 Category: Genetics & Stem Cells Source Type: research

Sequence Read Depth Analysis of a Monophyletic Cluster of Y Chromosomes Characterized by Structural Rearrangements in the AZFc Region Resulting in DYS448 Deletion and DYF387S1 Duplication
The azoospermia factor c region (AZFc), located in the long arm of the human Y chromosome, is frequently involved in chromosome rearrangements, mainly due to non-allelic homologous recombination events that occur between the nearly identical sequences (amplicon) that comprises it. These rearrangements may have major phenotypic effects like spermatogenic failure or other pathologies linked to male infertility. Moreover, they may also be relevant in forensic genetics, since some of the Y chromosome short tandem repeats (Y-STRs) commonly used in forensic analysis are located in amplicons or in inter-amplicon sequences of the ...
Source: Frontiers in Genetics - April 16, 2021 Category: Genetics & Stem Cells Source Type: research

A Major and Stable Quantitative Trait Locus qSS2 for Seed Size and Shape Traits in a Soybean RIL Population
Seed size and shape traits are important determinants of seed yield and appearance quality in soybean [Glycine max (L.) Merr.]. Understanding the genetic architecture of these traits is important to enable their genetic improvement through efficient and targeted selection in soybean breeding, and for the identification of underlying causal genes. To map seed size and shape traits in soybean, a recombinant inbred line (RIL) population developed from K099 (small seed size) × Fendou 16 (large seed size), was phenotyped in three growing seasons. A genetic map of the RIL population was developed using 1,485 genotyping by ...
Source: Frontiers in Genetics - April 16, 2021 Category: Genetics & Stem Cells Source Type: research

Novel Intronic Mutations Introduce Pseudoexons in DMD That Cause Muscular Dystrophy in Patients
Conclusion: This study defines three novel and one reported intronic mutations, which can result in DMD/BMD. We also emphasize the need to combine WES and cDNA-based methods to detect the variant in the very large DMD gene in which the mutational spectrum is complex. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - April 16, 2021 Category: Genetics & Stem Cells Source Type: research

Unearthing of Key Genes Driving the Pathogenesis of Alzheimer ’s Disease via Bioinformatics
Alzheimer’s disease (AD) is a neurodegenerative disease with unelucidated molecular pathogenesis. Herein, we aimed to identify potential hub genes governing the pathogenesis of AD. The AD datasets of GSE118553 and GSE131617 were collected from the NCBI GEO database. The weighted gene coexpression network analysis (WGCNA), differential gene expression analysis, and functional enrichment analysis were performed to reveal the hub genes and verify their role in AD. Hub genes were validated by machine learning algorithms. We identified modules and their corresponding hub genes from the temporal cortex (TC), frontal cortex...
Source: Frontiers in Genetics - April 16, 2021 Category: Genetics & Stem Cells Source Type: research

Genomic Risk Factors Driving Immune-Mediated Delayed Drug Hypersensitivity Reactions
Adverse drug reactions (ADRs) remain associated with significant mortality. Delayed hypersensitivity reactions (DHRs) that occur greater than 6 h following drug administration are T-cell mediated with many severe DHRs now associated with human leukocyte antigen (HLA) risk alleles, opening pathways for clinical prediction and prevention. However, incomplete negative predictive value (NPV), low positive predictive value (PPV), and a large number needed to test (NNT) to prevent one case have practically prevented large-scale and cost-effective screening implementation. Additional factors outside of HLA contributing to risk of...
Source: Frontiers in Genetics - April 16, 2021 Category: Genetics & Stem Cells Source Type: research

Analysis of mRNA Expression and DNA Methylation Datasets According to the Genomic Distribution of CpG Sites in Osteoarthritis
Conclusions the effect of DNA methylation on the transcriptional regulation is related to the distribution of methylated sites across the genome. Epigenetic studies on the positions of DMS in transcriptional units can inform a better understanding of the function of DNA methylation and its transcription regulation. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - April 15, 2021 Category: Genetics & Stem Cells Source Type: research

Identification of miRNA in Sheep Intramuscular Fat and the Role of miR-193a-5p in Proliferation and Differentiation of 3T3-L1
Intramuscular fat (IMF) is one of the most critical parameters affecting meat quality and mainly affected by genetic factors. MicroRNA as an important regulatory factor, which is still a lack of research in the development of sheep IMF deposition. We used RNA sequencing (RNA-seq) and cell-level validation to explore the role of miRNA in IMF deposition. As for this purpose, longissimus thoracis et lumborum (LTL) samples of 2 month-old (Mth-2) and 12 months-old (Mth-12) Aohan fine-wool sheep (AFWS) were used to identified miRNAs expression. We found 59 differentially expressed miRNAs (DE-miRNA) between these age groups and p...
Source: Frontiers in Genetics - April 15, 2021 Category: Genetics & Stem Cells Source Type: research

