Genes, Vol. 11, Pages 781: Can We Use Gene-Editing to Induce Apomixis in Sexual Plants?
ard Apomixis, the asexual formation of seeds, is a potentially valuable agricultural trait. Inducing apomixis in sexual crop plants would, for example, allow breeders to fix heterosis in hybrid seeds and rapidly generate doubled haploid crop lines. Molecular models explain the emergence of functional apomixis, i.e., apomeiosis + parthenogenesis + endosperm development, as resulting from a combination of genetic or epigenetic changes that coordinate altered molecular and developmental steps to form clonal seeds. Apomixis-like features and synthetic clonal seeds have been induced with limited success in the sexual plants...
Source: Genes - July 12, 2020 Category: Genetics & Stem Cells Authors: Armin Scheben Diego Hojsgaard Tags: Discussion Source Type: research

Genes, Vol. 11, Pages 782: Development of 14 Microsatellite Markers for Zoonotic Tapeworm Dibothriocephalus dendriticus (Cestoda: Diphyllobothriidea)
kírnisson Ivica Králová-Hromadová Dibothriocephalus dendriticus is one of the causative agents of the fish-borne zoonosis diphyllobothriosis. Polymorphic microsatellite markers were originally developed for future genetic studies using microsatellite library screening and next-generation sequencing (NGS). Out of 128 microsatellite candidates selected after NGS analysis, 126 yielded PCR products of the expected size. A declared repetitive motif was confirmed in 92 loci by Sanger sequencing. The level of polymorphism was tested by fragment analysis. Statistical tests for observed and expecte...
Source: Genes - July 12, 2020 Category: Genetics & Stem Cells Authors: Eva Bazsalovicsov á Gabriel Min árik Katar ína Šoltys Al žbeta Radačovská Jesper A. Kuhn Egil Karlsbakk Karl Sk írnisson Ivica Kr álová-Hromadová Tags: Technical Note Source Type: research

Genes, Vol. 11, Pages 778: Genetic Variation in Complex Traits in Transgenic α-Synuclein Strains of Caenorhabditis elegans
Genes, Vol. 11, Pages 778: Genetic Variation in Complex Traits in Transgenic α-Synuclein Strains of Caenorhabditis elegans Genes doi: 10.3390/genes11070778 Authors: Yiru A. Wang Lisa van Sluijs Yu Nie Mark G. Sterken Simon C. Harvey Jan E. Kammenga Different genetic backgrounds can modify the effect of mutated genes. Human α-synuclein (SNCA) gene encodes α-synuclein, and its oligomeric complexes accumulate with age and mediate the disruption of cellular homeostasis, resulting in the neuronal death that is characteristic of Parkinson’s Disease. Polymorphic va...
Source: Genes - July 11, 2020 Category: Genetics & Stem Cells Authors: Yiru A. Wang Lisa van Sluijs Yu Nie Mark G. Sterken Simon C. Harvey Jan E. Kammenga Tags: Article Source Type: research

Genes, Vol. 11, Pages 779: Genomic Selection in Winter Wheat Breeding Using a Recommender Approach
ter Achieving optimal predictive ability is key to increasing the relevance of implementing genomic selection (GS) approaches in plant breeding programs. The potential of an item-based collaborative filtering (IBCF) recommender system in the context of multi-trait, multi-environment GS has been explored. Different GS scenarios for IBCF were evaluated for a diverse population of winter wheat lines adapted to the Pacific Northwest region of the US. Predictions across years through cross-validations resulted in improved predictive ability when there is a high correlation between environments. Using multiple spectral trait...
Source: Genes - July 11, 2020 Category: Genetics & Stem Cells Authors: Dennis N. Lozada Arron H. Carter Tags: Article Source Type: research

Genes, Vol. 11, Pages 780: Linkage between Carbon Metabolism, Redox Status and Cellular Physiology in the Yeast Saccharomyces cerevisiae Devoid of SOD1 or SOD2 Gene
In this study, yeast cells devoid of the SOD1 or SOD2 gene and fermentative or respiratory conditions were used to unravel the connection between the type of metabolism and redox status of cells and also how this affects selected parameters of cellular physiology. The performed analysis provides an argument that the source of ROS depends on the type of metabolism and non-mitochondrial sources are an important pool of ROS in yeast cells, especially under fermentative metabolism. There is a strict interconnection between carbon metabolism and redox status, which in turn has an influence on the physiological efficiency of the...
Source: Genes - July 11, 2020 Category: Genetics & Stem Cells Authors: Roman Maslanka Renata Zadrag-Tecza Magdalena Kwolek-Mirek Tags: Article Source Type: research

Genes, Vol. 11, Pages 777: Evolution of NIN and NIN-like Genes in Relation to Nodule Symbiosis
ing Legumes and actinorhizal plants are capable of forming root nodules symbiosis with rhizobia and Frankia bacteria. All these nodulating species belong to the nitrogen fixation clade. Most likely, nodulation evolved once in the last common ancestor of this clade. NIN (NODULE INCEPTION) is a transcription factor that is essential for nodulation in all studied species. Therefore, it seems probable that it was recruited at the start when nodulation evolved. NIN is the founding member of the NIN-like protein (NLP) family. It arose by duplication, and this occurred before nodulation evolved. Therefore, several plant speci...
Source: Genes - July 11, 2020 Category: Genetics & Stem Cells Authors: Jieyu Liu Ton Bisseling Tags: Review Source Type: research

