Genes

12 pages, 2122 KiB

Open AccessArticle

Host-Diet Effect on the Metabolism of Bifidobacterium

by Maria Satti, Monica Modesto, Akihito Endo, Takeshi Kawashima, Paola Mattarelli and Masanori Arita

Genes 2021, 12(4), 609; https://doi.org/10.3390/genes12040609 - 20 Apr 2021

Cited by 22 | Viewed by 3809

Abstract

Bifidobacterium has a diverse host range and shows several beneficial properties to the hosts. Many species should have co-evolved with their hosts, but the phylogeny of Bifidobacterium is dissimilar to that of host animals. The discrepancy could be linked to the niche-specific evolution [...] Read more.

Bifidobacterium has a diverse host range and shows several beneficial properties to the hosts. Many species should have co-evolved with their hosts, but the phylogeny of Bifidobacterium is dissimilar to that of host animals. The discrepancy could be linked to the niche-specific evolution due to hosts’ dietary carbohydrates. We investigated the relationship between bifidobacteria and their host diet using a comparative genomics approach. Since carbohydrates are the main class of nutrients for bifidobacterial growth, we examined the distribution of carbohydrate-active enzymes, in particular glycoside hydrolases (GHs) that metabolize unique oligosaccharides. When bifidobacterial species are classified by their distribution of GH genes, five groups arose according to their hosts’ feeding behavior. The distribution of GH genes was only weakly associated with the phylogeny of the host animals or with genomic features such as genome size. Thus, the hosts’ dietary pattern is the key determinant of the distribution and evolution of GH genes. Full article

(This article belongs to the Special Issue Genetics and Genomics of Probiotic Organisms)

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29 pages, 3958 KiB

Open AccessArticle

Molecular Phylogeny and Evolution of Amazon Parrots in the Greater Antilles

by Sofiia Kolchanova, Alexey Komissarov, Sergei Kliver, Anyi Mazo-Vargas, Yashira Afanador, Jafet Velez-Valentín, Ricardo Valentín de la Rosa, Stephanie Castro-Marquez, Israel Rivera-Colon, Audrey J. Majeske, Walter W. Wolfsberger, Taylor Hains, André Corvelo, Juan-Carlos Martinez-Cruzado, Travis C. Glenn, Orlando Robinson, Klaus-Peter Koepfli and Taras K. Oleksyk

Genes 2021, 12(4), 608; https://doi.org/10.3390/genes12040608 - 20 Apr 2021

Cited by 3 | Viewed by 8450

Abstract

Amazon parrots (Amazona spp.) colonized the islands of the Greater Antilles from the Central American mainland, but there has not been a consensus as to how and when this happened. Today, most of the five remaining island species are listed as endangered, [...] Read more.

Amazon parrots (Amazona spp.) colonized the islands of the Greater Antilles from the Central American mainland, but there has not been a consensus as to how and when this happened. Today, most of the five remaining island species are listed as endangered, threatened, or vulnerable as a consequence of human activity. We sequenced and annotated full mitochondrial genomes of all the extant Amazon parrot species from the Greater Antillean (A. leucocephala (Cuba), A. agilis, A. collaria (both from Jamaica), A. ventralis (Hispaniola), and A. vittata (Puerto Rico)), A. albifrons from mainland Central America, and A. rhodocorytha from the Atlantic Forest in Brazil. The assembled and annotated mitogenome maps provide information on sequence organization, variation, population diversity, and evolutionary history for the Caribbean species including the critically endangered A. vittata. Despite the larger number of available samples from the Puerto Rican Parrot Recovery Program, the sequence diversity of the A. vittata population in Puerto Rico was the lowest among all parrot species analyzed. Our data support the stepping-stone dispersal and speciation hypothesis that has started approximately 3.47 MYA when the ancestral population arrived from mainland Central America and led to diversification across the Greater Antilles, ultimately reaching the island of Puerto Rico 0.67 MYA. The results are presented and discussed in light of the geological history of the Caribbean and in the context of recent parrot evolution, island biogeography, and conservation. This analysis contributes to understating evolutionary history and empowers subsequent assessments of sequence variation and helps design future conservation efforts in the Caribbean. Full article

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

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13 pages, 1867 KiB

Open AccessArticle

Application of Genome Sequencing from Blood to Diagnose Mitochondrial Diseases

by Rocio Rius, Alison G. Compton, Naomi L. Baker, AnneMarie E. Welch, David Coman, Maina P. Kava, Andre E. Minoche, Mark J. Cowley, David R. Thorburn and John Christodoulou

Genes 2021, 12(4), 607; https://doi.org/10.3390/genes12040607 - 20 Apr 2021

Cited by 7 | Viewed by 4861

Abstract

Mitochondrial diseases can be caused by pathogenic variants in nuclear or mitochondrial DNA-encoded genes that often lead to multisystemic symptoms and can have any mode of inheritance. Using a single test, Genome Sequencing (GS) can effectively identify variants in both genomes, but it [...] Read more.

Mitochondrial diseases can be caused by pathogenic variants in nuclear or mitochondrial DNA-encoded genes that often lead to multisystemic symptoms and can have any mode of inheritance. Using a single test, Genome Sequencing (GS) can effectively identify variants in both genomes, but it has not yet been universally used as a first-line approach to diagnosing mitochondrial diseases due to related costs and challenges in data analysis. In this article, we report three patients with mitochondrial disease molecularly diagnosed through GS performed on DNA extracted from blood to demonstrate different diagnostic advantages of this technology, including the detection of a low-level heteroplasmic pathogenic variant, an intragenic nuclear DNA deletion, and a large mtDNA deletion. Current technical improvements and cost reductions are likely to lead to an expanded routine diagnostic usage of GS and of the complementary “Omic” technologies in mitochondrial diseases. Full article

(This article belongs to the Special Issue Expanding the Genetic Landscape of Mitochondrial Diseases)

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12 pages, 3882 KiB

Open AccessReview

Genetic Interactions of Awnness Genes in Barley

by Biguang Huang, Weiren Wu and Zonglie Hong

Genes 2021, 12(4), 606; https://doi.org/10.3390/genes12040606 - 20 Apr 2021

Cited by 7 | Viewed by 3540

Abstract

Awns are extending structures from lemmas in grasses and are very active in photosynthesis, contributing directly to the filling of the developing grain. Barley (Hordeum vulgare L.) awns are highly diverse in shape and length and are known to be controlled by [...] Read more.

Awns are extending structures from lemmas in grasses and are very active in photosynthesis, contributing directly to the filling of the developing grain. Barley (Hordeum vulgare L.) awns are highly diverse in shape and length and are known to be controlled by multiple awn-related genes. The genetic effects of these genes on awn diversity and development in barley are multiplexed and include complementary effect, cumulative effect, duplicate effect, recessive epistasis, dominant epistasis, and inhibiting effect, each giving a unique modified Mendelian ratio of segregation. The complexity of gene interactions contributes to the awn diversity in barley. Excessive gene interactions create a challenging task for genetic mapping and specific strategies have to be developed for mapping genes with specific interactive effects. Awn gene interactions can occur at different levels of gene expression, from the transcription factor-mediated gene transcription to the regulation of enzymes and metabolic pathways. A better understanding of gene interactions will greatly facilitate deciphering the genetic mechanisms underlying barley awn diversity and development. Full article

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

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30 pages, 2615 KiB

Open AccessReview

Unraveling the Balance between Genes, Microbes, Lifestyle and the Environment to Improve Healthy Reproduction

by Valeria D’Argenio, Lara Dittfeld, Paolo Lazzeri, Rossella Tomaiuolo and Ennio Tasciotti

Genes 2021, 12(4), 605; https://doi.org/10.3390/genes12040605 - 20 Apr 2021

Cited by 8 | Viewed by 4848

Abstract

Humans’ health is the result of a complex and balanced interplay between genetic factors, environmental stimuli, lifestyle habits, and the microbiota composition. The knowledge about their single contributions, as well as the complex network linking each to the others, is pivotal to understand [...] Read more.

