Genes

20 pages, 3798 KiB

Open AccessArticle

Identification of Novel Interspersed DNA Repetitive Elements in the Trypanosoma cruzi Genome Associated with the 3′UTRs of Surface Multigenic Families

by Simone Guedes Calderano, Milton Yutaka Nishiyama Junior, Marjorie Marini, Nathan de Oliveira Nunes, Marcelo da Silva Reis, José Salvatore Leister Patané, José Franco da Silveira, Julia Pinheiro Chagas da Cunha and Maria Carolina Elias

Genes 2020, 11(10), 1235; https://doi.org/10.3390/genes11101235 - 21 Oct 2020

Cited by 2 | Viewed by 2979

Abstract

Trypanosoma cruzi is the etiological agent of Chagas disease, which affects millions of people in Latin America. No transcriptional control of gene expression has been demonstrated in this organism, and 50% of its genome consists of repetitive elements and members of multigenic families. [...] Read more.

Trypanosoma cruzi is the etiological agent of Chagas disease, which affects millions of people in Latin America. No transcriptional control of gene expression has been demonstrated in this organism, and 50% of its genome consists of repetitive elements and members of multigenic families. In this study, we applied a novel bioinformatics approach to predict new repetitive elements in the genome sequence of T. cruzi. A new repetitive sequence measuring 241 nt was identified and found to be interspersed along the genome sequence from strains of different DTUs. This new repeat was mostly on intergenic regions, and upstream and downstream regions of the 241 nt repeat were enriched in surface protein genes. RNAseq analysis revealed that the repeat was part of processed mRNAs and was predominantly found in the 3′ untranslated regions (UTRs) of genes of multigenic families encoding surface proteins. Moreover, we detected a correlation between the presence of the repeat in the 3′UTR of multigenic family genes and the level of differential expression of these genes when comparing epimastigote and trypomastigote transcriptomes. These data suggest that this sequence plays a role in the posttranscriptional regulation of the expression of multigenic families. Full article

(This article belongs to the Special Issue Kinetoplastid Genomics and Beyond)

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20 pages, 885 KiB

Open AccessArticle

Comparative Genomics of the Transport Proteins of Ten Lactobacillus Strains

by Hassan Zafar and Milton H. Saier, Jr.

Genes 2020, 11(10), 1234; https://doi.org/10.3390/genes11101234 - 21 Oct 2020

Cited by 16 | Viewed by 4324

Abstract

The genus Lactobacillus includes species that may inhabit different anatomical locations in the human body, but the greatest percentage of its species are inhabitants of the gut. Lactobacilli are well known for their probiotic characteristics, although some species may become pathogenic and exert [...] Read more.

The genus Lactobacillus includes species that may inhabit different anatomical locations in the human body, but the greatest percentage of its species are inhabitants of the gut. Lactobacilli are well known for their probiotic characteristics, although some species may become pathogenic and exert negative effects on human health. The transportome of an organism consists of the sum of the transport proteins encoded within its genome, and studies on the transportome help in the understanding of the various physiological processes taking place in the cell. In this communication we analyze the transport proteins and predict probable substrate specificities of ten Lactobacillus strains. Six of these strains (L. brevis, L. bulgaricus, L. crispatus, L. gasseri, L. reuteri, and L. ruminis) are currently believed to be only probiotic (OP). The remaining four strains (L. acidophilus, L. paracasei, L. planatarum, and L. rhamnosus) can play dual roles, being both probiotic and pathogenic (PAP). The characteristics of the transport systems found in these bacteria were compared with strains (E. coli, Salmonella, and Bacteroides) from our previous studies. Overall, the ten lactobacilli contain high numbers of amino acid transporters, but the PAP strains contain higher number of sugar, amino acid and peptide transporters as well as drug exporters than their OP counterparts. Moreover, some of the OP strains contain pore-forming toxins and drug exporters similar to those of the PAP strains, thus indicative of yet unrecognized pathogenic potential. The transportomes of the lactobacilli seem to be finely tuned according to the extracellular and probiotic lifestyles of these organisms. Taken together, the results of this study help to reveal the physiological and pathogenic potential of common prokaryotic residents in the human body. Full article

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

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18 pages, 2376 KiB

Open AccessArticle

GJB2 and GJB6 Genetic Variant Curation in an Argentinean Non-Syndromic Hearing-Impaired Cohort

by Paula Buonfiglio, Carlos D. Bruque, Leonela Luce, Florencia Giliberto, Vanesa Lotersztein, Sebastián Menazzi, Bibiana Paoli, Ana Belén Elgoyhen and Viviana Dalamón

Genes 2020, 11(10), 1233; https://doi.org/10.3390/genes11101233 - 21 Oct 2020

Cited by 12 | Viewed by 6179

Abstract

Genetic variants in GJB2 and GJB6 genes are the most frequent causes of hereditary hearing loss among several deaf populations worldwide. Molecular diagnosis enables proper genetic counseling and medical prognosis to patients. In this study, we present an update of testing [...] Read more.

Genetic variants in GJB2 and GJB6 genes are the most frequent causes of hereditary hearing loss among several deaf populations worldwide. Molecular diagnosis enables proper genetic counseling and medical prognosis to patients. In this study, we present an update of testing results in a cohort of Argentinean non-syndromic hearing-impaired individuals. A total of 48 different sequence variants were detected in genomic DNA from patients referred to our laboratory. They were manually curated and classified based on the American College of Medical Genetics and Genomics/Association for Molecular Pathology ACMG/AMP standards and hearing-loss-gene-specific criteria of the ClinGen Hearing Loss Expert Panel. More than 50% of sequence variants were reclassified from their previous categorization in ClinVar. These results provide an accurately interpreted set of variants to be taken into account by clinicians and the scientific community, and hence, aid the precise genetic counseling to patients. Full article

(This article belongs to the Special Issue Genetics of Hearing Impairment)

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17 pages, 3496 KiB

Open AccessArticle

bta-miR-23a Regulates the Myogenic Differentiation of Fetal Bovine Skeletal Muscle-Derived Progenitor Cells by Targeting MDFIC Gene

by Xin Hu, Yishen Xing, Ling Ren, Yahui Wang, Qian Li, Qiyuan Yang, Min Du, Lingyang Xu, Luc Willems, Junya Li and Lupei Zhang

Genes 2020, 11(10), 1232; https://doi.org/10.3390/genes11101232 - 20 Oct 2020

Cited by 5 | Viewed by 3035

Abstract

miR-23a, a member of the miR-23a/24-2/27a cluster, has been demonstrated to play pivotal roles in many cellular activities. However, the mechanisms of how bta-miR-23a controls the myogenic differentiation (MD) of PDGFRα⁻ bovine progenitor cells (bPCs) remain poorly understood. In the present work, [...] Read more.

miR-23a, a member of the miR-23a/24-2/27a cluster, has been demonstrated to play pivotal roles in many cellular activities. However, the mechanisms of how bta-miR-23a controls the myogenic differentiation (MD) of PDGFRα⁻ bovine progenitor cells (bPCs) remain poorly understood. In the present work, bta-miR-23a expression was increased during the MD of ^PDGFRα− bPCs. Moreover, bta-miR-23a overexpression significantly promoted the MD of ^PDGFRα− bPCs. Luciferase reporter assays showed that the 3’-UTR region of MDFIC (MyoD family inhibitor domain containing) could be a promising target of bta-miR-23a, which resulted in its post-transcriptional down-regulation. Additionally, the knockdown of MDFIC by siRNA facilitated the MD of ^PDGFRα− bPCs, while the overexpression of MDFIC inhibited the activating effect of bta-miR-23a during MD. Of note, MDFIC might function through the interaction between MyoG transcription factor and MEF2C promoter. This study reveals that bta-miR-23a can promote the MD of ^PDGFRα− bPCs through post-transcriptional downregulation of MDFIC. Full article

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13 pages, 1567 KiB

Open AccessArticle

Genome-Wide Co-Expression Distributions as a Metric to Prioritize Genes of Functional Importance

by Pâmela A. Alexandre, Nicholas J. Hudson, Sigrid A. Lehnert, Marina R. S. Fortes, Marina Naval-Sánchez, Loan T. Nguyen, Laercio R. Porto-Neto and Antonio Reverter

Genes 2020, 11(10), 1231; https://doi.org/10.3390/genes11101231 - 20 Oct 2020

Cited by 1 | Viewed by 5872

Abstract

Genome-wide gene expression analysis are routinely used to gain a systems-level understanding of complex processes, including network connectivity. Network connectivity tends to be built on a small subset of extremely high co-expression signals that are deemed significant, but this overlooks the vast majority [...] Read more.

