Exploring Prediction of Antimicrobial Resistance Based on Protein Solvent Accessibility Variation
Antimicrobial resistance (AMR) is a significant and growing public health threat. Sequencing of bacterial isolates is becoming more common, and therefore automatic identification of resistant bacterial strains is of pivotal importance for efficient, wide-spread AMR detection. To support this approach, several AMR databases and gene identification algorithms have been recently developed. A key problem in AMR detection, however, is the need for computational approaches detecting potential novel AMR genes or variants, which are not included in the reference databases. Toward this direction, here we study the relation between ...
Source: Frontiers in Genetics - January 22, 2021 Category: Genetics & Stem Cells Source Type: research

Independent Validation of Genomic Prediction in Strawberry Over Multiple Cycles
The University of Florida strawberry (Fragaria × ananassa) breeding program has implemented genomic prediction (GP) as a tool for choosing outstanding parents for crosses over the last five seasons. This has allowed the use of some parents 1 year earlier than with traditional methods, thus reducing the duration of the breeding cycle. However, as the number of breeding cycles increases over time, greater knowledge is needed on how multiple cycles can be used in the practical implementation of GP in strawberry breeding. Advanced selections and cultivars totaling 1,558 unique individuals were tested in field trials for ...
Source: Frontiers in Genetics - January 22, 2021 Category: Genetics & Stem Cells Source Type: research

Neonatal Screening and Genotype-Phenotype Correlation of 21-Hydroxylase Deficiency in the Chinese Population
Conclusions: This study suggested that neonatal screening effectively leads to the early diagnosis of 21-OHD and reduces fatal adrenal crisis. Our data provide additional information on the occurrence and genotype-phenotype correlation of 21-OHD in the Chinese population which can be used to better inform treatment and improve prognosis. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 22, 2021 Category: Genetics & Stem Cells Source Type: research

A Review of Statistical Methods for Identifying Trait-Relevant Tissues and Cell Types
Genome-wide association studies (GWASs) have identified and replicated many genetic variants that are associated with diseases and disease-related complex traits. However, the biological mechanisms underlying these identified associations remain largely elusive. Exploring the biological mechanisms underlying these associations requires identifying trait-relevant tissues and cell types, as genetic variants likely influence complex traits in a tissue- and cell type-specific manner. Recently, several statistical methods have been developed to integrate genomic data with GWASs for identifying trait-relevant tissues and cell ty...
Source: Frontiers in Genetics - January 22, 2021 Category: Genetics & Stem Cells Source Type: research

Stellate Genes and the piRNA Pathway in Speciation and Reproductive Isolation of Drosophila melanogaster
One of the main conditions of the species splitting from a common precursor lineage is the prevention of a gene flow between diverging populations. The study of Drosophila interspecific hybrids allows to reconstruct the speciation mechanisms and to identify hybrid incompatibility factors that maintain post-zygotic reproductive isolation between closely related species. The regulation, evolution, and maintenance of the testis-specific Ste-Su(Ste) genetic system in Drosophila melanogaster is the subject of investigation worldwide. X-linked tandem testis-specific Stellate genes encode proteins homologous to the regulatory &be...
Source: Frontiers in Genetics - January 22, 2021 Category: Genetics & Stem Cells Source Type: research

A Zero-Inflated Latent Dirichlet Allocation Model for Microbiome Studies
The human microbiome consists of a community of microbes in varying abundances and is shown to be associated with many diseases. An important first step in many microbiome studies is to identify possible distinct microbial communities in a given data set and to identify the important bacterial taxa that characterize these communities. The data from typical microbiome studies are high dimensional count data with excessive zeros due to both absence of species (structural zeros) and low sequencing depth or dropout. Although methods have been developed for identifying the microbial communities based on mixture models of counts...
Source: Frontiers in Genetics - January 22, 2021 Category: Genetics & Stem Cells Source Type: research

