Bioinformatics Analysis Discovers Microtubular Tubulin Beta 6 Class V (TUBB6) as a Potential Therapeutic Target in Glioblastoma
Glioblastoma (GBM) has long been a major clinical research challenge to scientists. The pivotal role of the mitochondria related gene family in the promotion of GBM tumorigenesis is not clear. We detected that microtubular tubulin beta 6 class V (TUBB6) was one of 33 differentially expressed mitochondrial-focused genes (DEMFGs) in GBM, and considered that TUBB6 is a potential therapeutic target in GBM. TUBB6 was vital for GBM and marked as the key prognostic gene in primary GBM. Mutations of TUBB6 in GBM were rare. Only four TUBB6 co-expressed hub genes (ANXA2, S100A11, FLNA, and MSN) exhibited poorer overall survival rate...
Source: Frontiers in Genetics - September 18, 2020 Category: Genetics & Stem Cells Source Type: research

Genetic Constraints, Transcriptome Plasticity, and the Evolutionary Response to Climate Change
In situ adaptation to climate change will be critical for the persistence of many ectotherm species due to their relative lack of dispersal capacity. Climate change is causing increases in both the mean and the variance of environmental temperature, each of which may act as agents of selection on different traits. Importantly, these traits may not be heritable or have the capacity to evolve independently from one another. When genetic constraints prevent the “baseline” values of thermal performance traits from evolving rapidly, phenotypic plasticity driven by gene expression might become critical. We review the...
Source: Frontiers in Genetics - September 18, 2020 Category: Genetics & Stem Cells Source Type: research

Plant miRNAs Reduce Cancer Cell Proliferation by Targeting MALAT1 and NEAT1: A Beneficial Cross-Kingdom Interaction
In conclusion, according to other recent discoveries, our study strengthens and expands the hypothesis that plant miRNAs can have a regulatory effect in mammals by targeting both protein-coding and non-coding RNA, thus suggesting new biotechnological applications. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - September 18, 2020 Category: Genetics & Stem Cells Source Type: research

Circular RNAs Are Regulators of Diverse Animal Transcriptomes: One Health Perspective
Derived from linear (parental) precursor mRNA, circRNA are recycled exons and introns whose ends are ligated. By titrating microRNAs and RNA binding proteins, circRNA interconnect networks of competing endogenous RNAs. Without altering chromosomal DNA, circRNA regulates skeletal muscle development and proliferation, lactation, ovulation, brain development, and responses to infections and metabolic stress. This review integrates emerging knowledge of circRNA activity coming from genome-wide characterizations in many clades of animals. circRNA research addresses one of the main pillars of the One Health vision – to imp...
Source: Frontiers in Genetics - September 18, 2020 Category: Genetics & Stem Cells Source Type: research

Comparative and Phylogenetic Analysis of the Complete Chloroplast Genomes of Three Paeonia Section Moutan Species (Paeoniaceae)
In this study, the complete chloroplast genomes of three sect. Moutan plants were sequenced and analyzed. Comparative and phylogenetic analyses of the complete chloroplast genomes of all eight species of sect. Moutan were then conducted. The three complete chloroplast genomes gained in this study showed four-part annular structures, and the genome length, structure, GC content, codon usage, and gene distribution were highly similar. There was greater variation in the noncoding regions of the sequences than in the conserved protein-coding regions. Sequence variations in the small single copy (SSC) regions and large single c...
Source: Frontiers in Genetics - September 18, 2020 Category: Genetics & Stem Cells Source Type: research

IFNAR2 Deficiency Causing Dysregulation of NK Cell Functions and Presenting With Hemophagocytic Lymphohistiocytosis
We describe a 2 year old boy with two previously undescribed frameshift mutations in the interferon (IFN)α/β receptor 2 (IFNAR2) gene presenting with hemophagocytic lymphohistiocytosis (HLH) following measles-mumps-rubella vaccination. Functional analyses show the absence of response to type I IFN in the patient’s cells, as revealed by the lack of phosphorylation of STAT1 and the lack of induction of interferon-stimulated genes upon ex vivo stimulation with IFNα. HLH has been reported in patients with inborn errors of type I IFN-mediated immune responses following vaccination with live-attenuated vir...
Source: Frontiers in Genetics - September 18, 2020 Category: Genetics & Stem Cells Source Type: research