Genes, Vol. 11, Pages 775: Evolutionary History of the Risk of SNPs for Diffuse-Type Gastric Cancer in the Japanese Population
Yoko Satta A genome wide association study reported that the T allele of rs2294008 in a cancer-related gene, PSCA, is a risk allele for diffuse-type gastric cancer. This allele has the highest frequency (0.63) in Japanese in Tokyo (JPT) among 26 populations in the 1000 Genomes Project database. FST ≈ 0.26 at this single nucleotide polymorphism is one of the highest between JPT and the genetically close Han Chinese in Beijing (CHB). To understand the evolutionary history of the alleles in PSCA, we addressed: (i) whether the C non-risk allele at rs2294008 is under positive selection, and (ii) why the mainl...
Source: Genes - July 10, 2020 Category: Genetics & Stem Cells Authors: Risa L. Iwasaki Koji Ishiya Hideaki Kanzawa-Kiriyama Yosuke Kawai Jun Gojobori Yoko Satta Tags: Article Source Type: research

Genes, Vol. 11, Pages 776: Pro12Ala PPAR- γ2 and +294T/C PPAR-δ Polymorphisms and Association with Metabolic Traits in Teenagers from Northern Mexico
Genes, Vol. 11, Pages 776: Pro12Ala PPAR-γ2 and +294T/C PPAR-δ Polymorphisms and Association with Metabolic Traits in Teenagers from Northern Mexico Genes doi: 10.3390/genes11070776 Authors: Martín A. Carrillo-Venzor Nancy R. Erives-Anchondo Janette G. Moreno-González Verónica Moreno-Brito Angel Licón-Trillo Everardo González-Rodríguez Pilar del Carmen Hernández-Rodríguez Sandra A. Reza-López Verónica Loera-Castañeda Irene Leal-Berumen Peroxisome proliferator-activated receptors (PPARs) play roles in glucose a...
Source: Genes - July 10, 2020 Category: Genetics & Stem Cells Authors: Mart ín A. Carrillo-Venzor Nancy R. Erives-Anchondo Janette G. Moreno-Gonz ález Ver ónica Moreno-Brito Angel Lic ón-Trillo Everardo Gonz ález-Rodríguez Pilar del Carmen Hern ández-Rodríguez Sandra A. Reza-L ópez Ver ónica Loera-Castañeda Irene Tags: Article Source Type: research

Genes, Vol. 11, Pages 772: Ectopic Expressions of the GhLETM1 Gene Reveal Sensitive Dose Effects on Precise Stamen Development and Male Fertility in Cotton
This report has important fundamental and practical significance in crop science, and has crucial prospects for genetic engineering of new cytoplasmic male sterility lines and breeding of crop hybrid varieties. (Source: Genes)
Source: Genes - July 9, 2020 Category: Genetics & Stem Cells Authors: Li Zhang Yao Zhang Yijie Fan Haixia Guo Huihui Guo Jianfei Wu Hongmei Wang Yunlei Zhao Xin Lian Zhongyuan Gou Yuxiao Sun Congcong Zheng Cuixia Chen Fanchang Zeng Tags: Communication Source Type: research

Genes, Vol. 11, Pages 773: PRPH2-Related Retinal Diseases: Broadening the Clinical Spectrum and Describing a New Mutation
We report the phenotype and genotype of eight families (24 patients) with retinal diseases associated with seven distinct PRPH2 gene mutations. We identified a new mutation, c.824_828+3delinsCATTTGGGCTCCTCATTTGG, in a patient with adult-onset vitelliform macular dystrophy (AVMD). One family with the p.Arg46Ter mutation presented with the already described AVMD phenotype, but another family presented with the same mutation and two heterozygous pathogenic mutations (p.Leu2027Phe and p.Gly1977Ser) in the ATP Binding Cassette Subfamily A Member 4 (ABCA4) gene that cause extensive chorioretinal atrophy (ECA), which could be a b...
Source: Genes - July 9, 2020 Category: Genetics & Stem Cells Authors: Rosa M. Coco-Martin Hortensia T. Sanchez-Tocino Carmen Desco Ricardo Usategui-Mart ín Juan J. Teller ía Tags: Article Source Type: research