Genome-wide gene expression analysis are routinely used to gain a systems-level understanding of complex processes, including network connectivity. Network connectivity tends to be built on a small subset of extremely high co-expression signals that are deemed significant, but this overlooks the vast majority of pairwise signals. Here, we developed a computational pipeline to assign to every gene its pair-wise genome-wide co-expression distribution to one of 8 template distributions shapes varying between unimodal, bimodal, skewed, or symmetrical, representing different proportions of positive and negative correlations. We then used a hypergeometric test to determine if specific genes (regulators versus non-regulators) and properties (differentially expressed or not) are associated with a particular distribution shape. We applied our methodology to five publicly available RNA sequencing (RNA-seq) datasets from four organisms in different physiological conditions and tissues. Our results suggest that genes can be assigned consistently to pre-defined distribution shapes, regarding the enrichment of differential expression and regulatory genes, in situations involving contrasting phenotypes, time-series, or physiological baseline data. There is indeed a striking additional biological signal present in the genome-wide distribution of co-expression values which would be overlooked by currently adopted approaches. Our method can be applied to extract further information from transcriptomic data and help uncover the molecular mechanisms involved in the regulation of complex biological process and phenotypes. Full article

(This article belongs to the Section Technologies and Resources for Genetics)

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4 pages, 182 KiB

Open AccessEditorial

Computational Methods for the Analysis of Genomic Data and Biological Processes

by Francisco Gómez-Vela, Federico Divina and Miguel García-Torres

Genes 2020, 11(10), 1230; https://doi.org/10.3390/genes11101230 - 20 Oct 2020

Cited by 2 | Viewed by 2327

Abstract

Today, new technologies, such as microarrays or high-performance sequencing, are producing more and more genomic data [...] Full article

(This article belongs to the Special Issue Computational Methods for the Analysis of Genomic Data and Biological Processes)

25 pages, 3994 KiB

Open AccessArticle

Genome-Wide Transcriptome Profiling Provides Insight on Cholesterol and Lithocholate Degradation Mechanisms in Nocardioides simplex VKM Ac-2033D

by Victoria Y. Shtratnikova, Mikhail I. Schelkunov, Victoria V. Fokina, Eugeny Y. Bragin, Tatyana G. Lobastova, Andrey A. Shutov, Alexey V. Kazantsev and Marina V. Donova

Genes 2020, 11(10), 1229; https://doi.org/10.3390/genes11101229 - 20 Oct 2020

Cited by 9 | Viewed by 3221

Abstract

Steroid microbial degradation plays a significant ecological role for biomass decomposition and removal/detoxification of steroid pollutants. In this study, the initial steps of cholesterol degradation and lithocholate bioconversion by a strain with enhanced 3-ketosteroid dehydrogenase (3-KSD) activity, Nocardioides simplex VKM Ac-2033D, were studied. [...] Read more.

Steroid microbial degradation plays a significant ecological role for biomass decomposition and removal/detoxification of steroid pollutants. In this study, the initial steps of cholesterol degradation and lithocholate bioconversion by a strain with enhanced 3-ketosteroid dehydrogenase (3-KSD) activity, Nocardioides simplex VKM Ac-2033D, were studied. Biochemical, transcriptomic, and bioinformatic approaches were used. Among the intermediates of sterol sidechain oxidation cholest-5-en-26-oic acid and 3-oxo-cholesta-1,4-dien-26-oic acid were identified as those that have not been earlier reported for N. simplex and related species. The transcriptomic approach revealed candidate genes of cholesterol and lithocholic acid (LCA) catabolism by the strain. A separate set of genes combined in cluster and additional 3-ketosteroid Δ¹-dehydrogenase and 3-ketosteroid 9α-hydroxylases that might be involved in LCA catabolism were predicted. Bioinformatic calculations based on transcriptomic data showed the existence of a previously unknown transcription factor, which regulates cholate catabolism gene orthologs. The results contribute to the knowledge on diversity of steroid catabolism regulation in actinobacteria and might be used at the engineering of microbial catalysts for ecological and industrial biotechnology. Full article

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

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39 pages, 13620 KiB

Open AccessArticle

Comparative Transcriptome Profiling of Skeletal Muscle from Black Muscovy Duck at Different Growth Stages Using RNA-seq

by Zhigang Hu, Junting Cao, Guangyu Liu, Huilin Zhang and Xiaolin Liu

Genes 2020, 11(10), 1228; https://doi.org/10.3390/genes11101228 - 20 Oct 2020

Cited by 19 | Viewed by 3283

Abstract

In China, the production for duck meat is second only to that of chicken, and the demand for duck meat is also increasing. However, there is still unclear on the internal mechanism of regulating skeletal muscle growth and development in duck. This study [...] Read more.

In China, the production for duck meat is second only to that of chicken, and the demand for duck meat is also increasing. However, there is still unclear on the internal mechanism of regulating skeletal muscle growth and development in duck. This study aimed to identity candidate genes related to growth of duck skeletal muscle and explore the potential regulatory mechanism. RNA-seq technology was used to compare the transcriptome of skeletal muscles in black Muscovy ducks at different developmental stages (day 17, 21, 27, 31, and 34 of embryos and postnatal 6-month-olds). The SNPs and InDels of black Muscovy ducks at different growth stages were mainly in “INTRON”, “SYNONYMOUS_CODING”, “UTR_3_PRIME”, and “DOWNSTREAM”. The average number of AS in each sample was 37,267, mainly concentrated in TSS and TTS. Besides, a total of 19 to 5377 DEGs were detected in each pairwise comparison. Functional analysis showed that the DEGs were mainly involved in the processes of cell growth, muscle development, and cellular activities (junction, migration, assembly, differentiation, and proliferation). Many of DEGs were well known to be related to growth of skeletal muscle in black Muscovy duck, such as MyoG, FBXO1, MEF2A, and FoxN2. KEGG pathway analysis identified that the DEGs were significantly enriched in the pathways related to the focal adhesion, MAPK signaling pathway and regulation of the actin cytoskeleton. Some DEGs assigned to these pathways were potential candidate genes inducing the difference in muscle growth among the developmental stages, such as FAF1, RGS8, GRB10, SMYD3, and TNNI2. Our study identified several genes and pathways that may participate in the regulation of skeletal muscle growth in black Muscovy duck. These results should serve as an important resource revealing the molecular basis of muscle growth and development in duck. Full article

(This article belongs to the Special Issue Genetics and Genomics Applied to Livestock Production)

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17 pages, 1688 KiB

Open AccessArticle

Metabolic Specialization and Codon Preference of Lignocellulolytic Genes in the White Rot Basidiomycete Ceriporiopsis subvermispora

by Alex Gonzalez, Gino Corsini, Sergio Lobos, Daniela Seelenfreund and Mario Tello

Genes 2020, 11(10), 1227; https://doi.org/10.3390/genes11101227 - 20 Oct 2020

Cited by 3 | Viewed by 2919

Abstract

Ceriporiopsis subvermispora is a white-rot fungus with a high specificity towards lignin mineralization when colonizing dead wood or lignocellulosic compounds. Its lignocellulose degrading system is formed by cellulose hydrolytic enzymes, manganese peroxidases, and laccases that catalyze the efficient depolymerization and mineralization of lignocellulose. [...] Read more.

