Genes, Vol. 12, Pages 1142: Comment on Tanmoy et al. CRISPR-Cas Diversity in Clinical Salmonella enterica Serovar Typhi Isolates from South Asian Countries. Genes 2020, 11, 1365
vier Weill Tanmoy et al. [...] (Source: Genes)
Source: Genes - July 28, 2021 Category: Genetics & Stem Cells Authors: Laetitia Fabre Elisabeth Njamkepo Fran çois-Xavier Weill Tags: Comment Source Type: research

Genes, Vol. 12, Pages 1147: Reply to Fabre et al. Comment on “Tanmoy et al. CRISPR-Cas Diversity in Clinical Salmonella enterica Serovar Typhi Isolates from South Asian Countries. Genes 2020, 11, 1365”
Genes, Vol. 12, Pages 1147: Reply to Fabre et al. Comment on “Tanmoy et al. CRISPR-Cas Diversity in Clinical Salmonella enterica Serovar Typhi Isolates from South Asian Countries. Genes 2020, 11, 1365” Genes doi: 10.3390/genes12081147 Authors: Arif Mohammad Tanmoy Chinmoy Saha Mohammad Saiful Islam Sajib Senjuti Saha Florence Komurian-Pradel Alex van Belkum Rogier Louwen Samir Kumar Saha Hubert P. Endtz We respectfully thank Fabre et al. [...] (Source: Genes)
Source: Genes - July 28, 2021 Category: Genetics & Stem Cells Authors: Arif Mohammad Tanmoy Chinmoy Saha Mohammad Saiful Islam Sajib Senjuti Saha Florence Komurian-Pradel Alex van Belkum Rogier Louwen Samir Kumar Saha Hubert P. Endtz Tags: Reply Source Type: research

Genes, Vol. 12, Pages 1148: Comparative Aspects of Annelid Regeneration: Towards Understanding the Mechanisms of Regeneration
zin The question of why animals vary in their ability to regenerate remains one of the most intriguing questions in biology. Annelids are a large and diverse phylum, many members of which are capable of extensive regeneration such as regrowth of a complete head or tail and whole-body regeneration, even from few segments. On the other hand, some representatives of both of the two major annelid clades show very limited tissue regeneration and are completely incapable of segmental regeneration. Here we review experimental and descriptive data on annelid regeneration, obtained at different levels of organization, from data...
Source: Genes - July 28, 2021 Category: Genetics & Stem Cells Authors: Roman P. Kostyuchenko Vitaly V. Kozin Tags: Review Source Type: research

Genes, Vol. 12, Pages 1149: The Genomic Architecture of Bladder Exstrophy Epispadias Complex
G. Newman The bladder exstrophy–epispadias complex (BEEC) is an abdominal midline malformation comprising a spectrum of congenital genitourinary abnormalities of the abdominal wall, pelvis, urinary tract, genitalia, anus, and spine. The vast majority of BEEC cases are classified as non-syndromic and the etiology of this malformation is still unknown. This review presents the current knowledge on this multifactorial disorder, including phenotypic and anatomical characterization, epidemiology, proposed developmental mechanisms, existing animal models, and implicated genetic and environmental components. (Source: Genes)
Source: Genes - July 28, 2021 Category: Genetics & Stem Cells Authors: Glenda M. Beaman Raimondo M. Cervellione David Keene Heiko Reutter William G. Newman Tags: Review Source Type: research

Genes, Vol. 12, Pages 1150: Molecular Pathways Involved in the Development of Congenital Erythrocytosis
Debeljak Patients with idiopathic erythrocytosis are directed to targeted genetic testing including nine genes involved in oxygen sensing pathway in kidneys, erythropoietin signal transduction in pre-erythrocytes and hemoglobin-oxygen affinity regulation in mature erythrocytes. However, in more than 60% of cases the genetic cause remains undiagnosed, suggesting that other genes and mechanisms must be involved in the disease development. This review aims to explore additional molecular mechanisms in recognized erythrocytosis pathways and propose new pathways associated with this rare hematological disorder. For this pur...
Source: Genes - July 28, 2021 Category: Genetics & Stem Cells Authors: Jana Tomc Nata ša Debeljak Tags: Review Source Type: research

Genes, Vol. 12, Pages 1151: Genetic Background of Congenital Erythrocytosis
n True erythrocytosis is present when the red cell mass is greater than 125% of predicted sex and body mass, which is reflected by elevated hemoglobin and hematocrit. Erythrocytosis can be primary or secondary and congenital or acquired. Congenital defects are often found in those diagnosed at a young age and with a family history of erythrocytosis. Primary congenital defects mainly include mutations in the Erythropoietin receptor gene but SH2B3 has also been implicated. Secondary congenital erythrocytosis can arise through a variety of genetic mechanisms, including mutations in the genes in the oxygen sensing pathway,...
Source: Genes - July 28, 2021 Category: Genetics & Stem Cells Authors: Mary Frances McMullin Tags: Review Source Type: research

Genes, Vol. 12, Pages 1152: Variant Transthyretin Amyloidosis (ATTRv) in Hungary: First Data on Epidemiology and Clinical Features
Conclusions: As TTR genotype influences the phenotype and clinical course of ATTRv, it is important to know the regional data. In Hungary, ATTRHis88Arg and ATTRIle107Val are the most common mutations in ATTRv, both presenting with mixed phenotype, but the median age at the time of the diagnosis is 9 years lower in patients with ATTRHis88Arg than in patients with ATTRIle107Val. (Source: Genes)
Source: Genes - July 28, 2021 Category: Genetics & Stem Cells Authors: Zolt án Pozsonyi Gergely Pesk ó Hedvig Tak ács Dorottya Csuka Vikt ória Nagy Ágnes Szilágyi Lidia Hategan Bal ázs Muk Be áta Csányi No émi Nyolczas L ívia Dézsi Judit M ária Molnár Anita Csillik Katalin R évész B éla Iványi Fruzsina Szab Tags: Article Source Type: research

