Genes

15 pages, 1410 KiB

Open AccessFeature PaperArticle

Evaluation of the CRISPR/Cas9 Genetic Constructs in Efficient Disruption of Porcine Genes for Xenotransplantation Purposes Along with an Assessment of the Off-Target Mutation Formation

by Natalia Ryczek, Magdalena Hryhorowicz, Daniel Lipiński, Joanna Zeyland and Ryszard Słomski

Genes 2020, 11(6), 713; https://doi.org/10.3390/genes11060713 - 26 Jun 2020

Cited by 8 | Viewed by 3946

Abstract

The increasing life expectancy of humans has led to an increase in the number of patients with chronic diseases and organ failure. However, the imbalance between the supply and the demand for human organs is a serious problem in modern transplantology. One of [...] Read more.

The increasing life expectancy of humans has led to an increase in the number of patients with chronic diseases and organ failure. However, the imbalance between the supply and the demand for human organs is a serious problem in modern transplantology. One of many solutions to overcome this problem is the use of xenotransplantation. The domestic pig (Sus scrofa domestica) is currently considered as the most suitable for human organ procurement. However, there are discrepancies between pigs and humans that lead to the creation of immunological barriers preventing the direct xenograft. The introduction of appropriate modifications to the pig genome to prevent xenograft rejection is crucial in xenotransplantation studies. In this study, porcine GGTA1, CMAH, β4GalNT2, vWF, ASGR1 genes were selected to introduce genetic modifications. The evaluation of three selected gRNAs within each gene was obtained, which enabled the selection of the best site for efficient introduction of changes. Modifications were examined after nucleofection of porcine primary kidney fibroblasts with CRISPR/Cas9 system genetic constructs, followed by the tracking of indels by decomposition (TIDE) analysis. In addition, off-target analysis was carried out for selected best gRNAs using the TIDE tool, which is new in the research conducted so far and shows the utility of this tool in these studies. Full article

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

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26 pages, 2765 KiB

Open AccessReview

Omics Approaches Applied to Penicillium chrysogenum and Penicillin Production: Revealing the Secrets of Improved Productivity

by Carlos García-Estrada, Juan F. Martín, Laura Cueto and Carlos Barreiro

Genes 2020, 11(6), 712; https://doi.org/10.3390/genes11060712 - 26 Jun 2020

Cited by 21 | Viewed by 8548

Abstract

Penicillin biosynthesis by Penicillium chrysogenum is one of the best-characterized biological processes from the genetic, molecular, biochemical, and subcellular points of view. Several omics studies have been carried out in this filamentous fungus during the last decade, which have contributed to gathering a [...] Read more.

Penicillin biosynthesis by Penicillium chrysogenum is one of the best-characterized biological processes from the genetic, molecular, biochemical, and subcellular points of view. Several omics studies have been carried out in this filamentous fungus during the last decade, which have contributed to gathering a deep knowledge about the molecular mechanisms underlying improved productivity in industrial strains. The information provided by these studies is extremely useful for enhancing the production of penicillin or other bioactive secondary metabolites by means of Biotechnology or Synthetic Biology. Full article

(This article belongs to the Special Issue Omics Studies Focused on Fungal Secondary Metabolism)

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15 pages, 1456 KiB

Open AccessReview

Reciprocal Regulation between Primary Cilia and mTORC1

by Yandong Lai and Yu Jiang

Genes 2020, 11(6), 711; https://doi.org/10.3390/genes11060711 - 26 Jun 2020

Cited by 21 | Viewed by 6945

Abstract

In quiescent cells, primary cilia function as a mechanosensor that converts mechanic signals into chemical activities. This unique organelle plays a critical role in restricting mechanistic target of rapamycin complex 1 (mTORC1) signaling, which is essential for quiescent cells to maintain their quiescence. [...] Read more.

In quiescent cells, primary cilia function as a mechanosensor that converts mechanic signals into chemical activities. This unique organelle plays a critical role in restricting mechanistic target of rapamycin complex 1 (mTORC1) signaling, which is essential for quiescent cells to maintain their quiescence. Multiple mechanisms have been identified that mediate the inhibitory effect of primary cilia on mTORC1 signaling. These mechanisms depend on several tumor suppressor proteins localized within the ciliary compartment, including liver kinase B1 (LKB1), AMP-activated protein kinase (AMPK), polycystin-1, and polycystin-2. Conversely, changes in mTORC1 activity are able to affect ciliogenesis and stability indirectly through autophagy. In this review, we summarize recent advances in our understanding of the reciprocal regulation of mTORC1 and primary cilia. Full article

(This article belongs to the Special Issue Cellular Growth Control by TOR Signaling)

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16 pages, 9382 KiB

Open AccessArticle

Comparative Proteomics Analysis of Anisakis simplex s.s.—Evaluation of the Response of Invasive Larvae to Ivermectin

by Iwona Polak, Elżbieta Łopieńska-Biernat, Robert Stryiński, Jesús Mateos and Mónica Carrera

Genes 2020, 11(6), 710; https://doi.org/10.3390/genes11060710 - 26 Jun 2020

Cited by 15 | Viewed by 4288

Abstract

Ivermectin (IVM), an antiparasitic drug, has a positive effect against Anisakis simplex s.s. infection and has been used for the treatment and prevention of anisakiasis in humans. However, the molecular mechanism of action of IVM on A. simplex s.s. remains unknown. Herein, tandem [...] Read more.

Ivermectin (IVM), an antiparasitic drug, has a positive effect against Anisakis simplex s.s. infection and has been used for the treatment and prevention of anisakiasis in humans. However, the molecular mechanism of action of IVM on A. simplex s.s. remains unknown. Herein, tandem mass tag (TMT) labeling and extensive liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) analysis were used to identify the effect of IVM on the proteome of A. simplex s.s. in vitro. During the study, 3433 proteins, of which 1247 had at least two protein unique peptides, were identified. Comparative proteomics analysis revealed that 59 proteins were differentially regulated (DRPs) in IVM-treated larvae, of which 14 proteins were upregulated and 38 were downregulated after 12 h of culture, but after 24 h, 12 proteins were upregulated and 22 were downregulated. The transcription level of five randomly selected DRPs was determined by real-time PCR as a supplement to the proteomic data. The functional enrichment analysis showed that most of the DRPs were involved in oxidoreductase activity, immunogenicity, protein degradation, and other biological processes. This study has, for the first time, provided comprehensive proteomics data on A. simplex s.s. response to IVM and might deliver new insight into the molecular mechanism by which IVM acts on invasive larvae of A. simplex s.s. Full article

(This article belongs to the Special Issue Novel Omics Studies on Anisakid Nematodes)

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Graphical abstract

14 pages, 2370 KiB

Open AccessArticle

Extensive Involvement of Alternative Polyadenylation in Single-Nucleus Neurons

by Ying Wang, Weixing Feng, Siwen Xu and Bo He

Genes 2020, 11(6), 709; https://doi.org/10.3390/genes11060709 - 26 Jun 2020

Cited by 3 | Viewed by 3224

Abstract

Cleavage and polyadenylation are essential processes that can impact many aspects of mRNA fate. Most eukaryotic genes have alternative polyadenylation (APA) events. While the heterogeneity of mRNA polyadenylation isoform choice has been studied in specific tissues, less attention has been paid to the [...] Read more.

