Genes

11 pages, 4667 KiB

Open AccessArticle

Identification and Expression of SAUR Genes in the CAM Plant Agave

by Gang Deng, Xing Huang, Li Xie, Shibei Tan, Thomas Gbokie, Jr., Yaning Bao, Zhouli Xie and Kexian Yi

Genes 2019, 10(7), 555; https://doi.org/10.3390/genes10070555 - 23 Jul 2019

Cited by 16 | Viewed by 4519

Abstract

Agave species are important crassulacean acid metabolism (CAM) plants and widely cultivated in tropical areas for producing tequila spirit and fiber. The hybrid H11648 of Agave ((A. amaniensis × A. angustifolia) × A. amaniensis) is the main cultivar for fiber [...] Read more.

Agave species are important crassulacean acid metabolism (CAM) plants and widely cultivated in tropical areas for producing tequila spirit and fiber. The hybrid H11648 of Agave ((A. amaniensis × A. angustifolia) × A. amaniensis) is the main cultivar for fiber production in Brazil, China, and African countries. Small Auxin Up-regulated RNA (SAUR) genes have broad effect on auxin signaling-regulated plant growth and development, while only few SAUR genes have been reported in Agave species. In this study, we identified 43, 60, 24, and 21 SAUR genes with full-length coding regions in A. deserti, A. tequilana, A. H11648, and A. americana, respectively. Although phylogenetic analysis revealed that rice contained a species-specific expansion pattern of SAUR gene, no similar phenomena were observed in Agave species. The in silico expression indicated that SAUR genes had a distinct expression pattern in A. H11648 compared with other Agave species; and four SAUR genes were differentially expressed during CAM diel cycle in A. americana. Additionally, an expression analysis was conducted to estimate SAUR gene expression during different leaf developmental stages, abiotic and biotic stresses in A. H11648. Together, we first characterized the SAUR genes of Agave based on previously published transcriptome datasets and emphasized the potential functions of SAUR genes in Agave’s leaf development and stress responses. The identification of which further expands our understanding on auxin signaling-regulated plant growth and development in Agave species. Full article

(This article belongs to the Special Issue Genetics, genomics, and evolution of CAM photosynthesis)

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27 pages, 7758 KiB

Open AccessArticle

Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3)

by Guoliang Li, Tongkai Sun, Huidan Chang, Liuyang Cai, Ping Hong and Qiangwei Zhou

Genes 2019, 10(7), 554; https://doi.org/10.3390/genes10070554 - 22 Jul 2019

Cited by 24 | Viewed by 8669

Abstract

Understanding chromatin interactions is important because they create chromosome conformation and link the cis- and trans- regulatory elements to their target genes for transcriptional regulation. Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing is a genome-wide high-throughput technology that detects chromatin interactions associated [...] Read more.

Understanding chromatin interactions is important because they create chromosome conformation and link the cis- and trans- regulatory elements to their target genes for transcriptional regulation. Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing is a genome-wide high-throughput technology that detects chromatin interactions associated with a specific protein of interest. We developed ChIA-PET Tool for ChIA-PET data analysis in 2010. Here, we present the updated version of ChIA-PET Tool (V3) as a computational package to process the next-generation sequence data generated from ChIA-PET experiments. It processes short-read and long-read ChIA-PET data with multithreading and generates statistics of results in an HTML file. In this paper, we provide a detailed demonstration of the design of ChIA-PET Tool V3 and how to install it and analyze RNA polymerase II (RNAPII) ChIA-PET data from human K562 cells with it. We compared our tool with existing tools, including ChiaSig, MICC, Mango and ChIA-PET2, by using the same public data set in the same computer. Most peaks detected by the ChIA-PET Tool V3 overlap with those of other tools. There is higher enrichment for significant chromatin interactions from ChIA-PET Tool V3 in aggregate peak analysis (APA) plots. The ChIA-PET Tool V3 is publicly available at GitHub. Full article

(This article belongs to the Special Issue 3D Genomics)

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19 pages, 2045 KiB

Open AccessReview

A Guide on Deep Learning for Complex Trait Genomic Prediction

by Miguel Pérez-Enciso and Laura M. Zingaretti

Genes 2019, 10(7), 553; https://doi.org/10.3390/genes10070553 - 20 Jul 2019

Cited by 100 | Viewed by 20260

Abstract

Deep learning (DL) has emerged as a powerful tool to make accurate predictions from complex data such as image, text, or video. However, its ability to predict phenotypic values from molecular data is less well studied. Here, we describe the theoretical foundations of [...] Read more.

Deep learning (DL) has emerged as a powerful tool to make accurate predictions from complex data such as image, text, or video. However, its ability to predict phenotypic values from molecular data is less well studied. Here, we describe the theoretical foundations of DL and provide a generic code that can be easily modified to suit specific needs. DL comprises a wide variety of algorithms which depend on numerous hyperparameters. Careful optimization of hyperparameter values is critical to avoid overfitting. Among the DL architectures currently tested in genomic prediction, convolutional neural networks (CNNs) seem more promising than multilayer perceptrons (MLPs). A limitation of DL is in interpreting the results. This may not be relevant for genomic prediction in plant or animal breeding but can be critical when deciding the genetic risk to a disease. Although DL technologies are not “plug-and-play”, they are easily implemented using Keras and TensorFlow public software. To illustrate the principles described here, we implemented a Keras-based code in GitHub. Full article

(This article belongs to the Special Issue Genomic Prediction Methods for Sequencing Data)

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19 pages, 4746 KiB

Open AccessArticle

Transcriptome Analysis of Landrace Pig Subcutaneous Preadipocytes during Adipogenic Differentiation

by Xitong Zhao, Shaokang Chen, Zhen Tan, Yuan Wang, Fengxia Zhang, Ting Yang, Yibing Liu, Hong Ao, Kai Xing and Chuduan Wang

Genes 2019, 10(7), 552; https://doi.org/10.3390/genes10070552 - 19 Jul 2019

Cited by 15 | Viewed by 4200

Abstract

Fat deposition in pigs, which significantly contributes to meat quality, fattening efficiency, reproductive performance, and immunity, is critically affected by preadipocyte adipogenic differentiation. We elucidated adipogenesis in pigs using transcriptome analysis. Preadipocytes from subcutaneous adipose tissue (SAT) of Landrace piglets were differentiated into [...] Read more.

Fat deposition in pigs, which significantly contributes to meat quality, fattening efficiency, reproductive performance, and immunity, is critically affected by preadipocyte adipogenic differentiation. We elucidated adipogenesis in pigs using transcriptome analysis. Preadipocytes from subcutaneous adipose tissue (SAT) of Landrace piglets were differentiated into adipocytes in vitro. RNA sequencing (RNA-seq) used to screen differentially expressed genes (DEGs) during preadipocyte differentiation up to day 8 revealed 15,918 known and 586 novel genes. We detected 21, 144, and 394 DEGs, respectively, including 16 genes differentially expressed at days 2, 4 and 8 compared to day 0. Th number of DEGs increased time-dependently. Lipid metabolism, cell differentiation and proliferation, peroxisome proliferator-activated receptor (PPAR), wingless-type MMTV integration site (Wnt), tumor necrosis factor (TNF) signaling, and steroid biosynthesis were significant at days 2, 4, and 8 compared to day 0 (adjusted p < 0.05). Short time-series expression miner (STEM) analysis obtained 26 clusters of differential gene expression patterns, and nine were significant (p < 0.05). Functional analysis showed many significantly enriched lipid deposition- and cellular process-related biological processes and pathways in profiles 9, 21, 22, and 24. Glycerolipid and fatty-acid metabolism, PPAR signaling, fatty-acid degradation, phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt), and TNF signaling were observed during preadipocyte differentiation in vitro. These findings will facilitate the comprehension of preadipocyte differentiation and fat deposition in pigs. Full article

(This article belongs to the Section Animal Genetics and Genomics)

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20 pages, 2713 KiB

Open AccessConcept Paper

When Three Isn’t a Crowd: A Digyny Concept for Treatment-Resistant, Near-Triploid Human Cancers

by Kristine Salmina, Bogdan I. Gerashchenko, Michael Hausmann, Ninel M. Vainshelbaum, Pawel Zayakin, Juris Erenpreiss, Talivaldis Freivalds, Mark S. Cragg and Jekaterina Erenpreisa

Genes 2019, 10(7), 551; https://doi.org/10.3390/genes10070551 - 19 Jul 2019

Cited by 14 | Viewed by 5498

Abstract

Near-triploid human tumors are frequently resistant to radio/chemotherapy through mechanisms that are unclear. We recently reported a tight association of male tumor triploidy with XXY karyotypes based on a meta-analysis of 15 tumor cohorts extracted from the Mitelman database. Here we provide a [...] Read more.