Evaluation of the Minimum Sampling Design for Population Genomic and Microsatellite Studies: An Analysis Based on Wild Maize
Massive parallel sequencing (MPS) is revolutionizing the field of molecular ecology by allowing us to understand better the evolutionary history of populations and species, and to detect genomic regions that could be under selection. However, the economic and computational resources needed generate a tradeoff between the amount of loci that can be obtained and the number of populations or individuals that can be sequenced. In this work, we analyzed and compared two simulated genomic datasets fitting a hierarchical structure, two extensive empirical genomic datasets, and a dataset comprising microsatellite information. For ...
Source: Frontiers in Genetics - September 18, 2020 Category: Genetics & Stem Cells Source Type: research

The Effects of Domestication on Secondary Metabolite Composition in Legumes
Legumes are rich in secondary metabolites, such as polyphenols, alkaloids, and saponins, which are important defense compounds to protect the plant against herbivores and pathogens, and act as signaling molecules between the plant and its biotic environment. Legume-sourced secondary metabolites are well known for their potential benefits to human health as pharmaceuticals and nutraceuticals. During domestication, the color, smell, and taste of crop plants have been the focus of artificial selection by breeders. Since these agronomic traits are regulated by secondary metabolites, the basis behind the genomic evolution was t...
Source: Frontiers in Genetics - September 18, 2020 Category: Genetics & Stem Cells Source Type: research

Chromatin Landscape During Skeletal Muscle Differentiation
Cellular commitment and differentiation involve highly coordinated mechanisms by which tissue-specific genes are activated while others are repressed. These mechanisms rely on the activity of specific transcription factors, chromatin remodeling enzymes, and higher-order chromatin organization in order to modulate transcriptional regulation on multiple cellular contexts. Tissue-specific transcription factors are key mediators of cell fate specification with the ability to reprogram cell types into different lineages. A classic example of a master transcription factor is the muscle specific factor MyoD, which belongs to the ...
Source: Frontiers in Genetics - September 18, 2020 Category: Genetics & Stem Cells Source Type: research

Integrated Analysis of lncRNA-miRNA-mRNA ceRNA Network Identified lncRNA EPB41L4A-AS1 as a Potential Biomarker in Non-small Cell Lung Cancer
ConclusionIn this study, we constructed a lncRNA-miRNA-mRNA ceRNA network to investigate potential prognostic biomarkers for NSCLC. We found that lncRNA EPB41L4A-AS1 could function as a regulator in the pathogenesis of NSCLC. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - September 18, 2020 Category: Genetics & Stem Cells Source Type: research

A Recurrent Pathogenic Variant of INPP5K Underlies Autosomal Recessive Congenital Muscular Dystrophy With Cataracts and Intellectual Disability: Evidence for a Founder Effect in Southern Italy
Inositol polyphosphate-5-phosphatase K [INPP5K (MIM: 607875)] acts as a PIP3 5-phosphatase and regulates actin cytoskeleton, insulin, and cell migration. Biallelic pathogenic variants in INPP5K have recently been reported in patients affected by a form of muscular dystrophy with childhood onset. Affected patients have limb girdle muscle weakness, often associated with bilateral cataracts, short stature, and intellectual disability. Here we report four patients affected by INPP5K-related muscle dystrophy, who were apparently unrelated but originated from the same geographical area in South Italy. These patients manifest a r...
Source: Frontiers in Genetics - September 18, 2020 Category: Genetics & Stem Cells Source Type: research

MicroRNA-7 Targets the KLF4 Gene to Regulate the Proliferation and Differentiation of Chicken Primary Myoblasts
In this study, we found that the expression levels of miR-7 and the Krüppel-like factor 4 (KLF4) gene were negatively correlated during the embryonic phase, and in vitro induced differentiation. A dual-luciferase assay and a rescue experiment show that there is a target relationship between miR-7 and the KLF4 gene. Meanwhile, the results show that overexpression of miR-7 inhibited the proliferation and differentiation of CPMs, while inhibition of miR-7 had the opposite effects. Furthermore, overexpression of the KLF4 gene was found to significantly promote the proliferation and differentiation of CPMs. Conversely, inh...
Source: Frontiers in Genetics - September 18, 2020 Category: Genetics & Stem Cells Source Type: research