Cleavage and polyadenylation are essential processes that can impact many aspects of mRNA fate. Most eukaryotic genes have alternative polyadenylation (APA) events. While the heterogeneity of mRNA polyadenylation isoform choice has been studied in specific tissues, less attention has been paid to the neuronal heterogeneity of APA selection at single-nucleus resolution. APA is highly controlled during development and neuronal activation, however, to what extent APA events vary in a specific neuronal cell population and the regulatory mechanisms are still unclear. In this paper, we investigated dynamic APA usage in different cell types using snRNA-seq data of 1424 human brain cells generated by single-cell 3′ RNA sequencing. We found that distal APA sites are not only favored by global neuronal cells, but that their usage also varies between the principal types of neuronal cell populations (excitatory neurons and inhibitory neurons). A motif analysis and a gene functional analysis indicated the enrichment of RNA-binding protein (RBP) binding sites and neuronal functions for the set of genes with neuron-enhanced distal PAS usage. Our results revealed the extensive involvement of APA regulation in neuronal populations at the single-nucleus level, providing new insights into roles for APA in specific neuronal cell populations, as well as utility in future functional studies. Full article

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

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11 pages, 1280 KiB

Open AccessArticle

Evaluation of the VISAGE Basic Tool for Appearance and Ancestry Prediction Using PowerSeq Chemistry on the MiSeq FGx System

by Leire Palencia-Madrid, Catarina Xavier, María de la Puente, Carsten Hohoff, Christopher Phillips, Manfred Kayser and Walther Parson

Genes 2020, 11(6), 708; https://doi.org/10.3390/genes11060708 - 26 Jun 2020

Cited by 31 | Viewed by 5025

Abstract

The study of DNA to predict externally visible characteristics (EVCs) and the biogeographical ancestry (BGA) from unknown samples is gaining relevance in forensic genetics. Technical developments in Massively Parallel Sequencing (MPS) enable the simultaneous analysis of hundreds of DNA markers, which improves successful [...] Read more.

The study of DNA to predict externally visible characteristics (EVCs) and the biogeographical ancestry (BGA) from unknown samples is gaining relevance in forensic genetics. Technical developments in Massively Parallel Sequencing (MPS) enable the simultaneous analysis of hundreds of DNA markers, which improves successful Forensic DNA Phenotyping (FDP). The EU-funded VISAGE (VISible Attributes through GEnomics) Consortium has developed various targeted MPS-based lab tools to apply FDP in routine forensic analyses. Here, we present an evaluation of the VISAGE Basic tool for appearance and ancestry prediction based on PowerSeq chemistry (Promega) on a MiSeq FGx System (Illumina). The panel consists of 153 single nucleotide polymorphisms (SNPs) that provide information about EVCs (41 SNPs for eye, hair and skin color from HIrisPlex-S) and continental BGA (115 SNPs; three overlap with the EVCs SNP set). The assay was evaluated for sensitivity, repeatability and genotyping concordance, as well as its performance with casework-type samples. This targeted MPS assay provided complete genotypes at all 153 SNPs down to 125 pg of input DNA and 99.67% correct genotypes at 50 pg. It was robust in terms of repeatability and concordance and provided useful results with casework-type samples. The results suggest that this MPS assay is a useful tool for basic appearance and ancestry prediction in forensic genetics for users interested in applying PowerSeq chemistry and MiSeq for this purpose. Full article

(This article belongs to the Special Issue Genes at Ten)

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9 pages, 1235 KiB

Open AccessArticle

A Private 16q24.2q24.3 Microduplication in a Boy with Intellectual Disability, Speech Delay and Mild Dysmorphic Features

by Orazio Palumbo, Pietro Palumbo, Ester Di Muro, Luigia Cinque, Antonio Petracca, Massimo Carella and Marco Castori

Genes 2020, 11(6), 707; https://doi.org/10.3390/genes11060707 - 26 Jun 2020

Cited by 11 | Viewed by 3101

Abstract

No data on interstitial microduplications of the 16q24.2q24.3 chromosome region are available in the medical literature and remain extraordinarily rare in public databases. Here, we describe a boy with a de novo 16q24.2q24.3 microduplication at the Single Nucleotide Polymorphism (SNP)-array analysis spanning ~2.2 [...] Read more.

No data on interstitial microduplications of the 16q24.2q24.3 chromosome region are available in the medical literature and remain extraordinarily rare in public databases. Here, we describe a boy with a de novo 16q24.2q24.3 microduplication at the Single Nucleotide Polymorphism (SNP)-array analysis spanning ~2.2 Mb and encompassing 38 genes. The patient showed mild-to-moderate intellectual disability, speech delay and mild dysmorphic features. In DECIPHER, we found six individuals carrying a “pure” overlapping microduplication. Although available data are very limited, genomic and phenotype comparison of our and previously annotated patients suggested a potential clinical relevance for 16q24.2q24.3 microduplication with a variable and not (yet) recognizable phenotype predominantly affecting cognition. Comparing the cytogenomic data of available individuals allowed us to delineate the smallest region of overlap involving 14 genes. Accordingly, we propose ANKRD11, CDH15, and CTU2 as candidate genes for explaining the related neurodevelopmental manifestations shared by these patients. To the best of our knowledge, this is the first time that a clinical and molecular comparison among patients with overlapping 16q24.2q24.3 microduplication has been done. This study broadens our knowledge of the phenotypic consequences of 16q24.2q24.3 microduplication, providing supporting evidence of an emerging syndrome. Full article

(This article belongs to the Special Issue Selected Papers from the International Workshop on Fragile X and Other Neurodevelopmental Disorders)

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9 pages, 1229 KiB

Open AccessFeature PaperArticle

Predicting Clinical Dementia Rating Using Blood RNA Levels

by Justin B. Miller and John S. K. Kauwe

Genes 2020, 11(6), 706; https://doi.org/10.3390/genes11060706 - 26 Jun 2020

Cited by 10 | Viewed by 3297

Abstract

The Clinical Dementia Rating (CDR) is commonly used to assess cognitive decline in Alzheimer’s disease patients and is included in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset. We divided 741 ADNI participants with blood microarray data into three groups based on their most [...] Read more.

The Clinical Dementia Rating (CDR) is commonly used to assess cognitive decline in Alzheimer’s disease patients and is included in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset. We divided 741 ADNI participants with blood microarray data into three groups based on their most recent CDR assessment: cognitive normal (CDR = 0), mild cognitive impairment (CDR = 0.5), and probable Alzheimer’s disease (CDR ≥ 1.0). We then used machine learning to predict cognitive status using only blood RNA levels. Only one probe for chloride intracellular channel 1 (CLIC1) was significant after correction. However, by combining individually nonsignificant probes with p-values less than 0.1, we averaged 87.87% (s = 1.02) predictive accuracy for classifying the three groups, compared to a 55.46% baseline for this study due to unequal group sizes. The best model had an overall precision of 0.902, recall of 0.895, and a receiver operating characteristic (ROC) curve area of 0.904. Although we identified one significant probe in CLIC1, CLIC1 levels alone were not sufficient to predict dementia status and cannot be used alone in a clinical setting. Additional analyses combining individually suggestive, but nonsignificant, blood RNA levels were significantly predictive and may improve diagnostic accuracy for Alzheimer’s disease. Therefore, we propose that patient features that do not individually predict cognitive status might still contribute to overall cognitive decline through interactions that can be elucidated through machine learning. Full article

(This article belongs to the Special Issue Genetics and Genomics of Alzheimer’s Disease)

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17 pages, 1435 KiB

Open AccessArticle

PPARG Pro12Ala Polymorphism with CKD in Asians: A Meta-Analysis Combined with a Case-Control Study—A Key for Reaching Null Association

by Hsiang-Cheng Chen, Wei-Teing Chen, Tzu-Ling Sung, Dung-Jang Tsai, Chin Lin, Hao Su, Yuh-Feng Lin, Hung-Yi Chiu and Sui-Lung Su

Genes 2020, 11(6), 705; https://doi.org/10.3390/genes11060705 - 26 Jun 2020

Cited by 1 | Viewed by 2676

Abstract

Background: So far, numerous meta-analyses have been published regarding the correlation between peroxisome proliferator-activated receptor gamma (PPARG) proline 12 alanine (Pro12Ala) gene polymorphism and chronic kidney disease (CKD); however, the results appear to be contradictory. Hence, this study is formulated with the objective [...] Read more.