QTL Mapping and Identification of Candidate Genes for Heat Tolerance at the Flowering Stage in Rice
In this study, the F2:3 population derived from a cross between Huanghuazhan (HHZ), a heat-tolerant cultivar, and 9311, a heat-sensitive variety, was used to map HT QTLs during the flowering stage in rice. A new major QTL, qHTT8, controlling HT was identified on chromosome 8 using the bulked-segregant analysis (BSA)-seq method. The QTL qHTT8 was mapped into the 3,555,000–4,520,000 bp, which had a size of 0.965 Mb. The candidate region of qHTT8 on chromosome 8 contained 65 predicted genes, and 10 putative predicted genes were found to be associated with abiotic stress tolerance. Furthermore, qRT-PCR was performed to a...
Source: Frontiers in Genetics - January 22, 2021 Category: Genetics & Stem Cells Source Type: research

Production of CFTR- ΔF508 Rabbits
Cystic Fibrosis (CF) is a lethal autosomal recessive disease caused by mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR). The most common mutation is the deletion of phenylalanine residue at position 508 (ΔF508). Here we report the production of CFTR-ΔF508 rabbits by CRISPR/Cas9-mediated gene editing. After microinjection and embryo transfer, 77 kits were born, of which five carried the ΔF508 mutation. To confirm the germline transmission, one male ΔF508 founder was bred with two wild-type females and produced 16 F1 generation kits, of which six are hetero...
Source: Frontiers in Genetics - January 22, 2021 Category: Genetics & Stem Cells Source Type: research

Quantifying the Stability of Coupled Genetic and Epigenetic Switches With Variational Methods
The Waddington landscape provides an intuitive metaphor to view development as a ball rolling down the hill, with distinct phenotypes as basins and differentiation pathways as valleys. Since, at a molecular level, cell differentiation arises from interactions among the genes, a mathematical definition for the Waddington landscape can, in principle, be obtained by studying the gene regulatory networks. For eukaryotes, gene regulation is inextricably and intimately linked to histone modifications. However, the impact of such modifications on both landscape topography and stability of attractor states is not fully understood....
Source: Frontiers in Genetics - January 22, 2021 Category: Genetics & Stem Cells Source Type: research

DeCban: Prediction of circRNA-RBP Interaction Sites by Using Double Embeddings and Cross-Branch Attention Networks
In this study, we propose a deep learning method to identify circRNA-RBP interactions, called DeCban, which is featured by hybrid double embeddings for representing RNA sequences and a cross-branch attention neural network for classification. To capture more information from RNA sequences, the double embeddings include pre-trained embedding vectors for both RNA segments and their converted amino acids. Meanwhile, the cross-branch attention network aims to address the learning of very long sequences by integrating features of different scales and focusing on important information. The experimental results on 37 benchmark da...
Source: Frontiers in Genetics - January 22, 2021 Category: Genetics & Stem Cells Source Type: research

Predicting Genome Architecture: Challenges and Solutions
Genome architecture plays a pivotal role in gene regulation. The use of high-throughput methods for chromatin profiling and 3-D interaction mapping provide rich experimental data sets describing genome organization and dynamics. These data challenge development of new models and algorithms connecting genome architecture with epigenetic marks. In this review, we describe how chromatin architecture could be reconstructed from epigenetic data using biophysical or statistical approaches. We discuss the applicability and limitations of these methods for understanding the mechanisms of chromatin organization. We also highlight t...
Source: Frontiers in Genetics - January 22, 2021 Category: Genetics & Stem Cells Source Type: research

Genetic and Epigenetic Consequence of Early-Life Social Stress on Depression: Role of Serotonin-Associated Genes
Early-life adversity caused by poor social bonding and deprived maternal care is known to affect mental wellbeing and physical health. It is a form of chronic social stress that persists because of a negative environment, and the consequences are long-lasting on mental health. The presence of social stress during early life can have an epigenetic effect on the body, possibly resulting in many complex mental disorders, including depression in later life. Here, we review the evidence for early-life social stress-induced epigenetic changes that modulate juvenile and adult social behavior (depression and anxiety). This review ...
Source: Frontiers in Genetics - January 22, 2021 Category: Genetics & Stem Cells Source Type: research

A Novel Framework to Predict Breast Cancer Prognosis Using Immune-Associated LncRNAs
Conclusion: We successfully constructed an immune-associated lncRNA signature that can accurately predict BC prognosis. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 21, 2021 Category: Genetics & Stem Cells Source Type: research