Insights Into the Albinism Mechanism for Two Distinct Color Morphs of Northern Snakehead, Channa argus Through Histological and Transcriptome Analyses
In this study, the melanocytes in the skin of two distinct color morphs C. argus were investigated and compared through employment of the microscopic analysis, hematoxylin and eosin (H&E) and Masson Fontana staining. Our results demonstrated the uneven distribution of melanocytes with extremely low density and most of them were in the state of aging or death. Meanwhile, there was no obvious pigment layer and melanocytes distribution pattern found in the albino-type (AT), while the melanocytes were evenly distributed with abundance in the bicolor-type (BT). The transcriptome analysis through Illumina HiSeq sequencing sh...
Source: Frontiers in Genetics - September 18, 2020 Category: Genetics & Stem Cells Source Type: research

Identification of QTLs for Domestication-Related Traits in Zombi Pea [Vigna vexillata (L.) A. Rich], a Lost Crop of Africa
In this study, the genetic basis of the following 13 domestication-related traits was investigated in an F2 population comprising 198 individuals derived from a cross between cultivated (var. macrosperma) and wild (var. vexillata) zombi pea accessions: seed dormancy, pod shattering, days-to-flowering, days-to-maturity, stem thickness, stem length, number of branches, leaf area, pod length, 100-seed weight, seed width, seed length, and seeds per pod. A genetic map containing 6,529 single nucleotide polymorphisms constructed for the F2 population was used to identify quantitative trait loci (QTLs) for these traits. A total o...
Source: Frontiers in Genetics - September 18, 2020 Category: Genetics & Stem Cells Source Type: research

Lysine Acetylome Study of Human Hepatocellular Carcinoma Tissues for Biomarkers and Therapeutic Targets Discovery
Lysine acetylation is a vital post-translational modification (PTM) of proteins, which plays an important role in cancer development. In healthy human liver tissues, multiple non-histone proteins were identified with acetylation modification, however, the role of acetylated proteins in hepatocellular carcinoma (HCC) development remains largely unknown. Here we performed a quantitative acetylome study of tumor and normal liver tissues from HCC patients. Overall, 598 lysine acetylation sites in 325 proteins were quantified, and almost 59% of their acetylation levels were significantly changed. The differentially acetylated p...
Source: Frontiers in Genetics - September 17, 2020 Category: Genetics & Stem Cells Source Type: research

Elucidating the Genetic Architecture of Fiber Quality in Hemp (Cannabis sativa L.) Using a Genome-Wide Association Study
This study provides new insights into the genetic architecture of fiber traits, identifies QTLs and candidate genes that form the basis for molecular breeding for high fiber quality hemp cultivars. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - September 17, 2020 Category: Genetics & Stem Cells Source Type: research

Identification of Signatures of Selection by Whole-Genome Resequencing of a Chinese Native Pig
Identification of genomic signatures of selection that help reveal genetic mechanisms underlying traits in domesticated pigs is of importance. Anqing six-end-white pig (ASP), a representative of the native breeds in China, has many distinguishing phenotypic characteristics. To identify the genomic signatures of selection of the ASP, whole-genome sequencing of 20 ASPs produced 469.01 Gb of sequence data and more than 26 million single-nucleotide polymorphisms. Combining these data with the available whole genomes of 13 Chinese wild boars, 157 selected regions harboring 48 protein-coding genes were identified by applying the...
Source: Frontiers in Genetics - September 17, 2020 Category: Genetics & Stem Cells Source Type: research

Prediction of Recombination Spots Using Novel Hybrid Feature Extraction Method via Deep Learning Approach
This study proposes an intelligent computational predictor called iRSpots-DNN for the identification of recombination spots. The proposed predictor is based on a novel feature extraction method and an optimized deep neural network (DNN). The DNN was employed as a classification engine whereas, the novel features extraction method was developed to extract meaningful features for the identification of hotspots and coldspots across the yeast genome. Unlike previous algorithms, the proposed feature extraction avoids bias among different selected features and preserved the sequence discriminant properties along with the sequenc...
Source: Frontiers in Genetics - September 17, 2020 Category: Genetics & Stem Cells Source Type: research