Background: So far, numerous meta-analyses have been published regarding the correlation between peroxisome proliferator-activated receptor gamma (PPARG) proline 12 alanine (Pro12Ala) gene polymorphism and chronic kidney disease (CKD); however, the results appear to be contradictory. Hence, this study is formulated with the objective of using existing meta-analysis data together with our research population to study the correlation between PPARG Pro12Ala gene polymorphism and CKD and evaluate whether an accurate result can be obtained. Methods: First, literature related to CKD and PPARG Pro12Ala available on the PubMed and EMBASE databases up to December 2016 was gathered from 20 publications. Then, the gathered results were combined with our case-control study of 1693 enrolled subjects and a trial sequential analysis (TSA) was performed to verify existing evidence and determine whether a firm conclusion can be drawn. Results: The TSA results showed that the cumulative sample size for the Asian sample was 6078 and was sufficient to support a definite result. The results of this study confirmed that there is no obvious correlation between PPARG Pro12Ala and CKD for Asians (OR = 0.82 (95% CI = 0.66–1.02), I² = 63.1%), but this was not confirmed for Caucasians. Furthermore, the case-control sample in our study was shown to be the key for reaching this conclusion. Conclusions: The meta-analysis results of this study suggest no significant correlation between PPARG Pro12Ala gene polymorphism and CKD for Asians after adding our samples, but not for Caucasian. Full article

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

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17 pages, 2289 KiB

Open AccessReview

Therapeutic Editing of the TP53 Gene: Is CRISPR/Cas9 an Option?

by Regina Mirgayazova, Raniya Khadiullina, Vitaly Chasov, Rimma Mingaleeva, Regina Miftakhova, Albert Rizvanov and Emil Bulatov

Genes 2020, 11(6), 704; https://doi.org/10.3390/genes11060704 - 25 Jun 2020

Cited by 39 | Viewed by 8944

Abstract

The TP53 gene encodes the transcription factor and oncosuppressor p53 protein that regulates a multitude of intracellular metabolic pathways involved in DNA damage repair, cell cycle arrest, apoptosis, and senescence. In many cases, alterations (e.g., mutations of the TP53 gene) negatively affect these [...] Read more.

The TP53 gene encodes the transcription factor and oncosuppressor p53 protein that regulates a multitude of intracellular metabolic pathways involved in DNA damage repair, cell cycle arrest, apoptosis, and senescence. In many cases, alterations (e.g., mutations of the TP53 gene) negatively affect these pathways resulting in tumor development. Recent advances in genome manipulation technologies, CRISPR/Cas9, in particular, brought us closer to therapeutic gene editing for the treatment of cancer and hereditary diseases. Genome-editing therapies for blood disorders, blindness, and cancer are currently being evaluated in clinical trials. Eventually CRISPR/Cas9 technology is expected to target TP53 as the most mutated gene in all types of cancers. A majority of TP53 mutations are missense which brings immense opportunities for the CRISPR/Cas9 system that has been successfully used for correcting single nucleotides in various models, both in vitro and in vivo. In this review, we highlight the recent clinical applications of CRISPR/Cas9 technology for therapeutic genome editing and discuss its perspectives for editing TP53 and regulating transcription of p53 pathway genes. Full article

(This article belongs to the Special Issue CRISPR-Cas: Interactions with Genome and Physiological Maintenance)

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17 pages, 2849 KiB

Open AccessArticle

Blockade of PD-1, PD-L1, and TIM-3 Altered Distinct Immune- and Cancer-Related Signaling Pathways in the Transcriptome of Human Breast Cancer Explants

by Reem Saleh, Salman M. Toor, Dana Al-Ali, Varun Sasidharan Nair and Eyad Elkord

Genes 2020, 11(6), 703; https://doi.org/10.3390/genes11060703 - 25 Jun 2020

Cited by 13 | Viewed by 4217

Abstract

Immune checkpoint inhibitors (ICIs) are yet to have a major advantage over conventional therapies, as only a fraction of patients benefit from the currently approved ICIs and their response rates remain low. We investigated the effects of different ICIs—anti-programmed cell death protein 1 [...] Read more.

Immune checkpoint inhibitors (ICIs) are yet to have a major advantage over conventional therapies, as only a fraction of patients benefit from the currently approved ICIs and their response rates remain low. We investigated the effects of different ICIs—anti-programmed cell death protein 1 (PD-1), anti-programmed death ligand-1 (PD-L1), and anti-T cell immunoglobulin and mucin-domain containing-3 (TIM-3)—on human primary breast cancer explant cultures using RNA-Seq. Transcriptomic data revealed that PD-1, PD-L1, and TIM-3 blockade follow unique mechanisms by upregulating or downregulating distinct pathways, but they collectively enhance immune responses and suppress cancer-related pathways to exert anti-tumorigenic effects. We also found that these ICIs upregulated the expression of other IC genes, suggesting that blocking one IC can upregulate alternative ICs, potentially giving rise to compensatory mechanisms by which tumor cells evade anti-tumor immunity. Overall, the transcriptomic data revealed some unique mechanisms of the action of monoclonal antibodies (mAbs) targeting PD-1, PD-L1, and TIM-3 in human breast cancer explants. However, further investigations and functional studies are warranted to validate these findings. Full article

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

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9 pages, 1415 KiB

Open AccessArticle

Molecular Cytogenetic Characterization of the Sicilian Endemic Pond Turtle Emys trinacris and the Yellow-Bellied Slider Trachemys scripta scripta (Testudines, Emydidae)

by Rita Scardino, Sofia Mazzoleni, Michail Rovatsos, Luca Vecchioni and Francesca Dumas

Genes 2020, 11(6), 702; https://doi.org/10.3390/genes11060702 - 25 Jun 2020

Cited by 12 | Viewed by 3607

Abstract

Turtles, a speciose group consisting of more than 300 species, demonstrate karyotypes with diploid chromosome numbers ranging from 2n = 26 to 2n = 68. However, cytogenetic analyses have been conducted only to 1/3rd of the turtle species, often limited to conventional staining [...] Read more.

Turtles, a speciose group consisting of more than 300 species, demonstrate karyotypes with diploid chromosome numbers ranging from 2n = 26 to 2n = 68. However, cytogenetic analyses have been conducted only to 1/3rd of the turtle species, often limited to conventional staining methods. In order to expand our knowledge of the karyotype evolution in turtles, we examined the topology of the (TTAGGG)_n telomeric repeats and the rDNA loci by fluorescence in situ hybridization (FISH) on the karyotypes of two emydids: the Sicilian pond turtle, Emys trinacris, and the yellow-bellied slider, Trachemys scripta scripta (family Emydidae). Furthermore, AT-rich and GC-rich chromosome regions were detected by DAPI and CMA₃ stains, respectively. The cytogenetic analysis revealed that telomeric sequences are restricted to the terminal ends of all chromosomes and the rDNA loci are localized in one pair of microchromosomes in both species. The karyotype of the Sicilian endemic E. trinacris with diploid number 2n = 50, consisting of 13 pairs of macrochromosomes and 12 pairs of microchromosomes, is presented here for first time. Our comparative examination revealed similar cytogenetic features in Emys trinacris and the closely related E. orbicularis, as well as to other previously studied emydid species, demonstrating a low rate of karyotype evolution, as chromosomal rearrangements are rather infrequent in this group of turtles. Full article

(This article belongs to the Special Issue Vertebrate Karyotype Evolution: How Far Have We Come, and Where Are We Going?)