Variations in the Mitochondrial Genome of a Goldfish-Like Hybrid [Koi Carp ( ♀) × Blunt Snout Bream (♂)] Indicate Paternal Leakage
Previously, a homodiploid goldfish-like fish (2n = 100; GF-L) was spontaneously generated by self-crossing a homodiploid red crucian carp-like fish (2n = 100; RCC-L), which was in turn produced via the distant hybridization of female koi carp (Cyprinus carpio haematopterus, KOC, 2n = 100) and male blunt snout bream (Megalobrama amblycephala, BSB, 2n = 48). The phenotypes and genotypes of RCC-L and GF-L differed from those of the parental species but were similar to diploid red crucian carp (2n = 100; RCC) and goldfish (2n = 100; GF), respectively. We sequenced the complete mitochondrial DNAs (mtDNAs) of the KOC, BSB, RCC-L...
Source: Frontiers in Genetics - January 21, 2021 Category: Genetics & Stem Cells Source Type: research

MeCP2: The Genetic Driver of Rett Syndrome Epigenetics
Mutations in methyl CpG binding protein 2 (MeCP2) are the major cause of Rett syndrome (RTT), a rare neurodevelopmental disorder with a notable period of developmental regression following apparently normal initial development. Such MeCP2 alterations often result in changes to DNA binding and chromatin clustering ability, and in the stability of this protein. Among other functions, MeCP2 binds to methylated genomic DNA, which represents an important epigenetic mark with broad physiological implications, including neuronal development. In this review, we will summarize the genetic foundations behind RTT, and the variable de...
Source: Frontiers in Genetics - January 21, 2021 Category: Genetics & Stem Cells Source Type: research

A Novel Prognostic Model of Early-Stage Lung Adenocarcinoma Integrating Methylation and Immune Biomarkers
Lung adenocarcinoma (LUAD) is caused by multiple biological factors. Therefore, it will be more meaningful to study the prognosis from the perspective of omics integration. Given the significance of epigenetic modification and immunity in tumorigenesis and development, we tried to combine aberrant methylation and tumor infiltration CD8 T cell-related genes to build a prognostic model, to explore the key biomarkers of early-stage LUAD. On the basis of RNA-seq and methylation microarray data downloaded from The Cancer Genome Atlas (TCGA), differentially expressed genes and aberrant methylated genes were calculated with &ldqu...
Source: Frontiers in Genetics - January 21, 2021 Category: Genetics & Stem Cells Source Type: research

Investigation on Potential Correlation Between Small Nuclear Ribonucleoprotein Polypeptide A and Lung Cancer
SNRPA (small nuclear ribonucleoprotein polypeptide A) gene is essential for the pre-mRNA splicing process. Using the available datasets of TCGA or GEO, we aimed at exploring the potential association between the SNRPA gene and lung cancer by several online tools (such as GEIPA2, MEXPRESS, Oncomine) and bioinformatics analysis software (R or GSEA). SNRPA was highly expressed in the tissues of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma tissue (LUSC), compared with control tissues. The high SNRPA expression was associated with a poor survival prognosis of LUAD cases, while the genetic alteration within SNRPA ...
Source: Frontiers in Genetics - January 21, 2021 Category: Genetics & Stem Cells Source Type: research

Construction and Analysis of a ceRNA Network in Cardiac Fibroblast During Fibrosis Based on in vivo and in vitro Data
ConclusionsThe CF-specific ceRNA network, including two lncRNA, three miRNA, and two mRNA, played a crucial role during cardiac fibrosis, which provided potential target genes in this field. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 21, 2021 Category: Genetics & Stem Cells Source Type: research

Gene Expression Changes and Associated Pathways Involved in the Progression of Prostate Cancer Advanced Stages
In this study, we performed a bioinformatic analysis of The Cancer Genome Atlas (TCGA) datasets, including RNA-Seq data from the prostate adenocarcinoma (PRAD; n = 55) and West Coast Dream Team – metastatic CRPC (WCDT-MCRPC; n = 84) projects, to evaluate the transcriptome changes associated with progression-free survival (PFS) for LAPC and CRPC, respectively. We identified the genes whose expression was positively/negatively correlated with PFS. In LAPC, the genes with the most significant negative correlations were ZC2HC1A, SQLE, and KIF11, and the genes with the most significant positive correlations were SOD3, LRR...
Source: Frontiers in Genetics - January 21, 2021 Category: Genetics & Stem Cells Source Type: research