Genes, Vol. 11, Pages 774: Mitochondrial PCK2 Missense Variant in Shetland Sheepdogs with Paroxysmal Exercise-Induced Dyskinesia (PED)
Andrea Tipold Tosso Leeb Four female Shetland Sheepdogs with hypertonic paroxysmal dyskinesia, mainly triggered by exercise and stress, were investigated in a retrospective multi-center investigation aiming to characterize the clinical phenotype and its underlying molecular etiology. Three dogs were closely related and their pedigree suggested autosomal dominant inheritance. Laboratory diagnostic findings included mild lactic acidosis and lactaturia, mild intermittent serum creatine kinase (CK) elevation and hypoglycemia. Electrophysiological tests and magnetic resonance imaging of the brain were unremarkable. A m...
Source: Genes - July 9, 2020 Category: Genetics & Stem Cells Authors: Jasmin Nessler Petra Hug Paul J. J. Mandigers Peter A. J. Leegwater Vidhya Jagannathan Anibh M. Das Marco Rosati Kaspar Matiasek Adrian C. Sewell Marion Kornberg Marina Hoffmann Petra Wolf Andrea Fischer Andrea Tipold Tosso Leeb Tags: Article Source Type: research

Genes, Vol. 11, Pages 770: Analyses of Hybrid Viability across a Hybrid Zone between Two Alnus Species Using Microsatellites and cpDNA Markers
Bohumil Mandák Diploid Alnus glutinosa s. str. and autotetraploid A. rohlenae form a narrow hybrid zone in a study area in southern Serbia, which results in triploid hybrid formation. The vast majority of previous studies have been focused on studies of maternal plants, but the offspring resulting from their crossing have not been much studied. Here, we use the variability of microsatellites and chloroplast DNA between these species and their putative hybrids to create an overall picture of the development of the hybrid zone and its predicted type. To elucidate the gene transfer within both species, the origi...
Source: Genes - July 9, 2020 Category: Genetics & Stem Cells Authors: Jan Šmíd Jan Douda Karol Krak Bohumil Mand ák Tags: Article Source Type: research

Genes, Vol. 11, Pages 771: Network Analysis Identifies Gene Regulatory Network Indicating the Role of RUNX1 in Human Intervertebral Disc Degeneration
In this study, we utilized a network medicine approach to uncover potential molecular mediators of IDD. Our systematic analyses of IDD associated with 284 genes included functional annotation clustering, interaction networks, network cluster analysis and Transcription factors (TFs)-target gene network analysis. The functional enrichment and protein–protein interaction network analysis highlighted the role of inflammatory genes and cytokine/chemokine signaling in IDD. Moreover, sub-network analysis identified significant clusters possessing organized networks of 24 cytokine and chemokine genes, which may be co...
Source: Genes - July 9, 2020 Category: Genetics & Stem Cells Authors: Nazir M. Khan Martha E Diaz-Hernandez Steven M. Presciutti Hicham Drissi Tags: Article Source Type: research

Genes, Vol. 11, Pages 762: Preventative Effect of Mebendazole against Malignancies in Neurofibromatosis 1
uan Bai Patients with RASopathy Neurofibromatosis 1 (NF1) are at a markedly increased risk of the development of benign and malignant tumors. Malignant tumors are often recalcitrant to treatments and associated with poor survival; however, no chemopreventative strategies currently exist. We thus evaluated the effect of mebendazole, alone or in combination with cyclooxygenase-2 (COX-2) inhibitors, on the prevention of NF1-related malignancies in a cis Nf1+/-;Tp53+/- (NPcis) mouse model of NF1. Our in vitro findings showed that mebendazole (MBZ) inhibits the growth of NF1-related malignant peripheral nerve sheath tumors ...
Source: Genes - July 8, 2020 Category: Genetics & Stem Cells Authors: Verena Staedtke Tyler Gray-Bethke Gregory J. Riggins Ren-Yuan Bai Tags: Article Source Type: research

Genes, Vol. 11, Pages 763: Quantitative Proteomics of Urinary Bladder Cancer Cell Lines Identify UAP1 as a Potential Therapeutic Target
In this study, we utilized a liquid-chromatography tandem mass spectrometry-based global proteomics approach to identify differentially expressed proteins in bladder cancer cell lines. A total of 3913 proteins were identified in this study, of which 479 proteins were overexpressed and 141 proteins were downregulated in 4 out of 6 BC cell lines when compared with normal human urothelial cell line (TERT-NHUC). We evaluated the role of UDP-N-acetylhexosamine pyrophosphorylase (UAP1) in bladder cancer pathogenesis. The silencing of UAP1 led to reduction in proliferation, invasion, colony formation and migration capability of b...
Source: Genes - July 8, 2020 Category: Genetics & Stem Cells Authors: Vinuth N. Puttamallesh Barnali Deb Kirti Gondkar Ankit Jain Bipin Nair Akhilesh Pandey Aditi Chatterjee Harsha Gowda Prashant Kumar Tags: Article Source Type: research

Genes, Vol. 11, Pages 764: Development of a Multilocus Sequence Typing Scheme for Giardia intestinalis
Juan David Ramírez Giardia intestinalis is an intestinal protozoan most commonly found in humans. It has been grouped into 8 assemblages (A-H). Markers such as the glutamate dehydrogenase gene, triose phosphate isomerase and beta-giardin (β-giardin) have been widely used for genotyping. In addition, different genetic targets have been proposed as a valuable alternative to assess diversity and genetics of this microorganism. Thus, our objective was to evaluate new markers for the study of the diversity and intra-taxa genetic structure of G. intestinalis in silico and in DNA obtained from stool sam...
Source: Genes - July 8, 2020 Category: Genetics & Stem Cells Authors: Adriana Higuera Marina Mu ñoz Myriam Consuelo L ópez Patricia Reyes Plutarco Urbano Oswaldo Villalobos Juan David Ram írez Tags: Article Source Type: research