Twenty Years Later: A Comprehensive Review of the X Chromosome Use in Forensic Genetics
The unique structure of the X chromosome shaped by evolution has led to the present gender-specific genetic differences, which are not shared by its counterpart, the Y chromosome, and neither by the autosomes. In males, recombination between the X and Y chromosomes is limited to the pseudoautosomal regions, PAR1 and PAR2; therefore, in males, the X chromosome is (almost) entirely transmitted to female offspring. On the other hand, the X chromosome is present in females with two copies that recombine along the whole chromosome during female meiosis and that is transmitted to both female and male descendants. These transmiss...
Source: Frontiers in Genetics - September 17, 2020 Category: Genetics & Stem Cells Source Type: research

Stemness Related Genes Revealed by Network Analysis Associated With Tumor Immune Microenvironment and the Clinical Outcome in Lung Adenocarcinoma
In conclusion, the 15 SRGs reported in our study may be used as potential candidate biomarkers for prognostic indicators and therapeutic targets after further validation. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - September 16, 2020 Category: Genetics & Stem Cells Source Type: research

Establishment of Quantitative PCR Assays for Active Long Interspersed Nuclear Element-1 Subfamilies in Mice and Applications to the Analysis of Aging-Associated Retrotransposition
The retrotransposon long interspersed nuclear element-1 (LINE-1) can autonomously increase its copy number within a host genome through the retrotransposition process. LINE-1 is active in the germline and in neural progenitor cells, and its somatic retrotransposition activity has a broad impact on neural development and susceptibility to neuropsychiatric disorders. The method to quantify the genomic copy number of LINE-1 would be important in unraveling the role of retrotransposition, especially in the brain. However, because of the species-specific evolution of LINE-1 sequences, methods for quantifying the copy number sho...
Source: Frontiers in Genetics - September 16, 2020 Category: Genetics & Stem Cells Source Type: research

Long Non-coding RNA LINC00115 Contributes to the Progression of Colorectal Cancer by Targeting miR-489-3p via the PI3K/AKT/mTOR Pathway
In conclusion, our findings demonstrated that LINC00115 serves as an oncogene in CRC metastasis. Deeper understanding of the LINC00115/miR-489-3p axis might provide potential therapeutic targets against CRC metastasis. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - September 16, 2020 Category: Genetics & Stem Cells Source Type: research

The Role of Genetically Determined Glycemic Traits in Breast Cancer: A Mendelian Randomization Study
ConclusionOur findings indicate a null association between genetically determined GTs and breast cancer risk among European women. Our findings may contribute to more complete characterizing of metabolic pathways in GTs and breast cancer. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - September 16, 2020 Category: Genetics & Stem Cells Source Type: research

Identifying Effective Antiviral Drugs Against SARS-CoV-2 by Drug Repositioning Through Virus-Drug Association Prediction
In this study, potential antiviral drugs against SARS-CoV-2 were identified by drug repositioning through Virus-Drug Association (VDA) prediction. 96 VDAs between 11 types of viruses similar to SARS-CoV-2 and 78 small molecular drugs were extracted and a novel VDA identification model (VDA-RLSBN) was developed to find potential VDAs related to SARS-CoV-2. The model integrated the complete genome sequences of the viruses, the chemical structures of drugs, a regularized least squared classifier (RLS), a bipartite local model, and the neighbor association information. Compared with five state-of-the-art association prediction...
Source: Frontiers in Genetics - September 16, 2020 Category: Genetics & Stem Cells Source Type: research

Familial Focal Segmental Glomerulosclerosis With Late-Onset Presentation and R229Q/R291W Podocin Mutations
ConclusionCoexistence of the two NPHS2 variants R229Q and R291W in compound heterozygosis was a determinant of the FSGS phenotype. The presence of these variants alone in heterozygosis did not cause significant proteinuria. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - September 16, 2020 Category: Genetics & Stem Cells Source Type: research