Technological Innovations for Improving Cassava Production in Sub-Saharan Africa
Cassava is crucial for food security of millions of people in sub-Saharan Africa. The crop has great potential to contribute to African development and is increasing its income-earning potential for small-scale farmers and related value chains on the continent. Therefore, it is critical to increase cassava production, as well as its quality attributes. Technological innovations offer great potential to drive this envisioned change. This paper highlights genomic tools and resources available in cassava. The paper also provides a glimpse of how these resources have been used to screen and understand the pattern of cassava ge...
Source: Frontiers in Genetics - January 21, 2021 Category: Genetics & Stem Cells Source Type: research

The Pontastacus leptodactylus (Astacidae) Repeatome Provides Insight Into Genome Evolution and Reveals Remarkable Diversity of Satellite DNA
Pontastacus leptodactylus is a native European crayfish species found in both freshwater and brackish environments. It has commercial importance for fisheries and aquaculture industries. Up till now, most studies concerning P. leptodactylus have focused onto gaining knowledge about its phylogeny and population genetics. However, little is known about the chromosomal evolution and genome organization of this species. Therefore, we performed clustering analysis of a low coverage genomic dataset to identify and characterize repetitive DNA in the P. leptodactylus genome. In addition, the karyogram of P. leptodactylus (2n = 180...
Source: Frontiers in Genetics - January 21, 2021 Category: Genetics & Stem Cells Source Type: research

Telomere Length as a Marker of Biological Age: State-of-the-Art, Open Issues, and Future Perspectives
Telomere shortening is a well-known hallmark of both cellular senescence and organismal aging. An accelerated rate of telomere attrition is also a common feature of age-related diseases. Therefore, telomere length (TL) has been recognized for a long time as one of the best biomarkers of aging. Recent research findings, however, indicate that TL per se can only allow a rough estimate of aging rate and can hardly be regarded as a clinically important risk marker for age-related pathologies and mortality. Evidence is obtained that other indicators such as certain immune parameters, indices of epigenetic age, etc., could be st...
Source: Frontiers in Genetics - January 21, 2021 Category: Genetics & Stem Cells Source Type: research

l-Isoaspartyl Methyltransferase Deficiency in Zebrafish Leads to Impaired Calcium Signaling in the Brain
Isomerization of l-aspartyl and l-asparaginyl residues to l-isoaspartyl residues is one type of protein damage that can occur under physiological conditions and leads to conformational changes, loss of function, and enhanced protein degradation. Protein l-isoaspartyl methyltransferase (PCMT) is a repair enzyme whose action initiates the reconversion of abnormal l-isoaspartyl residues to normal l-aspartyl residues in proteins. Many lines of evidence support a crucial role for PCMT in the brain, but the mechanisms involved remain poorly understood. Here, we investigated PCMT activity and function in zebrafish, a vertebrate m...
Source: Frontiers in Genetics - January 21, 2021 Category: Genetics & Stem Cells Source Type: research

Research on Components Assembly Platform of Biological Sequences Alignment Algorithm
After years of development, the complexity of the biological sequence alignment algorithm is gradually increasing, and the lack of high abstract level domain research leads to the complexity of its algorithm development and improvement. By applying the idea of software components to the design and development of algorithms, the development efficiency and reliability of biological sequence alignment algorithms can be effectively improved. The component assembly platform applies related assembly technology, which simplifies the operation difficulty of component assembly and facilitates the maintenance and optimization of the...
Source: Frontiers in Genetics - January 21, 2021 Category: Genetics & Stem Cells Source Type: research

Comparative mRNA and LncRNA Analysis of the Molecular Mechanisms Associated With Low Silk Production in Bombyx mori
In conclusion, our findings contribute to the lncRNA and mRNA database of Bombyx mori, and the identified differentially expressed mRNAs and lncRNAs help to reveal the molecular mechanisms of low silk production in Nd-sD and Nd, providing new insights for improvement of silk yield and elucidation of silk mechanical properties. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 21, 2021 Category: Genetics & Stem Cells Source Type: research