Genes, Vol. 11, Pages 765: Cardiac Involvement in Dystrophin-Deficient Females: Current Understanding and Implications for the Treatment of Dystrophinopathies
Yokota Duchenne muscular dystrophy (DMD) is a fatal X-linked recessive condition caused primarily by out-of-frame mutations in the dystrophin gene. In males, DMD presents with progressive body-wide muscle deterioration, culminating in death as a result of cardiac or respiratory failure. A milder form of DMD exists, called Becker muscular dystrophy (BMD), which is typically caused by in-frame dystrophin gene mutations. It should be emphasized that DMD and BMD are not exclusive to males, as some female dystrophin mutation carriers do present with similar symptoms, generally at reduced levels of severity. Cardiac involve...
Source: Genes - July 8, 2020 Category: Genetics & Stem Cells Authors: Kenji Rowel Q. Lim Narin Sheri Quynh Nguyen Toshifumi Yokota Tags: Review Source Type: research

Genes, Vol. 11, Pages 767: Identification of Loci and Pathways Associated with Heifer Conception Rate in U.S. Holsteins
Holly L. Neibergs Heifer conception rate (HCR) is defined as the percentage of inseminated heifers that become pregnant at each service. The genome-wide association analyses in this study focused on identifying the loci associated with Holstein heifer (n = 2013) conception rate at first service (HCR1) and the number of times bred (TBRD) to achieve a pregnancy. There were 348 unique loci associated (p < 5 × 10−8) with HCR1 and 615 unique loci associated (p < 5 × 10−8) with TBRD. The two phenotypes shared 302 loci, and 56 loci were validated in...
Source: Genes - July 8, 2020 Category: Genetics & Stem Cells Authors: Justine M. Galliou Jennifer N. Kiser Kayleen F. Oliver Christopher M. Seabury Joao G. N. Moraes Gregory W. Burns Thomas E. Spencer Joseph Dalton Holly L. Neibergs Tags: Article Source Type: research

Genes, Vol. 11, Pages 766: Matrix Metalloproteinase Genes (MMP1, MMP10, MMP12) on Chromosome 11q22 and the Risk of Non-Contact Anterior Cruciate Ligament Ruptures
Conclusions: Despite the fact that the current study did not support existing evidence suggesting that variants within the MMP1, MMP10, and MMP12 genes influence non-contact ACL rupture risk, future work should include high-throughput sequencing technologies to identify potential targeted polymorphisms to fully characterize the 11q22 region with susceptibility to non-contact ACL rupture susceptibility in a Polish cohort (Source: Genes)
Source: Genes - July 8, 2020 Category: Genetics & Stem Cells Authors: Ewelina Luli ńska Andrea Gibbon Mariusz Kaczmarczyk Agnieszka Maciejewska-Skrendo Krzysztof Ficek Agata Leo ńska-Duniec Micha ł Wilk Katarzyna Le źnicka Monika Micha łowska-Sawczyn Kinga Humi ńska-Lisowska Rafa ł Buryta Pawe ł Cięszczyk Ewelina M Tags: Article Source Type: research

Genes, Vol. 11, Pages 768: TLR4 Polymorphism, Nasopharyngeal Bacterial Colonization, and the Development of Childhood Asthma: A Prospective Birth-Cohort Study in Finnish Children
ltola Qiushui He We aimed to explore the role of TLR4 (rs4986790) polymorphism in the nasopharyngeal (NP) bacterial colonization and its consequent impact on the development of childhood asthma. A semi-quantitative culture of NP swabs was performed on 473 children at 2 months of age and on 213 children at 13 months of age. TLR4 polymorphism was analyzed for 396 children. Children were followed from birth to the age of 7.5 years and the final outcome was physician-diagnosed asthma. The associations between TLR4 genotype, bacterial colonization, and asthma were analyzed. Children with TLR4 AG or GG genotype were more o...
Source: Genes - July 8, 2020 Category: Genetics & Stem Cells Authors: Johanna T. Ter äsjärvi Laura Toivonen Juho Vuononvirta Jussi Mertsola Ville Peltola Qiushui He Tags: Communication Source Type: research

Genes, Vol. 11, Pages 769: Identification of Genes Encoding CENP-A and Heterochromatin Protein 1 of Lipomyces starkeyi and Functional Analysis Using Schizosaccharomyces pombe
a Centromeres function as a platform for the assembly of multiple kinetochore proteins and are essential for chromosome segregation. An active centromere is characterized by the presence of a centromere-specific histone H3 variant, CENP-A. Faithful centromeric localization of CENP-A is supported by heterochromatin in almost all eukaryotes; however, heterochromatin proteins have been lost in most Saccharomycotina. Here, identification of CENP-A (CENP-AL.s.) and heterochromatin protein 1 (Lsw1) in a Saccharomycotina species, the oleaginous yeast Lipomyces starkeyi, is reported. To determine if these proteins are function...
Source: Genes - July 8, 2020 Category: Genetics & Stem Cells Authors: Yuko Takayama Tags: Article Source Type: research