Prioritizing CircRNA –Disease Associations With Convolutional Neural Network Based on Multiple Similarity Feature Fusion
In this study, we propose a novel method named MSFCNN for the task of circRNA–disease association prediction, involving two-layer convolutional neural networks on a feature matrix that fuses multiple similarity kernels and interaction features among circRNAs, miRNAs, and diseases. First, four circRNA similarity kernels and seven disease similarity kernels are constructed based on the biological or topological properties of circRNAs and diseases. Subsequently, the similarity kernel fusion method is used to integrate the similarity kernels into one circRNA similarity kernel and one disease similarity kernel, respective...
Source: Frontiers in Genetics - September 16, 2020 Category: Genetics & Stem Cells Source Type: research

Interaction of Scientific Knowledge and Implementation of the Multilateral Environment Agreements in Relation to Digital Sequence Information on Genetic Resources
Integration of scientific knowledge into negotiations of the Multilateral Environment Agreements (MEAs) is crucial to effective implementation of those MEAs by ensuring uniformity in their terminology. Recent innovations in the field of biotechnology provoked a discussion over “Digital Sequence Information” (DSI) in fora of several MEAs. In the context of this discussion, the term DSI remains ambiguous and encompasses a wide range of concepts, including, at least, DNA/RNA base sequence data. We focused on how the term “DSI” was regarded in negotiations of the Convention on Biological Diversity and t...
Source: Frontiers in Genetics - September 16, 2020 Category: Genetics & Stem Cells Source Type: research

Identification and Validation of an Immunological Expression-Based Prognostic Signature in Breast Cancer
Conclusions: Our study revealed that a PIRDEG signature could be a candidate prognostic biomarker for predicting the overall survival (OS) of patients with BRCA. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - September 16, 2020 Category: Genetics & Stem Cells Source Type: research

Identification and Functional Analysis of Long Non-coding RNAs in Autism Spectrum Disorders
In conclusion, ASD-related lncRNAs participated in the pathogenesis of ASD through various known biological pathways, which may be differential in distinct brain regions. Detailed investigation into ASD-related lncRNAs can provide clues for developing potential ASD diagnosis biomarkers and therapy. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - September 16, 2020 Category: Genetics & Stem Cells Source Type: research

Genotypic and Phenotypic Analysis in Chinese Cohort With Autosomal Recessive Osteogenesis Imperfecta
This study recruited a Chinese cohort of 74 AR-OI families, aiming to establish the mutation spectrum and to examine the genotypic and phenotypic correlation. We identified 82 variants including 25 novel variants and 57 HGMD reported variants in these AR-OI patients, using whole exome sequencing/panel sequencing combined with Sanger sequencing. Pathogenic mutations were found at WNT1 (n = 30, 40.54%), SERPINF1 (n = 22, 29.73%), FKBP10 (n = 10, 13.51%), CRTAP (n = 3, 4.05%), P3H1 (n = 3, 4.05%), SERPINH1 (n = 2, 2.70%), SEC24D (n = 3, 4.05%), and PLOD2 (n = 1, 1.35%) respectively. Thus, WNT1 represents the most frequent pat...
Source: Frontiers in Genetics - September 15, 2020 Category: Genetics & Stem Cells Source Type: research

Transcriptomic Analysis Reveals Important Roles of Lignin and Flavonoid Biosynthetic Pathways in Rice Thermotolerance During Reproductive Stage
Rice is one of the major staple cereals in the world, but heat stress is increasingly threatening its yield. Analyzing the thermotolerance mechanism from new thermotolerant germplasms is very important for rice improvement. Here, physiological and transcriptome analyses were used to characterize the difference between two germplasms, heat-sensitive MH101 and heat-tolerant SDWG005. Two genotypes exhibited diverse heat responses in pollen viability, pollination characteristics, and antioxidant enzymatic activity in leaves and spikelets. Through cluster analysis, the global transcriptomic changes indicated that the ability of...
Source: Frontiers in Genetics - September 15, 2020 Category: Genetics & Stem Cells Source Type: research