Humans’ health is the result of a complex and balanced interplay between genetic factors, environmental stimuli, lifestyle habits, and the microbiota composition. The knowledge about their single contributions, as well as the complex network linking each to the others, is pivotal to understand the mechanisms underlying the onset of many diseases and can provide key information for their prevention, diagnosis and therapy. This applies also to reproduction. Reproduction, involving almost 10% of our genetic code, is one of the most critical human’s functions and is a key element to assess the well-being of a population. The last decades revealed a progressive decline of reproductive outcomes worldwide. As a consequence, there is a growing interest in unveiling the role of the different factors involved in human reproduction and great efforts have been carried out to improve its outcomes. As for many other diseases, it is now clear that the interplay between the underlying genetics, our commensal microbiome, the lifestyle habits and the environment we live in can either exacerbate the outcome or mitigate the adverse effects. Here, we aim to analyze how each of these factors contribute to reproduction highlighting their individual contribution and providing supporting evidence of how to modify their impact and overall contribution to a healthy reproductive status. Full article

(This article belongs to the Special Issue Genetics and Genomics of Reproductive Medicine)

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21 pages, 2276 KiB

Open AccessArticle

QTL Analysis of Five Morpho-Physiological Traits in Bread Wheat Using Two Mapping Populations Derived from Common Parents

by Paolo Vitale, Fabio Fania, Salvatore Esposito, Ivano Pecorella, Nicola Pecchioni, Samuela Palombieri, Francesco Sestili, Domenico Lafiandra, Francesca Taranto and Pasquale De Vita

Genes 2021, 12(4), 604; https://doi.org/10.3390/genes12040604 - 20 Apr 2021

Cited by 7 | Viewed by 3458

Abstract

Traits such as plant height (PH), juvenile growth habit (GH), heading date (HD), and tiller number are important for both increasing yield potential and improving crop adaptation to climate change. In the present study, these traits were investigated by using the same bi-parental [...] Read more.

Traits such as plant height (PH), juvenile growth habit (GH), heading date (HD), and tiller number are important for both increasing yield potential and improving crop adaptation to climate change. In the present study, these traits were investigated by using the same bi-parental population at early (F₂ and F₂-derived F₃ families) and late (F₆ and F₇, recombinant inbred lines, RILs) generations to detect quantitative trait loci (QTLs) and search for candidate genes. A total of 176 and 178 lines were genotyped by the wheat Illumina 25K Infinium SNP array. The two genetic maps spanned 2486.97 cM and 3732.84 cM in length, for the F₂ and RILs, respectively. QTLs explaining the highest phenotypic variation were found on chromosomes 2B, 2D, 5A, and 7D for HD and GH, whereas those for PH were found on chromosomes 4B and 4D. Several QTL detected in the early generations (i.e., PH and tiller number) were not detected in the late generations as they were due to dominance effects. Some of the identified QTLs co-mapped to well-known adaptive genes (i.e., Ppd-1, Vrn-1, and Rht-1). Other putative candidate genes were identified for each trait, of which PINE1 and PIF4 may be considered new for GH and TTN in wheat. The use of a large F₂ mapping population combined with NGS-based genotyping techniques could improve map resolution and allow closer QTL tagging. Full article

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

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9 pages, 601 KiB

Open AccessArticle

Identification of Genetic Variants in 65 Obesity Related Genes in a Cohort of Portuguese Obese Individuals

by Catarina Ginete, Bernardo Serrasqueiro, José Silva-Nunes, Luísa Veiga and Miguel Brito

Genes 2021, 12(4), 603; https://doi.org/10.3390/genes12040603 - 19 Apr 2021

Cited by 5 | Viewed by 3995

Abstract

Obesity is a major public health problem, which has a strong genetic component that interplays with environmental factors. Several genes are known to be implicated in the regulation of body weight. The identification of alleles that can be associated with obesity is a [...] Read more.

Obesity is a major public health problem, which has a strong genetic component that interplays with environmental factors. Several genes are known to be implicated in the regulation of body weight. The identification of alleles that can be associated with obesity is a key element to control this pandemic. On the basis of a Portuguese population, 65 obesity-related genes are sequenced using Next-Generation Sequencing (NGS) in 72 individuals with obesity, in order to identify variants associated with monogenic obesity and potential risk factors. A total of 429 variants are identified, 129 of which had already been associated with the phenotype. Comparing our results with the European and Global frequencies, from 1000 Genomes project, 23 potential risk variants are identified. Six new variants are discovered in heterozygous carriers: four missense (genes ALMS1-NM_015120.4:c.5552C>T; SORCS1-NM_001013031.2:c.1072A>G and NM_001013031.2: c.2491A>C; TMEM67-NM_153704.5:c.158A>G) and two synonymous (genes BBS1-NM_024649.4:c.1437C>T; TMEM67-NM_153704.5:c.2583T>C). Functional studies should be performed to validate these new findings and evaluate their penetrance and pathogenicity. Regardless of no cases of monogenic obesity being identified, this kind of investigational study is important when we are still trying to understand the aetiology and pathophysiology of obesity. This will allow the identification of rare variants associated with obesity and the study of their prevalence in specific populational groups. Full article

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

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14 pages, 5450 KiB

Open AccessArticle

Responses to Mineral Supplementation and Salmon Lice (Lepeophtheirus salmonis) Infestation in Skin Layers of Atlantic Salmon (Salmo salar L.)

by Lene Sveen, Aleksei Krasnov, Gerrit Timmerhaus and Andrè Sture Bogevik

Genes 2021, 12(4), 602; https://doi.org/10.3390/genes12040602 - 19 Apr 2021

Cited by 6 | Viewed by 3095

Abstract

The crustacean ectoparasite salmon louse (Lepeophtheirus salmonis), which severely affects Atlantic salmon health and welfare is one of the main problems of commercial aquaculture. In the present study, fish were fed a diet supplemented with extra minerals through the inclusion of [...] Read more.

The crustacean ectoparasite salmon louse (Lepeophtheirus salmonis), which severely affects Atlantic salmon health and welfare is one of the main problems of commercial aquaculture. In the present study, fish were fed a diet supplemented with extra minerals through the inclusion of a commercial additive (Biofeed Forte Salmon), substituting wheat in the control diet, before experimental infestation with salmon lice. Lice counts reduced with time but with no apparent effect of the diets. Further, fish fed the mineral diet had an overall higher number of blue (acidic) mucous cells, while the ratio of purple mucous cells was higher in the mineral diet. The transcriptional response in skin was enhanced at 7 dpc (copepodite life stage) in fish fed the mineral diet including immune and stress responses, while at 21 dpc (pre-adult life stage), the difference disappeared, or reversed with stronger induction in the control diet. Overall, 9.3% of the genes affected with lice also responded to the feed, with marked differences in outer (scale + epidermis) and inner (dermis) skin layers. A comparison of transcriptome data with five datasets from previous trials revealed common features and gene markers of responses to lice, stress, and mechanically induced wounds. Results suggested a prevalence of generic responses in wounded skin and lice-infected salmon. Full article

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

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10 pages, 1063 KiB

Open AccessArticle

Accurate Quantification of AAV Vector Genomes by Quantitative PCR

by Cristina Martinez-Fernandez de la Camara, Michelle E. McClements and Robert E. MacLaren

Genes 2021, 12(4), 601; https://doi.org/10.3390/genes12040601 - 19 Apr 2021

Cited by 16 | Viewed by 7056

Abstract

The ability to accurately determine the dose of an adeno-associated viral (AAV) therapeutic vector is critical to the gene therapy process. Quantitative PCR (qPCR) is one of the common methods to quantify the AAV vector titre, but different variables can lead to inconsistent [...] Read more.