Near-triploid human tumors are frequently resistant to radio/chemotherapy through mechanisms that are unclear. We recently reported a tight association of male tumor triploidy with XXY karyotypes based on a meta-analysis of 15 tumor cohorts extracted from the Mitelman database. Here we provide a conceptual framework of the digyny-like origin of this karyotype based on the germline features of malignant tumors and adaptive capacity of digyny, which supports survival in adverse conditions. Studying how the recombinatorial reproduction via diploidy can be executed in primary cancer samples and HeLa cells after DNA damage, we report the first evidence that diploid and triploid cell sub-populations constitutively coexist and inter-change genomes via endoreduplicated polyploid cells generated through genotoxic challenge. We show that irradiated triploid HeLa cells can enter tripolar mitosis producing three diploid sub-subnuclei by segregation and pairwise fusions of whole genomes. Considering the upregulation of meiotic genes in tumors, we propose that the reconstructed diploid sub-cells can initiate pseudo-meiosis producing two “gametes” (diploid “maternal” and haploid “paternal”) followed by digynic-like reconstitution of a triploid stemline that returns to mitotic cycling. This process ensures tumor survival and growth by (1) DNA repair and genetic variation, (2) protection against recessive lethal mutations using the third genome. Full article

(This article belongs to the Special Issue Chromosomal Heterogeneity and Human Diseases)

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7 pages, 1395 KiB

Open AccessArticle

Venous Thromboembolism in Prader–Willi Syndrome: A Questionnaire Survey

by Ann M. Manzardo, Janalee Heinemann, Barbara McManus, Carolyn Loker, James Loker and Merlin G. Butler

Genes 2019, 10(7), 550; https://doi.org/10.3390/genes10070550 - 19 Jul 2019

Cited by 12 | Viewed by 3627

Abstract

Prader–Willi Syndrome Association (USA) monitors the ongoing health and welfare of individuals with Prader–Willi syndrome (PWS) through active communication with members by membership surveys and data registries. Thromboembolism and blood clots have emerged in clinical studies as significant risk factors for injury and [...] Read more.

Prader–Willi Syndrome Association (USA) monitors the ongoing health and welfare of individuals with Prader–Willi syndrome (PWS) through active communication with members by membership surveys and data registries. Thromboembolism and blood clots have emerged in clinical studies as significant risk factors for injury and death in PWS. A 66-item questionnaire was developed by a panel of PWS medical and scientific experts, with input from Prader–Willi Syndrome Association (USA) leadership, so as to probe their membership on the frequency, risk, and protective factors for venous thromboembolism, pulmonary embolism, and related findings. The characteristics of those with and without a reported history of blood clots and related health factors were tabulated and analyzed. Responses were obtained for 1067 individuals with PWS (554 females and 513 males), and 38 (23 females and 15 males) had a history of blood clots. The individuals with clots did not differ by gender, but were significantly older 32.8 ± 15 years vs 20.4 ± 13 years, and were more likely to have a reported history of obesity (76%), edema (59%), hypertension (24%), vasculitis (33%), and family history of blood clots (33%) than those without clots. Growth hormone treatment was more common in individuals without clots. The risk factors for thromboembolism in PWS overlap those commonly observed for the general population. Full article

(This article belongs to the Special Issue Genetics of Prader-Willi syndrome)

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17 pages, 1848 KiB

Open AccessArticle

Characterization of Solanum melongena Thioesterases Related to Tomato Methylketone Synthase 2

by Vy Le Uyen Khuat, Vi Thi Tuong Bui, Huong Thi Diem Tran, Nuong Xuan Truong, Thien Chi Nguyen, Phuc Huynh Hanh Mai, Tuan Le Anh Dang, Hiep Minh Dinh, Hong Thi Anh Pham and Thuong Thi Hong Nguyen

Genes 2019, 10(7), 549; https://doi.org/10.3390/genes10070549 - 18 Jul 2019

Cited by 7 | Viewed by 3766

Abstract

2-Methylketones are involved in plant defense and fragrance and have industrial applications as flavor additives and for biofuel production. We isolated three genes from the crop plant Solanum melongena (eggplant) and investigated these as candidates for methylketone production. The wild tomato methylketone synthase [...] Read more.

2-Methylketones are involved in plant defense and fragrance and have industrial applications as flavor additives and for biofuel production. We isolated three genes from the crop plant Solanum melongena (eggplant) and investigated these as candidates for methylketone production. The wild tomato methylketone synthase 2 (ShMKS2), which hydrolyzes β-ketoacyl-acyl carrier proteins (ACP) to release β-ketoacids in the penultimate step of methylketone synthesis, was used as a query to identify three homologs from S. melongena: SmMKS2-1, SmMKS2-2, and SmMKS2-3. Expression and functional characterization of SmMKS2s in E. coli showed that SmMKS2-1 and SmMKS2-2 exhibited the thioesterase activity against different β-ketoacyl-ACP substrates to generate the corresponding saturated and unsaturated β-ketoacids, which can undergo decarboxylation to form their respective 2-methylketone products, whereas SmMKS2-3 showed no activity. SmMKS2-1 was expressed at high level in leaves, stems, roots, flowers, and fruits, whereas expression of SmMKS2-2 and SmMKS2-3 was mainly in flowers and fruits, respectively. Expression of SmMKS2-1 was induced in leaves by mechanical wounding, and by methyl jasmonate or methyl salicylate, but SmMKS2-2 and SmMKS2-3 genes were not induced. SmMKS2-1 is a candidate for methylketone-based defense in eggplant, and both SmMKS2-1 and SmMKS2-2 are novel MKS2 enzymes for biosynthesis of methylketones as feedstocks to biofuel production. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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15 pages, 644 KiB

Open AccessReview

Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data

by Peter Hansen, Michael Gargano, Jochen Hecht, Jonas Ibn-Salem, Guy Karlebach, Johannes T. Roehr and Peter N. Robinson

Genes 2019, 10(7), 548; https://doi.org/10.3390/genes10070548 - 18 Jul 2019

Cited by 5 | Viewed by 6016

Abstract

Hi-C, capture Hi-C (CHC) and Capture-C have contributed greatly to our present understanding of the three-dimensional organization of genomes in the context of transcriptional regulation by characterizing the roles of topological associated domains, enhancer promoter loops and other three-dimensional genomic interactions. The analysis [...] Read more.