Genes, Vol. 11, Pages 760: Protein Coding and Long Noncoding RNA (lncRNA) Transcriptional Landscape in SARS-CoV-2 Infected Bronchial Epithelial Cells Highlight a Role for Interferon and Inflammatory Response
lajez The global spread of COVID-19, caused by pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscores the need for an imminent response from medical research communities to better understand this rapidly spreading infection. Employing multiple bioinformatics and computational pipelines on transcriptome data from primary normal human bronchial epithelial cells (NHBE) during SARS-CoV-2 infection revealed activation of several mechanistic networks, including those involved in immunoglobulin G (IgG) and interferon lambda (IFNL) in host cells. Induction of acute inflammatory response and activat...
Source: Genes - July 7, 2020 Category: Genetics & Stem Cells Authors: Radhakrishnan Vishnubalaji Hibah Shaath Nehad M. Alajez Tags: Article Source Type: research

Genes, Vol. 11, Pages 761: Mutation Patterns of Human SARS-CoV-2 and Bat RaTG13 Coronavirus Genomes Are Strongly Biased Towards C & gt;U Transitions, Indicating Rapid Evolution in Their Hosts
Genes, Vol. 11, Pages 761: Mutation Patterns of Human SARS-CoV-2 and Bat RaTG13 Coronavirus Genomes Are Strongly Biased Towards C>U Transitions, Indicating Rapid Evolution in Their Hosts Genes doi: 10.3390/genes11070761 Authors: Roman Matyášek Aleš Kovařík The pandemic caused by the spread of SARS-CoV-2 has led to considerable interest in its evolutionary origin and genome structure. Here, we analyzed mutation patterns in 34 human SARS-CoV-2 isolates and a closely related RaTG13 isolated from Rhinolophus affinis (a horseshoe bat). We also evaluated the CpG dinucleotide contents...
Source: Genes - July 7, 2020 Category: Genetics & Stem Cells Authors: Roman Maty ášek Ale š Kovařík Tags: Article Source Type: research

Genes, Vol. 11, Pages 759: A SNP-Based Genome-Wide Association Study to Mine Genetic Loci Associated to Salinity Tolerance in Mungbean (Vigna radiata L.)
chafleitner Mungbean (Vigna radiata (L.) R. Wilzeck var. radiata) is a protein-rich short-duration legume that fits well as a rotation crop into major cereal production systems of East and South-East Asia. Salinity stress in arid areas affects mungbean, being more of a glycophyte than cereals. A significant portion of the global arable land is either salt or sodium affected. Thus, studies to understand and improve salt-stress tolerance are imminent. Here, we conducted a genome-wide association study (GWAS) to mine genomic loci underlying salt-stress tolerance during seed germination of mungbean. The World Vegetable Cen...
Source: Genes - July 7, 2020 Category: Genetics & Stem Cells Authors: Caleb Manamik Breria Ching-Hsiang Hsieh Tsair-Bor Yen Jo-Yi Yen Thomas J. Noble Roland Schafleitner Tags: Article Source Type: research

Genes, Vol. 11, Pages 754: Heat Diffusion Kernel Algorithm-Based Interpretation of the Disease Intervention Mechanism for DHA
In this study, we used HotNet2, a heat diffusion kernel algorithm, to calculate the gene regulatory networks of connectivity map (cMap)-derived agents (including DHA) based on gene expression profiles, aiming to interpret the disease intervention mechanism of DHA at the network level. As a result, significant gene regulatory networks for DHA and 676 cMap-derived agents were identified respectively. The biological functions of the DHA-regulated gene network provide preliminary insights into the mechanism by which DHA intervenes in disease. In addition, we compared the gene regulatory networks of DHA with those of cMap-deriv...
Source: Genes - July 7, 2020 Category: Genetics & Stem Cells Authors: Yuan Quan Hong-Yu Zhang Jiang-Hui Xiong Rui-Feng Xu Min Gao Tags: Letter Source Type: research

Genes, Vol. 11, Pages 755: Actions of L-thyroxine (T4) and Tetraiodothyroacetic Acid (Tetrac) on Gene Expression in Thyroid Cancer Cells
. Mousa The clinical behavior of thyroid cancers is seen to reflect inherent transcriptional activities of mutated genes and trophic effects on tumors of circulating pituitary thyrotropin (TSH). The thyroid hormone, L-thyroxine (T4), has been shown to stimulate proliferation of a large number of different forms of cancer. This activity of T4 is mediated by a cell surface receptor on the extracellular domain of integrin αvβ3. In this brief review, we describe what is known about T4 as a circulating trophic factor for differentiated (papillary and follicular) thyroid cancers. Given T4&p...
Source: Genes - July 7, 2020 Category: Genetics & Stem Cells Authors: Paul J. Davis Hung-Yun Lin Aleck Hercbergs Shaker A. Mousa Tags: Review Source Type: research