Pedigree Analysis of Warmblood Horses Participating in Competitions for Young Horses
The aim of the study was to characterize the population structure and assess the genetic diversity of warmblood horses used in the show jumping discipline. Pedigree data of 1,048 horses participating in the Polish Championships for Young Horses were analyzed. The pedigree of these animals included 12 863 individuals. The study consisted in analysis of the pedigree structure of the horses and characterization of the homozygosity and genetic diversity in the population. It was found that pedigree completeness and depth were sufficient for reliable assessment of the genetic diversity in the analyzed population. Although the a...
Source: Frontiers in Genetics - April 15, 2021 Category: Genetics & Stem Cells Source Type: research

Chromosomal Aneuploidy Associated With Clinical Characteristics of Pregnancy Loss
ObjectiveEmbryonic aneuploidy is found in about half of sporadic pregnancy losses and the associations between the chromosomal aneuploidy and clinical characteristics of pregnancy loss remain unclear. The aims of this study were to evaluate the associations between chromosomal aneuploidy of products of conception (POC) and clinical features of pregnancy loss.MethodsWe conducted a retrospective cohort study including 1,102 women experienced singleton pregnancy loss and underwent chromosomal microarray analysis (CMA) detection of POC in our hospital. The results of molecular karyotypes and clinical features including materna...
Source: Frontiers in Genetics - April 15, 2021 Category: Genetics & Stem Cells Source Type: research

The Promise of the Zebrafish Model for Parkinson ’s Disease: Today’s Science and Tomorrow’s Treatment
The second most prevalent neurodegenerative disorder in the elderly is Parkinson’s disease (PD). Its etiology is unclear and there are no available disease-modifying medicines. Therefore, more evidence is required concerning its pathogenesis. The use of the neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) is the basis of most animal models of PD. MPTP is metabolized by monoamine oxidase B (MAO B) to MPP + and induces the loss of dopaminergic neurons in the substantia nigra in mammals. Zebrafish have been commonly used in developmental biology as a model organism, but owing to its perfect mix of properti...
Source: Frontiers in Genetics - April 15, 2021 Category: Genetics & Stem Cells Source Type: research

Comparative Small RNA Profiling and Functional Exploration on Wheat With High- and Low-Cadmium Accumulation
In this study, high-cadmium-accumulating wheat cultivars (Annong9267) and low-cadmium-accumulating wheat cultivars (Qian 102032) were used as experimental models. The two cultivars were treated by Cd for 2 h to explore the microRNA profiles in root and leaf tissues through small RNA sequencing. Important small RNAs, such as tae-miR9663-5p and tae-miR6201, and potential small RNA-mediated mechanisms associated with cadmium accumulation were identified by summarizing specific microRNA profiling patterns and their respective target genes. At the wheat roots and leaves, differentially expressed small RNAs related to cadmium ac...
Source: Frontiers in Genetics - April 15, 2021 Category: Genetics & Stem Cells Source Type: research

Identification of a MicroRNA Signature Associated With Lymph Node Metastasis in Endometrial Endometrioid Cancer
ConclusionThe miRNA signature could work as a noninvasive method to detect LNM in EEC with a high prediction accuracy. In addition, miR-34c cluster may be a key biomarker referring LNM in endometrial cancer. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - April 15, 2021 Category: Genetics & Stem Cells Source Type: research

KLF4, a Key Regulator of a Transitive Triplet, Acts on the TGF- β Signaling Pathway and Contributes to High-Altitude Adaptation of Tibetan Pigs
Tibetan pigs are native mammalian species on the Tibetan Plateau that have evolved distinct physiological traits that allow them to tolerate high-altitude hypoxic environments. However, the genetic mechanism underlying this adaptation remains elusive. Here, based on multitissue transcriptional data from high-altitude Tibetan pigs and low-altitude Rongchang pigs, we performed a weighted correlation network analysis (WGCNA) and identified key modules related to these tissues. Complex network analysis and bioinformatics analysis were integrated to identify key genes and three-node network motifs. We found that among the six t...
Source: Frontiers in Genetics - April 15, 2021 Category: Genetics & Stem Cells Source Type: research

Genomic Prediction Using Bayesian Regression Models With Global –Local Prior
In this study, we introduced the global–local prior with unknown hyperparameter to Bayesian regression models for genomic prediction, which can trigger further investigations on model development. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - April 15, 2021 Category: Genetics & Stem Cells Source Type: research