Genes, Vol. 12, Pages 1153: Environmental Exposure to Endocrine Disrupting Chemicals Influences Genomic Imprinting, Growth, and Metabolism
tolomei Genomic imprinting is an epigenetic mechanism that results in monoallelic, parent-of-origin-specific expression of a small number of genes. Imprinted genes play a crucial role in mammalian development as their dysregulation result in an increased risk of human diseases. DNA methylation, which undergoes dynamic changes early in development, is one of the epigenetic marks regulating imprinted gene expression patterns during early development. Thus, environmental insults, including endocrine disrupting chemicals during critical periods of fetal development, can alter DNA methylation patterns, leading to inappropri...
Source: Genes - July 28, 2021 Category: Genetics & Stem Cells Authors: Nicole Robles-Matos Tre Artis Rebecca A. Simmons Marisa S. Bartolomei Tags: Review Source Type: research

Genes, Vol. 12, Pages 1156: Harnessing the Nucleolar DNA Damage Response in Cancer Therapy
e Sanij The nucleoli are subdomains of the nucleus that form around actively transcribed ribosomal RNA (rRNA) genes. They serve as the site of rRNA synthesis and processing, and ribosome assembly. There are 400–600 copies of rRNA genes (rDNA) in human cells and their highly repetitive and transcribed nature poses a challenge for DNA repair and replication machineries. It is only in the last 7 years that the DNA damage response and processes of DNA repair at the rDNA repeats have been recognized to be unique and distinct from the classic response to DNA damage in the nucleoplasm. In the last decade, the nucleolus ...
Source: Genes - July 28, 2021 Category: Genetics & Stem Cells Authors: Jiachen Xuan Kezia Gitareja Natalie Brajanovski Elaine Sanij Tags: Review Source Type: research

Genes, Vol. 12, Pages 1154: Circulating microRNAs from the Molecular Mechanisms to Clinical Biomarkers: A Focus on the Clear Cell Renal Cell Carcinoma
ella Calogero microRNAs (miRNAs) are emerging as relevant molecules in cancer development and progression. MiRNAs add a post-transcriptional level of control to the regulation of gene expression. The deregulation of miRNA expression results in changing the molecular circuitry in which miRNAs are involved, leading to alterations of cell fate determination. In this review, we describe the miRNAs that are emerging as innovative molecular biomarkers from liquid biopsies, not only for diagnosis, but also for post-surgery management in cancer. We focus our attention on renal cell carcinoma, in particular highlighting the cru...
Source: Genes - July 28, 2021 Category: Genetics & Stem Cells Authors: Claudia Tito Elena De Falco Paolo Rosa Alessia Iaiza Francesco Fazi Vincenzo Petrozza Antonella Calogero Tags: Review Source Type: research

Genes, Vol. 12, Pages 1155: bCNN-Methylpred: Feature-Based Prediction of RNA Sequence Modification Using Branch Convolutional Neural Network
ark RNA modification is vital to various cellular and biological processes. Among the existing RNA modifications, N6-methyladenosine (m6A) is considered the most important modification owing to its involvement in many biological processes. The prediction of m6A sites is crucial because it can provide a better understanding of their functional mechanisms. In this regard, although experimental methods are useful, they are time consuming. Previously, researchers have attempted to predict m6A sites using computational methods to overcome the limitations of experimental methods. Some of these approaches are based on classic...
Source: Genes - July 28, 2021 Category: Genetics & Stem Cells Authors: Naeem Islam Jaebyung Park Tags: Article Source Type: research

Genes, Vol. 12, Pages 1159: Clinical Phenotypic Spectrum of 4095 Individuals with Down Syndrome from Text Mining of Electronic Health Records
In this study, we examined the electronic health records of 4095 individuals with Down syndrome at the Children’s Hospital of Philadelphia to create a method to characterize the phenotypic spectrum digitally. We extracted Human Phenotype Ontology (HPO) terms from quality-filtered patient notes using a natural language processing (NLP) approach MetaMap. We catalogued the most common HPO terms related to Down syndrome patients and compared the terms with those from a baseline population. We characterized the top 100 HPO terms by their frequencies at different ages of clinical visits and highlighted selected terms that ...
Source: Genes - July 28, 2021 Category: Genetics & Stem Cells Authors: James Margolin Havrilla Mengge Zhao Cong Liu Chunhua Weng Ingo Helbig Elizabeth Bhoj Kai Wang Tags: Article Source Type: research

Genes, Vol. 12, Pages 1157: Rett Syndrome Spectrum in Monogenic Developmental-Epileptic Encephalopathies and Epilepsies: A Review
Conclusions: Patients share a complex neurodevelopmental and neurological phenotype (developmental delay, movement disorder) with impaired gait, abnormal tone and hand stereotypies. However, the presence and characteristics of regression and loss of language and functional hand use can differ. Finally, the frequency of additional supportive criteria and their distribution also vary widely. (Source: Genes)
Source: Genes - July 28, 2021 Category: Genetics & Stem Cells Authors: Carlotta Spagnoli Carlo Fusco Francesco Pisani Tags: Review Source Type: research