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14 pages, 7893 KiB

Open AccessArticle

Arabidopsis V-ATPase d2 Subunit Plays a Role in Plant Responses to Oxidative Stress

by Shuang Feng, Yun Peng, Enhui Liu, Hongping Ma, Kun Qiao, Aimin Zhou, Shenkui Liu and Yuanyuan Bu

Genes 2020, 11(6), 701; https://doi.org/10.3390/genes11060701 - 25 Jun 2020

Cited by 10 | Viewed by 3219

Abstract

Vacuolar-type H⁺-ATPase (V-ATPase), a multisubunit proton pump located on the endomembrane, plays an important role in plant growth. The Arabidopsis thaliana V-ATPase d subunit (VHA-d) consists of two isoforms; AtVHA-d1 and AtVHA-d2. In this study, the function of AtVHA-d2 was investigated. [...] Read more.

Vacuolar-type H⁺-ATPase (V-ATPase), a multisubunit proton pump located on the endomembrane, plays an important role in plant growth. The Arabidopsis thaliana V-ATPase d subunit (VHA-d) consists of two isoforms; AtVHA-d1 and AtVHA-d2. In this study, the function of AtVHA-d2 was investigated. Histochemical analysis revealed that the expression of AtVHA-d1 and AtVHA-d2 was generally highly overlapping in multiple tissues at different developmental stages of Arabidopsis. Subcellular localization revealed that AtVHA-d2 was mainly localized to the vacuole. AtVHA-d2 expression was significantly induced by oxidative stress. Analysis of phenotypic and H₂O₂ content showed that the atvha-d2 mutant was sensitive to oxidative stress. The noninvasive microtest monitoring demonstrated that the net H⁺ influx in the atvha-d2 roots was weaker than that in the wild-type under normal conditions. However, oxidative stress resulted in the H⁺ efflux in atvha-d2 roots, which was significantly different from that in the wild-type. RNA-seq combined with qPCR analysis showed that the expression of several members of the plasma membrane H⁺-ATPase gene (AtAHA) family in atvha-d2 was significantly different from that in the wild-type. Overall, our results indicate that AtVHA-d2 plays a role in Arabidopsis in response to oxidative stress by affecting H⁺ flux and AtAHA gene expression. Full article

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

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12 pages, 2451 KiB

Open AccessArticle

Differentially Expressed miRNA-Gene Targets Related to Intramuscular Fat in Musculus Longissimus Dorsi of Charolais × Holstein F₂-Crossbred Bulls

by Bilal Ahmad Mir, Henry Reyer, Katrin Komolka, Siriluck Ponsuksili, Christa Kühn and Steffen Maak

Genes 2020, 11(6), 700; https://doi.org/10.3390/genes11060700 - 25 Jun 2020

Cited by 11 | Viewed by 3853

Abstract

Intramuscular fat (IMF) is a meat quality indicator associated with taste and juiciness. IMF deposition, influenced by genetic and non-genetic factors, occurs through a transcriptionally coordinated process of adipogenesis. MicroRNAs (miRNAs) are transcriptional regulators of vital biological processes, including lipid metabolism and adipogenesis. [...] Read more.

Intramuscular fat (IMF) is a meat quality indicator associated with taste and juiciness. IMF deposition, influenced by genetic and non-genetic factors, occurs through a transcriptionally coordinated process of adipogenesis. MicroRNAs (miRNAs) are transcriptional regulators of vital biological processes, including lipid metabolism and adipogenesis. However, in bovines, limited data on miRNA profiling and association with divergent intramuscular fat content, regulated exclusively by genetic parameters, have been reported. Here, a microarray experiment was performed to identify and characterize the miRNA expression pattern in the Musculus longissimus dorsi of F₂-cross (Charolais × German Holstein) bulls with high and low IMF. A total of 38 differentially expressed miRNAs (DE miRNAs), including 33 upregulated and 5 downregulated (corrected p-value ≤ 0.05, FC ≥ ±1.2), were reported. Among DE miRNAs, the upregulated miRNAs miR-105a/b, miR-695, miR-1193, miR-1284, miR-1287-5p, miR-3128, miR-3178, miR-3910, miR-4443, miR-4445 and miR-4745, and the downregulated miRNAs miR-877-5p, miR-4487 and miR-4706 were identified as novel fat deposition regulators. DE miRNAs were further analyzed, along with previously identified differentially expressed genes (DEGs) from the same samples and predicted target genes, using multiple bioinformatic approaches, including target prediction tools and co-expression networks, as well as Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. We identified DE miRNAs and their gene targets associated with bovine intramuscular adipogenesis, and we provide a basis for further functional investigations. Full article

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

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18 pages, 602 KiB

Open AccessArticle

Identification of QTLs for Resistance to Fusarium Head Blight Using a Doubled Haploid Population Derived from Southeastern United States Soft Red Winter Wheat Varieties AGS 2060 and AGS 2035

by Alejandro Castro Aviles, Stephen Alan Harrison, Kelly Joseph Arceneaux, Gina Brown-Guidera, Richard Esten Mason and Niranjan Baisakh

Genes 2020, 11(6), 699; https://doi.org/10.3390/genes11060699 - 25 Jun 2020

Cited by 13 | Viewed by 3266

Abstract

Fusarium head blight (FHB), caused primarily by the fungus Fusarium graminearum, is one of the most damaging diseases of wheat, causing significant loss of yield and quality worldwide. Warm and wet conditions during flowering, a lack of resistant wheat varieties, and high [...] Read more.

Fusarium head blight (FHB), caused primarily by the fungus Fusarium graminearum, is one of the most damaging diseases of wheat, causing significant loss of yield and quality worldwide. Warm and wet conditions during flowering, a lack of resistant wheat varieties, and high inoculum pressure from corn stubble contribute to frequent FHB epidemics in the southern United States. The soft red winter wheat variety AGS 2060 is moderately susceptible (as opposed to susceptible) to FHB and regularly found in pedigrees of resistant breeding lines. AGS 2060 does not carry any known resistance genes or quantitative trait loci (QTL). A QTL mapping study was conducted to determine the location and genetic effect of its resistance using a doubled haploid mapping population produced from a cross between wheat varieties AGS 2060 and AGS 2035 (FHB susceptible). The population was genotyped using the Illumina iSelect single nucleotide polymorphism (SNP) array for wheat and phenotyped in Baton Rouge and Winnsboro, Louisiana and Newport, Arkansas in 2018 and 2019. The effect of genotype was significant for Fusarium damaged kernels (FDK) and deoxynivalenol (DON) content across all locations and years, indicating genetic variation in the population. The study detected 13 QTLs (one each on chromosome 1A, 1B, 1D, 2A, 2B, 6A, 6B, 7A, and 7B, and two each on 5A and 5B) responsible for the reduction of FDK and/or DON. Of these, nine QTLs for FHB resistance were identified in Winnsboro, Louisiana, in 2019. QTLs on chromosomes 2A and 7A could be valuable sources of resistance to both DON and FDK over several environments and were likely the best candidates for use in marker-assisted selection. Consistently expressed QTLs on chromosomes 5A, 6B, and 7A were potentially newly identified sources of resistance to FHB in soft red winter wheat. Full article

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

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12 pages, 1639 KiB

Open AccessArticle

Cross-Species BAC Mapping Highlights Conservation of Chromosome Synteny across Dragon Lizards (Squamata: Agamidae)

by Shayer Mahmood Ibney Alam, Marie Altmanová, Tulyawat Prasongmaneerut, Arthur Georges, Stephen D. Sarre, Stuart V. Nielsen, Tony Gamble, Kornsorn Srikulnath, Michail Rovatsos, Lukáš Kratochvíl and Tariq Ezaz

Genes 2020, 11(6), 698; https://doi.org/10.3390/genes11060698 - 25 Jun 2020

Cited by 6 | Viewed by 4556

Abstract

Dragon lizards (Squamata: Agamidae) comprise about 520 species in six subfamilies distributed across Asia, Australasia and Africa. Only five species are known to have sex chromosomes. All of them possess ZZ/ZW sex chromosomes, which are microchromosomes in four species from the subfamily Amphibolurinae, [...] Read more.