Immunohistochemical Expression of Five Protein Combinations Revealed as Prognostic Markers in Asian Oral Cancer
Oral squamous cell carcinoma (OSCC) has a high mortality rate (∼50%), and the 5-year overall survival rate is not optimal. Cyto- and histopathological examination of cancer tissues is the main strategy for diagnosis and treatment. In the present study, we aimed to uncover immunohistochemical (IHC) markers for prognosis in Asian OSCC. From the collected 742 synthetic lethal gene pairs (of various cancer types), we first filtered genes relevant to OSCC, performed 29 IHC stains at different cellular portions and combined these IHC stains into 398 distinct pairs. Next, we identified novel IHC prognostic markers in OSCC amo...
Source: Frontiers in Genetics - April 15, 2021 Category: Genetics & Stem Cells Source Type: research

Three-in-One Simultaneous Extraction of Proteins, Metabolites and Lipids for Multi-Omics
Elucidation of complex molecular networks requires integrative analysis of molecular features and changes at different levels of information flow and regulation. Accordingly, high throughput functional genomics tools such as transcriptomics, proteomics, metabolomics, and lipidomics have emerged to provide system-wide investigations. Unfortunately, analysis of different types of biomolecules requires specific sample extraction procedures in combination with specific analytical instrumentation. The most efficient extraction protocols often only cover a restricted type of biomolecules due to their different physicochemical pr...
Source: Frontiers in Genetics - April 15, 2021 Category: Genetics & Stem Cells Source Type: research

Meta-Analyses of Splicing and Expression Quantitative Trait Loci Identified Susceptibility Genes of Glioma
This study explored splicing quantitative trait loci (sQTL) as molecular QTL and improved the power of QTL mapping through meta-analyses of both cis eQTL and sQTL.MethodsWe first evaluated eQTLs and sQTLs of the CommonMind Consortium (CMC) and Genotype-Tissue Expression Project (GTEx) using genotyping, or whole-genome sequencing and RNA-seq data. Alternative splicing events were characterized using an annotation-free method that detected intron excision events. Then, we conducted meta-analyses by pooling the eQTL and sQTL results of CMC and GTEx using the inverse variance-weighted model. Afterward, we integrated QTL meta-analysis results (Q
Source: Frontiers in Genetics - April 15, 2021 Category: Genetics & Stem Cells Source Type: research

Transcriptome Based Estrogen Related Genes Biomarkers for Diagnosis and Prognosis in Non-small Cell Lung Cancer
ConclusionsThe expressions of FKBP4 and ADCY9 are related to the pathogenesis and prognosis of LUAD. FKBP4 and ADCY9 may serve as biomarkers in LUAD screening and prognosis prediction in clinical settings. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - April 14, 2021 Category: Genetics & Stem Cells Source Type: research

Xp11.2 Duplication in Females: Unique Features of a Rare Copy Number Variation
Among the diseases with X-linked inheritance and intellectual disability, duplication of the Xp11.23p11.22 region is indeed a rare phenomenon, with less than 90 cases known in the literature. Most of them have been recognized with the routine application of array techniques, as these copy number variations (CNVs) are highly variable in size, occurring in recurrent and non-recurrent forms. Its pathogenic role is not debated anymore, but the information available about the pathomechanism, especially in affected females, is still very limited. It has been observed that the phenotype in females varies from normal to severe, wh...
Source: Frontiers in Genetics - April 14, 2021 Category: Genetics & Stem Cells Source Type: research

Coming Out to Play: Privacy, Data Protection, Children ’s Health, and COVID-19 Research
The COVID-19 pandemic has underscored the need for new ways of thinking about data protection. This is especially so in the case of health research with children. The responsible use of children’s data plays a key role in promoting children’s well-being and securing their right to health and to privacy. In this article, we contend that a contextual approach that appropriately balances children’s legal and moral rights and interests is needed when thinking about data protection issues with children. We examine three issues in health research through a child-focused lens: consent to data processing, data re...
Source: Frontiers in Genetics - April 14, 2021 Category: Genetics & Stem Cells Source Type: research

Potential Prospective Biomarkers for Non-small Cell Lung Cancer: Mini-Chromosome Maintenance Proteins
Minichromosome maintenance proteins (MCMs) are considered to be essential factors coupling DNA replication to both cell cycle progression and checkpoint regulation. Previous studies have shown that dysregulation of MCMs are implicated in tumorigenesis of lung cancer. However, the distinct expression/mutation patterns and prognostic values of MCMs in lung cancer have yet to be systematically elucidated. In the present study, we analyzed the transcriptional levels, mutations, and prognostic value of MCM1-10 in non-small cell lung cancer (NSCLC) patients using multiple bioinformatics tools, including ONCOMINE, GEPIA, Kaplan&n...
Source: Frontiers in Genetics - April 14, 2021 Category: Genetics & Stem Cells Source Type: research