The ability to accurately determine the dose of an adeno-associated viral (AAV) therapeutic vector is critical to the gene therapy process. Quantitative PCR (qPCR) is one of the common methods to quantify the AAV vector titre, but different variables can lead to inconsistent results. The aim of this study was to analyze the influence of the conformation of the DNA used as the standard control, and the enzymatic digestion was performed to release the viral genome from the protein capsid on the physical genome titration of a clinically relevant AAV8.RPGR vector, made to good laboratory practice standards in an academic setting. The results of this study showed that the conformation of the DNA used as standard has a significant impact on the accuracy of absolute quantification by qPCR. The use of supercoiled undigested plasmid DNA template generated a higher apparent titer, as compared to the use of linearized plasmid as the standard. In contrast to previous studies, the pre-treatment of the samples with Proteinase K, in addition to the high temperature step used after DNase I digestion, resulted in a reduction on AAV titers. Ideally, all AAV documentation should state which form of reference plasmid and which pre-treatment of the samples have been used to calculate titers, so that appropriate comparisons relating to dose toxicity and transduction efficacy can be made in the clinical scenario. Full article

(This article belongs to the Special Issue Genomics and Therapeutics of Hereditary Eye Disease)

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21 pages, 1852 KiB

Open AccessReview

Inosine in Biology and Disease

by Sundaramoorthy Srinivasan, Adrian Gabriel Torres and Lluís Ribas de Pouplana

Genes 2021, 12(4), 600; https://doi.org/10.3390/genes12040600 - 19 Apr 2021

Cited by 59 | Viewed by 11948

Abstract

The nucleoside inosine plays an important role in purine biosynthesis, gene translation, and modulation of the fate of RNAs. The editing of adenosine to inosine is a widespread post-transcriptional modification in transfer RNAs (tRNAs) and messenger RNAs (mRNAs). At the wobble position of [...] Read more.

The nucleoside inosine plays an important role in purine biosynthesis, gene translation, and modulation of the fate of RNAs. The editing of adenosine to inosine is a widespread post-transcriptional modification in transfer RNAs (tRNAs) and messenger RNAs (mRNAs). At the wobble position of tRNA anticodons, inosine profoundly modifies codon recognition, while in mRNA, inosines can modify the sequence of the translated polypeptide or modulate the stability, localization, and splicing of transcripts. Inosine is also found in non-coding and exogenous RNAs, where it plays key structural and functional roles. In addition, molecular inosine is an important secondary metabolite in purine metabolism that also acts as a molecular messenger in cell signaling pathways. Here, we review the functional roles of inosine in biology and their connections to human health. Full article

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

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47 pages, 2531 KiB

Open AccessArticle

Human Mitochondrial Control Region and mtGenome: Design and Forensic Validation of NGS Multiplexes, Sequencing and Analytical Software

by Cydne L. Holt, Kathryn M. Stephens, Paulina Walichiewicz, Keenan D. Fleming, Elmira Forouzmand and Shan-Fu Wu

Genes 2021, 12(4), 599; https://doi.org/10.3390/genes12040599 - 19 Apr 2021

Cited by 21 | Viewed by 6331

Abstract

Forensic mitochondrial DNA (mtDNA) analysis conducted using next-generation sequencing (NGS), also known as massively parallel sequencing (MPS), as compared to Sanger-type sequencing brings modern advantages, such as deep coverage per base (herein referred to as read depth per base pair (bp)), simultaneous sequencing [...] Read more.

Forensic mitochondrial DNA (mtDNA) analysis conducted using next-generation sequencing (NGS), also known as massively parallel sequencing (MPS), as compared to Sanger-type sequencing brings modern advantages, such as deep coverage per base (herein referred to as read depth per base pair (bp)), simultaneous sequencing of multiple samples (libraries) and increased operational efficiencies. This report describes the design and developmental validation, according to forensic quality assurance standards, of end-to-end workflows for two multiplexes, comprised of ForenSeq mtDNA control region and mtDNA whole-genome kits the MiSeq FGx^TM instrument and ForenSeq universal analysis software (UAS) 2.0/2.1. Polymerase chain reaction (PCR) enrichment and a tiled amplicon approach target small, overlapping amplicons (60–150 bp and 60–209 bp for the control region and mtGenome, respectively). The system provides convenient access to data files that can be used outside of the UAS if desired. Studies assessed a range of environmental and situational variables, including but not limited to buccal samples, rootless hairs, dental and skeletal remains, concordance of control region typing between the two multiplexes and as compared to orthogonal data, assorted sensitivity studies, two-person DNA mixtures and PCR-based performance testing. Limitations of the system and implementation considerations are discussed. Data indicated that the two mtDNA multiplexes, MiSeq FGx and ForenSeq software, meet or exceed forensic DNA quality assurance (QA) guidelines with robust, reproducible performance on samples of various quantities and qualities. Full article

(This article belongs to the Special Issue Forensic Mitochondrial Genomics)

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10 pages, 700 KiB

Open AccessArticle

piRNA-823 Is a Unique Potential Diagnostic Non-Invasive Biomarker in Colorectal Cancer Patients

by Norhan A. Sabbah, Wael M. Abdalla, Walid A. Mawla, Nagla AbdAlMonem, Amal F. Gharib, Ahmed Abdul-Saboor, Abdallah S. Abdelazem and Nermin Raafat

Genes 2021, 12(4), 598; https://doi.org/10.3390/genes12040598 - 19 Apr 2021

Cited by 26 | Viewed by 2995

Abstract

Early detection of colorectal cancer (CRC) is the most important factor in deciding its prognosis, so the need to develop an accurate screening test is a must. P-element induced wimpy testis (PIWI) RNA-823 (piR-823) is one of the first piRNAs recognized to be [...] Read more.

Early detection of colorectal cancer (CRC) is the most important factor in deciding its prognosis, so the need to develop an accurate screening test is a must. P-element induced wimpy testis (PIWI) RNA-823 (piR-823) is one of the first piRNAs recognized to be linked to malignancy. We aimed to investigate the expression levels of piR-823 in both serum and tissues of colorectal cancer patients and the ability to use its serum level as a non-invasive diagnostic biomarker to detect colorectal cancer. We determined piR-823 expression levels in 84 serum samples of CRC patients, 75 serum samples of healthy controls, and biological specimens obtained from the 84 patients with colorectal cancer from both the tumor tissues and the normal neighboring tissues using quantitative real-time reverse transcriptase-PCR. We showed that piR-823 had significantly higher serum and tissue expression levels in CRC patients compared to the controls. We observed a significant positive correlation between piR-823 serum levels and the staging of CRC, with significantly higher levels exhibiting advanced stages of CRC (III and IV). This translates into poorer differentiation and lymph node metastasis. The receiver operating characteristic curve (ROC curve) test showed 83.3% sensitivity and 89.3% specificity at a cut-off value of >5.98-fold change, with an area under the curve of 0.933 (p < 0.0001) concerning the ability of piR-823 in diagnosing patients with colorectal carcinoma. piR-823 expression is upregulated in colorectal cancer patients’ serum and tissues, and it can be used as a diagnostic noninvasive biomarker for CRC. Full article

(This article belongs to the Special Issue Non-coding RNAs in Human Health and Diseases)

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11 pages, 276 KiB

Open AccessReview

MicroRNA Changes in Gastric Carcinogenesis: Differential Dysregulation during Helicobacter pylori and EBV Infection

by Christian Prinz, Kemal Mese and David Weber

Genes 2021, 12(4), 597; https://doi.org/10.3390/genes12040597 - 19 Apr 2021

Cited by 13 | Viewed by 2916

Abstract

Despite medical advances, gastric-cancer (GC) mortality remains high in Europe. Bacterial infection with Helicobacter pylori (H. pylori) and viral infection with the Epstein–Barr virus (EBV) are associated with the development of both distal and proximal gastric cancer. Therefore, the detection of [...] Read more.