Comparative Transcriptome Analysis During the Seven Developmental Stages of Channel Catfish (Ictalurus punctatus) and Tra Catfish (Pangasianodon hypophthalmus) Provides Novel Insights for Terrestrial Adaptation
This study provides a foundational data resource for functional genomic studies in air-breathing function in tra catfish and sheds light on the adaptation of aquatic organisms to the terrestrial environment. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 21, 2021 Category: Genetics & Stem Cells Source Type: research

Analysis of Genome DNA Methylation at Inherited Coat Color Dilutions of Rex Rabbits
Conclusion: These findings provide evidence that there is an association between inherited color dilution and DNA methylation alterations in hair follicles, greatly contributing to our understanding of the epigenetic regulation of rabbit pigmentation. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 21, 2021 Category: Genetics & Stem Cells Source Type: research

Genomic Prediction Based on SNP Functional Annotation Using Imputed Whole-Genome Sequence Data in Korean Hanwoo Cattle
This study aimed to improve the predictive performance of the customized Hanwoo 50 k SNP panel for four carcass traits in commercial Hanwoo population by adding highly predictive variants from sequence data. A total of 16,892 Hanwoo cattle with phenotypes (i.e., backfat thickness, carcass weight, longissimus muscle area, and marbling score), 50 k genotypes, and WGS imputed genotypes were used. We partitioned imputed WGS data according to functional annotation [intergenic (IGR), intron (ITR), regulatory (REG), synonymous (SYN), and non-synonymous (NSY)] to characterize the genomic regions that will deliver higher predictive...
Source: Frontiers in Genetics - January 21, 2021 Category: Genetics & Stem Cells Source Type: research

Characteristics of Genetic Variations Associated With Lennox-Gastaut Syndrome in Korean Families
Lennox-Gastaut syndrome (LGS) is a severe type of childhood-onset epilepsy characterized by multiple types of seizures, specific discharges on electroencephalography, and intellectual disability. Most patients with LGS do not respond well to drug treatment and show poor long-term prognosis. Approximately 30% of patients without brain abnormalities have unidentifiable causes. Therefore, accurate diagnosis and treatment of LGS remain challenging. To identify causative mutations of LGS, we analyzed the whole-exome sequencing data of 17 unrelated Korean families, including patients with LGS and LGS-like epilepsy without brain ...
Source: Frontiers in Genetics - January 20, 2021 Category: Genetics & Stem Cells Source Type: research

Prior Biological Knowledge Improves Genomic Prediction of Growth-Related Traits in Arabidopsis thaliana
In conclusion, prior knowledge about trait-specific groups of genes can be directly translated into improved genomic prediction. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 20, 2021 Category: Genetics & Stem Cells Source Type: research

Identification of Protein Subcellular Localization With Network and Functional Embeddings
In this study, we present an embedding-based method for predicting the subcellular localization of proteins. We first learn the functional embeddings of KEGG/GO terms, which are further used in representing proteins. Then, we characterize the network embeddings of proteins on a protein–protein network. The functional and network embeddings are combined as novel representations of protein locations for the construction of the final classification model. In our collected benchmark dataset with 4,861 proteins from 16 locations, the best model shows a Matthews correlation coefficient of 0.872 and is thus superior to mult...
Source: Frontiers in Genetics - January 20, 2021 Category: Genetics & Stem Cells Source Type: research

CDAE: A Cascade of Denoising Autoencoders for Noise Reduction in the Clustering of Single-Particle Cryo-EM Images
In this study, we design an effective cryo-EM image denoising model, CDAE, i.e., a cascade of denoising autoencoders. The new model comprises stacked blocks of deep neural networks to reduce noise in a progressive manner. Each block contains a convolutional autoencoder, pre-trained by simulated data of different SNRs and fine-tuned by target data set. We assess this new model on three simulated test sets and a real data set. CDAE achieves very competitive PSNR (peak signal-to-noise ratio) in the comparison of the state-of-the-art image denoising methods. Moreover, the denoised images have significantly enhanced clustering ...
Source: Frontiers in Genetics - January 20, 2021 Category: Genetics & Stem Cells Source Type: research