Genes, Vol. 11, Pages 756: ShadowCaster: Compositional Methods under the Shadow of Phylogenetic Models to Detect Horizontal Gene Transfers in Prokaryotes
Sánchez-Rodríguez Horizontal gene transfer (HGT) plays an important role for evolutionary innovations within prokaryotic communities and is a crucial event for their survival. Several computational approaches have arisen to identify HGT events in recipient genomes. However, this has been proven to be a complex task due to the generation of a great number of false positives and the prediction disagreement among the existing methods. Phylogenetic reconstruction methods turned out to be the most reliable ones, but they are not extensible to all genes/species and are computationally demanding when dealing wi...
Source: Genes - July 7, 2020 Category: Genetics & Stem Cells Authors: Daniela S ánchez-Soto Guillermin Ag üero-Chapin Vinicio Armijos-Jaramillo Yunierkis Perez-Castillo Eduardo Tejera Agostinho Antunes Aminael S ánchez-Rodríguez Tags: Article Source Type: research

Genes, Vol. 11, Pages 757: The Need for Establishing a Universal CTG Sizing Method in Myotonic Dystrophy Type 1
o-Melo Alejandro Lucia Darren G. Monckton Sarah A. Cumming Alba Ramos-Fransi Alicia Martínez-Piñeiro Gisela Nogales-Gadea The number of cytosine-thymine-guanine (CTG) repeats (‘CTG expansion size’) in the 3′untranslated region (UTR) region of the dystrophia myotonica-protein kinase (DMPK) gene is a hallmark of myotonic dystrophy type 1 (DM1), which has been related to age of disease onset and clinical severity. However, accurate determination of CTG expansion size is challenging due to its characteristic instability. We compared five different approach...
Source: Genes - July 7, 2020 Category: Genetics & Stem Cells Authors: Alfonsina Ballester-Lopez Ian Linares-Pardo Emma Koehorst Judit N úñez-Manchón Guillem Pintos-Morell Jaume Coll-Cant í Miriam Almendrote Giuseppe Lucente Andrea Arbex Jonathan J. Maga ña Nadia M. Murillo-Melo Alejandro Lucia Darren G. Monckton Sarah Tags: Brief Report Source Type: research

Genes, Vol. 11, Pages 758: Semen Modulates the Expression of NGF, ABHD2, VCAN, and CTEN in the Reproductive Tract of Female Rabbits
z-Rodriguez Semen changes the gene expression in endometrial and oviductal tissues modulating important processes for reproduction. We tested the hypothesis that mating and/or sperm-free seminal plasma deposition in the reproductive tract affect the expression of genes associated with sperm-lining epithelium interactions, ovulation, and pre-implantation effects (nerve growth factor, NGF; α/β hydrolase domain-containing protein 2, ABHD2; C-terminal tensin-like protein, CTEN or TNS4; and versican, VCAN) in the period 10–72 h post-mating. In Experiment 1, does (n = 9) were treated ...
Source: Genes - July 7, 2020 Category: Genetics & Stem Cells Authors: Jaume Gardela Amaia Jauregi-Miguel Cristina A. Martinez Heriberto Rodriguez-Martinez Manel Lopez-Bejar Manuel Alvarez-Rodriguez Tags: Article Source Type: research

Genes, Vol. 11, Pages 747: Precision and Personalized Medicine: How Genomic Approach Improves the Management of Cardiovascular and Neurodegenerative Disease
ria Rosaria Rusciano Life expectancy has gradually grown over the last century. This has deeply affected healthcare costs, since the growth of an aging population is correlated to the increasing burden of chronic diseases. This represents the interesting challenge of how to manage patients with chronic diseases in order to improve health care budgets. Effective primary prevention could represent a promising route. To this end, precision, together with personalized medicine, are useful instruments in order to investigate pathological processes before the appearance of clinical symptoms and to guide physicians to choose ...
Source: Genes - July 6, 2020 Category: Genetics & Stem Cells Authors: Oriana Strianese Francesca Rizzo Michele Ciccarelli Gennaro Galasso Ylenia D ’Agostino Annamaria Salvati Carmine Del Giudice Paola Tesorio Maria Rosaria Rusciano Tags: Review Source Type: research

Genes, Vol. 11, Pages 748: Spatial and Temporal Dynamics of Contact Zones Between Chromosomal Races of House Mice, Mus musculus domesticus, on Madeira Island
This study investigates the present (2012–2014) and past (1998–2002) distribution of two parapatric house mouse chromosomal races—PEDC (Estreito da Calheta) and PADC (Achadas da Cruz)—on Madeira Island, aiming to identify changes in the location and width of their contact. We also extended the 1998–2002 sampling area into the range of another chromosomal race—PLDB (Lugar de Baixo). Clinal analysis indicates no major geographic alterations in the distribution and chromosomal characteristics of the PEDC and PADC races but exhibited a signific...
Source: Genes - July 6, 2020 Category: Genetics & Stem Cells Authors: Joaquim T. Tapisso Sofia I. Gabriel Ana Mota Cerveira Janice Britton-Davidian Guila Ganem Jeremy B. Searle Maria da Gra ça Ramalhinho Maria da Luz Mathias Tags: Article Source Type: research