Despite medical advances, gastric-cancer (GC) mortality remains high in Europe. Bacterial infection with Helicobacter pylori (H. pylori) and viral infection with the Epstein–Barr virus (EBV) are associated with the development of both distal and proximal gastric cancer. Therefore, the detection of these infections and the prediction of further cancer development could be clinically significant. To this end, microRNAs (miRNAs) could serve as promising new tools. MiRNAs are highly conserved noncoding RNAs that play an important role in gene silencing, mainly acting via translational repression and the degradation of mRNA targets. Recent reports demonstrate the downregulation of numerous miRNAs in GC, especially miR-22, miR-145, miR-206, miR-375, and miR-490, and these changes seem to promote cancer-cell invasion and tumor spreading. The dysregulation of miR-106b, miR-146a, miR-155, and the Let-7b/c complex seems to be of particular importance during H. pylori infection or gastric carcinogenesis. In contrast, many reports describe changes in host miRNA expression and outline the effects of bamHI-A region rightward transcript (BART) miRNA in EBV-infected tissue. The differential regulation of these miRNA, acting alone or in close interaction when both infections coexist, may therefore enable us to detect cancer earlier. In this review, we focus on the two different etiologies of gastric cancer and outline the molecular pathways through which H. pylori- or EBV-induced changes might synergistically act via miR-155 dysregulation to potentiate cancer risk. The three markers, namely, H. pylori presence, EBV infection, and miR-155 expression, may be checked in routine biopsies to evaluate the risk of developing gastric cancer. Full article

(This article belongs to the Special Issue The Role of MicroRNA in Cancer)

15 pages, 1149 KiB

Open AccessCommunication

Protective Role of a TMPRSS2 Variant on Severe COVID-19 Outcome in Young Males and Elderly Women

by Maria Monticelli, Bruno Hay Mele, Elisa Benetti, Chiara Fallerini, Margherita Baldassarri, Simone Furini, Elisa Frullanti, Francesca Mari, GEN-COVID Multicenter Study, Giuseppina Andreotti, Maria Vittoria Cubellis and Alessandra Renieri

Genes 2021, 12(4), 596; https://doi.org/10.3390/genes12040596 - 19 Apr 2021

Cited by 42 | Viewed by 6434

Abstract

The protease encoded by the TMPRSS2 gene facilitates viral infections and has been implicated in the pathogenesis of SARS-CoV-2. We analyzed the TMPRSS2 sequence and correlated the protein variants with the clinical features of a cohort of 1177 patients affected by COVID-19 in [...] Read more.

The protease encoded by the TMPRSS2 gene facilitates viral infections and has been implicated in the pathogenesis of SARS-CoV-2. We analyzed the TMPRSS2 sequence and correlated the protein variants with the clinical features of a cohort of 1177 patients affected by COVID-19 in Italy. Nine relatively common variants (allele frequency > 0.01) and six missense variants which may affect the protease activity according to PolyPhen-2 in HumVar-trained mode were identified. Among them, p.V197M (p.Val197Met) (rs12329760) emerges as a common variant that has a deleterious effect on the protease and a protective effect on the patients. Its role appears particularly relevant in two subgroups of patients—young males and elderly women—and among those affected by co-morbidities, where the variant frequency is higher among individuals who were mildly affected by the disease and did not need hospitalization or oxygen therapy than among those more severely affected, who required oxygen therapy, ventilation or intubation. This study provides useful information for the identification of patients at risk of developing a severe form of COVID-19, and encourages the usage of drugs affecting the expression of TMPRSS2 or inhibiting protein activity. Full article

(This article belongs to the Special Issue COVID-19 and Molecular Genetics)

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10 pages, 624 KiB

Open AccessCommunication

Microsatellite DNA Analysis for Diversity Study, Individual Identification and Parentage Control in Pig Breeds in Poland

by Anna Radko, Grzegorz Smołucha and Anna Koseniuk

Genes 2021, 12(4), 595; https://doi.org/10.3390/genes12040595 - 19 Apr 2021

Cited by 6 | Viewed by 2897

Abstract

Swine DNA profiling is of high importance for animal identification and parentage verification. The aim of this study was to test a set of 14 microsatellite (STR) markers recommended by ISAG for parentage verification in Polish Landrace (PL, n = 900), Polish Large [...] Read more.

Swine DNA profiling is of high importance for animal identification and parentage verification. The aim of this study was to test a set of 14 microsatellite (STR) markers recommended by ISAG for parentage verification in Polish Landrace (PL, n = 900), Polish Large White (PLW, n = 482), Pulawska (PUL, n = 127), and Duroc pigs (DU n = 108). The studied breeds showed a medium level of genetic differentiation. The average value of heterozygosity and degree of polymorphism (PIC) were above 0.5 for the studied breeds, except for the DU breed (PIC = 0.477). The population inbreeding coefficient indicates an absence of inbreeding in the studied breeds (an average value of F_IS = 0.007). The cumulative power of discrimination for all breeds reached high values close to 1.0, while the probability of identity (P_ID) was low, with P_ID values ranging between 10⁻⁹ (for DU) and 10⁻¹² (for PLW). The cumulative exclusion probability for PE₁ and PE₂ showed that the parentage can be confirmed with a probability of from 92.75% to 99.01% and from 99.49% to 99.97%, respectively. Full article

(This article belongs to the Special Issue Genetic Structure of World Animal Populations)

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11 pages, 1936 KiB

Open AccessArticle

Further Delineation of Phenotype and Genotype of Primary Microcephaly Syndrome with Cortical Malformations Associated with Mutations in the WDR62 Gene

by Ryszard Slezak, Robert Smigiel, Ewa Obersztyn, Agnieszka Pollak, Mateusz Dawidziuk, Wojciech Wiszniewski, Monika Bekiesinska-Figatowska, Malgorzata Rydzanicz, Rafal Ploski and Pawel Gawlinski

Genes 2021, 12(4), 594; https://doi.org/10.3390/genes12040594 - 19 Apr 2021

Cited by 8 | Viewed by 3124

Abstract

Type 2 congenital microcephaly (MCPH2) is a brain development disorder characterized by primary microcephaly with or without brain malformations. MCPH2 is caused by mutations in the WDR62 gene. We present three new patients with MCPH2 and compound heterozygous mutations in the WDR62 gene. [...] Read more.