Hi-C, capture Hi-C (CHC) and Capture-C have contributed greatly to our present understanding of the three-dimensional organization of genomes in the context of transcriptional regulation by characterizing the roles of topological associated domains, enhancer promoter loops and other three-dimensional genomic interactions. The analysis is based on counts of chimeric read pairs that map to interacting regions of the genome. However, the processing and quality control presents a number of unique challenges. We review here the experimental and computational foundations and explain how the characteristics of restriction digests, sonication fragments and read pairs can be exploited to distinguish technical artefacts from valid read pairs originating from true chromatin interactions. Full article

(This article belongs to the Special Issue 3D Genomics)

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14 pages, 2434 KiB

Open AccessArticle

Single-Nucleotide Polymorphisms Sequencing Identifies Candidate Functional Variants at Prostate Cancer Risk Loci

by Peng Zhang, Lori S. Tillmans, Stephen N. Thibodeau and Liang Wang

Genes 2019, 10(7), 547; https://doi.org/10.3390/genes10070547 - 18 Jul 2019

Cited by 7 | Viewed by 4000

Abstract

Genome-wide association studies have identified over 150 risk loci that increase prostate cancer risk. However, few causal variants and their regulatory mechanisms have been characterized. In this study, we utilized our previously developed single-nucleotide polymorphisms sequencing (SNPs-seq) technology to test allele-dependent protein binding [...] Read more.

Genome-wide association studies have identified over 150 risk loci that increase prostate cancer risk. However, few causal variants and their regulatory mechanisms have been characterized. In this study, we utilized our previously developed single-nucleotide polymorphisms sequencing (SNPs-seq) technology to test allele-dependent protein binding at 903 SNP sites covering 28 genomic regions. All selected SNPs have shown significant cis-association with at least one nearby gene. After preparing nuclear extract using LNCaP cell line, we first mixed the extract with dsDNA oligo pool for protein–DNA binding incubation. We then performed sequencing analysis on protein-bound oligos. SNPs-seq analysis showed protein-binding differences (>1.5-fold) between reference and variant alleles in 380 (42%) of 903 SNPs with androgen treatment and 403 (45%) of 903 SNPs without treatment. From these significant SNPs, we performed a database search and further narrowed down to 74 promising SNPs. To validate this initial finding, we performed electrophoretic mobility shift assay in two SNPs (rs12246440 and rs7077275) at CTBP2 locus and one SNP (rs113082846) at NCOA4 locus. This analysis showed that all three SNPs demonstrated allele-dependent protein-binding differences that were consistent with the SNPs-seq. Finally, clinical association analysis of the two candidate genes showed that CTBP2 was upregulated, while NCOA4 was downregulated in prostate cancer (p < 0.02). Lower expression of CTBP2 was associated with poor recurrence-free survival in prostate cancer. Utilizing our experimental data along with bioinformatic tools provides a strategy for identifying candidate functional elements at prostate cancer susceptibility loci to help guide subsequent laboratory studies. Full article

(This article belongs to the Special Issue Prostate Cancer Genetics and the Emergence of Targeted Therapies Based on Molecular Profiling)

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16 pages, 3412 KiB

Open AccessArticle

Genetic Analyses of Tanzanian Local Chicken Ecotypes Challenged with Newcastle Disease Virus

by Muhammed Walugembe, James R. Mushi, Esinam N. Amuzu-Aweh, Gaspar H. Chiwanga, Peter L. Msoffe, Ying Wang, Perot Saelao, Terra Kelly, Rodrigo A. Gallardo, Huaijun Zhou, Susan J. Lamont, Amandus P. Muhairwa and Jack C.M. Dekkers

Genes 2019, 10(7), 546; https://doi.org/10.3390/genes10070546 - 17 Jul 2019

Cited by 19 | Viewed by 4353

Abstract

Newcastle Disease (ND) is a continuing global threat to domestic poultry, especially in developing countries, where severe outbreaks of velogenic ND virus (NDV) often cause major economic losses to households. Local chickens are of great importance to rural family livelihoods through provision of [...] Read more.

Newcastle Disease (ND) is a continuing global threat to domestic poultry, especially in developing countries, where severe outbreaks of velogenic ND virus (NDV) often cause major economic losses to households. Local chickens are of great importance to rural family livelihoods through provision of high-quality protein. To investigate the genetic basis of host response to NDV, three popular Tanzanian chicken ecotypes (regional populations) were challenged with a lentogenic (vaccine) strain of NDV at 28 days of age. Various host response phenotypes, including anti-NDV antibody levels (pre-infection and 10 days post-infection, dpi), and viral load (2 and 6 dpi) were measured, in addition to growth rate. We estimated genetic parameters and conducted genome-wide association study analyses by genotyping 1399 chickens using the Affymetrix 600K chicken SNP chip. Estimates of heritability of the evaluated traits were moderate (0.18–0.35). Five quantitative trait loci (QTL) associated with growth and/or response to NDV were identified by single-SNP analyses, with some regions explaining ≥1% of genetic variance based on the Bayes-B method. Immune related genes, such as ETS1, TIRAP, and KIRREL3, were located in regions associated with viral load at 6 dpi. The moderate estimates of heritability and identified QTL indicate that NDV response traits may be improved through selective breeding of chickens to enhance increased NDV resistance and vaccine efficacy in Tanzanian local ecotypes. Full article

(This article belongs to the Section Animal Genetics and Genomics)

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17 pages, 1376 KiB

Open AccessReview

Yeast as a Tool for Deeper Understanding of Human Manganese-Related Diseases

by Louise Thines, Antoine Deschamps, Jiri Stribny and Pierre Morsomme

Genes 2019, 10(7), 545; https://doi.org/10.3390/genes10070545 - 17 Jul 2019

Cited by 9 | Viewed by 4240

Abstract

The biological importance of manganese lies in its function as a key cofactor for numerous metalloenzymes and as non-enzymatic antioxidant. Due to these two essential roles, it appears evident that disturbed manganese homeostasis may trigger the development of pathologies in humans. In this [...] Read more.

The biological importance of manganese lies in its function as a key cofactor for numerous metalloenzymes and as non-enzymatic antioxidant. Due to these two essential roles, it appears evident that disturbed manganese homeostasis may trigger the development of pathologies in humans. In this context, yeast has been extensively used over the last decades to gain insight into how cells regulate intra-organellar manganese concentrations and how human pathologies may be related to disturbed cellular manganese homeostasis. This review first summarizes how manganese homeostasis is controlled in yeast cells and how this knowledge can be extrapolated to human cells. Several manganese-related pathologies whose molecular mechanisms have been studied in yeast are then presented in the light of the function of this cation as a non-enzymatic antioxidant or as a key cofactor of metalloenzymes. In this line, we first describe the Transmembrane protein 165-Congenital Disorder of Glycosylation (TMEM165-CDG) and Friedreich ataxia pathologies. Then, due to the established connection between manganese cations and neurodegeneration, the Kufor–Rakeb syndrome and prion-related diseases are finally presented. Full article

(This article belongs to the Special Issue Humanized Yeast Models)

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13 pages, 3524 KiB

Open AccessArticle

Seasonal Stability and Dynamics of DNA Methylation in Plants in a Natural Environment

by Tasuku Ito, Haruki Nishio, Yoshiaki Tarutani, Naoko Emura, Mie N. Honjo, Atsushi Toyoda, Asao Fujiyama, Tetsuji Kakutani and Hiroshi Kudoh

Genes 2019, 10(7), 544; https://doi.org/10.3390/genes10070544 - 17 Jul 2019

Cited by 21 | Viewed by 5627

Abstract

DNA methylation has been considered a stable epigenetic mark but may respond to fluctuating environments. However, it is unclear how they behave in natural environments. Here, we analyzed seasonal patterns of genome-wide DNA methylation in a single clone from a natural population of [...] Read more.