Genes, Vol. 11, Pages 749: Genetic and Genomic Landscape of Secondary and Therapy-Related Acute Myeloid Leukemia
hah A subset of acute myeloid leukemia (AML) arises either from an antecedent myeloid malignancy (secondary AML, sAML) or as a complication of DNA-damaging therapy for other cancers (therapy-related myeloid neoplasm, t-MN). These secondary leukemias have unique biological and clinical features that distinguish them from de novo AML. Over the last decade, molecular techniques have unraveled the complex subclonal architecture of sAML and t-MN. In this review, we compare and contrast biological and clinical features of de novo AML with sAML and t-MN. We discuss the role of genetic mutations, including those involved in RN...
Source: Genes - July 6, 2020 Category: Genetics & Stem Cells Authors: Alexandra Higgins Mithun Vinod Shah Tags: Review Source Type: research

Genes, Vol. 11, Pages 751: Prognostic Significance of RAS Mutations and P53 Expression in Cutaneous Squamous Cell Carcinomas
The objective of our study was to evaluate the frequency of p53 expression and RAS mutations in cSCC and correlate them with clinicopathological features and patient outcome. We performed immunohistochemistry for p53 and genetic profiling for RAS mutations in a retrospective series of cSCC. The predictive value of p53 expression, RAS mutations, and clinicopathological parameters was assessed using logistic regression models. The overall frequency of RAS mutations was 9.3% (15/162), and 82.1% of the cases (133/162) had p53 overexpression. RAS mutations rate was 3.2% (1/31) of in situ cSCCs and 10.7% (14/131) of invasive cSC...
Source: Genes - July 6, 2020 Category: Genetics & Stem Cells Authors: Manuel Ant ónio Campos Sofia Macedo Margarida S á Fernandes Ana Pestana Joana Pardal Rui Batista Jo ão Vinagre Agostinho Sanches Armando Baptista Jos é Manuel Lopes Paula Soares Tags: Article Source Type: research

Genes, Vol. 11, Pages 750: Detection of Multiple Transgene Fragments in a Mouse Model of Gene Doping Based on Plasmid Vector Using TaqMan-qPCR Assay
kekoshi The World Anti-Doping Agency has prohibited gene doping in the context of progress in gene therapy. There is a risk that the augmentation of genes using plasmids could be applied for gene doping. However, no gold standard method to detect this has been established. Here, we aimed to develop a method to detect multiple transgene fragments as proof of gene doping. Firstly, gene delivery model mice as a mimic of gene doping were created by injecting firefly luciferase plasmid with polyethylenimine (PEI) into the abdominal cavity. The results confirmed successful establishment of the model, with sufficient luminesc...
Source: Genes - July 6, 2020 Category: Genetics & Stem Cells Authors: Takehito Sugasawa Kai Aoki Kouki Yanazawa Kazuhiro Takekoshi Tags: Article Source Type: research

Genes, Vol. 11, Pages 752: The Importance of ATM and ATR in Physcomitrella patens DNA Damage Repair, Development, and Gene Targeting
d Reiss Coordinated by ataxia-telangiectasia-mutated (ATM) and ATM and Rad3-related (ATR), two highly conserved kinases, DNA damage repair ensures genome integrity and survival in all organisms. The Arabidopsis thaliana (A. thaliana) orthologues are well characterized and exhibit typical mammalian characteristics. We mutated the Physcomitrella patens (P. patens) PpATM and PpATR genes by deleting functionally important domains using gene targeting. Both mutants showed growth abnormalities, indicating that these genes, particularly PpATR, are important for normal vegetative development. ATR was also required for repair o...
Source: Genes - July 6, 2020 Category: Genetics & Stem Cells Authors: Martin Martens Ralf Horres Edelgard Wendeler Bernd Reiss Tags: Article Source Type: research

Genes, Vol. 11, Pages 753: Hybridization of Russian Sturgeon (Acipenser gueldenstaedtii, Brandt and Ratzeberg, 1833) and American Paddlefish (Polyodon spathula, Walbaum 1792) and Evaluation of Their Progeny
oacute;s Bercsényi Mariann Molnár Eszter Patakiné Várkonyi Two species from the families Acipenseridae and Polyodontidae, Russian sturgeon (Acipenser gueldenstaedtii, Brandt and Ratzeberg, 1833; functional tetraploid) and American paddlefish (Polyodon spathula, Walbaum 1792, functional diploid) were hybridized. The hybridization was repeated using eggs from three sturgeon and sperm from four paddlefish individuals. Survival in all hybrid family groups ranged from 62% to 74% 30 days after hatching. This was the first successful hybridization between these two species and between members o...
Source: Genes - July 6, 2020 Category: Genetics & Stem Cells Authors: Jen ő Káldy Attila Mozs ár Gy öngyvér Fazekas M óni Farkas Dorottya Lilla Fazekas Georgina Lea Fazekas Katalin Goda Zsuzsanna Gy öngy Bal ázs Kovács Kenneth Semmens Mikl ós Bercsényi Mariann Moln ár Eszter Patakin é Várkonyi Tags: Article Source Type: research