Dragon lizards (Squamata: Agamidae) comprise about 520 species in six subfamilies distributed across Asia, Australasia and Africa. Only five species are known to have sex chromosomes. All of them possess ZZ/ZW sex chromosomes, which are microchromosomes in four species from the subfamily Amphibolurinae, but much larger in Phrynocephalus vlangalii from the subfamily Agaminae. In most previous studies of these sex chromosomes, the focus has been on Australian species from the subfamily Amphibolurinae, but only the sex chromosomes of the Australian central bearded dragon (Pogona vitticeps) are well-characterized cytogenetically. To determine the level of synteny of the sex chromosomes of P. vitticeps across agamid subfamilies, we performed cross-species two-colour FISH using two bacterial artificial chromosome (BAC) clones from the pseudo-autosomal regions of P. vitticeps. We mapped these two BACs across representative species from all six subfamilies as well as two species of chameleons, the sister group to agamids. We found that one of these BAC sequences is conserved in macrochromosomes and the other in microchromosomes across the agamid lineages. However, within the Amphibolurinae, there is evidence of multiple chromosomal rearrangements with one of the BACs mapping to the second-largest chromosome pair and to the microchromosomes in multiple species including the sex chromosomes of P. vitticeps. Intriguingly, no hybridization signal was observed in chameleons for either of these BACs, suggesting a likely agamid origin of these sequences. Our study shows lineage-specific evolution of sequences/syntenic blocks and successive rearrangements and reveals a complex history of sequences leading to their association with important biological processes such as the evolution of sex chromosomes and sex determination. Full article

(This article belongs to the Special Issue Vertebrate Karyotype Evolution: How Far Have We Come, and Where Are We Going?)

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11 pages, 3666 KiB

Open AccessCase Report

In Vitro Fertilisation (IVF) Associated with Preimplantation Genetic Testing for Monogenic Diseases (PGT-M) in a Romanian Carrier Couple for Congenital Disorder of Glycosylation Type Ia (CDG-Ia): A Case Report

by Bogdan Doroftei, Loredana Nemtanu, Ovidiu-Dumitru Ilie, Gabriela Simionescu, Iuliu Ivanov, Emil Anton, Maria Puiu and Radu Maftei

Genes 2020, 11(6), 697; https://doi.org/10.3390/genes11060697 - 25 Jun 2020

Cited by 1 | Viewed by 3456

Abstract

Background: Congenital disorder of glycosylation (CDG) is a severe morphogenic and metabolic disorder that affects all of the systems of organs and is caused by a mutation of the gene PMM2, having a mortality rate of 20% during the first months of [...] Read more.

Background: Congenital disorder of glycosylation (CDG) is a severe morphogenic and metabolic disorder that affects all of the systems of organs and is caused by a mutation of the gene PMM2, having a mortality rate of 20% during the first months of life. Results: Here we report the outcome of an in vitro fertilisation (IVF) cycle associated with preimplantation genetic testing for monogenic diseases (PGT-M) in a Romanian carrier couple for CDG type Ia with distinct mutations of the PMM2 gene. The embryonic biopsy was performed on day five of the blastocyst stage for six embryos. The amplification of the whole genome had been realized by using the PicoPLEX WGA kit. Using the Array Comparative Genomic Hybridisation technique, we detected both euploid and aneuploid embryos. The identification of the PMM2 mutation on exon 5 and exon 6 was performed for the euploid embryos through Sanger Sequencing with specific primers on ABI 3500. Of the six embryos tested, only three were euploid. One had compound heterozygosity and the remaining two were simple heterozygotes. Conclusion: PGT-M should be strongly considered for optimising embryo selection in partners with single-gene mutations in order to prevent transmission to the offspring. Full article

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

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14 pages, 6966 KiB

Open AccessArticle

Comparative Pathway Integrator: A Framework of Meta-Analytic Integration of Multiple Transcriptomic Studies for Consensual and Differential Pathway Analysis

by Xiangrui Zeng, Wei Zong, Chien-Wei Lin, Zhou Fang, Tianzhou Ma, David A. Lewis, John F. Enwright and George C. Tseng

Genes 2020, 11(6), 696; https://doi.org/10.3390/genes11060696 - 24 Jun 2020

Cited by 6 | Viewed by 2907

Abstract

Pathway enrichment analysis provides a knowledge-driven approach to interpret differentially expressed genes associated with disease status. Many tools have been developed to analyze a single study. However, when multiple studies of different conditions are jointly analyzed, novel integrative tools are needed. In addition, [...] Read more.

Pathway enrichment analysis provides a knowledge-driven approach to interpret differentially expressed genes associated with disease status. Many tools have been developed to analyze a single study. However, when multiple studies of different conditions are jointly analyzed, novel integrative tools are needed. In addition, pathway redundancy introduced by combining multiple public pathway databases hinders interpretation and knowledge discovery. We present a meta-analytic integration tool, Comparative Pathway Integrator (CPI), to address these issues using adaptively weighted Fisher’s method to discover consensual and differential enrichment patterns, a tight clustering algorithm to reduce pathway redundancy, and a text mining algorithm to assist interpretation of the pathway clusters. We applied CPI to jointly analyze six psychiatric disorder transcriptomic studies to demonstrate its effectiveness, and found functions confirmed by previous biological studies as well as novel enrichment patterns. CPI’s R package is accessible online on Github metaOmics/MetaPath. Full article

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

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20 pages, 4230 KiB

Open AccessArticle

Sequence Composition Underlying Centromeric and Heterochromatic Genome Compartments of the Pacific Oyster Crassostrea gigas

by Monika Tunjić Cvitanić, Tanja Vojvoda Zeljko, Juan J. Pasantes, Daniel García-Souto, Tena Gržan, Evelin Despot-Slade, Miroslav Plohl and Eva Šatović

Genes 2020, 11(6), 695; https://doi.org/10.3390/genes11060695 - 24 Jun 2020

Cited by 7 | Viewed by 4529

Abstract

Segments of the genome enriched in repetitive sequences still present a challenge and are omitted in genome assemblies. For that reason, the exact composition of DNA sequences underlying the heterochromatic regions and the active centromeres are still unexplored for many organisms. The centromere [...] Read more.