Soybean Endo-1,3-Beta-Glucanase (GmGLU) Interaction With Soybean mosaic virus-Encoded P3 Protein May Contribute to the Intercelluar Movement
This study provides evidence that the soybean (Glycine max) endo-1,3-beta-glucanase protein (designated as GmGLU) interacts with SMV-P3 by using a yeast two-hybrid system to screen a soybean cDNA library. A bimolecular fluorescence complementation assay further confirmed the interaction, which occurred on the cytomembrane in Nicotiana benthamiana cells. Subcellular localization experiment indicated that GmGLU localized in cytomembrane and could co-localized at PD with PD marker. The transient expression of GmGLU promoted the coupling of Turnip mosaic virus replication and cell-to-cell movement in N. benthamiana. Meanwhile,...
Source: Frontiers in Genetics - September 15, 2020 Category: Genetics & Stem Cells Source Type: research

Preclinical and Clinical Epigenetic-Based Reconsideration of Beckwith-Wiedemann Syndrome
Epigenetics has achieved a profound impact in the biomedical field, providing new experimental opportunities and innovative therapeutic strategies to face a plethora of diseases. In the rare diseases scenario, Beckwith-Wiedemann syndrome (BWS) is a pediatric pathological condition characterized by a complex molecular basis, showing alterations in the expression of different growth-regulating genes. The molecular origin of BWS is associated with impairments in the genomic imprinting of two domains at the 11p15.5 chromosomal region. The first domain contains three different regions: insulin growth like factor gene (IGF2), H1...
Source: Frontiers in Genetics - September 15, 2020 Category: Genetics & Stem Cells Source Type: research

Terminus-Associated Non-coding RNAs: Trash or Treasure?
3′ untranslated regions (3′ UTRs) of protein-coding genes are well known for their important roles in determining the fate of mRNAs in diverse processes, including trafficking, stabilization, translation, and RNA–protein interactions. However, non-coding RNAs (ncRNAs) scattered around 3′ termini of the protein-coding genes, here referred to as terminus-associated non-coding RNAs (TANRs), have not attracted wide attention in RNA research. Indeed, whether TANRs are transcriptional noise, degraded mRNA products, alternative 3′ UTRs, or functional molecules has remained unclear for a long time. As...
Source: Frontiers in Genetics - September 15, 2020 Category: Genetics & Stem Cells Source Type: research

Systematic Identification of Hub Genes in Placenta Accreta Spectrum Based on Integrated Transcriptomic and Proteomic Analysis
In this study, placenta tissues from 5 patients with PAS and 5 healthy pregnant women were collected for transcriptomic and proteomic sequencing and integrated analysis. A total of 728 messenger RNAs and 439 proteins were found to be significantly different between PAS group and non-PAS group, in which 23 hub genes were differentially expressed in both transcriptome and proteome. Functional enrichment analysis showed that the differentially expressed genes were mainly related to cell proliferation, migration and vascular development. Totally 18 long non-coding RNA were found that might regulate the expression of hub genes....
Source: Frontiers in Genetics - September 15, 2020 Category: Genetics & Stem Cells Source Type: research

Construction and Characterization of a Synergistic lncRNA –miRNA Network Reveals a Crucial and Prognostic Role of lncRNAs in Colon Cancer
In this study, we constructed and characterized an lncRNA–miRNA synergistic network following a four-step approach by integrating the regulatory pairs and expression profiles. The synergistic interactions with more shared regulatory mRNAs were found to have higher interactional intensity. Through the analysis of nodes in the network, we found that lncRNAs played roles that are more central and had similar synergistic interactions with their neighbors when compared with miRNAs. In addition, known colon adenocarcinoma (COAD)-related RNAs were found to be enriched in this synergistic network, with higher degrees, betwee...
Source: Frontiers in Genetics - September 15, 2020 Category: Genetics & Stem Cells Source Type: research