Genes, Vol. 12, Pages 1160: Genotype Pattern Mining for Pairs of Interacting Variants Underlying Digenic Traits
Jurg Ott Some genetic diseases (“digenic traits”) are due to the interaction between two DNA variants, which presumably reflects biochemical interactions. For example, certain forms of Retinitis Pigmentosa, a type of blindness, occur in the presence of two mutant variants, one each in the ROM1 and RDS genes, while the occurrence of only one such variant results in a normal phenotype. Detecting variant pairs underlying digenic traits by standard genetic methods is difficult and is downright impossible when individual variants alone have minimal effects. Frequent pattern mining (FPM) methods are known to det...
Source: Genes - July 28, 2021 Category: Genetics & Stem Cells Authors: Atsuko Okazaki Sukanya Horpaopan Qingrun Zhang Matthew Randesi Jurg Ott Tags: Article Source Type: research

Genes, Vol. 12, Pages 1158: Post-Translational Modification of MRE11: Its Implication in DDR and Diseases
ongwei Zhou Maintaining genomic stability is vital for cells as well as individual organisms. The meiotic recombination-related gene MRE11 (meiotic recombination 11) is essential for preserving genomic stability through its important roles in the resection of broken DNA ends, DNA damage response (DDR), DNA double-strand breaks (DSBs) repair, and telomere maintenance. The post-translational modifications (PTMs), such as phosphorylation, ubiquitination, and methylation, regulate directly the function of MRE11 and endow MRE11 with capabilities to respond to cellular processes in promptly, precisely, and with more diversif...
Source: Genes - July 28, 2021 Category: Genetics & Stem Cells Authors: Ruiqing Lu Han Zhang Yinan Jiang Zhaoqi Wang Litao Sun Zhongwei Zhou Tags: Review Source Type: research

Genes, Vol. 12, Pages 1161: Heat Stress Reduces the Susceptibility of Caenorhabditis elegans to Orsay Virus Infection
E. Kammenga The nematode Caenorhabditis elegans has been a versatile model for understanding the molecular responses to abiotic stress and pathogens. In particular, the response to heat stress and virus infection has been studied in detail. The Orsay virus (OrV) is a natural virus of C. elegans and infection leads to intracellular infection and proteostatic stress, which activates the intracellular pathogen response (IPR). IPR related gene expression is regulated by the genes pals-22 and pals-25, which also control thermotolerance and immunity against other natural pathogens. So far, we have a limited understanding of ...
Source: Genes - July 28, 2021 Category: Genetics & Stem Cells Authors: Yuqing Huang Mark G. Sterken Koen van Zwet Lisa van Sluijs Gorben P. Pijlman Jan E. Kammenga Tags: Article Source Type: research

Genes, Vol. 12, Pages 1162: HFE Genotype, Ferritin Levels and Transferrin Saturation in Patients with Suspected Hereditary Hemochromatosis
kon Reikvam HFE hemochromatosis is characterized by increased iron absorption and iron overload due to variants of the iron-regulating HFE gene. Overt disease is mainly associated with homozygosity for the C282Y variant, although the H63D variant in compound heterozygosity with C282Y (C282Y/H63D) contributes to disease manifestation. In this observational study, we describe the association between biochemical findings, age, gender and HFE genotype in patients referred from general practice to a tertiary care referral center for diagnostic workup based on suspected hemochromatosis due to persistent hyperferritinemia and...
Source: Genes - July 28, 2021 Category: Genetics & Stem Cells Authors: Miriam Sandnes Marta Vorland Rune J. Ulvik H åkon Reikvam Tags: Article Source Type: research

Genes, Vol. 12, Pages 1139: Bioinformatic Analysis of Two TOR (Target of Rapamycin)-Like Proteins Encoded by Entamoeba histolytica Revealed Structural Similarities with Functional Homologs
e;pez Marco A. Ramos-Ibarra The target of rapamycin (TOR), also known as FKBP-rapamycin associated protein (FRAP), is a protein kinase belonging to the PIKK (phosphatidylinositol 3-kinase (PI3K)-related kinases) family. TOR kinases are involved in several signaling pathways that control cell growth and proliferation. Entamoeba histolytica, the protozoan parasite that causes human amoebiasis, contains two genes encoding TOR-like proteins: EhFRAP and EhTOR2. To assess their potential as drug targets to control the cell proliferation of E. histolytica, we studied the structural features of EhFRAP and EhTOR2 using a bioc...
Source: Genes - July 28, 2021 Category: Genetics & Stem Cells Authors: Patricia L. A. Mu ñoz-Muñoz Rosa E. Mares-Alejandre Samuel G. Mel éndez-López Marco A. Ramos-Ibarra Tags: Article Source Type: research

Genes, Vol. 12, Pages 1140: Multiple Acyl-CoA Dehydrogenase Deficiency with Variable Presentation Due to a Homozygous Mutation in a Bedouin Tribe
We report on six patients from a single Bedouin tribe, five of whom were sequenced and found to be homozygous to the same variant in the ETFDH gene, with variable severity and age of presentation. The variant, NM_004453.3 (ETFDH): c.524G>A, p.(R175H), was previously recognized as pathogenic, although it has not been reported in the literature in a homozygous state before. R175H is located near the FAD binding site, likely affecting the affinity of FAD for EFT:QO. The single homozygous ETFDH pathogenic variant was found to be causing MADD in this cohort with an unexpectedly variable severity of presentation. The ...
Source: Genes - July 28, 2021 Category: Genetics & Stem Cells Authors: Orna Staretz-Chacham Shirly Amar Shlomo Almashanu Ben Pode-Shakked Ann Saada Ohad Wormser Eli Hershkovitz Tags: Article Source Type: research