Segments of the genome enriched in repetitive sequences still present a challenge and are omitted in genome assemblies. For that reason, the exact composition of DNA sequences underlying the heterochromatic regions and the active centromeres are still unexplored for many organisms. The centromere is a crucial region of eukaryotic chromosomes responsible for the accurate segregation of genetic material. The typical landmark of centromere chromatin is the rapidly-evolving variant of the histone H3, CenH3, while DNA sequences packed in constitutive heterochromatin are associated with H3K9me3-modified histones. In the Pacific oyster Crassostrea gigas we identified its centromere histone variant, Cg-CenH3, that shows stage-specific distribution in gonadal cells. In order to investigate the DNA composition of genomic regions associated with the two specific chromatin types, we employed chromatin immunoprecipitation followed by high-throughput next-generation sequencing of the Cg-CenH3- and H3K9me3-associated sequences. CenH3-associated sequences were assigned to six groups of repetitive elements, while H3K9me3-associated-ones were assigned only to three. Those associated with CenH3 indicate the lack of uniformity in the chromosomal distribution of sequences building the centromeres, being also in the same time dispersed throughout the genome. The heterochromatin of C. gigas exhibited general paucity and limited chromosomal localization as predicted, with H3K9me3-associated sequences being predominantly constituted of DNA transposons. Full article

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

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32 pages, 1340 KiB

Open AccessFeature PaperReview

Orphan G Protein Coupled Receptors in Affective Disorders

by Lyndsay R. Watkins and Cesare Orlandi

Genes 2020, 11(6), 694; https://doi.org/10.3390/genes11060694 - 24 Jun 2020

Cited by 42 | Viewed by 11241

Abstract

G protein coupled receptors (GPCRs) are the main mediators of signal transduction in the central nervous system. Therefore, it is not surprising that many GPCRs have long been investigated for their role in the development of anxiety and mood disorders, as well as [...] Read more.

G protein coupled receptors (GPCRs) are the main mediators of signal transduction in the central nervous system. Therefore, it is not surprising that many GPCRs have long been investigated for their role in the development of anxiety and mood disorders, as well as in the mechanism of action of antidepressant therapies. Importantly, the endogenous ligands for a large group of GPCRs have not yet been identified and are therefore known as orphan GPCRs (oGPCRs). Nonetheless, growing evidence from animal studies, together with genome wide association studies (GWAS) and post-mortem transcriptomic analysis in patients, pointed at many oGPCRs as potential pharmacological targets. Among these discoveries, we summarize in this review how emotional behaviors are modulated by the following oGPCRs: ADGRB2 (BAI2), ADGRG1 (GPR56), GPR3, GPR26, GPR37, GPR50, GPR52, GPR61, GPR62, GPR88, GPR135, GPR158, and GPRC5B. Full article

(This article belongs to the Special Issue Genes and Biomarkers of Mood and Anxiety Disorders)

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18 pages, 6392 KiB

Open AccessArticle

Mass Spectrometry Based-Proteomic Analysis of Anisakis spp.: A Preliminary Study towards a New Diagnostic Tool

by Valeria Marzano, Stefania Pane, Gianluca Foglietta, Stefano Levi Mortera, Pamela Vernocchi, Andrea Onetti Muda and Lorenza Putignani

Genes 2020, 11(6), 693; https://doi.org/10.3390/genes11060693 - 24 Jun 2020

Cited by 23 | Viewed by 3692

Abstract

Anisakiasis is nowadays a well-known infection, mainly caused by the accidental ingestion of Anisakis larvae, following the consumption of raw or undercooked fishes and cephalopods. Due to the similarity of symptoms with those of common gastrointestinal disorders, this infection is often underestimated, and [...] Read more.

Anisakiasis is nowadays a well-known infection, mainly caused by the accidental ingestion of Anisakis larvae, following the consumption of raw or undercooked fishes and cephalopods. Due to the similarity of symptoms with those of common gastrointestinal disorders, this infection is often underestimated, and the need for new specific diagnostic tools is becoming crucial. Given the remarkable impact that MALDI–TOF MS biotyping had in the last decade in clinical routine practice for the recognition of bacterial and fungi strains, a similar scenario could be foreseen for the identification of parasites, such as nematodes. In this work, a MALDI–TOF MS profiling of Anisakis proteome was pursued with a view to constructing a first spectral library for the diagnosis of Anisakis infections. At the same time, a shotgun proteomics approach by LC–ESI–MS/MS was performed on the two main fractions obtained from protein extraction, to evaluate the protein species enriched by the protocol. A set of MALDI–TOF MS signals associated with proteins originating in the ribosomal fraction of the nematode extract was selected as a potential diagnostic tool for the identification of Anisakis spp. Full article

(This article belongs to the Special Issue Novel Omics Studies on Anisakid Nematodes)

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9 pages, 252 KiB

Open AccessFeature PaperArticle

Combined Preimplantation Genetic Testing for Autosomal Dominant Polycystic Kidney Disease: Consequences for Embryos Available for Transfer

by Pere Mir Pardo, José Antonio Martínez-Conejero, Julio Martín, Carlos Simón and Ana Cervero

Genes 2020, 11(6), 692; https://doi.org/10.3390/genes11060692 - 24 Jun 2020

Cited by 9 | Viewed by 2906

Abstract

Autosomal dominant polycystic kidney disease (ADPKD) is the most common hereditary kidney disease and presents with genetic and clinical heterogeneity. ADPKD can also manifest extra-renally, and seminal cysts have been associated with male infertility in some cases. ADPKD-linked male infertility, along with female [...] Read more.

Autosomal dominant polycystic kidney disease (ADPKD) is the most common hereditary kidney disease and presents with genetic and clinical heterogeneity. ADPKD can also manifest extra-renally, and seminal cysts have been associated with male infertility in some cases. ADPKD-linked male infertility, along with female age, have been proposed as factors that may influence the clinical outcomes of preimplantation genetic testing (PGT) for monogenic disorders (PGT-M). Large PGT for aneuploidy assessment (PGT-A) studies link embryo aneuploidy to increasing female age; other studies suggest that embryo aneuploidy is also linked to severe male-factor infertility. We aimed to assess the number of aneuploid embryos and the number of cycles with transferable embryos in ADPKD patients after combined-PGT. The combined-PGT protocol, involving PGT-M by PCR and PGT-A by next-generation sequencing, was performed in single trophectoderm biopsies from 289 embryos in 83 PGT cycles. Transferable embryos were obtained in 69.9% of cycles. The number of aneuploid embryos and cycles with transferable embryos did not differ when the male or female had the ADPKD mutation. However, a significantly higher proportion of aneuploid embryos was found in the advanced maternal age (AMA) group, but not in the male factor (MF) group, when compared to non-AMA and non-MF groups, respectively. Additionally, no significant differences in the percentage of cycles with transferable embryos were found in any of the groups. Our results indicate that AMA couples among ADPKD patients have an increased risk of aneuploid embryos, but ADPKD-linked male infertility does not promote an increased aneuploidy rate. Full article

(This article belongs to the Special Issue EmbryoGenetics)

18 pages, 682 KiB

Open AccessReview

From Genes to -Omics: The Evolving Molecular Landscape of Malignant Peripheral Nerve Sheath Tumor

by Kathryn M. Lemberg, Jiawan Wang and Christine A. Pratilas

Genes 2020, 11(6), 691; https://doi.org/10.3390/genes11060691 - 24 Jun 2020

Cited by 29 | Viewed by 4683

Abstract

Malignant peripheral nerve sheath tumors (MPNST) are rare, aggressive soft tissue sarcomas that occur with significantly increased incidence in people with the neuro-genetic syndrome neurofibromatosis type I (NF1). These complex karyotype sarcomas are often difficult to resect completely due to the involvement of [...] Read more.