Genome- and Transcriptome-Wide Identification of C3Hs in Common Bean (Phaseolus vulgaris L.) and Structural and Expression-Based Analyses of Their Functions During the Sprout Stage Under Salt-Stress Conditions
CCCH (C3H) zinc-finger proteins are involved in plant biotic and abiotic stress responses, growth and development, and disease resistance. However, studies on C3H genes in Phaseolus vulgaris L. (common bean) are limited. Here, 29 protein-encoding C3H genes, located on 11 different chromosomes, were identified in P. vulgaris. A phylogenetic analysis categorized the PvC3Hs into seven subfamilies on the basis of distinct features, such as exon–intron structure, cis-regulatory elements, and MEME motifs. A collinearity analysis revealed connections among the PvC3Hs in the same and different species. The PvC3H genes showed...
Source: Frontiers in Genetics - September 15, 2020 Category: Genetics & Stem Cells Source Type: research

Insulin-Independent and Dependent Glucose Transporters in Brain Mural Cells in CADASIL
Typical cerebral autosomal-dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is caused by mutations in the human NOTCH3 gene. Cerebral autosomal-dominant arteriopathy with subcortical infarcts and leukoencephalopathy is characterized by subcortical ischemic strokes due to severe arteriopathy and fibrotic thickening of small vessels. Blood regulating vascular smooth muscle cells (VSMCs) appear as the key target in CADASIL but the pathogenic mechanisms remain unclear. With the hypothesis that brain glucose metabolism is disrupted in VSMCs in CADASIL, we investigated post-mortem tissues and VSM...
Source: Frontiers in Genetics - September 15, 2020 Category: Genetics & Stem Cells Source Type: research

Genes and Pathways Implicated in Tetralogy of Fallot Revealed by Ultra-Rare Variant Burden Analysis in 231 Genome Sequences
Recent genome-wide studies of rare genetic variants have begun to implicate novel mechanisms for tetralogy of Fallot (TOF), a severe congenital heart defect (CHD). To provide statistical support for case-only data without parental genomes, we re-analyzed genome sequences of 231 individuals with TOF (n = 175) or related CHD. We adapted a burden test originally developed for de novo variants to assess ultra-rare variant burden in individual genes, and in gene-sets corresponding to functional pathways and mouse phenotypes, accounting for highly correlated gene-sets and for multiple testing. For truncating variants, the gene b...
Source: Frontiers in Genetics - September 15, 2020 Category: Genetics & Stem Cells Source Type: research

Editorial: Role of Epigenetic Modifications on Diet-Induced Metabolic Diseases
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - September 15, 2020 Category: Genetics & Stem Cells Source Type: research

Pharmacological Effects of Novel Peptide Drugs on Allergic Rhinitis at the Small Ribonucleic Acids Level
Using an allergic rhinitis (AR) model, we evaluated the pharmacological effects of novel peptide drugs (P-ONE and P-TWO) at the small RNA (sRNA) level. Using high-throughput sequencing, we assessed the sRNA expression profile of the negative control, AR antagonist (positive control), P-ONE, and P-TWO groups. By functional clustering and Gene Ontology and KEGG pathway analyses, we found that sRNA target genes have a specific enrichment pattern and may contribute to the effects of the novel peptides. Small RNA sequencing confirmed the biological foundations of novel and traditional AR treatments and suggested unique pharmaco...
Source: Frontiers in Genetics - September 11, 2020 Category: Genetics & Stem Cells Source Type: research

Novel Compound Heterozygous TMPRSS15 Gene Variants Cause Enterokinase Deficiency
ConclusionWe reported an EKD patient with novel compound heterozygous variants in the TMPRSS15 gene, expanding the genotypic and phenotypic spectrum of EKD. The functional characterization in vitro demonstrated that the c.1921G> A variant alters pre-mRNA splicing and the p.Val799Asp variant leads to a decrease in protein expression and enzyme activity. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - September 11, 2020 Category: Genetics & Stem Cells Source Type: research

Maternal High-Sucrose Diet Affects Phenotype Outcome in Adult Male Offspring: Role of Zbtb16
Overnutrition in pregnancy and lactation affects fetal and early postnatal development, which can result in metabolic disorders in adulthood. We tested a hypothesis that variation of the Zbtb16 gene, a significant energy metabolism regulator, modulates the effect of maternal high-sucrose diet (HSD) on metabolic and transcriptomic profiles of the offspring. We used the spontaneously hypertensive rat (SHR) strain and a minimal congenic rat strain SHR-Zbtb16, carrying the Zbtb16 gene allele originating from the PD/Cub rat, a metabolic syndrome model. Sixteen-week-old SHR and SHR-Zbtb16 rat dams were fed either standard diet (...
Source: Frontiers in Genetics - September 11, 2020 Category: Genetics & Stem Cells Source Type: research