Ceriporiopsis subvermispora is a white-rot fungus with a high specificity towards lignin mineralization when colonizing dead wood or lignocellulosic compounds. Its lignocellulose degrading system is formed by cellulose hydrolytic enzymes, manganese peroxidases, and laccases that catalyze the efficient depolymerization and mineralization of lignocellulose. To determine if this metabolic specialization has modified codon usage of the lignocellulolytic system, improving its adaptation to the fungal translational machine, we analyzed the adaptation to host codon usage (CAI), tRNA pool (tAI, and AAtAI), codon pair bias (CPB), and the number of effective codons (Nc). These indexes were correlated with gene expression of C. subvermispora, in the presence of glucose and Aspen wood. General gene expression was not correlated with the index values. However, in media containing Aspen wood, the induction of expression of lignocellulose-degrading genes, showed significantly (p < 0.001) higher values of CAI, AAtAI, CPB, tAI, and lower values of Nc than non-induced genes. Cellulose-binding proteins and manganese peroxidases presented the highest adaptation values. We also identified an expansion of genes encoding glycine and glutamic acid tRNAs. Our results suggest that the metabolic specialization to use wood as the sole carbon source has introduced a bias in the codon usage of genes involved in lignocellulose degradation. This bias reduces codon diversity and increases codon usage adaptation to the tRNA pool available in C. subvermispora. To our knowledge, this is the first study showing that codon usage is modified to improve the translation efficiency of a group of genes involved in a particular metabolic process. Full article

(This article belongs to the Special Issue Microbial Genomics and Evolution)

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11 pages, 2228 KiB

Open AccessArticle

Expression Profile of Porcine TRIM26 and Its Inhibitory Effect on Interferon-β Production and Antiviral Response

by Hui Huang, Mona Sharma, Yanbing Zhang, Chenxi Li, Ke Liu, Jianchao Wei, Donghua Shao, Beibei Li, Zhiyong Ma, Ruibing Cao and Yafeng Qiu

Genes 2020, 11(10), 1226; https://doi.org/10.3390/genes11101226 - 19 Oct 2020

Cited by 7 | Viewed by 2939

Abstract

TRIM26, a member of the tripartite motif (TRIM) family has been shown to be involved in modulation of innate antiviral response. However, the functional characteristics of porcine TRIM26 (porTRIM26) are unclear. In this study, we used a synthesized antigen peptide to generate a [...] Read more.

TRIM26, a member of the tripartite motif (TRIM) family has been shown to be involved in modulation of innate antiviral response. However, the functional characteristics of porcine TRIM26 (porTRIM26) are unclear. In this study, we used a synthesized antigen peptide to generate a polyclonal antibody against porTRIM26 with which to study the expression and function of porTRIM26. We demonstrated that polyinosinic:polycytidylic acid (poly (I:C)) stimulation and viral infection (vesicular stomatitis (VSV) or porcine reproductive and respiratory syndrome virus (PRRSV)) induce expression of porTRIM26, whereas knock-down expression of porTRIM26 promotes interferon (IFN)-β production after poly (I:C) stimulation and virus infection (VSV or PRRSV). The importance of the porTRIM26-mediated modulation of the antiviral response was also shown in VSV- or PRRSV-infected cells. In summary, these findings show that porTRIM26 has an inhibitory role in IFN-β expression and the antiviral response. Full article

(This article belongs to the Special Issue Pig Genomics and Genetics)

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15 pages, 1961 KiB

Open AccessArticle

Systems Level Analysis and Identification of Pathways and Key Genes Associated with Delirium

by Yukiko Takahashi, Tomoyoshi Terada and Yoshinori Muto

Genes 2020, 11(10), 1225; https://doi.org/10.3390/genes11101225 - 19 Oct 2020

Cited by 8 | Viewed by 2942

Abstract

Delirium is a complex pathophysiological process, and multiple contributing mechanisms have been identified. However, it is largely unclear how the genes associated with delirium contribute and which of them play key roles. In this study, the genes associated with delirium were retrieved from [...] Read more.

Delirium is a complex pathophysiological process, and multiple contributing mechanisms have been identified. However, it is largely unclear how the genes associated with delirium contribute and which of them play key roles. In this study, the genes associated with delirium were retrieved from the Comparative Toxicogenomics Database (CTD) and integrated through a protein–protein interaction (PPI) network. Delirium-associated genes formed a highly interconnected PPI subnetwork, indicating a high tendency to interact and agglomerate. Using the Molecular Complex Detection (MCODE) algorithm, we identified the top two delirium-relevant network modules, M1 and M5, that have the most significant enrichments for the delirium-related gene sets. Functional enrichment analysis showed that genes related to neurotransmitter receptor activity were enriched in both modules. Moreover, analyses with genes located in human accelerated regions (HARs) provided evidence that HAR-Brain genes were overrepresented in the delirium-relevant network modules. We found that four of the HAR-Brain genes, namely APP, PLCB1, NPY, and HTR2A, in the M1 module were highly connected and appeared to exhibit hub properties, which might play vital roles in delirium development. Further understanding of the function of the identified modules and member genes could help to identify therapeutic intervention targets and diagnostic biomarkers for delirium. Full article

(This article belongs to the Section Human Genomics and Genetic Diseases)

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18 pages, 1500 KiB

Open AccessReview

DNA Damage and Repair in Pulmonary Arterial Hypertension

by Samantha Sharma and Micheala A. Aldred

Genes 2020, 11(10), 1224; https://doi.org/10.3390/genes11101224 - 19 Oct 2020

Cited by 26 | Viewed by 4257

Abstract

Pulmonary arterial hypertension (PAH) is a complex multifactorial disease with both genetic and environmental dynamics contributing to disease progression. Over the last decade, several studies have demonstrated the presence of genomic instability and increased levels of DNA damage in PAH lung vascular cells, [...] Read more.

Pulmonary arterial hypertension (PAH) is a complex multifactorial disease with both genetic and environmental dynamics contributing to disease progression. Over the last decade, several studies have demonstrated the presence of genomic instability and increased levels of DNA damage in PAH lung vascular cells, which contribute to their pathogenic apoptosis-resistant and proliferating characteristics. In addition, the dysregulated DNA damage response pathways have been indicated as causal factors for the presence of persistent DNA damage. To understand the significant implications of DNA damage and repair in PAH pathogenesis, the current review summarizes the recent advances made in this field. This includes an overview of the observed DNA damage in the nuclear and mitochondrial genome of PAH patients. Next, the irregularities observed in various DNA damage response pathways and their role in accumulating DNA damage, escaping apoptosis, and proliferation under a DNA damaging environment are discussed. Although the current literature establishes the pertinence of DNA damage in PAH, additional studies are required to understand the temporal sequence of the above-mentioned events. Further, an exploration of different types of DNA damage in conjunction with associated impaired DNA damage response in PAH will potentially stimulate early diagnosis of the disease and development of novel therapeutic strategies. Full article

(This article belongs to the Special Issue Genetics and Genomics of Pulmonary Arterial Hypertension)

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19 pages, 2265 KiB

Open AccessArticle

QTL Mapping for Domestication-Related Characteristics in Field Cress (Lepidium campestre)—A Novel Oil Crop for the Subarctic Region

by Cecilia Hammenhag, Ganapathi Varma Saripella, Rodomiro Ortiz and Mulatu Geleta

Genes 2020, 11(10), 1223; https://doi.org/10.3390/genes11101223 - 19 Oct 2020

Cited by 2 | Viewed by 3777

Abstract

Domestication of a new crop requires identification and improvement of desirable characteristics Field cress (Lepidium campestre) is being domesticated as a new oilseed crop, particularly for northern temperate regions.. In the present study, an F₂ mapping population and its F₃ progenies [...] Read more.