Type 2 congenital microcephaly (MCPH2) is a brain development disorder characterized by primary microcephaly with or without brain malformations. MCPH2 is caused by mutations in the WDR62 gene. We present three new patients with MCPH2 and compound heterozygous mutations in the WDR62 gene. In all the cases, the parents were healthy and unrelated. All children were clinically diagnosed with congenital microcephaly and retardation of motor and speech development. Sequencing results in the presented patients revealed five new variants in the WDR62 gene (c.4273C>T, c.1711_1712insTA, c.1777_1778delGA, c.1642+2T>G, c.194T>A) and one previously described in the German population (c.2864_2867delACAG). In two of the presented cases, variants in the SMAD4, DKC1, and ATRX genes were also found with unknown effects on the course of the disease. Moreover, in the article we collected and compared the most common clinical symptoms, dysmorphic features, and changes in radiographic examinations of the brain observed in 120 patients with recessive primary microcephaly type 2 caused by mutations in the WDR62 gene. Full article

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

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15 pages, 3022 KiB

Open AccessArticle

Unique Variant Spectrum in a Jordanian Cohort with Inherited Retinal Dystrophies

by Bilal Azab, Zain Dardas, Dunia Aburizeg, Muawyah Al-Bdour, Mohammed Abu-Ameerh, Tareq Saleh, Raghda Barham, Ranad Maswadi, Nidaa A Ababneh, Mohammad Alsalem, Hana Zouk, Sami Amr and Abdalla Awidi

Genes 2021, 12(4), 593; https://doi.org/10.3390/genes12040593 - 19 Apr 2021

Cited by 3 | Viewed by 3528

Abstract

Whole Exome Sequencing (WES) is a powerful approach for detecting sequence variations in the human genome. The aim of this study was to investigate the genetic defects in Jordanian patients with inherited retinal dystrophies (IRDs) using WES. WES was performed on proband patients’ [...] Read more.

Whole Exome Sequencing (WES) is a powerful approach for detecting sequence variations in the human genome. The aim of this study was to investigate the genetic defects in Jordanian patients with inherited retinal dystrophies (IRDs) using WES. WES was performed on proband patients’ DNA samples from 55 Jordanian families. Sanger sequencing was used for validation and segregation analysis of the detected, potential disease-causing variants (DCVs). Thirty-five putatively causative variants (6 novel and 29 known) in 21 IRD-associated genes were identified in 71% of probands (39 of the 55 families). Three families showed phenotypes different from the typically reported clinical findings associated with the causative genes. To our knowledge, this is the largest genetic analysis of IRDs in the Jordanian population to date. Our study also confirms that WES is a powerful tool for the molecular diagnosis of IRDs in large patient cohorts. Full article

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

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24 pages, 3910 KiB

Open AccessReview

Neuromesodermal Lineage Contribution to CNS Development in Invertebrate and Vertebrate Chordates

by Clare Hudson and Hitoyoshi Yasuo

Genes 2021, 12(4), 592; https://doi.org/10.3390/genes12040592 - 17 Apr 2021

Cited by 13 | Viewed by 4122

Abstract

Ascidians are invertebrate chordates and the closest living relative to vertebrates. In ascidian embryos a large part of the central nervous system arises from cells associated with mesoderm rather than ectoderm lineages. This seems at odds with the traditional view of vertebrate nervous [...] Read more.

Ascidians are invertebrate chordates and the closest living relative to vertebrates. In ascidian embryos a large part of the central nervous system arises from cells associated with mesoderm rather than ectoderm lineages. This seems at odds with the traditional view of vertebrate nervous system development which was thought to be induced from ectoderm cells, initially with anterior character and later transformed by posteriorizing signals, to generate the entire anterior-posterior axis of the central nervous system. Recent advances in vertebrate developmental biology, however, show that much of the posterior central nervous system, or spinal cord, in fact arises from cells that share a common origin with mesoderm. This indicates a conserved role for bi-potential neuromesoderm precursors in chordate CNS formation. However, the boundary between neural tissue arising from these distinct neural lineages does not appear to be fixed, which leads to the notion that anterior-posterior patterning and neural fate formation can evolve independently. Full article

(This article belongs to the Special Issue The Evolution of Invertebrate Animals)

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19 pages, 5199 KiB

Open AccessFeature PaperReview

Structures of the ß-Keratin Filaments and Keratin Intermediate Filaments in the Epidermal Appendages of Birds and Reptiles (Sauropsids)

by David A.D. Parry

Genes 2021, 12(4), 591; https://doi.org/10.3390/genes12040591 - 17 Apr 2021

Cited by 7 | Viewed by 3399

Abstract

The epidermal appendages of birds and reptiles (the sauropsids) include claws, scales, and feathers. Each has specialized physical properties that facilitate movement, thermal insulation, defence mechanisms, and/or the catching of prey. The mechanical attributes of each of these appendages originate from its fibril-matrix [...] Read more.

The epidermal appendages of birds and reptiles (the sauropsids) include claws, scales, and feathers. Each has specialized physical properties that facilitate movement, thermal insulation, defence mechanisms, and/or the catching of prey. The mechanical attributes of each of these appendages originate from its fibril-matrix texture, where the two filamentous structures present, i.e., the corneous ß-proteins (CBP or ß-keratins) that form 3.4 nm diameter filaments and the α-fibrous molecules that form the 7–10 nm diameter keratin intermediate filaments (KIF), provide much of the required tensile properties. The matrix, which is composed of the terminal domains of the KIF molecules and the proteins of the epidermal differentiation complex (EDC) (and which include the terminal domains of the CBP), provides the appendages, with their ability to resist compression and torsion. Only by knowing the detailed structures of the individual components and the manner in which they interact with one another will a full understanding be gained of the physical properties of the tissues as a whole. Towards that end, newly-derived aspects of the detailed conformations of the two filamentous structures will be discussed and then placed in the context of former knowledge. Full article

(This article belongs to the Special Issue Genomics and Evolution of Sauropsid Traits in the Genomics Era)

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15 pages, 3264 KiB

Open AccessArticle

Identification of a Candidate Gene for the Novel Cytoplasmic Male Sterility Derived from Inter-Subspecific Crosses in Rice (Oryza sativa L.)

by Zhuo Jin, Jeonghwan Seo, Backki Kim, Seung Young Lee and Hee-Jong Koh

Genes 2021, 12(4), 590; https://doi.org/10.3390/genes12040590 - 17 Apr 2021

Cited by 4 | Viewed by 2990

Abstract

Tetep-cytoplasmic male sterility (CMS) was developed through successive backcrosses between subspecies indica and japonica in rice (Oryza sativa L.), which showed abnormal anther dehiscence phenotypes. Whole genome sequencing and de novo assembly of the mitochondrial genome identified the chimeric gene orf312, [...] Read more.

Tetep-cytoplasmic male sterility (CMS) was developed through successive backcrosses between subspecies indica and japonica in rice (Oryza sativa L.), which showed abnormal anther dehiscence phenotypes. Whole genome sequencing and de novo assembly of the mitochondrial genome identified the chimeric gene orf312, which possesses a transmembrane domain and overlaps with two mitotype-specific sequences (MSSs) that are unique to the Tetep-CMS line. The encoded peptide of orf312 was toxic to Escherichia coli and inhibited cell growth compared to the control under isopropyl-β-D-1-thiogalactopyranoside (IPTG) induction. The peptide of orf312 contains COX11-interaction domains, which are thought to be a main functional domain for WA352c in the wild abortive (WA-CMS) line of rice. A QTL for Rf-Tetep (restorer-of-fertility gene(s) originating from Tetep) was identified on chromosome 10. In this region, several restorer genes, Rf1a, Rf1b, and Rf4, have previously been reported. Collectively, the interactions of orf312, a candidate gene for Tetep-CMS, and Rf-Tetep, a restorer QTL, confer male sterility and fertility restoration, respectively, which enables a hybrid rice breeding system. Further studies on orf312 and isolation of Rf-Tetep will help to identify the underlying molecular mechanism of mitochondrial ORFs with the COX11-interaction domains. Full article

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

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16 pages, 3547 KiB

Open AccessArticle

LncMyoD Promotes Skeletal Myogenesis and Regulates Skeletal Muscle Fiber-Type Composition by Sponging miR-370-3p

by Peiwen Zhang, Jingjing Du, Xinyu Guo, Shuang Wu, Jin He, Xinrong Li, Linyuan Shen, Lei Chen, Bohong Li, Jingjun Zhang, Yuhao Xie, Lili Niu, Dongmei Jiang, Xuewei Li, Shunhua Zhang and Li Zhu

Genes 2021, 12(4), 589; https://doi.org/10.3390/genes12040589 - 17 Apr 2021

Cited by 14 | Viewed by 2671

Abstract

The development of skeletal muscle is a highly ordered and complex biological process. Increasing evidence has shown that noncoding RNAs, especially long-noncoding RNAs (lncRNAs) and microRNAs, play a vital role in the development of myogenic processes. In this study, we observed that lncMyoD [...] Read more.