Genes, Vol. 12, Pages 1135: Glaucoma Heritability: Molecular Mechanisms of Disease
s A. Ciulla Glaucoma is one of the world’s leading causes of irreversible blindness. A complex, multifactorial disease, the underlying pathogenesis and reasons for disease progression are not fully understood. The most common form of glaucoma, primary open-angle glaucoma (POAG), was traditionally understood to be the result of elevated intraocular pressure (IOP), leading to optic nerve damage and functional vision loss. Recently, researchers have suggested that POAG may have an underlying genetic component. In fact, studies of genetic association and heritability have yielded encouraging results showing that glau...
Source: Genes - July 27, 2021 Category: Genetics & Stem Cells Authors: Ryan Zukerman Alon Harris Francesco Oddone Brent Siesky Alice Verticchio Vercellin Thomas A. Ciulla Tags: Review Source Type: research

Genes, Vol. 12, Pages 1136: Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates, and the Putative Contribution of Genetic Conflict
ctor Escriva About eight million animal species are estimated to live on Earth, and all except those belonging to one subphylum are invertebrates. Invertebrates are incredibly diverse in their morphologies, life histories, and in the range of the ecological niches that they occupy. A great variety of modes of reproduction and sex determination systems is also observed among them, and their mosaic-distribution across the phylogeny shows that transitions between them occur frequently and rapidly. Genetic conflict in its various forms is a long-standing theory to explain what drives those evolutionary transitions. Here, w...
Source: Genes - July 27, 2021 Category: Genetics & Stem Cells Authors: Marion Anne Lise Picard Beatriz Vicoso St éphanie Bertrand Hector Escriva Tags: Review Source Type: research

Genes, Vol. 12, Pages 1137: Meiotic Silencing in Pigs: A Case Study in a Translocated Azoospermic Boar
Ducos Alain Pinton Carriers of balanced constitutional reciprocal translocations usually present a normal phenotype, but often show reproductive disorders. For the first time in pigs, we analyzed the meiotic process of an autosome–autosome translocation associated with azoospermia. Meiotic process analysis revealed the presence of unpaired autosomal segments with histone γH2AX accumulation sometimes associated with the XY body. Additionally, γH2AX signals were observed on apparently synapsed autosomes other than the SSC1 or SSC15, as previously observed in Ataxia with oculomotor apraxia type 2 patie...
Source: Genes - July 27, 2021 Category: Genetics & Stem Cells Authors: Nicolas Mary Anne Calgaro Harmonie Barasc Nathalie Bonnet St éphane Ferchaud Isabelle Raymond-Letron Alain Ducos Alain Pinton Tags: Article Source Type: research

Genes, Vol. 12, Pages 1138: A Rapid and Cost-Effective Identification of Invertebrate Pests at the Borders Using MinION Sequencing of DNA Barcodes
Cherie Gambley The rapid and accurate identification of invertebrate pests detected at the border is a challenging task. Current diagnostic methods used at the borders are mainly based on time consuming visual and microscopic examinations. Here, we demonstrate a rapid in-house workflow for DNA extraction, PCR amplification of the barcode region of the mitochondrial cytochrome oxidase subunit I (COI) gene and Oxford Nanopore Technologies (ONT) MinION sequencing of amplified products multiplexed after barcoding on ONT Flongle flow cells. A side-by-side comparison was conducted of DNA barcode sequencing-based identificat...
Source: Genes - July 27, 2021 Category: Genetics & Stem Cells Authors: Shamila Weerakoon Abeynayake Sonia Fiorito Adrian Dinsdale Mark Whattam Bill Crowe Kate Sparks Paul Richard Campbell Cherie Gambley Tags: Article Source Type: research

Genes, Vol. 12, Pages 1143: DNA-Dependent Protein Kinase Catalytic Subunit: The Sensor for DNA Double-Strand Breaks Structurally and Functionally Related to Ataxia Telangiectasia Mutated
Shimada The DNA-dependent protein kinase (DNA-PK) is composed of a DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and Ku70/Ku80 heterodimer. DNA-PK is thought to act as the “sensor” for DNA double-stranded breaks (DSB), which are considered the most deleterious type of DNA damage. In particular, DNA-PKcs and Ku are shown to be essential for DSB repair through nonhomologous end joining (NHEJ). The phenotypes of animals and human individuals with defective DNA-PKcs or Ku functions indicate their essential roles in these developments, especially in neuronal and immune systems. DNA-PKcs are structura...
Source: Genes - July 27, 2021 Category: Genetics & Stem Cells Authors: Yoshihisa Matsumoto Anie Day D. C. Asa Chaity Modak Mikio Shimada Tags: Review Source Type: research

Genes, Vol. 12, Pages 1141: Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling
te Danny Geelen Roots are composed of different root types and, in the dicotyledonous Arabidopsis, typically consist of a primary root that branches into lateral roots. Adventitious roots emerge from non-root tissue and are formed upon wounding or other types of abiotic stress. Here, we investigated adventitious root (AR) formation in Arabidopsis hypocotyls under conditions of altered abscisic acid (ABA) signaling. Exogenously applied ABA suppressed AR formation at 0.25 µM or higher doses. AR formation was less sensitive to the synthetic ABA analog pyrabactin (PB). However, PB was a more potent inhibitor at con...
Source: Genes - July 27, 2021 Category: Genetics & Stem Cells Authors: Yinwei Zeng Inge Verstraeten Hoang Khai Trinh Thomas Heugebaert Christian V. Stevens Irene Garcia-Maquilon Pedro L. Rodriguez Steffen Vanneste Danny Geelen Tags: Article Source Type: research