DNA methylation has been considered a stable epigenetic mark but may respond to fluctuating environments. However, it is unclear how they behave in natural environments. Here, we analyzed seasonal patterns of genome-wide DNA methylation in a single clone from a natural population of the perennial Arabidopsis halleri. The genome-wide pattern of DNA methylation was primarily stable, and most of the repetitive regions were methylated across the year. Although the proportion was small, we detected seasonally methylated cytosines (SeMCs) in the genome. SeMCs in the CHH context were detected predominantly at repetitive sequences in intergenic regions. In contrast, gene-body CG methylation (gbM) itself was generally stable across seasons, but the levels of gbM were positively associated with seasonal stability of RNA expression of the genes. These results suggest the existence of two distinct aspects of DNA methylation in natural environments: sources of epigenetic variation and epigenetic marks for stable gene expression. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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15 pages, 4588 KiB

Open AccessArticle

A Homeostasis Hypothesis of Avian Influenza Resistance in Chickens

by Jing An, Jinxiu Li, Ying Wang, Jing Wang, Qinghe Li, Huaijun Zhou, Xiaoxiang Hu, Yiqiang Zhao and Ning Li

Genes 2019, 10(7), 543; https://doi.org/10.3390/genes10070543 - 17 Jul 2019

Cited by 6 | Viewed by 4940

Abstract

Avian influenza has caused significant damage to the poultry industry globally. Consequently, efforts have been made to elucidate the disease mechanisms as well as the mechanisms of disease resistance. Here, by investigating two chicken breeds with distinct responses to avian influenza virus (AIV), [...] Read more.

Avian influenza has caused significant damage to the poultry industry globally. Consequently, efforts have been made to elucidate the disease mechanisms as well as the mechanisms of disease resistance. Here, by investigating two chicken breeds with distinct responses to avian influenza virus (AIV), Leghorn GB2 and Fayoumi M43, we compared their genome, methylation, and transcriptome differences. MX1, HSP90AB1, and HSP90B1 exhibited high degrees of genetic differentiation (F_ST) between the two species. Except for the MX1-involved direct anti-virus mechanism, we found that at the methylation and transcriptome levels, the more AIV-resistant breed, Fayoumi, exhibited less variation compared with Leghorn after AIV inoculation, which included change trends in differentially expressed regions, top-fold change genes with FDR-corrected p < 0.05, immune response related genes, and housekeeping genes. Fayoumi also showed better consistency regarding changes in methylation and changes at the transcriptome level. Our results suggest a homeostasis hypothesis for avian influenza resistance, with Fayoumi maintaining superior homeostasis at both the epigenetic and gene expression levels. Three candidate genes—MX1, HSP90AB1, and HSP90B1—showed genetic differentiation and altered gene expression, methylation, and protein expression, which merit attention in further functional studies. Full article

(This article belongs to the Special Issue Genomics of Avian Viral Infections)

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13 pages, 7647 KiB

Open AccessArticle

Variable Number Tandem Repeats in the Mitochondrial DNA of Lentinula edodes

by Sinil Kim, Yelin Song, Byeongsuk Ha, Yoon Jung Moon, Minseek Kim, Hojin Ryu and Hyeon-Su Ro

Genes 2019, 10(7), 542; https://doi.org/10.3390/genes10070542 - 17 Jul 2019

Cited by 8 | Viewed by 4226

Abstract

Variable number tandem repeats (VNTRs) in mitochondrial DNA (mtDNA) of Lentinula edodes are of interest for their role in mtDNA variation and their application as genetic marker. Sequence analysis of three L. edodes mtDNAs revealed the presence of VNTRs of two categories. Type [...] Read more.

Variable number tandem repeats (VNTRs) in mitochondrial DNA (mtDNA) of Lentinula edodes are of interest for their role in mtDNA variation and their application as genetic marker. Sequence analysis of three L. edodes mtDNAs revealed the presence of VNTRs of two categories. Type I VNTRs consist of two types of repeat units in a symmetric distribution, whereas Type II VNTRs contain tandemly arrayed repeats of 7- or 17-bp DNA sequences. The number of repeat units was variable depending on the mtDNA of different strains. Using the variations in VNTRs as a mitochondrial marker and the A mating type as a nuclear type marker, we demonstrated that one of the two nuclei in the donor dikaryon preferentially enters into the monokaryotic cytoplasm to establish a new dikaryon which still retains the mitochondria of the monokaryon in the individual mating. Interestingly, we found 6 VNTRs with newly added repeat units from the 22 mates, indicating that elongation of VNTRs occurs during replication of mtDNA. This, together with comparative analysis of the repeating pattern, enables us to propose a mechanistic model that explains the elongation of Type I VNTRs through reciprocal incorporation of basic repeat units, 5’-TCCCTTTAGGG-3’ and its complementary sequence (5’-CCCTAAAGGGA-3’). Full article

(This article belongs to the Section Microbial Genetics and Genomics)

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15 pages, 8692 KiB

Open AccessArticle

The CaAP2/ERF064 Regulates Dual Functions in Pepper: Plant Cell Death and Resistance to Phytophthora capsici

by Jing-Hao Jin, Huai-Xia Zhang, Muhammad Ali, Ai-Min Wei, De-Xu Luo and Zhen-Hui Gong

Genes 2019, 10(7), 541; https://doi.org/10.3390/genes10070541 - 17 Jul 2019

Cited by 19 | Viewed by 4077

Abstract

Phytophthora blight is one of the most destructive diseases of pepper (Capsicum annuum L.) globally. The APETALA2/Ethylene Responsive Factors (AP2/ERF) genes play a crucial role in plant response to biotic stresses but, to date, have not been studied in the [...] Read more.

Phytophthora blight is one of the most destructive diseases of pepper (Capsicum annuum L.) globally. The APETALA2/Ethylene Responsive Factors (AP2/ERF) genes play a crucial role in plant response to biotic stresses but, to date, have not been studied in the context of Phytophthora resistance in pepper. Here, we documented potential roles for the pepper CaAP2/ERF064 gene in inducing cell death and conferring resistance to Phytophthora capsici (P. capsici) infection. Results revealed that the N-terminal, AP2 domain, and C-terminal of CaAP2/ERF064 protein is responsible for triggering cell death in Nicotiana benthamiana (N. benthamiana). Moreover, the transcription of CaAP2/ERF064 in plant is synergistically regulated by the Methyl-Jasmonate (MeJA) and ethephon (ET) signaling pathway. CaAP2/ERF064 was found to regulate the expression of CaBPR1, which is a pathogenesis-related (PR) gene of pepper. Furthermore, the silencing of CaAP2/ERF064 compromised the pepper plant resistance to P. capsici by reducing the transcript level of defense-related genes CaBPR1, CaPO2, and CaSAR82, while the ectopic expression of CaAP2/ERF064 in N. benthamiana plant elevated the expression level of NbPR1b and enhanced resistance to P. capsici. These results suggest that CaAP2/ERF064 could positively regulate the defense response against P. capsici by modulating the transcription of PR genes in the plant. Full article

(This article belongs to the Special Issue Genetics and Epigenetics of Biotic Stress Response in Plants)

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6 pages, 797 KiB

Open AccessArticle

The Caribou (Rangifer tarandus) Genome

by Rebecca S. Taylor, Rebekah L. Horn, Xi Zhang, G. Brian Golding, Micheline Manseau and Paul J. Wilson

Genes 2019, 10(7), 540; https://doi.org/10.3390/genes10070540 - 17 Jul 2019

Cited by 17 | Viewed by 6332

Abstract

Rangifer tarandus, known as caribou or reindeer, is a widespread circumpolar species which presents significant variability in their morphology, ecology, and genetics. A genome was sequenced from a male boreal caribou (R. t. caribou) from Manitoba, Canada. Both paired end [...] Read more.