Domestication of a new crop requires identification and improvement of desirable characteristics Field cress (Lepidium campestre) is being domesticated as a new oilseed crop, particularly for northern temperate regions.. In the present study, an F₂ mapping population and its F₃ progenies were used to identify quantitative trait loci (QTLs) for plant height (PH), number of stems per plant (NS), stem growth orientation (SO), flowering habit (FH), earliness (ER), seed yield per plant (SY), pod shattering resistance (SHR), and perenniality (PE). A highly significant correlation (p < 0.001) was observed between several pairs of characteristics, including SY and ER (negative) or ER and PE (positive). The inclusive composite interval mapping approach was used for QTL mapping using 2330 single nucleotide polymorphism (SNP) markers mapped across the eight field cress linkage groups. Nine QTLs were identified with NS, PH, SO, and PE having 3, 3, 2, and 1 QTLs, explaining 21.3%, 29.5%, 3.8%, and 7.2% of the phenotypic variation, respectively. Candidate genes behind three of the QTLs and favorable marker alleles for different classes of each characteristic were identified. Following their validation through further study, the identified QTLs and associated favorable marker alleles can be used in marker-aided breeding to speed up the domestication of field cress. Full article

(This article belongs to the Special Issue Evolutionary Genetics of Plant Crop-Wild Complexes: From Fundamental to Applied Research)

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17 pages, 2265 KiB

Open AccessArticle

Fine-Tuning of Alanyl-tRNA Synthetase Quality Control Alleviates Global Dysregulation of the Proteome

by Paul Kelly, Arundhati Kavoor and Michael Ibba

Genes 2020, 11(10), 1222; https://doi.org/10.3390/genes11101222 - 18 Oct 2020

Cited by 2 | Viewed by 3035

Abstract

One integral step in the transition from a nucleic acid encoded-genome to functional proteins is the aminoacylation of tRNA molecules. To perform this activity, aminoacyl-tRNA synthetases (aaRSs) activate free amino acids in the cell forming an aminoacyl-adenylate before transferring the amino acid on [...] Read more.

One integral step in the transition from a nucleic acid encoded-genome to functional proteins is the aminoacylation of tRNA molecules. To perform this activity, aminoacyl-tRNA synthetases (aaRSs) activate free amino acids in the cell forming an aminoacyl-adenylate before transferring the amino acid on to its cognate tRNA. These newly formed aminoacyl-tRNA (aa-tRNA) can then be used by the ribosome during mRNA decoding. In Escherichia coli, there are twenty aaRSs encoded in the genome, each of which corresponds to one of the twenty proteinogenic amino acids used in translation. Given the shared chemicophysical properties of many amino acids, aaRSs have evolved mechanisms to prevent erroneous aa-tRNA formation with non-cognate amino acid substrates. Of particular interest is the post-transfer proofreading activity of alanyl-tRNA synthetase (AlaRS) which prevents the accumulation of Ser-tRNA^Ala and Gly-tRNA^Ala in the cell. We have previously shown that defects in AlaRS proofreading of Ser-tRNA^Ala lead to global dysregulation of the E. coli proteome, subsequently causing defects in growth, motility, and antibiotic sensitivity. Here we report second-site AlaRS suppressor mutations that alleviate the aforementioned phenotypes, revealing previously uncharacterized residues within the AlaRS proofreading domain that function in quality control. Full article

(This article belongs to the Special Issue tRNAs in Biology)

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18 pages, 1964 KiB

Open AccessArticle

Genetic Architecture Underpinning Yield Components and Seed Mineral–Nutrients in Sesame

by Naama Teboul, Yaron Gadri, Zipi Berkovich, Ram Reifen and Zvi Peleg

Genes 2020, 11(10), 1221; https://doi.org/10.3390/genes11101221 - 18 Oct 2020

Cited by 18 | Viewed by 4376

Abstract

Genetic dissection of yield components and seed mineral-nutrient is crucial for understanding plant physiological and biochemical processes and alleviate nutrient malnutrition. Sesame (Sesamum indicum L.) is an orphan crop that harbors rich allelic repertoire for seed mineral–nutrients. Here, we harness this wide [...] Read more.

Genetic dissection of yield components and seed mineral-nutrient is crucial for understanding plant physiological and biochemical processes and alleviate nutrient malnutrition. Sesame (Sesamum indicum L.) is an orphan crop that harbors rich allelic repertoire for seed mineral–nutrients. Here, we harness this wide diversity to study the genetic architecture of yield components and seed mineral–nutrients using a core-collection of worldwide genotypes and segregating mapping population. We also tested the association between these traits and the effect of seed nutrients concentration on their bio-accessibility. Wide genetic diversity for yield components and seed mineral–nutrients was found among the core-collection. A high-density linkage map consisting of 19,309 markers was constructed and used for genetic mapping of 84 QTL associated with yield components and 50 QTL for seed minerals. To the best of our knowledge, this is the first report on mineral–nutrients QTL in sesame. Genomic regions with a cluster of overlapping QTL for several morphological and nutritional traits were identified and considered as genomic hotspots. Candidate gene analysis revealed potential functional associations between QTL and corresponding genes, which offers unique opportunities for synchronous improvement of mineral–nutrients. Our findings shed-light on the genetic architecture of yield components, seed mineral–nutrients and their inter- and intra- relationships, which may facilitate future breeding efforts to develop bio-fortified sesame cultivars. Full article

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

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18 pages, 2442 KiB

Open AccessArticle

Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes

by Roshan Kulkarni, Ratan Chopra, Jennifer Chagoya, Charles E. Simpson, Michael R. Baring, Andrew Hillhouse, Naveen Puppala, Kelly Chamberlin and Mark D. Burow

Genes 2020, 11(10), 1220; https://doi.org/10.3390/genes11101220 - 18 Oct 2020

Cited by 3 | Viewed by 3458

Abstract

The use of molecular markers in plant breeding has become a routine practice, but the cost per accession can be a hindrance to the routine use of Quantitative Trait Loci (QTL) identification in breeding programs. In this study, we demonstrate the use of [...] Read more.