Genes, Vol. 12, Pages 1145: Nitric Oxide Synthase Dependency in Hydroxyurea Inhibition of Erythroid Progenitor Growth
dan P. Čokić Hydroxyurea (HU) causes nitric oxide (NO) bioactivation, acting as both a NO donor and a stimulator of NO synthase (NOS). To examine whether HU effects are NO mediated by chemical degradation or enzymatic induction, we studied human and mouse erythroid cells during proliferation, apoptosis, and differentiation. The HU and NO donor demonstrated persisted versus temporary inhibition of erythroid cell growth during differentiation, as observed by γ- and β-globin gene expression. HU decreased the percentage of erythroleukemic K562 cells in the G2/M phase that was reversed by N-nitro l-arginine met...
Source: Genes - July 27, 2021 Category: Genetics & Stem Cells Authors: Tijana Suboti čki Olivera Mitrovi ć Ajtić Dragoslava Đikić Juan F. Santibanez Milica To šić Vladan P. Čokić Tags: Article Source Type: research

Genes, Vol. 12, Pages 1146: DNA Polymerase θ: A Cancer Drug Target with Reverse Transcriptase Activity
Genes, Vol. 12, Pages 1146: DNA Polymerase θ: A Cancer Drug Target with Reverse Transcriptase Activity Genes doi: 10.3390/genes12081146 Authors: Xiaojiang S. Chen Richard T. Pomerantz The emergence of precision medicine from the development of Poly (ADP-ribose) polymerase (PARP) inhibitors that preferentially kill cells defective in homologous recombination has sparked wide interest in identifying and characterizing additional DNA repair enzymes that are synthetic lethal with HR factors. DNA polymerase theta (Polθ) is a validated anti-cancer drug target that is synthetic lethal with HR factors and oth...
Source: Genes - July 27, 2021 Category: Genetics & Stem Cells Authors: Xiaojiang S. Chen Richard T. Pomerantz Tags: Review Source Type: research

Genes, Vol. 12, Pages 1144: The Genetics of Myelodysplastic Syndromes: Clinical Relevance
nni Della Porta Myelodysplastic syndromes (MDS) are a clonal disease arising from hematopoietic stem cells, that are characterized by ineffective hematopoiesis (leading to peripheral blood cytopenia) and by an increased risk of evolution into acute myeloid leukemia. MDS are driven by a complex combination of genetic mutations that results in heterogeneous clinical phenotype and outcome. Genetic studies have enabled the identification of a set of recurrently mutated genes which are central to the pathogenesis of MDS and can be organized into a limited number of cellular pathways, including RNA splicing (SF3B1, SRSF2, ZR...
Source: Genes - July 27, 2021 Category: Genetics & Stem Cells Authors: Chiara Chiereghin Erica Travaglino Matteo Zampini Elena Saba Claudia Saitta Elena Riva Matteo Bersanelli Matteo Giovanni Della Porta Tags: Review Source Type: research

Genes, Vol. 12, Pages 1132: Upregulation of 15 Antisense Long Non-Coding RNAs in Osteosarcoma
In this study, we investigated the expression patterns of antisense lncRNAs from osteosarcoma and healthy bone samples (24 tumour-16 bone samples) using RNA sequencing. We identified 15 antisense lncRNAs (RUSC1-AS1, TBX2-AS1, PTOV1-AS1, UBE2D3-AS1, ERCC8-AS1, ZMIZ1-AS1, RNF144A-AS1, RDH10-AS1, TRG-AS1, GSN-AS1, HMGA2-AS1, ZNF528-AS1, OTUD6B-AS1, COX10-AS1 and SLC16A1-AS1) that were upregulated in tumour samples compared to bone sample controls. Further, we performed real-time polymerase chain reaction (RT-qPCR) to validate the expressions of the antisense lncRNAs in 8 different osteosarcoma cell lines (SaOS-2, G-292, HOS, ...
Source: Genes - July 26, 2021 Category: Genetics & Stem Cells Authors: Emel Rothzerg Xuan Dung Ho Jiake Xu David Wood Aare M ärtson Sulev K õks Tags: Article Source Type: research

Genes, Vol. 12, Pages 1133: The Mechanisms of CHD8 in Neurodevelopment and Autism Spectrum Disorders
ott Chromodomain-helicase-DNA-binding protein 8 (CHD8) has been identified as one of the genes with the strongest association with autism. The CHD8 protein is a transcriptional regulator that is expressed in nearly all cell types and has been implicated in multiple cellular processes, including cell cycle, cell adhesion, neuronal development, myelination, and synaptogenesis. Considering the central role of CHD8 in the genetics of autism, a deeper understanding of the physiological functions of CHD8 is important to understand the development of the autism phenotype and potential therapeutic targets. Different CHD8 mutan...
Source: Genes - July 26, 2021 Category: Genetics & Stem Cells Authors: Orly Weissberg Evan Elliott Tags: Review Source Type: research

Genes, Vol. 12, Pages 1134: Mitochondrial Genomes from Two Specialized Subfamilies of Reduviidae (Insecta: Hemiptera) Reveal Novel Gene Rearrangements of True Bugs
In this study, the first mitogenomes of Holoptilinae (Ptilocnemus lemur) and Emesinae (Ischnobaenella hainana) were sequenced. Two novel gene orders were detected in the newly sequenced mitogenomes. Combined 421 heteropteran mitogenomes, we identified 21 different gene orders and six gene rearrangement units located in three gene blocks. Comparative analyses of the diversity of gene order for each unit reveal that the tRNA gene cluster trnI-trnQ-trnM is the hotspot of heteropteran gene rearrangement. Furthermore, combined analyses of the gene rearrangement richness of each unit and the whole mitogenome among heteropteran l...
Source: Genes - July 26, 2021 Category: Genetics & Stem Cells Authors: Fei Ye Hu Li Qiang Xie Tags: Article Source Type: research