Identification of Metastasis-Associated Biomarkers in Synovial Sarcoma Using Bioinformatics Analysis
Synovial sarcoma (SS) is a highly aggressive soft tissue tumor with high risk of local recurrence and metastasis. However, the mechanisms underlying SS metastasis are still largely unclear. The purpose of this study is to screen metastasis-associated biomarkers in SS by integrated bioinformatics analysis. Two mRNA datasets (GSE40018 and GSE40021) were selected to analyze the differentially expressed genes (DEGs). Using the Database for Annotation, Visualization and Integrated Discovery (DAVID) and gene set enrichment analysis (GSEA), functional and pathway enrichment analyses were performed for DEGs. Then, the protein-prot...
Source: Frontiers in Genetics - September 11, 2020 Category: Genetics & Stem Cells Source Type: research

PacBio Long-Read Sequencing Transcriptome Dataset of Adult Harmonia axyridis Under Diapause Inducing and Reproductive Inducing Photoperiod
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - September 11, 2020 Category: Genetics & Stem Cells Source Type: research

Genetic Diversity and Population Structure of Cannabis Based on the Genome-Wide Development of Simple Sequence Repeat Markers
Cannabis has been used as a source of nutrition, medicine, and fiber. However, lack of genomic simple sequence repeat (SSR) markers had limited the genetic research on Cannabis species. In the present study, 92,409 motifs were identified, and 63,707 complementary SSR primer pairs were developed. The most abundant SSR motifs had six repeat units (36.60%). The most abundant type of motif was dinucleotides (70.90%), followed by trinucleotides, tetranucleotides, and pentanucleotides. We randomly selected 80 pairs of genomic SSR markers, of which 69 (86.25%) were amplified successfully; 59 (73.75%) of these were polymorphic. Ge...
Source: Frontiers in Genetics - September 11, 2020 Category: Genetics & Stem Cells Source Type: research

Progesterone Receptor Signaling Selectively Modulates Cytokine-Induced Global Gene Expression in Human Cervical Stromal Cells
Preterm birth (PTB) is the leading cause of morbidity and mortality in infants
Source: Frontiers in Genetics - September 11, 2020 Category: Genetics & Stem Cells Source Type: research

Phenotypically Selective Genotyping Realizes More Genetic Gains in a Rainbow Trout Breeding Program in the Presence of Genotype-by-Environment Interactions
In conclusion, we recommend phenotypic genotyping of top and bottom fish in C and top fish in B for the purpose of selecting breeding animals and random genotyping of individuals in B and C for the purpose of estimating variance components when a genomic breeding program for rainbow trout aims to improve animals’ performance in C. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - September 11, 2020 Category: Genetics & Stem Cells Source Type: research

Comprehensive Analysis of Respiratory Burst Oxidase Homologs (Rboh) Gene Family and Function of GbRboh5/18 on Verticillium Wilt Resistance in Gossypium barbadense
This study sheds fresh light on the molecular evolutionary properties and function of Rboh genes in cotton, and provides a reference for improving cotton’s responses to the pathogen V. dahliae. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - September 11, 2020 Category: Genetics & Stem Cells Source Type: research

Synergistic Enhancement of Cancer Therapy Using HDAC Inhibitors: Opportunity for Clinical Trials
Chemotherapy is one of the most established and effective treatments for almost all types of cancer. However, the elevated toxicity due to the non-tumor-associated effects, development of secondary malignancies, infertility, radiation-induced fibrosis and resistance to treatment limit the effectiveness and safety of treatment. In addition, these multiple factors significantly impact quality of life. Over the last decades, our increased understanding of cancer epigenetics has led to new therapeutic approaches and the promise of improved patient outcomes. Epigenetic alterations are commonly found in cancer, especially the in...
Source: Frontiers in Genetics - September 11, 2020 Category: Genetics & Stem Cells Source Type: research