Sea Urchin as a Universal Model for Studies of Gene Networks
The purple sea urchin Strongylocentrotus purpuratus has been used for over 150 years as a model organism in developmental biology. Using this model species, scientists have been able to describe, in detail, the mechanisms of cell cycle control and cell adhesion, fertilization, calcium signaling, cell differentiation, and death. Massive parallel sequencing of the sea urchin genome enabled the deciphering of the main components of gene regulatory networks during the activation of embryonic signaling pathways. This knowledge helped to extrapolate aberrations in somatic cells that may lead to diseases, including cancer in huma...
Source: Frontiers in Genetics - January 20, 2021 Category: Genetics & Stem Cells Source Type: research

Genetic Structure and Evolutionary History of Rhinopithecus roxellana in Qinling Mountains, Central China
The Qinling mountainous region is one of the world's biodiversity hotspots and provides refuges for many endangered endemic animals. The golden snub-nosed monkeys (Rhinopithecus roxellana) are considered as a flagship species in this area. Here, we depicted the genetic structure and evolutionary history via microsatellite markers and combination with the ecological niche models (ENMs) to elucidate the intraspecific divergent and the impacts of the population demography on our focal species. Our results revealed three distinct subpopulations of R. roxellana and also uncovered asymmetric historical and symmetric contemporary...
Source: Frontiers in Genetics - January 20, 2021 Category: Genetics & Stem Cells Source Type: research

Mutational Dynamics of Aroid Chloroplast Genomes II
The co-occurrence among single nucleotide polymorphisms (SNPs), insertions-deletions (InDels), and oligonucleotide repeats has been reported in prokaryote, eukaryote, and chloroplast genomes. Correlations among SNPs, InDels, and repeats have been investigated in the plant family Araceae previously using pair-wise sequence alignments of the chloroplast genomes of two morphotypes of one species, Colocasia esculenta belonging to subfamily Aroideae (crown group), and four species from the subfamily Lemnoideae, a basal group. The family Araceae is a large family comprising 3,645 species in 144 genera, grouped into eight subfami...
Source: Frontiers in Genetics - January 20, 2021 Category: Genetics & Stem Cells Source Type: research

Integrating Somatic Mutations for Breast Cancer Survival Prediction Using Machine Learning Methods
Breast cancer is the most common malignancy in women, and because it has a high mortality rate, it is urgent to develop computational methods to increase the accuracy of breast cancer survival predictive models. Although multi-omics data such as gene expression have been extensively used in recent studies, the accurate prognosis of breast cancer remains a challenge. Somatic mutations are another important and promising data source for studying cancer development, and its effect on the prognosis of breast cancer remains to be further explored. Meanwhile, these omics datasets are high-dimensional and redundant. Therefore, we...
Source: Frontiers in Genetics - January 18, 2021 Category: Genetics & Stem Cells Source Type: research

Genomic Characterization of WRKY Transcription Factors Related to Andrographolide Biosynthesis in Andrographis paniculata
This study laid a foundation for understanding the regulatory mechanism of andrographolide biosynthesis and the improvement and breeding of Andrographis paniculata varieties. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 18, 2021 Category: Genetics & Stem Cells Source Type: research

The Susceptibility and Potential Functions of the LBX1 Gene in Adolescent Idiopathic Scoliosis
Genome-wide association studies have identified many susceptibility genes for adolescent idiopathic scoliosis (AIS). However, most of the results are hard to be replicated in multi-ethnic populations. LBX1 is the most promising candidate gene in the etiology of AIS. We aimed to appraise the literature for the association of LBX1 gene polymorphisms with susceptibility and curve progression in AIS. We also reviewed the function of the LBX1 gene in muscle progenitor cell migration and neuronal determination processes. Three susceptibility loci (rs11190870, rs625039, and rs11598564) near the LBX1 gene, as well as another susce...
Source: Frontiers in Genetics - January 18, 2021 Category: Genetics & Stem Cells Source Type: research