Rangifer tarandus, known as caribou or reindeer, is a widespread circumpolar species which presents significant variability in their morphology, ecology, and genetics. A genome was sequenced from a male boreal caribou (R. t. caribou) from Manitoba, Canada. Both paired end and Chicago libraries were constructed and sequenced on Illumina platforms. The final assembly consists of approximately 2.205 Gb, and has a scaffold N50 of 11.765 Mb. BUSCO (Benchmarking Universal Single-Copy Orthologs) reconstructed 3820 (93.1%) complete mammalian genes, and genome annotation identified the locations of 33,177 protein-coding genes. An alignment to the bovine genome was carried out, indicating sequence coverage on all bovine chromosomes. A high-quality reference genome will be invaluable for evolutionary research and for conservation efforts for the species. Further information about the genome, including a FASTA file of the assembly and the annotation files, is available on our caribou genome website. Raw sequence data is available at the National Centre for Biotechnology Information (NCBI), under the BioProject accession number PRJNA549927. Full article

(This article belongs to the Section Animal Genetics and Genomics)

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18 pages, 4794 KiB

Open AccessArticle

Transcriptome Analysis of Differentially Expressed Genes Related to the Growth and Development of the Jinghai Yellow Chicken

by Fuxiang Chen, Pengfei Wu, Manman Shen, Mingliang He, Lan Chen, Cong Qiu, Huiqiang Shi, Tao Zhang, Jiahong Wang, Kaizhou Xie, Guojun Dai, Jinyu Wang and Genxi Zhang

Genes 2019, 10(7), 539; https://doi.org/10.3390/genes10070539 - 17 Jul 2019

Cited by 22 | Viewed by 4918

Abstract

The growth traits are important traits in chickens. Compared to white feather broiler breeds, Chinese local broiler breeds have a slow growth rate. The main genes affecting the growth traits of local chickens in China are still unclear and need to be further [...] Read more.

The growth traits are important traits in chickens. Compared to white feather broiler breeds, Chinese local broiler breeds have a slow growth rate. The main genes affecting the growth traits of local chickens in China are still unclear and need to be further explored. This experiment used fast-growth and slow-growth groups of the Jinghai Yellow chicken as the research objects. Three males and three females with similar body weights were selected from the two groups at four weeks old and eight weeks old, respectively, with a total of 24 individuals selected. After slaughter, their chest muscles were taken for transcriptome sequencing. In the differentially expressed genes screening, all of the genes obtained were screened by fold change ≥ 2 and false discovery rate (FDR) < 0.05. For four-week-old chickens, a total of 172 differentially expressed genes were screened in males, where there were 68 upregulated genes and 104 downregulated genes in the fast-growth group when compared with the slow-growth group. A total of 31 differentially expressed genes were screened in females, where there were 11 upregulated genes and 20 downregulated genes in the fast-growth group when compared with the slow-growth group. For eight-week-old chickens, a total of 37 differentially expressed genes were screened in males. The fast-growth group had 28 upregulated genes and 9 downregulated genes when compared with the slow-growth group. A total of 44 differentially expressed genes were screened in females. The fast-growth group had 13 upregulated genes and 31 downregulated genes when compared with the slow-growth group. Through gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, many genes were found to be related to cell proliferation and differentiation, muscle growth, and cell division such as SNCG, MCL1, ARNTL, PLPPR4, VAMP1, etc. Real-time PCR results were consistent with the RNA-Seq data and validated the findings. The results of this study will help to understand the regulation mechanism of the growth and development of Jinghai Yellow chicken and provide a theoretical basis for improving the growth rate of Chinese local chicken breeds. Full article

(This article belongs to the Section Animal Genetics and Genomics)

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13 pages, 1013 KiB

Open AccessArticle

Contrasting Asymptomatic and Drug Resistance Gene Prevalence of Plasmodium falciparum in Ghana: Implications on Seasonal Malaria Chemoprevention

by Cheikh Cambel Dieng, Lauren Gonzalez, Kareen Pestana, Shittu B. Dhikrullahi, Linda E. Amoah, Yaw A. Afrane and Eugenia Lo

Genes 2019, 10(7), 538; https://doi.org/10.3390/genes10070538 - 16 Jul 2019

Cited by 16 | Viewed by 4696

Abstract

Malaria is a significant public health problem in Ghana. Seasonal Malaria Chemoprevention (SMC) using a combination of sulfadoxine-pyrimethamine and amodiaquine has been implemented since 2015 in northern Ghana where malaria transmission is intense and seasonal. In this study, we estimated the prevalence of [...] Read more.

Malaria is a significant public health problem in Ghana. Seasonal Malaria Chemoprevention (SMC) using a combination of sulfadoxine-pyrimethamine and amodiaquine has been implemented since 2015 in northern Ghana where malaria transmission is intense and seasonal. In this study, we estimated the prevalence of asymptomatic P. falciparum carriers in three ecological zones of Ghana, and compared the sensitivity and specificity of different molecular methods in identifying asymptomatic infections. Moreover, we examined the frequency of mutations in pfcrt, pfmdr1, pfdhfr, and pfdhps that relate to the ongoing SMC. A total of 535 asymptomatic schoolchildren were screened by microscopy and PCR (18s rRNA and TARE-2) methods. Among all samples, 28.6% were detected as positive by 18S nested PCR, whereas 19.6% were detected by microscopy. A high PCR-based asymptomatic prevalence was observed in the north (51%) compared to in the central (27.8%) and south (16.9%). The prevalence of pfdhfr-N51I/C59R/S108N/pfdhps-A437G quadruple mutant associated with sulfadoxine-pyrimethamine resistance was significantly higher in the north where SMC was implemented. Compared to 18S rRNA, TARE-2 serves as a more sensitive molecular marker for detecting submicroscopic asymptomatic infections in high and low transmission settings. These findings establish a baseline for monitoring P. falciparum prevalence and resistance in response to SMC over time. Full article

(This article belongs to the Special Issue Genetics and Genomics of Malaria Parasites)

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15 pages, 2658 KiB

Open AccessArticle

Genome-Wide Identification and Characterization of Xyloglucan Endotransglycosylase/Hydrolase in Ananas comosus during Development

by Qingyun Li, Huayang Li, Chongyang Yin, Xiaotong Wang, Qing Jiang, Rui Zhang, Fangfang Ge, Yudong Chen and Long Yang

Genes 2019, 10(7), 537; https://doi.org/10.3390/genes10070537 - 16 Jul 2019

Cited by 21 | Viewed by 4574

Abstract

Xyloglucan endotransglycosylase/hydrolase (XTH) is a cell-wall-modifying enzyme participating in diverse cell morphogenetic processes and adaptation to stress. In this study, 48 XTH genes were identified from two pineapple (Ananas comosus) cultivars (‘F153’ and ‘MD2’) and designated Ac(F153)XTH1 to -24 and Ac(MD2)XTH1 [...] Read more.