The use of molecular markers in plant breeding has become a routine practice, but the cost per accession can be a hindrance to the routine use of Quantitative Trait Loci (QTL) identification in breeding programs. In this study, we demonstrate the use of targeted re-sequencing as a proof of concept of a cost-effective approach to retrieve highly informative allele information, as well as develop a bioinformatics strategy to capture the genome-specific information of a polyploid species. SNPs were identified from alignment of raw transcriptome reads (2 × 50 bp) to a synthetic tetraploid genome using BWA followed by a GATK pipeline. Regions containing high polymorphic SNPs in both A genome and B genomes were selected as targets for the resequencing study. Targets were amplified using multiplex PCR followed by sequencing on an Illumina HiSeq. Eighty-one percent of the SNP calls in diploids and 68% of the SNP calls in tetraploids were confirmed. These results were also confirmed by KASP validation. Based on this study, we find that targeted resequencing technologies have potential for obtaining maximum allele information in allopolyploids at reduced cost. Full article

(This article belongs to the Special Issue Food Legume Genomics)

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17 pages, 1682 KiB

Open AccessArticle

Genomic Characterization of Methicillin-Resistant Staphylococcus aureus (MRSA) by High-Throughput Sequencing in a Tertiary Care Hospital

by May Sherif Soliman, Noha Salah Soliman, Arwa Ramadan El-Manakhly, Shahira AbdelSalam ElBanna, Ramy Karam Aziz and Amani Ali El-Kholy

Genes 2020, 11(10), 1219; https://doi.org/10.3390/genes11101219 - 17 Oct 2020

Cited by 14 | Viewed by 4688

Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) strains are associated with serious complications and poor clinical outcome. In Egypt, they contribute to more than 70% of S. aureus healthcare-associated infections. This study combined whole-genome sequencing, bioinformatics, and statistical analyses to identify the phylogeny, resistome, virulome and [...] Read more.

Methicillin-resistant Staphylococcus aureus (MRSA) strains are associated with serious complications and poor clinical outcome. In Egypt, they contribute to more than 70% of S. aureus healthcare-associated infections. This study combined whole-genome sequencing, bioinformatics, and statistical analyses to identify the phylogeny, resistome, virulome and potential genotype–phenotype–clinical correlation among 18 clinical isolates of MRSA in a tertiary hospital in Cairo, Egypt. The ST1535-V MRSA clone was the most frequently isolated (16.6%), followed by ST5-VI, ST1-V and ST239-III (11.1% each). SCCmec V, VI, IV and III types were detected at frequencies of 50%, 16.6%, 11.1% and 11.1%, respectively. None of the tested virulence genes were detected in all isolates, but they ranged in distribution from 1/18 to 17/18. The Panton–Valentine leukocidin (PVL)-encoding genes were detected in only four isolates and were enriched in isolates causing non-severe cases. Phylogenetic analysis revealed relatedness between three ST1535-Vs, two ST5-VIs, two ST239-IIIs and two ST1-Vs; however, only the two genetically related ST1-V isolates were epidemiologically linked. While disease outcome and source of infection had no correlation with a particular genotypic pattern, the sequence type was the most correlated factor with phylogeny and genotypic patterns, and a few genes were associated with non-severe cases. Full article

(This article belongs to the Special Issue Genetics of Antimicrobial Resistance)

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17 pages, 2225 KiB

Open AccessArticle

Landscape Genomics of a Widely Distributed Snake, Dolichophis caspius (Gmelin, 1789) across Eastern Europe and Western Asia

by Sarita Mahtani-Williams, William Fulton, Amelie Desvars-Larrive, Sara Lado, Jean Pierre Elbers, Bálint Halpern, Dávid Herczeg, Gergely Babocsay, Boris Lauš, Zoltán Tamás Nagy, Daniel Jablonski, Oleg Kukushkin, Pablo Orozco-terWengel, Judit Vörös and Pamela Anna Burger

Genes 2020, 11(10), 1218; https://doi.org/10.3390/genes11101218 - 17 Oct 2020

Cited by 6 | Viewed by 6634

Abstract

Across the distribution of the Caspian whipsnake (Dolichophis caspius), populations have become increasingly disconnected due to habitat alteration. To understand population dynamics and this widespread but locally endangered snake’s adaptive potential, we investigated population structure, admixture, and effective migration patterns. We [...] Read more.

Across the distribution of the Caspian whipsnake (Dolichophis caspius), populations have become increasingly disconnected due to habitat alteration. To understand population dynamics and this widespread but locally endangered snake’s adaptive potential, we investigated population structure, admixture, and effective migration patterns. We took a landscape-genomic approach to identify selected genotypes associated with environmental variables relevant to D. caspius. With double-digest restriction-site associated DNA (ddRAD) sequencing of 53 samples resulting in 17,518 single nucleotide polymorphisms (SNPs), we identified 8 clusters within D. caspius reflecting complex evolutionary patterns of the species. Estimated Effective Migration Surfaces (EEMS) revealed higher-than-average gene flow in most of the Balkan Peninsula and lower-than-average gene flow along the middle section of the Danube River. Landscape genomic analysis identified 751 selected genotypes correlated with 7 climatic variables. Isothermality correlated with the highest number of selected genotypes (478) located in 41 genes, followed by annual range (127) and annual mean temperature (87). We conclude that environmental variables, especially the day-to-night temperature oscillation in comparison to the summer-to-winter oscillation, may have an important role in the distribution and adaptation of D. caspius. Full article

(This article belongs to the Special Issue Genome Diversity of Adaptation and Speciation)

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18 pages, 639 KiB

Open AccessArticle

Point Mutations in the 14-α Sterol Demethylase Cyp51A or Cyp51C Could Contribute to Azole Resistance in Aspergillus flavus

by Jose Lucio, Irene Gonzalez-Jimenez, Olga Rivero-Menendez, Ana Alastruey-Izquierdo, Teresa Pelaez, Laura Alcazar-Fuoli and Emilia Mellado

Genes 2020, 11(10), 1217; https://doi.org/10.3390/genes11101217 - 17 Oct 2020

Cited by 19 | Viewed by 3721

Abstract

Infections caused by Aspergillus species are being increasingly reported. Aspergillus flavus is the second most common species within this genus causing invasive infections in humans, and isolates showing azole resistance have been recently described. A. flavus has three cyp51-related genes (cyp [...] Read more.

Infections caused by Aspergillus species are being increasingly reported. Aspergillus flavus is the second most common species within this genus causing invasive infections in humans, and isolates showing azole resistance have been recently described. A. flavus has three cyp51-related genes (cyp51A, cyp51B, and cyp51C) encoding 14-α sterol demethylase-like enzymes which are the target of azole drugs. In order to study triazole drug resistance in A. flavus, three strains showing reduced azole susceptibility and 17 azole susceptible isolates were compared. The three cyp51-related genes were amplified and sequenced. A comparison of the deduced Cyp51A, Cyp51B, and Cyp51C protein sequences with other protein sequences from orthologous genes in different filamentous fungi led to a protein identity that ranged from 50% to 80%. Cyp51A and Cyp51C presented several synonymous and non-synonymous point mutations among both susceptible and non-susceptible strains. However, two amino acid mutations were present only in two resistant isolates: one strain harbored a P214L substitution in Cyp51A, and another a H349R in Cyp51C that also showed an increase of cyp51A and cyp51C gene expression compared to the susceptible strain ATCC2004304. Isolates that showed reduced in vitro susceptibility to clinical azoles exhibited a different susceptibility profile to demethylation inhibitors (DMIs). Although P214L substitution might contribute to azole resistance, the role of H349R substitution together with changes in gene expression remains unclear. Full article

(This article belongs to the Special Issue Human Fungal Pathogens and Emerging Antifungal Resistance—A Global Public Health Problem?)

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28 pages, 3832 KiB

Open AccessArticle

Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene Networks

by Angelika Voronova, Martha Rendón-Anaya, Pär Ingvarsson, Ruslan Kalendar and Dainis Ruņģis

Genes 2020, 11(10), 1216; https://doi.org/10.3390/genes11101216 - 16 Oct 2020

Cited by 10 | Viewed by 4842

Abstract

Sequencing the giga-genomes of several pine species has enabled comparative genomic analyses of these outcrossing tree species. Previous studies have revealed the wide distribution and extraordinary diversity of transposable elements (TEs) that occupy the large intergenic spaces in conifer genomes. In this study, [...] Read more.