The development of skeletal muscle is a highly ordered and complex biological process. Increasing evidence has shown that noncoding RNAs, especially long-noncoding RNAs (lncRNAs) and microRNAs, play a vital role in the development of myogenic processes. In this study, we observed that lncMyoD regulates myogenesis and changes myofiber-type composition. miR-370-3p, which is directly targeted by lncMyoD, promoted myoblast proliferation and inhibited myoblast differentiation in the C2C12 cell line, which serves as a valuable model for studying muscle development. In addition, the inhibition of miR-370-3p promoted fast-twitch fiber transition. Further analysis indicated that acyl-Coenzyme A dehydrogenase, short/branched chain (ACADSB) is a target gene of miR-370-3p, which is also involved in myoblast differentiation and fiber-type transition. Furthermore, our data suggested that miR-370-3p was sponged by lncMyoD. In contrast with miR-370-3p, lncMyoD promoted fast-twitch fiber transition. Taken together, our results suggest that miR-370-3p regulates myoblast differentiation and muscle fiber transition and is sponged by lncMyoD. Full article

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

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11 pages, 1564 KiB

Open AccessArticle

Maternal Uniparental Disomy of Chromosome 20 (UPD(20)mat) as Differential Diagnosis of Silver Russell Syndrome: Identification of Three New Cases

by Pierpaola Tannorella, Daniele Minervino, Sara Guzzetti, Alessandro Vimercati, Luciano Calzari, Giuseppa Patti, Mohamad Maghnie, Anna Elsa Maria Allegri, Donatella Milani, Giulietta Scuvera, Milena Mariani, Piergiorgio Modena, Angelo Selicorni, Lidia Larizza and Silvia Russo

Genes 2021, 12(4), 588; https://doi.org/10.3390/genes12040588 - 17 Apr 2021

Cited by 12 | Viewed by 3644

Abstract

Silver Russell Syndrome (SRS, MIM #180860) is a rare growth retardation disorder in which clinical diagnosis is based on six features: pre- and postnatal growth failure, relative macrocephaly, prominent forehead, body asymmetry, and feeding difficulties (Netchine–Harbison clinical scoring system (NH-CSS)). The molecular mechanisms [...] Read more.

Silver Russell Syndrome (SRS, MIM #180860) is a rare growth retardation disorder in which clinical diagnosis is based on six features: pre- and postnatal growth failure, relative macrocephaly, prominent forehead, body asymmetry, and feeding difficulties (Netchine–Harbison clinical scoring system (NH-CSS)). The molecular mechanisms consist in (epi)genetic deregulations at multiple loci: the loss of methylation (LOM) at the paternal H19/IGF2:IG-DMR (chr11p15.5) (50%) and the maternal uniparental disomy of chromosome 7 (UPD(7)mat) (10%) are the most frequent causes. Thus far, about 40% of SRS remains undiagnosed, pointing to the need to define the rare mechanisms in such a consistent fraction of unsolved patients. Within a cohort of 176 SRS with an NH-CSS ≥ 3, a molecular diagnosis was disclosed in about 45%. Among the remaining patients, we identified in 3 probands (1.7%) with UPD(20)mat (Mulchandani–Bhoj–Conlin syndrome, OMIM #617352), a molecular mechanism deregulating the GNAS locus and described in 21 cases, characterized by severe feeding difficulties associated with failure to thrive, preterm birth, and intrauterine/postnatal growth retardation. Our patients share prominent forehead, feeding difficulties, postnatal growth delay, and advanced maternal age. Their clinical assessment and molecular diagnostic flowchart contribute to better define the characteristics of this rare imprinting disorder and to rank UPD(20)mat as the fourth most common pathogenic molecular defect causative of SRS. Full article

(This article belongs to the Special Issue Genomic Imprinting and the Regulation of Growth and Metabolism)

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27 pages, 746 KiB

Open AccessReview

MTHFR C677T and A1298C Polymorphisms in Breast Cancer, Gliomas and Gastric Cancer: A Review

by Igor Petrone, Paula Sabbo Bernardo, Everton Cruz dos Santos and Eliana Abdelhay

Genes 2021, 12(4), 587; https://doi.org/10.3390/genes12040587 - 17 Apr 2021

Cited by 32 | Viewed by 10141

Abstract

Folate (vitamin B9) is found in some water-soluble foods or as a synthetic form of folic acid and is involved in many essential biochemical processes. Dietary folate is converted into tetrahydrofolate, a vital methyl donor for most methylation reactions, including DNA methylation. 5,10-methylene [...] Read more.

Folate (vitamin B9) is found in some water-soluble foods or as a synthetic form of folic acid and is involved in many essential biochemical processes. Dietary folate is converted into tetrahydrofolate, a vital methyl donor for most methylation reactions, including DNA methylation. 5,10-methylene tetrahydrofolate reductase (MTHFR) is a critical enzyme in the folate metabolism pathway that converts 5,10-methylenetetrahydrofolate into 5-methyltetrahydrofolate, which produces a methyl donor for the remethylation of homocysteine to methionine. MTHFR polymorphisms result in reduced enzyme activity and altered levels of DNA methylation and synthesis. MTHFR polymorphisms have been linked to increased risks of several pathologies, including cancer. Breast cancer, gliomas and gastric cancer are highly heterogeneous and aggressive diseases associated with high mortality rates. The impact of MTHFR polymorphisms on these tumors remains controversial in the literature. This review discusses the relationship between the MTHFR C677T and A1298C polymorphisms and the increased risk of breast cancer, gliomas, and gastric cancer. Additionally, we highlight the relevance of ethnic and dietary aspects of population-based studies and histological stratification of highly heterogeneous tumors. Finally, this review discusses these aspects as potential factors responsible for the controversial literature concerning MTHFR polymorphisms. Full article

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

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12 pages, 665 KiB

Open AccessReview

Role of the Non-Canonical RNAi Pathway in the Antifungal Resistance and Virulence of Mucorales

by José Tomás Cánovas-Márquez, María Isabel Navarro-Mendoza, Carlos Pérez-Arques, Carlos Lax, Ghizlane Tahiri, José Antonio Pérez-Ruiz, Damaris Lorenzo-Gutiérrez, Silvia Calo, Sergio López-García, Eusebio Navarro, Francisco Esteban Nicolás, Victoriano Garre and Laura Murcia

Genes 2021, 12(4), 586; https://doi.org/10.3390/genes12040586 - 17 Apr 2021

Cited by 5 | Viewed by 3338

Abstract

Mucorales are the causal agents for the lethal disease known as mucormycosis. Mortality rates of mucormycosis can reach up to 90%, due to the mucoralean antifungal drug resistance and the lack of effective therapies. A concerning urgency among the medical and scientific community [...] Read more.