Genes, Vol. 12, Pages 1127: Plant Variety Protection: Current Practices and Insights
ung Breeders persistently supply farmers with the best varieties in order to exceed consumer demand through plant-breeding processes that are resource-intensive. In order to motivate continuous innovation in variety development, a system needs to provide incentives for plant breeders to develop superior varieties, for example, exclusive ownership to produce and market those varieties. The most common system is the acquisition of intellectual property protection through plant variety protection, also known as the breeder’s right. Most countries have adopted the system established by the International Union for the...
Source: Genes - July 25, 2021 Category: Genetics & Stem Cells Authors: Ju-Kyung Yu Yong-Suk Chung Tags: Review Source Type: research

Genes, Vol. 12, Pages 1128: Allelic Variants in Established Hypopituitarism Genes Expand Our Knowledge of the Phenotypic Spectrum
In conclusion, we have found allelic variants in three genes in hypopituitarism patients. We discuss these variants and associated patient phenotypes in relation to previously reported variants in these genes, expanding our knowledge of the phenotypic spectrum in patient populations. (Source: Genes)
Source: Genes - July 25, 2021 Category: Genetics & Stem Cells Authors: Marilena Nakaguma Nathalia Garcia Bianchi Pereira Ferreira Anna Flavia Figueredo Benedetti Mariana Cotarelli Madi Juliana Moreira Silva Jun Z. Li Qianyi Ma Ayse Bilge Ozel Qing Fang Amanda de Moraes Narcizo La ís Cavalca Cardoso Luciana Ribeiro Montenegr Tags: Article Source Type: research

Genes, Vol. 12, Pages 1129: Transposons-Based Clonal Diversity in Trematode Involves Parts of CR1 (LINE) in Eu- and Heterochromatin
Podgornaya Trematode parthenitae have long been believed to form clonal populations, but clonal diversity has been discovered in this asexual stage of the lifecycle. Clonal polymorphism in the model species Himasthla elongata has been previously described, but the source of this phenomenon remains unknown. In this work, we traced cercarial clonal diversity using a simplified amplified fragment length polymorphism (SAFLP) method and characterised the nature of fragments in diverse electrophoretic bands. The repetitive elements were identified in both the primary sequence of the H. elongata genome and in the transcripto...
Source: Genes - July 25, 2021 Category: Genetics & Stem Cells Authors: Anna Solovyeva Ivan Levakin Evgeny Zorin Leonid Adonin Yuri Khotimchenko Olga Podgornaya Tags: Article Source Type: research

Genes, Vol. 12, Pages 1130: GNAI2 Promotes Proliferation and Decreases Apoptosis in Rabbit Melanocytes
Yang Chen GNAI2 (G protein subunit alpha i2) is a signaling modulator or transducer, involved in several transmembrane signaling systems, that plays a vital role in the melanogenesis signaling pathway. However, whether GNAI2 regulates cell proliferation and apoptosis in rabbit melanocytes is not known. We found that GNAI2 was differentially expressed in rabbits with different coat colors using qRT-PCR and Wes assays. Furthermore, it was observed that the rabbits with black skin had the highest GNAI2 levels, and those with white skin had the lowest expression. The coding sequence of GNAI2 was successfully cloned and i...
Source: Genes - July 25, 2021 Category: Genetics & Stem Cells Authors: Shuaishuai Hu Yingying Dai Shaocheng Bai Bohao Zhao Xinsheng Wu Yang Chen Tags: Article Source Type: research

Genes, Vol. 12, Pages 1131: Genomic Characterization of Fluoroquinolone-Resistant Thermophilic Campylobacter Strains Isolated from Layer Chicken Feces in Gangneung, South Korea by Whole-Genome Sequencing
havendra G. Amachawadi Thermophilic Campylobacter species of poultry origin have been associated with up to 80% of human campylobacteriosis cases. Layer chickens have received less attention as possible reservoirs of Campylobacter species. Initially, the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of two archived Campylobacter isolates (Campylobacter jejuni strain 200605 and Campylobacter coli strain 200606) from layer chickens to five antimicrobials (ciprofloxacin, nalidixic acid, erythromycin, tetracycline, and gentamicin) were determined using broth microdilution while the pre...
Source: Genes - July 25, 2021 Category: Genetics & Stem Cells Authors: Noel Gahamanyi Dae-Geun Song Kye-Yoon Yoon Leonard E. G. Mboera Mecky I. Matee Dieudonn é Mutangana Erick V. G. Komba Cheol-Ho Pan Raghavendra G. Amachawadi Tags: Article Source Type: research

Genes, Vol. 12, Pages 1126: Novel FGFR1 Variants Are Associated with Congenital Scoliosis
In conclusion, FGFR1 variants identified in our patients led to only mild disruption to protein function, caused milder skeletal and cardiac phenotypes than those reported previously. (Source: Genes)
Source: Genes - July 24, 2021 Category: Genetics & Stem Cells Authors: Shengru Wang Xiran Chai Zihui Yan Sen Zhao Yang Yang Xiaoxin Li Yuchen Niu Guanfeng Lin Zhe Su Zhihong Wu Terry Jianguo Zhang Nan Wu Tags: Article Source Type: research

Genes, Vol. 12, Pages 1122: Characterization of the Role of the Neoxanthin Synthase Gene BoaNXS in Carotenoid Biosynthesis in Chinese Kale
In this study, the function of the neoxanthin synthase gene (BoaNXS) in Chinese kale was investigated. BoaNXS, which had a 699-bp coding sequence, was cloned from the white flower cultivar of Chinese kale and was expressed in all developmental stages and organs of Chinese kale; its expression was highest in young seeds. The subcellular localization indicated that BoaNXS was localized in the chloroplast. BoaNXS-overexpressed plants were obtained via Agrobacterium-mediated transient overexpression methodology, and the gene overexpression efficiencies ranged from 2.10- to 4.24-fold. The color in the leaves of BoaNXS-overexpre...
Source: Genes - July 24, 2021 Category: Genetics & Stem Cells Authors: Yue Jian Chenlu Zhang Yating Wang Zhiqing Li Jing Chen Wenting Zhou Wenli Huang Min Jiang Hao Zheng Mengyao Li Huiying Miao Fen Zhang Huanxiu Li Qiaomei Wang Bo Sun Tags: Article Source Type: research