Malignant peripheral nerve sheath tumors (MPNST) are rare, aggressive soft tissue sarcomas that occur with significantly increased incidence in people with the neuro-genetic syndrome neurofibromatosis type I (NF1). These complex karyotype sarcomas are often difficult to resect completely due to the involvement of neurovascular bundles, and are relatively chemotherapy- and radiation-insensitive. The lifetime risk of developing MPNST in the NF1 population has led to great efforts to characterize the genetic changes that drive the development of these tumors and identify mutations that may be used for diagnostic or therapeutic purposes. Advancements in genetic sequencing and genomic technologies have greatly enhanced researchers’ abilities to broadly and deeply investigate aberrations in human MPNST genomes. Here, we review genetic sequencing efforts in human MPNST samples over the past three decades. Particularly for NF1-associated MPNST, these overall sequencing efforts have converged on a set of four common genetic changes that occur in most MPNST, including mutations in neurofibromin 1 (NF1), CDKN2A, TP53, and members of the polycomb repressor complex 2 (PRC2). However, broader genomic studies have also identified recurrent but less prevalent genetic variants in human MPNST that also contribute to the molecular landscape of MPNST and may inform further research. Future studies to further define the molecular landscape of human MPNST should focus on collaborative efforts across multiple institutions in order to maximize information gathered from large numbers of well-annotated MPNST patient samples, both in the NF1 and the sporadic MPNST populations. Full article

(This article belongs to the Special Issue Genomics and Models of Nerve Sheath Tumors)

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14 pages, 834 KiB

Open AccessReview

Aspects of Multicellularity in Saccharomyces cerevisiae Yeast: A Review of Evolutionary and Physiological Mechanisms

by Monika Opalek and Dominika Wloch-Salamon

Genes 2020, 11(6), 690; https://doi.org/10.3390/genes11060690 - 24 Jun 2020

Cited by 18 | Viewed by 4567

Abstract

The evolutionary transition from single-celled to multicellular growth is a classic and intriguing problem in biology. Saccharomyces cerevisiae is a useful model to study questions regarding cell aggregation, heterogeneity and cooperation. In this review, we discuss scenarios of group formation and how this [...] Read more.

The evolutionary transition from single-celled to multicellular growth is a classic and intriguing problem in biology. Saccharomyces cerevisiae is a useful model to study questions regarding cell aggregation, heterogeneity and cooperation. In this review, we discuss scenarios of group formation and how this promotes facultative multicellularity in S. cerevisiae. We first describe proximate mechanisms leading to aggregation. These mechanisms include staying together and coming together, and can lead to group heterogeneity. Heterogeneity is promoted by nutrient limitation, structured environments and aging. We then characterize the evolutionary benefits and costs of facultative multicellularity in yeast. We summarize current knowledge and focus on the newest state-of-the-art discoveries that will fuel future research programmes aiming to understand facultative microbial multicellularity. Full article

(This article belongs to the Special Issue Genetic Aspects of Yeast: Cell Biology, Ecology and Biotechnology)

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27 pages, 4995 KiB

Open AccessArticle

Genetic Basis of Maize Resistance to Multiple Insect Pests: Integrated Genome-Wide Comparative Mapping and Candidate Gene Prioritization

by A. Badji, D. B. Kwemoi, L. Machida, D. Okii, N. Mwila, S. Agbahoungba, F. Kumi, A. Ibanda, A. Bararyenya, M. Solemanegy, T. Odong, P. Wasswa, M. Otim, G. Asea, M. Ochwo-Ssemakula, H. Talwana, S. Kyamanywa and P. Rubaihayo

Genes 2020, 11(6), 689; https://doi.org/10.3390/genes11060689 - 24 Jun 2020

Cited by 21 | Viewed by 7080

Abstract

Several species of herbivores feed on maize in field and storage setups, making the development of multiple insect resistance a critical breeding target. In this study, an association mapping panel of 341 tropical maize lines was evaluated in three field environments for resistance [...] Read more.

Several species of herbivores feed on maize in field and storage setups, making the development of multiple insect resistance a critical breeding target. In this study, an association mapping panel of 341 tropical maize lines was evaluated in three field environments for resistance to fall armyworm (FAW), whilst bulked grains were subjected to a maize weevil (MW) bioassay and genotyped with Diversity Array Technology’s single nucleotide polymorphisms (SNPs) markers. A multi-locus genome-wide association study (GWAS) revealed 62 quantitative trait nucleotides (QTNs) associated with FAW and MW resistance traits on all 10 maize chromosomes, of which, 47 and 31 were discovered at stringent Bonferroni genome-wide significance levels of 0.05 and 0.01, respectively, and located within or close to multiple insect resistance genomic regions (MIRGRs) concerning FAW, SB, and MW. Sixteen QTNs influenced multiple traits, of which, six were associated with resistance to both FAW and MW, suggesting a pleiotropic genetic control. Functional prioritization of candidate genes (CGs) located within 10–30 kb of the QTNs revealed 64 putative GWAS-based CGs (GbCGs) showing evidence of involvement in plant defense mechanisms. Only one GbCG was associated with each of the five of the six combined resistance QTNs, thus reinforcing the pleiotropy hypothesis. In addition, through in silico co-functional network inferences, an additional 107 network-based CGs (NbCGs), biologically connected to the 64 GbCGs, and differentially expressed under biotic or abiotic stress, were revealed within MIRGRs. The provided multiple insect resistance physical map should contribute to the development of combined insect resistance in maize. Full article

(This article belongs to the Special Issue Genetics and Physiology of Multiple-Stress Tolerance in Crops)

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10 pages, 4841 KiB

Open AccessArticle

Leukocyte Nucleolus and Anisakis pegreffii—When Falling Apart Means Falling in Place

by Ivona Mladineo and Jerko Hrabar

Genes 2020, 11(6), 688; https://doi.org/10.3390/genes11060688 - 23 Jun 2020

Cited by 1 | Viewed by 2658

Abstract

The view of the nucleolus as a mere ribosomal factory has been recently expanded, highlighting its essential role in immune and stress-related signalling and orchestrating. It has been shown that the nucleolus structure, formed around nucleolus organiser regions (NORs) and attributed Cajal bodies, [...] Read more.

The view of the nucleolus as a mere ribosomal factory has been recently expanded, highlighting its essential role in immune and stress-related signalling and orchestrating. It has been shown that the nucleolus structure, formed around nucleolus organiser regions (NORs) and attributed Cajal bodies, is prone to disassembly and reassembly correlated to various physiological and pathological stimuli. To evaluate the effect of parasite stimulus on the structure of the leukocyte nucleolus, we exposed rat peripheral blood mononuclear cells (PBMC) to the crude extract of the nematode A. pegreffii (Anisakidae), and compared the observed changes to the effect of control (RPMI-1640 media), immunosuppressive (MPA) and immunostimulant treatment (bacterial lipopolysaccharide (LPS) and viral analogue polyinosinic:polycytidylic acid (poly I:C)) by confocal microscopy. Poly I:C triggered the most accentuated changes such as nucleolar fragmentation and structural unravelling, LPS induced nucleolus thickening reminiscent of cell activation, while MPA induced disassembly of dense fibrillar and granular components. A. pegreffii crude extract triggered nucleolar segregation, expectedly more enhanced in treatment with a higher dose. This is the first evidence that leukocyte nucleoli already undergo structural changes 12 h post-parasitic stimuli, although these are likely to subside after successful cell activation. Full article

(This article belongs to the Special Issue Novel Omics Studies on Anisakid Nematodes)

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18 pages, 1097 KiB

Open AccessArticle

Autosomal Dominantly Inherited GREB1L Variants in Individuals with Profound Sensorineural Hearing Impairment

by Isabelle Schrauwen, Khurram Liaqat, Isabelle Schatteman, Thashi Bharadwaj, Abdul Nasir, Anushree Acharya, Wasim Ahmad, Guy Van Camp and Suzanne M. Leal

Genes 2020, 11(6), 687; https://doi.org/10.3390/genes11060687 - 23 Jun 2020

Cited by 24 | Viewed by 4685

Abstract

Congenital hearing impairment is a sensory disorder that is genetically highly heterogeneous. By performing exome sequencing in two families with congenital nonsyndromic profound sensorineural hearing loss (SNHL), we identified autosomal dominantly inherited missense variants [p.(Asn283Ser); p.(Thr116Ile)] in GREB1L, a neural crest regulatory [...] Read more.