Xyloglucan endotransglycosylase/hydrolase (XTH) is a cell-wall-modifying enzyme participating in diverse cell morphogenetic processes and adaptation to stress. In this study, 48 XTH genes were identified from two pineapple (Ananas comosus) cultivars (‘F153’ and ‘MD2’) and designated Ac(F153)XTH1 to -24 and Ac(MD2)XTH1 to -24 based on their orthology with Arabidopsis thaliana genes. Endoglucanase family 16 members were identified in addition to XTHs of glycoside hydrolase family 16. Phylogenetic analysis clustered the XTHs into three major groups (Group I/II, III and Ancestral Group) and Group III was subdivided into Group IIIA and Group IIIB. Similar gene structure and motif number were observed within a group. Two highly conserved domains, glycosyl hydrolase family 16 (GH16-XET) and xyloglucan endotransglycosylase C-terminus (C-XET), were detected by multiple sequences alignment of all XTHs. Segmental replication were detected in the two cultivars, with only the paralogous pair Ac(F153)XTH7-Ac(F153)XTH18 presented in ‘F153’ prior to genomic expansion. Transcriptomic analysis indicated that XTHs were involved in the regulation of fruit ripening and crassulacean acid metabolism with tissue specificity and quantitative real-time PCR analysis suggested that Ac(MD2)XTH18 was involved in root growth. The results enhance our understanding of XTHs in the plant kingdom and provide a basis for further studies of functional diversity in A. comosus. Full article

(This article belongs to the Special Issue Genetics, genomics, and evolution of CAM photosynthesis)

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13 pages, 3502 KiB

Open AccessArticle

Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Peanut

by Xiaobo Zhao, Liming Gan, Caixia Yan, Chunjuan Li, Quanxi Sun, Juan Wang, Cuiling Yuan, Hao Zhang, Shihua Shan and Jian Ning Liu

Genes 2019, 10(7), 536; https://doi.org/10.3390/genes10070536 - 15 Jul 2019

Cited by 19 | Viewed by 4765

Abstract

Long non-coding RNAs (lncRNAs) are involved in various regulatory processes although they do not encode protein. Presently, there is little information regarding the identification of lncRNAs in peanut (Arachis hypogaea Linn.). In this study, 50,873 lncRNAs of peanut were identified from large-scale [...] Read more.

Long non-coding RNAs (lncRNAs) are involved in various regulatory processes although they do not encode protein. Presently, there is little information regarding the identification of lncRNAs in peanut (Arachis hypogaea Linn.). In this study, 50,873 lncRNAs of peanut were identified from large-scale published RNA sequencing data that belonged to 124 samples involving 15 different tissues. The average lengths of lncRNA and mRNA were 4335 bp and 954 bp, respectively. Compared to the mRNAs, the lncRNAs were shorter, with fewer exons and lower expression levels. The 4713 co-expression lncRNAs (expressed in all samples) were used to construct co-expression networks by using the weighted correlation network analysis (WGCNA). LncRNAs correlating with the growth and development of different peanut tissues were obtained, and target genes for 386 hub lncRNAs of all lncRNAs co-expressions were predicted. Taken together, these findings can provide a comprehensive identification of lncRNAs in peanut. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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12 pages, 1048 KiB

Open AccessArticle

Altered in Vitro Metabolomic Response of the Human Microbiota to Sweeteners

by Emanuel Vamanu, Diana Pelinescu, Florentina Gatea and Ionela Sârbu

Genes 2019, 10(7), 535; https://doi.org/10.3390/genes10070535 - 15 Jul 2019

Cited by 27 | Viewed by 5998

Abstract

Non-nutritive sweeteners represent an ingredient class that directly affects human health, via the development of inflammatory processes that promote chronic diseases related to microbiota dysbiosis. Several in vitro tests were conducted in the static GIS1 simulator. The aim of the study was to [...] Read more.

Non-nutritive sweeteners represent an ingredient class that directly affects human health, via the development of inflammatory processes that promote chronic diseases related to microbiota dysbiosis. Several in vitro tests were conducted in the static GIS1 simulator. The aim of the study was to highlight the effect of sweeteners on the microbiota pattern of healthy individuals, associated with any alteration in the metabolomic response, through the production of organic acids and ammonium. The immediate effect of the in vitro treatment and the influence of the specific sweetener type on the occurrence of dysbiosis were evaluated by determining the biomarkers of the microbiota response. The presence of the steviol reduced the ammonium level (minimum of 410 mg/L), while the addition of cyclamate and saccharin caused a decrease in the number of microorganisms, in addition to lowering the total quantity of synthesized short-chain fatty acids (SCFAs). The bifidobacteria appeared to decrease below 10² genomes/mL in all the analyzed samples at the end of the in vitro simulation period. Barring the in vitro treatment of steviol, all the sweeteners tested exerted a negative influence on the fermentative profile, resulting in a decline in the fermentative processes, a rise in the colonic pH, and uniformity of the SCFA ratio. Full article

(This article belongs to the Special Issue Human Microbiome or Microbial Communities Related with Humans)

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19 pages, 1138 KiB

Open AccessReview

Ketogenic Diet and Microbiota: Friends or Enemies?

by Antonio Paoli, Laura Mancin, Antonino Bianco, Ewan Thomas, João Felipe Mota and Fabio Piccini

Genes 2019, 10(7), 534; https://doi.org/10.3390/genes10070534 - 15 Jul 2019

Cited by 186 | Viewed by 45270

Abstract

Over the last years, a growing body of evidence suggests that gut microbial communities play a fundamental role in many aspects of human health and diseases. The gut microbiota is a very dynamic entity influenced by environment and nutritional behaviors. Considering the influence [...] Read more.

Over the last years, a growing body of evidence suggests that gut microbial communities play a fundamental role in many aspects of human health and diseases. The gut microbiota is a very dynamic entity influenced by environment and nutritional behaviors. Considering the influence of such a microbial community on human health and its multiple mechanisms of action as the production of bioactive compounds, pathogens protection, energy homeostasis, nutrients metabolism and regulation of immunity, establishing the influences of different nutritional approach is of pivotal importance. The very low carbohydrate ketogenic diet is a very popular dietary approach used for different aims: from weight loss to neurological diseases. The aim of this review is to dissect the complex interactions between ketogenic diet and gut microbiota and how this large network may influence human health. Full article

(This article belongs to the Special Issue Genetic and Epigenetic Modulation of Cell Functions by Physical Exercise)

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11 pages, 1272 KiB

Open AccessArticle

The First Complete Mitochondrial Genome of the Flathead Cociella crocodilus (Scorpaeniformes: Platycephalidae) and the Phylogenetic Relationships within Scorpaeniformes Based on Whole Mitogenomes

by Lei Cui, Rongbo Cao, Yuelei Dong, Xingchen Gao, Jingyi Cen and Songhui Lu

Genes 2019, 10(7), 533; https://doi.org/10.3390/genes10070533 - 15 Jul 2019

Cited by 5 | Viewed by 3623

Abstract

Complete mitochondrial genomes (mitogenomes) are important molecular markers for understanding the phylogenetics of various species. Although recent studies on the mitogenomes of the Scorpaeniformes species have been greatly advanced, information regarding molecular studies and the taxonomic localization of Platycephalidae is still sparse. To [...] Read more.