Mucorales are the causal agents for the lethal disease known as mucormycosis. Mortality rates of mucormycosis can reach up to 90%, due to the mucoralean antifungal drug resistance and the lack of effective therapies. A concerning urgency among the medical and scientific community claims to find targets for the development of new treatments. Here, we reviewed different studies describing the role and machinery of a novel non-canonical RNAi pathway (NCRIP) only conserved in Mucorales. Its non-canonical features are the independence of Dicer and Argonaute proteins. Conversely, NCRIP relies on RNA-dependent RNA Polymerases (RdRP) and an atypical ribonuclease III (RNase III). NCRIP regulates the expression of mRNAs by degrading them in a specific manner. Its mechanism binds dsRNA but only cuts ssRNA. NCRIP exhibits a diversity of functional roles. It represses the epimutational pathway and the lack of NCRIP increases the generation of drug resistant strains. NCRIP also regulates the control of retrotransposons expression, playing an essential role in genome stability. Finally, NCRIP regulates the response during phagocytosis, affecting the multifactorial process of virulence. These critical NCRIP roles in virulence and antifungal drug resistance, along with its exclusive presence in Mucorales, mark this pathway as a promising target to fight against mucormycosis. 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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16 pages, 9573 KiB

Open AccessReview

Growth Restriction and Genomic Imprinting-Overlapping Phenotypes Support the Concept of an Imprinting Network

by Thomas Eggermann, Justin H. Davies, Maithé Tauber, Erica van den Akker, Anita Hokken-Koelega, Gudmundur Johansson and Irène Netchine

Genes 2021, 12(4), 585; https://doi.org/10.3390/genes12040585 - 17 Apr 2021

Cited by 24 | Viewed by 5552

Abstract

Intrauterine and postnatal growth disturbances are major clinical features of imprinting disorders, a molecularly defined group of congenital syndromes caused by molecular alterations affecting parentally imprinted genes. These genes are expressed monoallelically and in a parent-of-origin manner, and they have an impact on [...] Read more.

Intrauterine and postnatal growth disturbances are major clinical features of imprinting disorders, a molecularly defined group of congenital syndromes caused by molecular alterations affecting parentally imprinted genes. These genes are expressed monoallelically and in a parent-of-origin manner, and they have an impact on human growth and development. In fact, several genes with an exclusive expression from the paternal allele have been shown to promote foetal growth, whereas maternally expressed genes suppress it. The evolution of this correlation might be explained by the different interests of the maternal and paternal genomes, aiming for the conservation of maternal resources for multiple offspring versus extracting maximal maternal resources. Since not all imprinted genes in higher mammals show the same imprinting pattern in different species, the findings from animal models are not always transferable to human. Therefore, human imprinting disorders might serve as models to understand the complex regulation and interaction of imprinted loci. This knowledge is a prerequisite for the development of precise diagnostic tools and therapeutic strategies for patients affected by imprinting disorders. In this review we will specifically overview the current knowledge on imprinting disorders associated with growth retardation, and its increasing relevance in a personalised medicine direction and the need for a multidisciplinary therapeutic approach. Full article

(This article belongs to the Special Issue Genomic Imprinting and the Regulation of Growth and Metabolism)

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18 pages, 8248 KiB

Open AccessArticle

Identification of Novel Loci and Candidate Genes for Resistance to Powdery Mildew in a Resequenced Cucumber Germplasm

by Xiaoping Liu, Xingfang Gu, Hongwei Lu, Panna Liu, Han Miao, Yuling Bai and Shengping Zhang

Genes 2021, 12(4), 584; https://doi.org/10.3390/genes12040584 - 16 Apr 2021

Cited by 19 | Viewed by 3873

Abstract

Powdery mildew (PM) is one of the most serious diseases in cucumber and causes huge yield loss. Multiple quantitative trait loci (QTLs) for PM resistance have been reported in previous studies using a limited number of cucumber accessions. In this study, a cucumber [...] Read more.

Powdery mildew (PM) is one of the most serious diseases in cucumber and causes huge yield loss. Multiple quantitative trait loci (QTLs) for PM resistance have been reported in previous studies using a limited number of cucumber accessions. In this study, a cucumber core germplasm (CG) consisting of 94 resequenced lines was evaluated for PM resistance in four trials across three years (2013, 2014, and 2016). These trials were performed on adult plants in the field with natural infection. Using genome-wide association study (GWAS), 13 loci (pmG1.1, pmG1.2, pmG2.1, pmG2.2, pmG3.1, pmG4.1, pmG4.2, pmG5.1, pmG5.2, pmG5.3, pmG5.4, pmG6.1, and pmG6.2) associated with PM resistance were detected on all chromosomes except for Chr.7. Among these loci, ten were mapped to chromosomal intervals where QTLs had been reported in previous studies, while, three (pmG2.1, pmG3.1, and pmG4.1) were novel. The loci of pmG2.1, pmG5.2, pmG5.3 showed stronger signal in four trials. Based on the annotation of homologous genes in Arabidopsis and pairwise LD correlation analysis, candidate genes located in the QTL intervals were predicted. SNPs in these candidate genes were analyzed between haplotypes of highly resistant (HR) and susceptible (HS) CG lines, which were defined based on combing disease index data of all trials. Furthermore, candidate genes (Csa5G622830 and CsGy5G015660) reported in previous studies for PM resistance and cucumber orthologues of several PM susceptibility (S) genes (PMR5, PMR-6, and MLO) that are colocalized with certain QTLs, were analyzed for their potential contribution to the QTL effect on both PM and DM in the CG population. This study shows that the CG germplasm is a very valuable resource carrying known and novel QTLs for both PM and DM resistance, which can be exploited in cucumber breeding. Full article

(This article belongs to the Special Issue Powdery Mildew Resistance Genetics)

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24 pages, 4101 KiB

Open AccessArticle

Computational and Transcriptomic Analysis Unraveled OsMATE34 as a Putative Anthocyanin Transporter in Black Rice (Oryza sativa L.) Caryopsis

by Enerand Mackon, Yafei Ma, Guibeline Charlie Jeazet Dongho Epse Mackon, Babar Usman, Yitong Zhao, Qiufeng Li and Piqing Liu

Genes 2021, 12(4), 583; https://doi.org/10.3390/genes12040583 - 16 Apr 2021

Cited by 15 | Viewed by 3495

Abstract

Anthocyanin is a flavonoid compound with potential antioxidant properties beneficial to human health and sustains plant growth and development under different environmental stresses. In black rice, anthocyanin can be found in the stems, leaves, stigmas, and caryopsis. Although the anthocyanin biosynthesis in rice [...] Read more.