Sequencing the giga-genomes of several pine species has enabled comparative genomic analyses of these outcrossing tree species. Previous studies have revealed the wide distribution and extraordinary diversity of transposable elements (TEs) that occupy the large intergenic spaces in conifer genomes. In this study, we analyzed the distribution of TEs in gene regions of the assembled genomes of Pinus taeda and Pinus lambertiana using high-performance computing resources. The quality of draft genomes and the genome annotation have significant consequences for the investigation of TEs and these aspects are discussed. Several TE families frequently inserted into genes or their flanks were identified in both species’ genomes. Potentially important sequence motifs were identified in TEs that could bind additional regulatory factors, promoting gene network formation with faster or enhanced transcription initiation. Node genes that contain many TEs were observed in multiple potential transposable element-associated networks. This study demonstrated the increased accumulation of TEs in the introns of stress-responsive genes of pines and suggests the possibility of rewiring them into responsive networks and sub-networks interconnected with node genes containing multiple TEs. Many such regulatory influences could lead to the adaptive environmental response clines that are characteristic of naturally spread pine populations. Full article

(This article belongs to the Special Issue Transposable Elements in Plant Genomes)

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8 pages, 1229 KiB

Open AccessCase Report

SLC19A3 Loss-of-Function Variant in Yorkshire Terriers with Leigh-Like Subacute Necrotizing Encephalopathy

by Michaela Drögemüller, Anna Letko, Kaspar Matiasek, Vidhya Jagannathan, Daniele Corlazzoli, Marco Rosati, Konrad Jurina, Susanne Medl, Thomas Gödde, Stefan Rupp, Andrea Fischer, Alejandro Luján Feliu-Pascual and Cord Drögemüller

Genes 2020, 11(10), 1215; https://doi.org/10.3390/genes11101215 - 16 Oct 2020

Cited by 4 | Viewed by 3050

Abstract

Sporadic occurrence of juvenile-onset necrotizing encephalopathy (SNE) has been previously reported in Yorkshire terriers. However, so far, no causative genetic variant has been found for this breed-specific form of suspected mitochondrial encephalomyopathy. Affected dogs showed gait abnormalities, central visual defects, and/or seizures. Histopathological [...] Read more.

Sporadic occurrence of juvenile-onset necrotizing encephalopathy (SNE) has been previously reported in Yorkshire terriers. However, so far, no causative genetic variant has been found for this breed-specific form of suspected mitochondrial encephalomyopathy. Affected dogs showed gait abnormalities, central visual defects, and/or seizures. Histopathological analysis revealed the presence of major characteristics of human Leigh syndrome and SNE in Alaskan huskies. The aim of this study was to characterize the genetic etiology of SNE-affected purebred Yorkshire terriers. After SNP genotyping and subsequent homozygosity mapping, we identified a single loss-of-function variant by whole-genome sequencing in the canine SLC19A3 gene situated in a 1.7 Mb region of homozygosity on chromosome 25. All ten cases were homozygous carriers of a mutant allele, an indel variant in exon 2, that is predicted to lead to a frameshift and to truncate about 86% of the wild type coding sequence. This study reports a most likely pathogenic variant in SLC19A3 causing a form of SNE in Yorkshire terriers and enables selection against this fatal neurodegenerative recessive disorder. This is the second report of a pathogenic alteration of the SLC19A3 gene in dogs with SNE. Full article

(This article belongs to the Special Issue Molecular Basis of Inherited Diseases in Companion Animals)

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21 pages, 4241 KiB

Open AccessArticle

Developmental scRNAseq Trajectories in Gene- and Cell-State Space—The Flatworm Example

by Maria Schmidt, Henry Loeffler-Wirth and Hans Binder

Genes 2020, 11(10), 1214; https://doi.org/10.3390/genes11101214 - 16 Oct 2020

Cited by 13 | Viewed by 4430

Abstract

Single-cell RNA sequencing has become a standard technique to characterize tissue development. Hereby, cross-sectional snapshots of the diversity of cell transcriptomes were transformed into (pseudo-) longitudinal trajectories of cell differentiation using computational methods, which are based on similarity measures distinguishing cell phenotypes. Cell [...] Read more.

Single-cell RNA sequencing has become a standard technique to characterize tissue development. Hereby, cross-sectional snapshots of the diversity of cell transcriptomes were transformed into (pseudo-) longitudinal trajectories of cell differentiation using computational methods, which are based on similarity measures distinguishing cell phenotypes. Cell development is driven by alterations of transcriptional programs e.g., by differentiation from stem cells into various tissues or by adapting to micro-environmental requirements. We here complement developmental trajectories in cell-state space by trajectories in gene-state space to more clearly address this latter aspect. Such trajectories can be generated using self-organizing maps machine learning. The method transforms multidimensional gene expression patterns into two dimensional data landscapes, which resemble the metaphoric Waddington epigenetic landscape. Trajectories in this landscape visualize transcriptional programs passed by cells along their developmental paths from stem cells to differentiated tissues. In addition, we generated developmental “vector fields” using RNA-velocities to forecast changes of RNA abundance in the expression landscapes. We applied the method to tissue development of planarian as an illustrative example. Gene-state space trajectories complement our data portrayal approach by (pseudo-)temporal information about changing transcriptional programs of the cells. Future applications can be seen in the fields of tissue and cell differentiation, ageing and tumor progression and also, using other data types such as genome, methylome, and also clinical and epidemiological phenotype data. Full article

(This article belongs to the Special Issue Disentangling Mechanisms of Genomic Regulation of Cell Functions at the Gene Level)

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16 pages, 4014 KiB

Open AccessReview

Genetics and Genomics of Pediatric Pulmonary Arterial Hypertension

by Carrie L. Welch and Wendy K. Chung

Genes 2020, 11(10), 1213; https://doi.org/10.3390/genes11101213 - 16 Oct 2020

Cited by 23 | Viewed by 4398

Abstract

Pulmonary arterial hypertension (PAH) is a rare disease with high mortality despite recent therapeutic advances. The disease is caused by both genetic and environmental factors and likely gene–environment interactions. While PAH can manifest across the lifespan, pediatric-onset disease is particularly challenging because it [...] Read more.

Pulmonary arterial hypertension (PAH) is a rare disease with high mortality despite recent therapeutic advances. The disease is caused by both genetic and environmental factors and likely gene–environment interactions. While PAH can manifest across the lifespan, pediatric-onset disease is particularly challenging because it is frequently associated with a more severe clinical course and comorbidities including lung/heart developmental anomalies. In light of these differences, it is perhaps not surprising that emerging data from genetic studies of pediatric-onset PAH indicate that the genetic basis is different than that of adults. There is a greater genetic burden in children, with rare genetic factors contributing to ~42% of pediatric-onset PAH compared to ~12.5% of adult-onset PAH. De novo variants are frequently associated with PAH in children and contribute to at least 15% of all pediatric cases. The standard of medical care for pediatric PAH patients is based on extrapolations from adult data. However, increased etiologic heterogeneity, poorer prognosis, and increased genetic burden for pediatric-onset PAH calls for a dedicated pediatric research agenda to improve molecular diagnosis and clinical management. A genomics-first approach will improve the understanding of pediatric PAH and how it is related to other rare pediatric genetic disorders. Full article

(This article belongs to the Special Issue Genetics and Genomics of Pulmonary Arterial Hypertension)

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14 pages, 1743 KiB

Open AccessReview

Thiopurine Drugs in the Treatment of Ulcerative Colitis: Identification of a Novel Deleterious Mutation in TPMT

by Pierre-Olivier Harmand and Jérôme Solassol

Genes 2020, 11(10), 1212; https://doi.org/10.3390/genes11101212 - 16 Oct 2020

Cited by 18 | Viewed by 6129

Abstract

Chronic inflammatory bowel disease (IBD) includes Crohn’s disease and ulcerative colitis. Both are characterized by inflammation of part of the digestive tract lining. Azathioprine (AZA) is a well-known immunosuppressant that has been known for many years for its ability to provide long-term disease [...] Read more.