Complete mitochondrial genomes (mitogenomes) are important molecular markers for understanding the phylogenetics of various species. Although recent studies on the mitogenomes of the Scorpaeniformes species have been greatly advanced, information regarding molecular studies and the taxonomic localization of Platycephalidae is still sparse. To further analyze the phylogeny of Platycephalidae, we sequenced the complete mitogenome of Cociella crocodilus of the Platycephalidae family within Scorpaeniformes for the first time. The mitogenome was 17,314 bp in length, contained two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and two typical noncoding control regions (the control region (CR) and origin of the light strand (OL)). All PCGs used standard initiation codons ATG, apart from cox1. The majority of the tRNA genes could be folded into cloverleaf secondary structures, whereas the secondary structure of tRNASer (AGN) lacked a dihydrouridine (DHU) stem. The CR contained several conserved sequence blocks (CSBs) and eight tandem repeats. In addition, the phylogenetic relationship based on the concatenated nucleotides sequences of 13 PCGs indicated that the Platycephalidae species are relatively basal in the phylogenetic relationships of Scorpaeniformes. Our results may not only advance the origin and the evolution of Scorpaeniformes, but also provide information for the genetic evolution and taxonomy of the teleostean species. Full article

(This article belongs to the Section Population and Evolutionary Genetics and Genomics)

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14 pages, 2987 KiB

Open AccessArticle

Maternally Inherited Differences within Mitochondrial Complex I Control Murine Healthspan

by Misa Hirose, Paul Schilf, Kim Zarse, Hauke Busch, Georg Fuellen, Olaf Jöhren, Rüdiger Köhling, Inke R. König, Barbara Richer, Jan Rupp, Markus Schwaninger, Karsten Seeger, Christian Sina, Michael Ristow and Saleh M. Ibrahim

Genes 2019, 10(7), 532; https://doi.org/10.3390/genes10070532 - 13 Jul 2019

Cited by 8 | Viewed by 4558

Abstract

Mitochondrial complex I—the largest enzyme complex of the mitochondrial oxidative phosphorylation machinery—has been proposed to contribute to a variety of age-related pathological alterations as well as longevity. The enzyme complex-consisting proteins are encoded by both nuclear (nDNA) and mitochondrial DNA (mtDNA). While some [...] Read more.

Mitochondrial complex I—the largest enzyme complex of the mitochondrial oxidative phosphorylation machinery—has been proposed to contribute to a variety of age-related pathological alterations as well as longevity. The enzyme complex-consisting proteins are encoded by both nuclear (nDNA) and mitochondrial DNA (mtDNA). While some association studies of mtDNA encoded complex I genes and lifespan in humans have been reported, experimental evidence and the functional consequence of such variants is limited to studies using invertebrate models. Here, we present experimental evidence that a homoplasmic mutation in the mitochondrially encoded complex I gene mt-Nd2 modulates lifespan by altering cellular tryptophan levels and, consequently, ageing-related pathways in mice. A conplastic mouse strain carrying a mutation at m.4738C > A in mt-Nd2 lived slightly, but significantly, shorter than the controls did. The same mutation led to a higher susceptibility to glucose intolerance induced by high-fat diet feeding. These phenotypes were not observed in mice carrying a mutation in another mtDNA encoded complex I gene, mt-Nd5, suggesting the functional relevance of particular mutations in complex I to ageing and age-related diseases. Full article

(This article belongs to the Special Issue Mitochondrial DNA Mutations in Human Diseases)

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17 pages, 3334 KiB

Open AccessArticle

SCINA: A Semi-Supervised Subtyping Algorithm of Single Cells and Bulk Samples

by Ze Zhang, Danni Luo, Xue Zhong, Jin Huk Choi, Yuanqing Ma, Stacy Wang, Elena Mahrt, Wei Guo, Eric W Stawiski, Zora Modrusan, Somasekar Seshagiri, Payal Kapur, Gary C. Hon, James Brugarolas and Tao Wang

Genes 2019, 10(7), 531; https://doi.org/10.3390/genes10070531 - 12 Jul 2019

Cited by 129 | Viewed by 15054

Abstract

Advances in single-cell RNA sequencing (scRNA-Seq) have allowed for comprehensive analyses of single cell data. However, current analyses of scRNA-Seq data usually start from unsupervised clustering or visualization. These methods ignore prior knowledge of transcriptomes and the probable structures of the data. Moreover, [...] Read more.

Advances in single-cell RNA sequencing (scRNA-Seq) have allowed for comprehensive analyses of single cell data. However, current analyses of scRNA-Seq data usually start from unsupervised clustering or visualization. These methods ignore prior knowledge of transcriptomes and the probable structures of the data. Moreover, cell identification heavily relies on subjective and possibly inaccurate human inspection afterwards. To address these analytical challenges, we developed SCINA (Semi-supervised Category Identification and Assignment), a semi-supervised model that exploits previously established gene signatures using an expectation–maximization (EM) algorithm. SCINA is applicable to scRNA-Seq and flow cytometry/CyTOF data, as well as other data of similar format. We applied SCINA to a wide range of datasets, and showed its accuracy, stability and efficiency, which exceeded most popular unsupervised approaches. SCINA discovered an intermediate stage of oligodendrocytes from mouse brain scRNA-Seq data. SCINA also detected immune cell population changes in cytometry data in a genetically-engineered mouse model. Furthermore, SCINA performed well with bulk gene expression data. Specifically, we identified a new kidney tumor clade with similarity to FH-deficient tumors (FHD), which we refer to as FHD-like tumors (FHDL). Overall, SCINA provides both methodological advances and biological insights from perspectives different from traditional analytical methods. Full article

(This article belongs to the Special Issue Genetic Variation and Splicing from Single Cell RNA-Sequencing)

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12 pages, 1487 KiB

Open AccessArticle

groEL Gene-Based Phylogenetic Analysis of Lactobacillus Species by High-Throughput Sequencing

by Miaoqi Xie, Mingluo Pan, Yang Jiang, Xiaoming Liu, Wenwei Lu, Jianxin Zhao, Hao Zhang and Wei Chen

Genes 2019, 10(7), 530; https://doi.org/10.3390/genes10070530 - 12 Jul 2019

Cited by 22 | Viewed by 4688

Abstract

Lactobacillus is a fairly diverse genus of bacteria with more than 260 species and subspecies. Many profiling methods have been developed to carry out phylogenetic analysis of this complex and diverse genus, but limitations remain since there is still a lack of comprehensive [...] Read more.

Lactobacillus is a fairly diverse genus of bacteria with more than 260 species and subspecies. Many profiling methods have been developed to carry out phylogenetic analysis of this complex and diverse genus, but limitations remain since there is still a lack of comprehensive and accurate analytical method to profile this genus at species level. To overcome these limitations, a Lactobacillus-specific primer set was developed targeting a hypervariable region in the groEL gene—a single-copy gene that has undergone rapid mutation and evolution. The results showed that this methodology could accurately perform taxonomic identification of Lactobacillus down to the species level. Its detection limit was as low as 10⁴ colony-forming units (cfu)/mL for Lactobacillus species. The assessment of detection specificity using the Lactobacillus groEL profiling method found that Lactobacillus, Pediococcus, Weissella, and Leuconostoc genus could be distinguished, but non-Lactobacillus Genus Complex could not be detected. The groEL gene sequencing and Miseq high-throughput approach were adopted to estimate the richness and diversity of Lactobacillus species in different ecosystems. The method was tested using kurut (fermented yak milk) samples and fecal samples of human, rat, and mouse. The results indicated that Lactobacillus mucosae was the predominant gut Lactobacillus species among Chinese, and L. johnsonii accounted for the majority of lactobacilli in rat and mouse gut. Meanwhile, L. delbrueckii subsp. bulgaricus had the highest relative abundance of Lactobacillus in kurut. Thus, this groEL gene profiling method is expected to promote the application of Lactobacillus for industrial production and therapeutic purpose. Full article

(This article belongs to the Special Issue Human Microbiome or Microbial Communities Related with Humans)

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14 pages, 10926 KiB

Open AccessArticle

Three New Mutations and Mild, Asymmetrical Phenotype in the Highly Distinctive LAMM Syndrome: A Report of Eight Further Cases

by Amina Al Yassin, Felice D’Arco, Matías Morín, Waheeda Pagarkar, Katherine Harrop-Griffiths, Azhar Shaida, Elena Fernández, Tom Cullup, Bianca De-Souza, Miguel Angel Moreno-Pelayo and Maria Bitner-Glindzicz

Genes 2019, 10(7), 529; https://doi.org/10.3390/genes10070529 - 12 Jul 2019

Cited by 10 | Viewed by 3759

Abstract

Labyrinthine aplasia, microtia, and microdontia (LAMM) is an autosomal recessive condition causing profound congenital deafness, complete absence of inner ear structures (usually Michel’s aplasia), microtia (usually type 1) and microdontia. To date, several families have been described with this condition and a number [...] Read more.