The Dynamic Expression of Potential Mediators of Severe Acute Respiratory Syndrome Coronavirus 2 Cellular Entry in Fetal, Neonatal, and Adult Rhesus Monkeys
The coronavirus disease 2019 (COVID-19) pandemic, induced by the pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread rapidly all over the world. There is considerable variability among neonates, children, and adults in the incidence of infection and severe disease following exposure to SARS-CoV-2. In our study, we analyzed the transcriptome data of primate animal model of Rhesus monkeys to evaluate the expression levels of possible SARS-CoV-2 receptors and proteases and immunologic features in the lungs, colons, livers, and brains at different developmental stages. Our results revealed that ...
Source: Frontiers in Genetics - January 18, 2021 Category: Genetics & Stem Cells Source Type: research

Identification of a Five-Gene Prognostic Model and Its Potential Drug Repurposing in Colorectal Cancer Based on TCGA, GTEx and GEO Databases
Colorectal cancer (CRC) is a major cause of cancer deaths worldwide. Unfortunately, many CRC patients are still being diagnosed at an advanced stage of the cancer, and the 5-year survival rate is only ~30%. Effective prognostic markers of CRC are therefore urgently needed. To address this issue, we performed a detailed bioinformatics analysis based on the Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Gene Expression Omnibus (GEO) databases to identify prognostic biomarkers for CRC, which in turn help in exploring potential drug-repurposing. We identified five hub genes (PGM2, PODXL, RHNO1, SCD, and SEP...
Source: Frontiers in Genetics - January 18, 2021 Category: Genetics & Stem Cells Source Type: research

Metagenomic Approaches to Analyze Antimicrobial Resistance: An Overview
Antimicrobial resistance is a major global public health problem, which develops when pathogens acquire antimicrobial resistance genes (ARGs), primarily through genetic recombination between commensal and pathogenic microbes. The resistome is a collection of all ARGs. In microorganisms, the primary method of ARG acquisition is horizontal gene transfer (HGT). Thus, understanding and identifying HGTs, can provide insight into the mechanisms of antimicrobial resistance transmission and dissemination. The use of high-throughput sequencing technologies has made the analysis of ARG sequences feasible and accessible. In particula...
Source: Frontiers in Genetics - January 18, 2021 Category: Genetics & Stem Cells Source Type: research

A Multi-Locus Association Model Framework for Nested Association Mapping With Discriminating QTL Effects in Various Subpopulations
Nested association mapping (NAM) has been an invaluable approach for plant genetics community and can dissect the genetic architecture of complex traits. As the most popular NAM analysis strategy, joint multifamily mapping can combine all information from diverse genetic backgrounds and increase population size. However, it is influenced by the genetic heterogeneity of quantitative trait locus (QTL) across various subpopulations. Multi-locus association mapping has been proven to be powerful in many cases of QTL mapping and genome-wide association studies. Therefore, we developed a multi-locus association model of multiple...
Source: Frontiers in Genetics - January 18, 2021 Category: Genetics & Stem Cells Source Type: research

SNP-Density Crossover Maps of Polymorphic Transposable Elements and HLA Genes Within MHC Class I Haplotype Blocks and Junction
The genomic region (~4 Mb) of the human major histocompatibility complex (MHC) on chromosome 6p21 is a prime model for the study and understanding of conserved polymorphic sequences (CPSs) and structural diversity of ancestral haplotypes (AHs)/conserved extended haplotypes (CEHs). The aim of this study was to use a set of 95 MHC genomic sequences downloaded from a publicly available BioProject database at NCBI to identify and characterise polymorphic human leukocyte antigen (HLA) class I genes and pseudogenes, MICA and MICB, and retroelement indels as haplotypic lineage markers, and single-nucleotide polymorphism (SNP) cro...
Source: Frontiers in Genetics - January 18, 2021 Category: Genetics & Stem Cells Source Type: research

Hierarchical Microbial Functions Prediction by Graph Aggregated Embedding
Matching 16S rRNA gene sequencing data to a metabolic reference database is a meaningful way to predict the metabolic function of bacteria and archaea, bringing greater insight to the working of the microbial community. However, some operational taxonomy units (OTUs) cannot be functionally profiled, especially for microbial communities from non-human samples cultured in defective media. Therefore, we herein report the development of Hierarchical micrObial functions Prediction by graph aggregated Embedding (HOPE), which utilizes co-occurring patterns and nucleotide sequences to predict microbial functions. HOPE integrates t...
Source: Frontiers in Genetics - January 18, 2021 Category: Genetics & Stem Cells Source Type: research