Anthocyanin is a flavonoid compound with potential antioxidant properties beneficial to human health and sustains plant growth and development under different environmental stresses. In black rice, anthocyanin can be found in the stems, leaves, stigmas, and caryopsis. Although the anthocyanin biosynthesis in rice has been extensively studied, limited knowledge underlying the storage mechanism and transporters is available. This study undertook the complementation of computational and transcriptome analysis to decipher a potential multidrug and toxic compound extrusion (MATE) gene candidate for anthocyanin transportation in black rice caryopsis. The phylogenetic analysis showed that OsMATE34 has the same evolutionary history and high similarities with VvAM1, VvAM3, MtMATE2, SlMATE/MTP77, RsMATE8, AtFFT, and AtTT12 involved in anthocyanin transportation. RNA sequencing analysis in black caryopsis (Bc; Bc11, Bc18, Bc25) and white caryopsis (Wc; Wc11, Wc18, Wc25), respectively, at 11 days after flowering (DAF), 18 DAF, and 25 DAF revealed a total of 36,079 expressed genes, including 33,157 known genes and 2922 new genes. The differentially expressed genes (DEGs) showed 15,573 genes commonly expressed, with 1804 and 1412 genes uniquely expressed in Bc and Wc, respectively. Pairwise comparisons showed 821 uniquely expressed genes out of 15,272 DEGs for Wc11 vs. Bc11, 201 uniquely expressed genes out of 16,240 DEGs for Wc18 vs. Bc18, and 2263 uniquely expressed genes out of 16,240 DEGs for Wc25 vs. Bc25. Along with anthocyanin biosynthesis genes (OsPAL, OsCHS, OsCHI, OsF3H, OsDFR, OsANS, and OsUFGT/Os3GT), OsMATE34 expression was significantly upregulated in all Bc but not in Wc. OsMATE34 expression was similar to OsGSTU34, a transporter of anthocyanin in rice leaves. Taken together, our results highlighted OsMATE34 (Os08g0562800) as a candidate anthocyanin transporter in rice caryopsis. This study provides a new finding and a clue to enhance the accumulation of anthocyanin in rice caryopsis. Full article

(This article belongs to the Special Issue Advances in Rice Genetics and Breeding)

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13 pages, 1965 KiB

Open AccessArticle

Expression of Estrogen Receptor- and Progesterone Receptor-Regulating MicroRNAs in Breast Cancer

by Tatiana Kalinina, Vladislav Kononchuk, Efim Alekseenok, Darya Obukhova, Sergey Sidorov, Dmitry Strunkin and Lyudmila Gulyaeva

Genes 2021, 12(4), 582; https://doi.org/10.3390/genes12040582 - 16 Apr 2021

Cited by 11 | Viewed by 3344

Abstract

In ~70% of breast cancer (BC) cases, estrogen and progesterone receptors (ER and PR) are overexpressed, which can change during tumor progression. Expression changes of these receptors during cancer initiation and progression can be caused by alterations in microRNA (miR, miRNA) expression. To [...] Read more.

In ~70% of breast cancer (BC) cases, estrogen and progesterone receptors (ER and PR) are overexpressed, which can change during tumor progression. Expression changes of these receptors during cancer initiation and progression can be caused by alterations in microRNA (miR, miRNA) expression. To assess the association of BC progression with aberrant expression of miRNAs that target ER and PR mRNAs, we quantified miR-19b, -222, -22, -378a, and -181a in BC samples (n = 174) by real-time PCR. Underexpression of miR-222 and miR-378a in stage T2–T4 BC was characteristic for HER2-overexpressing tumors. In addition, the expression of miR-181a and miR-378a was higher in these tumors than in tumors with a HER2 IHC score of 0 or 1+. In tumors with a Ki-67 index ≥ 14%, all tested miRNAs were underexpressed in BC with a high Allred PR score (6–8). In ER-and-PR–negative tumors, miR-22, miR-222, miR-181a, and miR-378a underexpression was associated with Ki-67 index > 35% (median value). MiR-19b and miR-22 underexpression could be a marker of lymph node metastasis in ER- and/or PR-positive tumors with HER2 IHC score 0. Thus, the association of miR-19b, miR-22, miR-222, miR-378a, and miR-181a levels with BC characteristics is influenced by the status of tumor ER, PR, HER2, and Ki-67. Full article

(This article belongs to the Special Issue The Role of MicroRNA in Cancer)

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10 pages, 2346 KiB

Open AccessArticle

Mosaic Segmental and Whole-Chromosome Upd(11)mat in Silver-Russell Syndrome

by Laura Pignata, Angela Sparago, Orazio Palumbo, Elena Andreucci, Elisabetta Lapi, Romano Tenconi, Massimo Carella, Andrea Riccio and Flavia Cerrato

Genes 2021, 12(4), 581; https://doi.org/10.3390/genes12040581 - 16 Apr 2021

Cited by 6 | Viewed by 2723

Abstract

Molecular defects altering the expression of the imprinted genes of the 11p15.5 cluster are responsible for the etiology of two congenital disorders characterized by opposite growth disturbances, Silver–Russell syndrome (SRS), associated with growth restriction, and Beckwith–Wiedemann syndrome (BWS), associated with overgrowth. At the [...] Read more.

Molecular defects altering the expression of the imprinted genes of the 11p15.5 cluster are responsible for the etiology of two congenital disorders characterized by opposite growth disturbances, Silver–Russell syndrome (SRS), associated with growth restriction, and Beckwith–Wiedemann syndrome (BWS), associated with overgrowth. At the molecular level, SRS and BWS are characterized by defects of opposite sign, including loss (LoM) or gain (GoM) of methylation at the H19/IGF2:intergenic differentially methylated region (H19/IGF2:IG-DMR), maternal or paternal duplication (dup) of 11p15.5, maternal (mat) or paternal (pat) uniparental disomy (upd), and gain or loss of function mutations of CDKN1C. However, while upd(11)pat is found in 20% of BWS cases and in the majority of them it is segmental, upd(11)mat is extremely rare, being reported in only two SRS cases to date, and in both of them is extended to the whole chromosome. Here, we report on two novel cases of mosaic upd(11)mat with SRS phenotype. The upd is mosaic and isodisomic in both cases but covers the entire chromosome in one case and is restricted to 11p14.1-pter in the other case. The segmental upd(11)mat adds further to the list of molecular defects of opposite sign in SRS and BWS, making these two imprinting disorders even more specular than previously described. Full article

(This article belongs to the Special Issue Genomic Imprinting and the Regulation of Growth and Metabolism)

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13 pages, 1075 KiB

Open AccessArticle

Molecular and Genetic Mechanism of Non-Syndromic Congenital Cataracts. Mutation Screening in Spanish Families

by Celia Fernández-Alcalde, María Nieves-Moreno, Susana Noval, Jesús M. Peralta, Victoria E. F. Montaño, Ángela del Pozo, Fernando Santos-Simarro and Elena Vallespín

Genes 2021, 12(4), 580; https://doi.org/10.3390/genes12040580 - 16 Apr 2021

Cited by 18 | Viewed by 4277

Abstract

Our purpose was to identify mutations responsible for non-syndromic congenital cataracts through the implementation of next-generation sequencing (NGS) in our center. A sample of peripheral blood was obtained from probands and willing family members and genomic DNA was extracted from leukocytes. DNA was [...] Read more.

Our purpose was to identify mutations responsible for non-syndromic congenital cataracts through the implementation of next-generation sequencing (NGS) in our center. A sample of peripheral blood was obtained from probands and willing family members and genomic DNA was extracted from leukocytes. DNA was analyzed implementing a panel (OFTv2.1) including 39 known congenital cataracts disease genes. 62 probands from 51 families were recruited. Pathogenic or likely pathogenic variants were identified in 32 patients and 25 families; in 16 families (64%) these were de novo mutations. The mutation detection rate was 49%. Almost all reported mutations were autosomal dominant. Mutations in crystallin genes were found in 30% of the probands. Mutations in membrane proteins were detected in seven families (two in GJA3 and five in GJA8). Mutations in LIM2 and MIP were each found in three families. Other mutations detected affected EPHA2, PAX6, HSF4 and PITX3. Variants classified as of unknown significance were found in 5 families (9.8%), affecting CRYBB3, LIM2, EPHA2, ABCB6 and TDRD7. Mutations lead to different cataract phenotypes within the same family. Full article

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

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