Chronic inflammatory bowel disease (IBD) includes Crohn’s disease and ulcerative colitis. Both are characterized by inflammation of part of the digestive tract lining. Azathioprine (AZA) is a well-known immunosuppressant that has been known for many years for its ability to provide long-term disease remission in IBDs, but has important side effects, most of which are related to a single nucleotide polymorphism in the gene for thiopurine methyltransferase (TPMT), which ensures the degradation and efficacy of AZA. Since a direct correlation between TPMT gene polymorphisms and the haematological toxicity of the AZA treatment has been widely demonstrated, TPMT genotyping has been made necessary prior to any introduction of AZA. The monitoring of thiopurine metabolites presents one of the factors that limit wide adaptation of these thiopurines in clinical practice. Thus, identifying patients with asymmetric metabolism could help clinicians provide an ideal treatment recommendation to improve response and reduce adverse effects. Here, we review the role of AZA in the treatment of IBD and discuss the usefulness of TPMT genotyping to guide clinical decision-making. In addition, we report the identification of a new molecular alteration, never described, TPMT mutation affecting the TPMT activity and responsible for deleterious side effects in a clinical case of a 20-year-old woman patient. Full article

(This article belongs to the Special Issue Pharmacogenomic Determinants of Interindividual Drug Response Variability: From Discovery to Implementation)

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7 pages, 34186 KiB

Open AccessCase Report

A Case Report of Left Atrial Isomerism in a Syndromic Context

by Aurora Ilian, Andrei Motoc, Ligia Balulescu, Cristina Secosan, Dorin Grigoras and Laurentiu Pirtea

Genes 2020, 11(10), 1211; https://doi.org/10.3390/genes11101211 - 16 Oct 2020

Cited by 1 | Viewed by 2449

Abstract

The objective of our paper is to underline the importance of assessing microarray genetic analysis for the detection of chromosomal abnormalities in rare cases such as left atrial isomerism, mostly in the context of antenatally detected syndromes. We present the case of a [...] Read more.

The objective of our paper is to underline the importance of assessing microarray genetic analysis for the detection of chromosomal abnormalities in rare cases such as left atrial isomerism, mostly in the context of antenatally detected syndromes. We present the case of a 26-year-old primipara, at 26 weeks of gestation, with prior first trimester normal anomaly scan, who presented in our department accusing lower abdominal pain. An anomaly ultrasound examination of the fetus revealed cardiomegaly with increased size of the right atrium, non-visualization of the atrial septum or the foramen ovale, malalignment of the three-vessel view, location of the superior vena cava above the two-vessel view, slight pericardial effusion, and no interruption of the inferior vena cava nor presence of azygos vein being noted. Associated extracardiac abnormalities, such as small kidneys at the level of the iliac fossa, micrognathia, dolichocephaly with hypoplasia of the cerebellum, increased nuchal fold, and reduced fetal movements were also reported. A diagnostic amniocentesis was performed, and, while the conventional rapid prenatal diagnostic test of the multiplex quantitative fluorescent polymerase chain reaction (PCR) came as normal, the microarray analysis (ChAS, NCBI Built 37 hg 19, detection of microdeletions or microduplications larger than 100 kb) revealed two chromosomal abnormalities: a 22.84 Mb loss of genetic material in the 18q21.31–18q23 chromosomal region and a gain of 22.31 Mb of genetic material in the 20p13–20p11.21 chromosomal region. After the termination of pregnancy, a necropsy of the fetus was performed, confirming heterotaxy syndrome with a common atrium, no atrial septum, superior vena cava draining medianly, and pulmonary veins that drained into the lower segment of the left atrium due to an anatomically enlarged single common atrium. The extracardiac findings consisted of two bilobar lungs, dysmorphic facies, low-set ears, nuchal fold edema, and small kidneys located in the iliac fossa. These findings are conclusive evidence that left atrial isomerism is a more complex syndrome. The genetic tests of the parents did not reveal any translocations of chromosomes 18 and 20 when the Fluorescent in situ Hybridization (FISH) analysis was assessed. The antenatal detection of corroboration between different structural abnormalities using serial ultrasound examinations and cardiac abnormalities, together with the detection of the affected chromosomes, improves the genetic counseling regarding the prognosis of the fetus and the recurrence rate of the condition for siblings. Full article

(This article belongs to the Special Issue Genetic Research in Fetal Medicine)

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20 pages, 3879 KiB

Open AccessReview

The Biochemical and Genetic Basis for the Biosynthesis of Bioactive Compounds in Hypericum perforatum L., One of the Largest Medicinal Crops in Europe

by Paride Rizzo, Lothar Altschmied, Beena M. Ravindran, Twan Rutten and John C. D’Auria

Genes 2020, 11(10), 1210; https://doi.org/10.3390/genes11101210 - 16 Oct 2020

Cited by 39 | Viewed by 7185

Abstract

Hypericum perforatum L. commonly known as Saint John’s Wort (SJW), is an important medicinal plant that has been used for more than 2000 years. Although H. perforatum produces several bioactive compounds, its importance is mainly linked to two molecules highly relevant for the [...] Read more.

Hypericum perforatum L. commonly known as Saint John’s Wort (SJW), is an important medicinal plant that has been used for more than 2000 years. Although H. perforatum produces several bioactive compounds, its importance is mainly linked to two molecules highly relevant for the pharmaceutical industry: the prenylated phloroglucinol hyperforin and the naphtodianthrone hypericin. The first functions as a natural antidepressant while the second is regarded as a powerful anticancer drug and as a useful compound for the treatment of Alzheimer’s disease. While the antidepressant activity of SJW extracts motivate a multi-billion dollar industry around the world, the scientific interest centers around the biosynthetic pathways of hyperforin and hypericin and their medical applications. Here, we focus on what is known about these processes and evaluate the possibilities of combining state of the art omics, genome editing, and synthetic biology to unlock applications that would be of great value for the pharmaceutical and medical industries. Full article

(This article belongs to the Special Issue Genetic and Molecular Mechanisms in Plant-Derived Compounds for Industrial Purposes)

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31 pages, 869 KiB

Open AccessReview

Interplay between Regulatory RNAs and Signal Transduction Systems during Bacterial Infection

by Emma Piattelli, Johann Peltier and Olga Soutourina

Genes 2020, 11(10), 1209; https://doi.org/10.3390/genes11101209 - 16 Oct 2020

Cited by 8 | Viewed by 4361

Abstract

The ability of pathogenic bacteria to stably infect the host depends on their capacity to respond and adapt to the host environment and on the efficiency of their defensive mechanisms. Bacterial envelope provides a physical barrier protecting against environmental threats. It also constitutes [...] Read more.