Labyrinthine aplasia, microtia, and microdontia (LAMM) is an autosomal recessive condition causing profound congenital deafness, complete absence of inner ear structures (usually Michel’s aplasia), microtia (usually type 1) and microdontia. To date, several families have been described with this condition and a number of mutations has been reported. We report on eight further cases of LAMM syndrome including three novel mutations, c. 173T>C p.L58P; c. 284G>A p.(Arg95Gln) and c.325_327delinsA p.(Glu109Thrfs*18). Congenital deafness was the primary presenting feature in all affected individuals and consanguinity in all but two families. We compare the features in our patients to those previously reported in LAMM, and describe a milder, asymmetrical phenotype associated with FGF3 mutations. Full article

(This article belongs to the Special Issue Genetic Epidemiology of Deafness)

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15 pages, 3470 KiB

Open AccessArticle

Defining the Clinical, Molecular and Ultrastructural Characteristics in Occipital Horn Syndrome: Two New Cases and Review of the Literature

by Aude Beyens, Kyaran Van Meensel, Lore Pottie, Riet De Rycke, Michiel De Bruyne, Femke Baeke, Piet Hoebeke, Frank Plasschaert, Bart Loeys, Sofie De Schepper, Sofie Symoens and Bert Callewaert

Genes 2019, 10(7), 528; https://doi.org/10.3390/genes10070528 - 12 Jul 2019

Cited by 22 | Viewed by 9407

Abstract

Occipital horn syndrome (OHS) is a rare connective tissue disorder caused by pathogenic variants in ATP7A, encoding a copper transporter. The main clinical features, including cutis laxa, bony exostoses, and bladder diverticula are attributed to a decreased activity of lysyl oxidase (LOX), a [...] Read more.

Occipital horn syndrome (OHS) is a rare connective tissue disorder caused by pathogenic variants in ATP7A, encoding a copper transporter. The main clinical features, including cutis laxa, bony exostoses, and bladder diverticula are attributed to a decreased activity of lysyl oxidase (LOX), a cupro-enzyme involved in collagen crosslinking. The absence of large case series and natural history studies precludes efficient diagnosis and management of OHS patients. This study describes the clinical and molecular characteristics of two new patients and 32 patients previously reported in the literature. We report on the need for long-term specialized care and follow-up, in which MR angiography, echocardiography and spirometry should be incorporated into standard follow-up guidelines for OHS patients, next to neurodevelopmental, orthopedic and urological follow-up. Furthermore, we report on ultrastructural abnormalities including increased collagen diameter, mild elastic fiber abnormalities and multiple autophagolysosomes reflecting the role of lysyl oxidase and defective ATP7A trafficking as pathomechanisms of OHS. Full article

(This article belongs to the Special Issue Molecular Genetics and Pathogenesis of Ehlers–Danlos Syndrome and Related Connective Tissue Disorders)

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17 pages, 5158 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of the Metacaspase Gene Family in Gossypium Species

by Senmiao Fan, Aiying Liu, Zhen Zhang, Xianyan Zou, Xiao Jiang, Jinyong Huang, Liqiang Fan, Zhibin Zhang, Xiaoying Deng, Qun Ge, Wankui Gong, Junwen Li, Juwu Gong, Yuzhen Shi, Kang Lei, Shuya Zhang, Tingting Jia, Lipeng Zhang, Youlu Yuan and Haihong Shang

Genes 2019, 10(7), 527; https://doi.org/10.3390/genes10070527 - 12 Jul 2019

Cited by 10 | Viewed by 3611

Abstract

Metacaspases (MCs) are cysteine proteases that are important for programmed cell death (PCD) in plants. In this study, we identified 89 MC genes in the genomes of four Gossypium species (Gossypium raimondii, Gossypium barbadense, Gossypium hirsutum, and Gossypium arboreum [...] Read more.

Metacaspases (MCs) are cysteine proteases that are important for programmed cell death (PCD) in plants. In this study, we identified 89 MC genes in the genomes of four Gossypium species (Gossypium raimondii, Gossypium barbadense, Gossypium hirsutum, and Gossypium arboreum), and classified them as type-I or type-II genes. All of the type-I and type-II MC genes contain a sequence encoding the peptidase C14 domain. During developmentally regulated PCD, type-II MC genes may play an important role related to fiber elongation, while type-I genes may affect the thickening of the secondary wall. Additionally, 13 genes were observed to be differentially expressed between two cotton lines with differing fiber strengths, and four genes (GhMC02, GhMC04, GhMC07, and GhMC08) were predominantly expressed in cotton fibers at 5–30 days post-anthesis (DPA). During environmentally induced PCD, the expression levels of four genes were affected in the root, stem, and leaf tissues within 6 h of an abiotic stress treatment. In general, the MC gene family affects the development of cotton fibers, including fiber elongation and fiber thickening while four prominent fiber- expressed genes were identified. The effects of the abiotic stress and hormone treatments imply that the cotton MC gene family may be important for fiber development. The data presented herein may form the foundation for future investigations of the MC gene family in Gossypium species. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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16 pages, 1990 KiB

Open AccessArticle

miR403a and SA Are Involved in NbAGO2 Mediated Antiviral Defenses Against TMV Infection in Nicotiana benthamiana

by Pengfei Diao, Qimeng Zhang, Hongyu Sun, Wenjie Ma, Aiping Cao, Ruonan Yu, Jiaojiao Wang, Yiding Niu and Hada Wuriyanghan

Genes 2019, 10(7), 526; https://doi.org/10.3390/genes10070526 - 12 Jul 2019

Cited by 25 | Viewed by 4584

Abstract

RNAi (RNA interference) is an important defense response against virus infection in plants. The core machinery of the RNAi pathway in plants include DCL (Dicer Like), AGO (Argonaute) and RdRp (RNA dependent RNA polymerase). Although involvement of these RNAi components in virus infection [...] Read more.

RNAi (RNA interference) is an important defense response against virus infection in plants. The core machinery of the RNAi pathway in plants include DCL (Dicer Like), AGO (Argonaute) and RdRp (RNA dependent RNA polymerase). Although involvement of these RNAi components in virus infection responses was demonstrated in Arabidopsis thaliana, their contribution to antiviral immunity in Nicotiana benthamiana, a model plant for plant-pathogen interaction studies, is not well understood. In this study, we investigated the role of N. benthamiana NbAGO2 gene against TMV (Tomato mosaic virus) infection. Silencing of NbAGO2 by transient expression of an hpRNA construct recovered GFP (Green fluorescent protein) expression in GFP-silenced plant, demonstrating that NbAGO2 participated in RNAi process in N. benthamiana. Expression of NbAGO2 was transcriptionally induced by both MeSA (Methylsalicylate acid) treatment and TMV infection. Down-regulation of NbAGO2 gene by amiR-NbAGO2 transient expression compromised plant resistance against TMV infection. Inhibition of endogenous miR403a, a predicted regulatory microRNA of NbAGO2, reduced TMV infection. Our study provides evidence for the antiviral role of NbAGO2 against a Tobamovirus family virus TMV in N. benthamiana, and SA (Salicylic acid) mediates this by induction of NbAGO2 expression upon TMV infection. Our data also highlighted that miR403a was involved in TMV defense by regulation of target NbAGO2 gene in N. Benthamiana. Full article

(This article belongs to the Special Issue Plant miRNA Mediated Defense Response)

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