Genes, Vol. 12, Pages 1121: The Chloroplast Epitranscriptome: Factors, Sites, Regulation, and Detection Methods
;rg Meurer Modifications in nucleic acids are present in all three domains of life. More than 170 distinct chemical modifications have been reported in cellular RNAs to date. Collectively termed as epitranscriptome, these RNA modifications are often dynamic and involve distinct regulatory proteins that install, remove, and interpret these marks in a site-specific manner. Covalent nucleotide modifications-such as methylations at diverse positions in the bases, polyuridylation, and pseudouridylation and many others impact various events in the lifecycle of an RNA such as folding, localization, processing, stability, ribo...
Source: Genes - July 24, 2021 Category: Genetics & Stem Cells Authors: Nikolay Manavski Alexandre Vicente Wei Chi J örg Meurer Tags: Review Source Type: research

Genes, Vol. 12, Pages 1123: The Role of Preclinical Models in Creatine Transporter Deficiency: Neurobiological Mechanisms, Biomarkers and Therapeutic Development
Laura Baroncelli Creatine (Cr) Transporter Deficiency (CTD) is an X-linked metabolic disorder, mostly caused by missense mutations in the SLC6A8 gene and presenting with intellectual disability, autistic behavior, and epilepsy. There is no effective treatment for CTD and patients need lifelong assistance. Thus, the research of novel intervention strategies is a major scientific challenge. Animal models are an excellent tool to dissect the disease pathogenetic mechanisms and drive the preclinical development of therapeutics. This review illustrates the current knowledge about Cr metabolism and CTD clinical aspects, wit...
Source: Genes - July 24, 2021 Category: Genetics & Stem Cells Authors: Elsa Ghirardini Francesco Calugi Giulia Sagona Federica Di Vetta Martina Palma Roberta Battini Giovanni Cioni Tommaso Pizzorusso Laura Baroncelli Tags: Review Source Type: research

Genes, Vol. 12, Pages 1124: Advances with Long Non-Coding RNAs in Alzheimer ’s Disease as Peripheral Biomarker
Genes, Vol. 12, Pages 1124: Advances with Long Non-Coding RNAs in Alzheimer’s Disease as Peripheral Biomarker Genes doi: 10.3390/genes12081124 Authors: Maria Garofalo Cecilia Pandini Daisy Sproviero Orietta Pansarasa Cristina Cereda Stella Gagliardi One of the most compelling needs in the study of Alzheimer’s disease (AD) is the characterization of cognitive decline peripheral biomarkers. In this context, the theme of altered RNA processing has emerged as a contributing factor to AD. In particular, the significant role of long non-coding RNAs (lncRNAs) associated to AD is opening new perspecti...
Source: Genes - July 24, 2021 Category: Genetics & Stem Cells Authors: Maria Garofalo Cecilia Pandini Daisy Sproviero Orietta Pansarasa Cristina Cereda Stella Gagliardi Tags: Review Source Type: research

Genes, Vol. 12, Pages 1125: RNA Modifications in Pathogenic Bacteria: Impact on Host Adaptation and Virulence
Stefano Marzi RNA modifications are involved in numerous biological processes and are present in all RNA classes. These modifications can be constitutive or modulated in response to adaptive processes. RNA modifications play multiple functions since they can impact RNA base-pairings, recognition by proteins, decoding, as well as RNA structure and stability. However, their roles in stress, environmental adaptation and during infections caused by pathogenic bacteria have just started to be appreciated. With the development of modern technologies in mass spectrometry and deep sequencing, recent examples of modifications r...
Source: Genes - July 24, 2021 Category: Genetics & Stem Cells Authors: Laura Antoine Roberto Bahena-Ceron Heemee Devi Bunwaree Martin Gobry Victor Loegler Pascale Romby Stefano Marzi Tags: Review Source Type: research

Genes, Vol. 12, Pages 1115: DNA Methylation Alterations in Blood Cells of Toddlers with Down Syndrome
rigorenko Recent research has provided evidence on genome-wide alterations in DNA methylation patterns due to trisomy 21, which have been detected in various tissues of individuals with Down syndrome (DS) across different developmental stages. Here, we report new data on the systematic genome-wide DNA methylation perturbations in blood cells of individuals with DS from a previously understudied age group—young children. We show that the study findings are highly consistent with those from the prior literature. In addition, utilizing relevant published data from two other developmental stages, neonatal and adult, ...
Source: Genes - July 23, 2021 Category: Genetics & Stem Cells Authors: Oxana Yu. Naumova Rebecca Lipschutz Sergey Yu. Rychkov Olga V. Zhukova Elena L. Grigorenko Tags: Article Source Type: research

Genes, Vol. 12, Pages 1116: Novel STAG1 Frameshift Mutation in a Patient Affected by a Syndromic Form of Neurodevelopmental Disorder
arella Orazio Palumbo The cohesin complex is a large evolutionary conserved functional unit which plays an essential role in DNA repair and replication, chromosome segregation and gene expression. It consists of four core proteins, SMC1A, SMC3, RAD21, and STAG1/2, and by proteins regulating the interaction between the complex and the chromosomes. Mutations in the genes coding for these proteins have been demonstrated to cause multisystem developmental disorders known as “cohesinopathies”. The most frequent and well recognized among these distinctive clinical conditions are the Cornelia de Lange syndrome (...
Source: Genes - July 23, 2021 Category: Genetics & Stem Cells Authors: Ester Di Muro Pietro Palumbo Mario Benvenuto Maria Accadia Marilena Carmela Di Giacomo Sergio Manieri Maria Rosaria Abate Maria Tagliente Stefano Castellana Tommaso Mazza Massimo Carella Orazio Palumbo Tags: Case Report Source Type: research