The ability of pathogenic bacteria to stably infect the host depends on their capacity to respond and adapt to the host environment and on the efficiency of their defensive mechanisms. Bacterial envelope provides a physical barrier protecting against environmental threats. It also constitutes an important sensory interface where numerous sensing systems are located. Signal transduction systems include Two-Component Systems (TCSs) and alternative sigma factors. These systems are able to sense and respond to the ever-changing environment inside the host, altering the bacterial transcriptome to mitigate the impact of the stress. The regulatory networks associated with signal transduction systems comprise small regulatory RNAs (sRNAs) that can be directly involved in the expression of virulence factors. The aim of this review is to describe the importance of TCS- and alternative sigma factor-associated sRNAs in human pathogens during infection. The currently available genome-wide approaches for studies of TCS-regulated sRNAs will be discussed. The differences in the signal transduction mediated by TCSs between bacteria and higher eukaryotes and the specificity of regulatory RNAs for their targets make them appealing targets for discovery of new strategies to fight against multi-resistant bacteria. Full article

(This article belongs to the Special Issue Genomics of Host-Pathogen Interactions)

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28 pages, 4568 KiB

Open AccessArticle

Fenugreek Stimulates the Expression of Genes Involved in Milk Synthesis and Milk Flow through Modulation of Insulin/GH/IGF-1 Axis and Oxytocin Secretion

by Thomas Sevrin, Clair-Yves Boquien, Alexis Gandon, Isabelle Grit, Pierre de Coppet, Dominique Darmaun and Marie-Cécile Alexandre-Gouabau

Genes 2020, 11(10), 1208; https://doi.org/10.3390/genes11101208 - 16 Oct 2020

Cited by 17 | Viewed by 5680

Abstract

We previously demonstrated galactagogue effect of fenugreek in a rat model of lactation challenge, foreshadowing its use in women’s breastfeeding management. To assess longitudinal molecular mechanisms involved in milk synthesis/secretion in dams submitted to fenugreek supplementation, inguinal mammary, pituitary glands and plasma were [...] Read more.

We previously demonstrated galactagogue effect of fenugreek in a rat model of lactation challenge, foreshadowing its use in women’s breastfeeding management. To assess longitudinal molecular mechanisms involved in milk synthesis/secretion in dams submitted to fenugreek supplementation, inguinal mammary, pituitary glands and plasma were isolated in forty-three rats nursing large 12 pups-litters and assigned to either a control (CTL) or a fenugreek-supplemented (FEN) diet during lactation. RT-PCR were performed at days 12 and 18 of lactation (L12 and L18) and the first day of involution (Inv1) to measure the relative expression of genes related to both milk synthesis and its regulation in the mammary gland and lactogenic hormones in the pituitary gland. Plasma hormone concentrations were measured by ELISA. FEN diet induced 2- to 3-times higher fold change in relative expression of several genes related to macronutrient synthesis (Fasn, Acaca, Fabp3, B4galt1, Lalba and Csn2) and energy metabolism (Cpt1a, Acads) and in IGF-1 receptor in mammary gland, mainly at L12. Pituitary oxytocin expression and plasma insulin concentration (+77.1%) were also significantly increased. Altogether, these findings suggest fenugreek might extend duration of peak milk synthesis through modulation of the insulin/GH/IGF-1 axis and increase milk ejection by activation of oxytocin secretion. Full article

(This article belongs to the Special Issue Gene Analysis of Mammary Gland Development and Breast Cancers)

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15 pages, 2561 KiB

Open AccessArticle

Vertical and Horizontal Transmission of ESBL Plasmid from Escherichia coli O104:H4

by Sandra Daniel, Kelly Goldlust, Valentin Quebre, Minjia Shen, Christian Lesterlin, Jean-Yves Bouet and Yoshiharu Yamaichi

Genes 2020, 11(10), 1207; https://doi.org/10.3390/genes11101207 - 16 Oct 2020

Cited by 4 | Viewed by 4719

Abstract

Multidrug resistance (MDR) often results from the acquisition of mobile genetic elements (MGEs) that encode MDR gene(s), such as conjugative plasmids. The spread of MDR plasmids is founded on their ability of horizontal transference, as well as their faithful inheritance in progeny cells. [...] Read more.

Multidrug resistance (MDR) often results from the acquisition of mobile genetic elements (MGEs) that encode MDR gene(s), such as conjugative plasmids. The spread of MDR plasmids is founded on their ability of horizontal transference, as well as their faithful inheritance in progeny cells. Here, we investigated the genetic factors involved in the prevalence of the IncI conjugative plasmid pESBL, which was isolated from the Escherichia coli O104:H4 outbreak strain in Germany in 2011. Using transposon-insertion sequencing, we identified the pESBL partitioning locus (par). Genetic, biochemical and microscopic approaches allowed pESBL to be characterized as a new member of the Type Ib partitioning system. Inactivation of par caused mis-segregation of pESBL followed by post-segregational killing (PSK), resulting in a great fitness disadvantage but apparent plasmid stability in the population of viable cells. We constructed a variety of pESBL derivatives with different combinations of mutations in par, conjugational transfer (oriT) and pnd toxin-antitoxin (TA) genes. Only the triple mutant exhibited plasmid-free cells in viable cell populations. Time-lapse tracking of plasmid dynamics in microfluidics indicated that inactivation of pnd improved the survival of plasmid-free cells and allowed oriT-dependent re-acquisition of the plasmid. Altogether, the three factors—active partitioning, toxin-antitoxin and conjugational transfer—are all involved in the prevalence of pESBL in the E. coli population. Full article

(This article belongs to the Special Issue Horizontal Gene Transfer in Bacteria)

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18 pages, 1119 KiB

Open AccessArticle

Genetic Risk of Autism Spectrum Disorder in a Pakistani Population

by Madiha Khalid, Hashim Raza, Terri M. Driessen, Paul J. Lee, Leon Tejwani, Abdul Sami, Muhammad Nawaz, Shahid Mehmood Baig, Janghoo Lim and Ghazala Kaukab Raja

Genes 2020, 11(10), 1206; https://doi.org/10.3390/genes11101206 - 15 Oct 2020

Cited by 13 | Viewed by 4988

Abstract

Autism spectrum disorder (ASD) is a group of complex multifactorial neurodevelopmental and neuropsychiatric disorders in children characterized by impairment of communication and social interaction. Several genes with associated single nucleotide polymorphisms (SNPs) have been identified for ASD in different genetic association studies, meta-analyses, [...] Read more.

Autism spectrum disorder (ASD) is a group of complex multifactorial neurodevelopmental and neuropsychiatric disorders in children characterized by impairment of communication and social interaction. Several genes with associated single nucleotide polymorphisms (SNPs) have been identified for ASD in different genetic association studies, meta-analyses, and genome-wide association studies (GWAS). However, associations between different SNPs and ASD vary from population to population. Four SNPs in genes CNTNAP2, EIF4E, ATP2B2, CACNA1C, and SNP rs4307059 (which is found between CDH9 and CDH10 genes) have been identified and reported as candidate risk factors for ASD. The aim of the present study was, for the first time, to assess the association of SNPs in these genes with ASD in the Pakistani population. PCR-based genotyping was performed using allele-specific primers in 93 ASD and 93 control Pakistani individuals. All genetic associations, genotype frequencies, and allele frequencies were computed as odds’ ratios (ORs) using logistic regression with a threshold of p ≤ 0.01 to determine statistical significance. We found that the homozygous genotypes of mutant T alleles of CNTNAP2 and ATP2B2 were significantly associated with Pakistani ASD patients in unadjusted ORs (p < 0.01), but their significance score was lost in the adjusted model. Other SNPs such as rs4307059, rs17850950 of EIF4E, and rs1006737 of CACNA1C were not statistically significant. Based on this, we conclude that SNPs are not associated with, or are not the main cause of, autism in the Pakistani population, indicating the involvement of additional players, which need to be investigated in future studies in a large population size. One of the limitations of present study is its small sample size. However, this study, being the first on Pakistani ASD patients, may lay the foundations for future studies in larger samples. Full article

(This article belongs to the Special Issue Genetics of Psychiatric Disorders)

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