The FpPPR1 Gene Encodes a Pentatricopeptide Repeat Protein That Is Essential for Asexual Development, Sporulation, and Pathogenesis in Fusarium pseudograminearum
In this study, we characterized FpPPR1, a gene that encodes a protein with 12 pentatricopeptide repeat (PPR) motifs. The radial growth rate of the ΔFpppr1 deletion mutant was significantly slower than the wild type strain WZ-8A on potato dextrose agar plates and exhibited significantly smaller colonies with sector mutations. The aerial mycelium of the mutant was almost absent in culture tubes. The ΔFpppr1 mutant was able to produce spores, but spores of abnormal size and altered conidium septum shape were produced with a significant reduction in sporulation compared to wild type. ΔFpppr1 failed to cause d...
Source: Frontiers in Genetics - January 15, 2021 Category: Genetics & Stem Cells Source Type: research

Use of Multivariable Mendelian Randomization to Address Biases Due to Competing Risk Before Recruitment
Conclusion: MR studies of harmful exposures on late-onset diseases with shared etiology need to be conceptualized within a mechanistic understanding so as to identify any potential bias due to survival to recruitment on both genetically instrumented exposure and competing risk of the outcome, which may then be investigated using multivariable MR or estimated analytically and results interpreted accordingly. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 15, 2021 Category: Genetics & Stem Cells Source Type: research

Identification of Key MicroRNAs and Mechanisms in Prostate Cancer Evolution Based on Biomarker Prioritization Model and Carcinogenic Survey
Conclusion: Biomarker miRNAs together with the associated miRNA-mRNA relations were computationally identified and analyzed for PCa management and carcinogenic deciphering. Further experimental and clinical validations using low-throughput techniques and human samples are expected for future translational studies. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 15, 2021 Category: Genetics & Stem Cells Source Type: research

The Effects of Feed Restriction and Isolated or Group Rearing on the Measurement of Individual Feed Intake and Estimation of Feed Conversion Ratio in Juvenile Nile Tilapia (Oreochromis niloticus) for Selective Breeding Purposes
Accurately measuring the phenotype at the individual level is critical to the success of selective breeding programs. Feed efficiency is a key sustainability trait and is typically approached through feed conversion ratio (FCR). This requires measurements of body weight gain (BWG) and feed intake (FI), the latter being technically challenging in fish. We assessed two of the principal methods for measuring feed intake in fish over consecutive days: (1) group rearing 10 fish per group and video recording the meals and (2) rearing fish individually on a restricted ration. Juvenile Nile tilapia (Oreochromis niloticus) from the...
Source: Frontiers in Genetics - January 15, 2021 Category: Genetics & Stem Cells Source Type: research

The Characteristics of Chemosensory and Opsin Genes in Newly Emerged and Sexually Mature Agrilus planipennis, an Important Quarantine Forest Beetle
This study forms the basis for further investigation of the chemosensory and visual system of A. planipennis, and these differentially expressed genes between newly emerged and sexually mature stages may serve as targets for the management of this destructive forest pest after sexual maturity. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - January 15, 2021 Category: Genetics & Stem Cells Source Type: research

Cell Type-Specific Predictive Models Perform Prioritization of Genes and Gene Sets Associated With Autism
Bulk transcriptomic analyses of autism spectrum disorder (ASD) have revealed dysregulated pathways, while the brain cell type-specific molecular pathology of ASD still needs to be studied. Machine learning-based studies can be conducted for ASD, prioritizing high-confidence gene candidates and promoting the design of effective interventions. Using human brain nucleus gene expression of ASD and controls, we construct cell type-specific predictive models for ASD based on individual genes and gene sets, respectively, to screen cell type-specific ASD-associated genes and gene sets. These two kinds of predictive models can pred...
Source: Frontiers in Genetics - January 15, 2021 Category: Genetics & Stem Cells Source Type: research