Congenital hearing impairment is a sensory disorder that is genetically highly heterogeneous. By performing exome sequencing in two families with congenital nonsyndromic profound sensorineural hearing loss (SNHL), we identified autosomal dominantly inherited missense variants [p.(Asn283Ser); p.(Thr116Ile)] in GREB1L, a neural crest regulatory molecule. The p.(Thr116Ile) variant was also associated with bilateral cochlear aplasia and cochlear nerve aplasia upon temporal bone imaging, an ultra-rare phenotype previously seen in patients with de novo GREB1L variants. An important role of GREB1L in normal ear development has also been demonstrated by greb1l^−/− zebrafish, which show an abnormal sensory epithelia innervation. Last, we performed a review of all disease-associated variation described in GREB1L, as it has also been implicated in renal, bladder and genital malformations. We show that the spectrum of features associated with GREB1L is broad, variable and with a high level of reduced penetrance, which is typically characteristic of neurocristopathies. So far, seven GREB1L variants (14%) have been associated with ear-related abnormalities. In conclusion, these results show that autosomal dominantly inherited variants in GREB1L cause profound SNHL. Furthermore, we provide an overview of the phenotypic spectrum associated with GREB1L variants and strengthen the evidence of the involvement of GREB1L in human hearing. Full article

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

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13 pages, 514 KiB

Open AccessFeature PaperArticle

Clinical Relevance of +936 C>T VEGFA and c.233C>T bFGF Polymorphisms in Chronic Lymphocytic Leukemia

by Sandra Ballester, Begoña Pineda, Patricia Rodrigues, Eduardo Tormo, María José Terol and Pilar Eroles

Genes 2020, 11(6), 686; https://doi.org/10.3390/genes11060686 - 23 Jun 2020

Cited by 5 | Viewed by 2420

Abstract

Angiogenesis process contributes to the pathogenesis of B-cell chronic lymphocytic leukemia (B-CLL) being the levels of VEGFA and bFGF higher in patients than in healthy controls. Our aim was to evaluate the implication of angiogenesis factors genetic variants in the predisposition to B-CLL [...] Read more.

Angiogenesis process contributes to the pathogenesis of B-cell chronic lymphocytic leukemia (B-CLL) being the levels of VEGFA and bFGF higher in patients than in healthy controls. Our aim was to evaluate the implication of angiogenesis factors genetic variants in the predisposition to B-CLL and their association with clinical factors and survival. We performed a population-based case-control study in 224 Spanish B-CLL patients and 476 healthy randomly selected controls to evaluate susceptibility to developing B-CLL. Six polymorphisms were evaluated: rs1109324, rs1547651, rs3025039 (+936 C>T), rs833052 of the VEGFA gene, rs1449683 (c.233C>T) of the bFGF gene and (−710 C>T) of the VEGFR1 gene. The association between clinical parameters and patient outcome was analyzed. Carriers of the CT/TT variants of rs3025039 showed a significant protective effect against developing B-CLL. The CT/TT variants of rs1449683 show a tendency towards the development of the disease and the same variants associated significantly with higher genetic risk and with reduced disease free survival. Moreover, the association persisted in the early-stage disease subgroup. Our study provides evidence of the protective effect of the T/- rs3025039 VEGFA variant against B-CLL development and the association of CT/TT variants of the rs1449683 bFGF gene with genetic risk and an adverse survival. Full article

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

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11 pages, 416 KiB

Open AccessArticle

Array-Based Epigenetic Aging Indices May Be Racially Biased

by Robert Philibert, Steven R.H. Beach, Man-Kit Lei, Frederick X. Gibbons, Meg Gerrard, Ronald L. Simons and Meeshanthini V. Dogan

Genes 2020, 11(6), 685; https://doi.org/10.3390/genes11060685 - 22 Jun 2020

Cited by 22 | Viewed by 3503

Abstract

Epigenetic aging (EA) indices are frequently used as predictors of mortality and other important health outcomes. However, each of the commonly used array-based indices has significant heritable components which could tag ethnicity and potentially confound comparisons across racial and ethnic groups. To determine [...] Read more.

Epigenetic aging (EA) indices are frequently used as predictors of mortality and other important health outcomes. However, each of the commonly used array-based indices has significant heritable components which could tag ethnicity and potentially confound comparisons across racial and ethnic groups. To determine if this was possible, we examined the relationship of DNA methylation in cord blood from 203 newborns (112 African American (AA) and 91 White) at the 513 probes from the Levine PhenoAge Epigenetic Aging index to ethnicity. Then, we examined all sites significantly associated with race in the newborn sample to determine if they were also associated with an index of ethnic genetic heritage in a cohort of 505 AA adults. After Bonferroni correction, methylation at 50 CpG sites was significantly associated with ethnicity in the newborn cohort. The five most significant sites predicted ancestry with a receiver operator characteristic area under the curve of 0.97. Examination of the top 50 sites in the AA adult cohort showed that methylation status at 11 of those sites was also associated with percentage European ancestry. We conclude that the Levine PhenoAge Index is influenced by cryptic ethnic-specific genetic influences. This influence may extend to similarly constructed EA indices and bias cross-race comparisons. Full article

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

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18 pages, 2292 KiB

Open AccessReview

DNA Hypermethylation and Unstable Repeat Diseases: A Paradigm of Transcriptional Silencing to Decipher the Basis of Pathogenic Mechanisms

by Loredana Poeta, Denise Drongitis, Lucia Verrillo and Maria Giuseppina Miano

Genes 2020, 11(6), 684; https://doi.org/10.3390/genes11060684 - 22 Jun 2020

Cited by 16 | Viewed by 5660

Abstract

Unstable repeat disorders comprise a variable group of incurable human neurological and neuromuscular diseases caused by an increase in the copy number of tandem repeats located in various regions of their resident genes. It has become clear that dense DNA methylation in hyperexpanded [...] Read more.

Unstable repeat disorders comprise a variable group of incurable human neurological and neuromuscular diseases caused by an increase in the copy number of tandem repeats located in various regions of their resident genes. It has become clear that dense DNA methylation in hyperexpanded non-coding repeats induces transcriptional silencing and, subsequently, insufficient protein synthesis. However, the ramifications of this paradigm reveal a far more profound role in disease pathogenesis. This review will summarize the significant progress made in a subset of non-coding repeat diseases demonstrating the role of dense landscapes of 5-methylcytosine (5mC) as a common disease modifier. However, the emerging findings suggest context-dependent models of 5mC-mediated silencing with distinct effects of excessive DNA methylation. An in-depth understanding of the molecular mechanisms underlying this peculiar group of human diseases constitutes a prerequisite that could help to discover novel pathogenic repeat loci, as well as to determine potential therapeutic targets. In this regard, we report on a brief description of advanced strategies in DNA methylation profiling for the identification of unstable Guanine-Cytosine (GC)-rich regions and on promising examples of molecular targeted therapies for Fragile X disease (FXS) and Friedrich ataxia (FRDA) that could pave the way for the application of this technique in other hypermethylated expansion disorders. Full article

(This article belongs to the Special Issue DNA Methylation in Health and Diseases)

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