Genes, Vol. 12, Pages 1117: i4mC-Deep: An Intelligent Predictor of N4-Methylcytosine Sites Using a Deep Learning Approach with Chemical Properties
In this study, we propose i4mC-Deep, an intelligent predictor based on a convolutional neural network (CNN) that predicts 4mC modification sites in DNA samples. The CNN is capable of automatically extracting important features from input samples during training. Nucleotide chemical properties and nucleotide density, which together represent a DNA sequence, act as CNN input data. The outcome of the proposed method outperforms several state-of-the-art predictors. When i4mC-Deep was used to analyze G. subterruneus DNA, the accuracy of the results was improved by 3.9% and MCC increased by 10.5% compared to a conventional predi...
Source: Genes - July 23, 2021 Category: Genetics & Stem Cells Authors: Waleed Alam Hilal Tayara Kil To Chong Tags: Article Source Type: research

Genes, Vol. 12, Pages 1118: T-Cell Acute Lymphoblastic Leukemia: Biomarkers and Their Clinical Usefulness
berta La Starza T-cell acute lymphoblastic leukemias (T-ALL) are immature lymphoid tumors localizing in the bone marrow, mediastinum, central nervous system, and lymphoid organs. They account for 10–15% of pediatric and about 25% of adult acute lymphoblastic leukemia (ALL) cases. It is a widely heterogeneous disease that is caused by the co-occurrence of multiple genetic abnormalities, which are acquired over time, and once accumulated, lead to full-blown leukemia. Recurrently affected genes deregulate pivotal cell processes, such as cycling (CDKN1B, RB1, TP53), signaling transduction (RAS pathway, IL7R/JAK/STAT,...
Source: Genes - July 23, 2021 Category: Genetics & Stem Cells Authors: Valentina Bardelli Silvia Arniani Valentina Pierini Danika Di Giacomo Tiziana Pierini Paolo Gorello Cristina Mecucci Roberta La Starza Tags: Review Source Type: research

Genes, Vol. 12, Pages 1119: Biochemical and Molecular Effects Induced by Triacontanol in Acquired Tolerance of Rice to Drought Stress
assan To assess the effect of triacontanol (TRIA) on rice plants grown under normal or drought conditions, rice seeds were presoaked in TRIA (35 ppm) for two hours. After 20 days of sowing, rice seedlings developed from TRIA-treated or untreated seeds were subjected to drought stress. After 10 days of plant exposure to drought stress, data of major growth attributes and the content of photosynthetic pigments were recorded. Moreover, the effect of drought stress on stomatal conductance and the photochemical efficiency of PSII (Fv/Fm) were followed. The data obtained indicated that the species of rice (Oryza sativa L.) c...
Source: Genes - July 23, 2021 Category: Genetics & Stem Cells Authors: Basmah M. Alharbi Awatif Mahfouz Abdulmajeed Heba Hassan Tags: Article Source Type: research

Genes, Vol. 12, Pages 1120: Expression of a Truncated Yeast Ccc1 Vacuolar Transporter Increases the Accumulation of Endogenous Iron
tor Sergi Puig Iron is an essential micronutrient for all eukaryotic organisms because it participates as a redox cofactor in multiple metabolic processes. Iron bioavailability is highly restricted due to the low solubility of its oxidized form, frequently leading to iron deficiency anemia. The baker’s yeast Saccharomyces cerevisiae is used as a model organism for iron homeostasis studies, but also as a food supplement and fermentative microorganism in the food industry. Yeast cells use the vacuolar Ccc1 transporter to detoxify and store excess iron in the vacuoles. Here, we modulate CCC1 expression and propert...
Source: Genes - July 23, 2021 Category: Genetics & Stem Cells Authors: Raquel Sorribes-Dauden Mar ía Teresa Martínez-Pastor Sergi Puig Tags: Article Source Type: research

Genes, Vol. 12, Pages 1109: Maternal Phylogenetic Relationships and Genetic Variation among Rare, Phenotypically Similar Donkey Breeds
In conclusion, we found that the primeval haplotypes, haplogroup variability, and a large number of maternal lineages were preserved in MF and RG; thus, these breeds play putative pivotal roles in the phyletic relationships of donkey breeds. Maternal inheritance is indispensable genetic information required to evaluate inheritance, variability, and breeding programs. (Source: Genes)
Source: Genes - July 22, 2021 Category: Genetics & Stem Cells Authors: Andrea Mazzatenta Massimo Vignoli Maurizio Caputo Giorgio Vignola Roberto Tamburro Francesco De Sanctis Jordi Mir ò Roig Roberta Bucci Domenico Robbe Augusto Carluccio Tags: Article Source Type: research

Genes, Vol. 12, Pages 1110: Genetic Dissection of Growth and Eco-Physiological Traits Associated with Altitudinal Adaptation in Sakhalin Fir (Abies sachalinensis) Based on QTL Mapping
Conclusion: The QTLs detected in this study include potentially important genomic regions linked to altitudinal adaptation in Sakhalin fir. (Source: Genes)
Source: Genes - July 22, 2021 Category: Genetics & Stem Cells Authors: Susumu Goto Hideki Mori Kentaro Uchiyama Wataru Ishizuka Haruhiko Taneda Masaru Kono Hiromi Kajiya-Kanegae Hiroyoshi Iwata Tags: Article Source Type: research