Genes, Vol. 11, Pages 746: Profile of the Nicotinic Cholinergic Receptor Alpha 7 Subunit Gene Expression is Associated with Response to Varenicline Treatment
Conclusion: This exploratory clinical study, searching for a possible predictor of effectiveness for varenicline, reaffirmed the association of the α7 nAChR subunit for nicotine dependence and smoking therapy effectiveness with varenicline. (Source: Genes)
Source: Genes - July 6, 2020 Category: Genetics & Stem Cells Authors: Juliana Rocha Santos Paulo Roberto Xavier Tomaz Jaqueline Ribeiro Scholz Patr ícia Viviane Gaya T ânia Ogawa Abe Jos é Eduardo Krieger Alexandre Costa Pereira Paulo Caleb J únior de Lima Santos Tags: Article Source Type: research

Genes, Vol. 11, Pages 745: A New Intra-Specific and High-Resolution Genetic Map of Eggplant Based on a RIL Population, and Location of QTLs Related to Plant Anthocyanin Pigmentation and Seed Vigour.
Sunseri Lanteri Rotino Eggplant is the second most important solanaceous berry-producing crop after tomato. Despite mapping studies based on bi-parental progenies and GWAS approaches having been performed, an eggplant intraspecific high-resolution map is still lacking. We developed a RIL population from the intraspecific cross ‘305E40′, (androgenetic introgressed line carrying the locus Rfo-Sa1 conferring Fusarium resistance) x ‘67/3′ (breeding line whose genome sequence was recently released). One hundred and sixty-three RILs were genotyped by a genotyp...
Source: Genes - July 4, 2020 Category: Genetics & Stem Cells Authors: Toppino Barchi Mercati Acciarri Perrone Martina Gattolin Sala Fadda Mauceri Ciriaci Carimi Portis Sunseri Lanteri Rotino Tags: Article Source Type: research

Genes, Vol. 11, Pages 739: Atypical Genotypes for Canine Agouti Signaling Protein Suggest Novel Chromosomal Rearrangement
J. Ekenstedt Canine coat color is a readily observed phenotype of great interest to dog enthusiasts; it is also an excellent avenue to explore the mechanisms of genetics and inheritance. As such, multiple commercial testing laboratories include basic color alleles in their popular screening panels, allowing for the creation of genotyped datasets at a scale not before appreciated in canine genetic research. These vast datasets have revealed rare genotype anomalies that encourage further exploration of color and pattern inheritance. We previously reported the simultaneous presence of greater than two allele variants at ...
Source: Genes - July 3, 2020 Category: Genetics & Stem Cells Authors: Dayna L. Dreger Heidi Anderson Jonas Donner Jessica A. Clark Arlene Dykstra Angela M. Hughes Kari J. Ekenstedt Tags: Article Source Type: research

Genes, Vol. 11, Pages 740: SpCas9- and LbCas12a-Mediated DNA Editing Produce Different Gene Knockout Outcomes in Zebrafish Embryos
ej Frolov CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein) genome editing is a powerful technology widely used in current genetic research. In the most simple and straightforward way it can be applied for a gene knockout resulting from repair errors, induced by dsDNA cleavage by Cas nuclease. For decades, zebrafish (Danio rerio) has been known as a convenient model object of developmental biology. Both commonly used nucleases SpCas9 (Streptococcus pyogenes Cas9) and LbCas12a (Lachnospiraceae bacterium Cas12a) are extensively used in this model. Among them, LbCas12a is fea...
Source: Genes - July 3, 2020 Category: Genetics & Stem Cells Authors: Darya A. Meshalkina Aleksei S. Glushchenko Elana V. Kysil Igor V. Mizgirev Andrej Frolov Tags: Communication Source Type: research

Genes, Vol. 11, Pages 741: Analysis of ACE2 Genetic Variability among Populations Highlights a Possible Link with COVID-19-Related Neurological Complications
Raffaella Cascella Angiotensin-converting enzyme 2 (ACE2) has been recognized as the entry receptor of the novel severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2). Structural and sequence variants in ACE2 gene may affect its expression in different tissues and determine a differential response to SARS-Cov-2 infection and the COVID-19-related phenotype. The present study investigated the genetic variability of ACE2 in terms of single nucleotide variants (SNVs), copy number variations (CNVs), and expression quantitative loci (eQTLs) in a cohort of 268 individuals representative of the general Italian populati...
Source: Genes - July 3, 2020 Category: Genetics & Stem Cells Authors: Claudia Strafella Valerio Caputo Andrea Termine Shila Barati Stefano Gambardella Paola Borgiani Carlo Caltagirone Giuseppe Novelli Emiliano Giardina Raffaella Cascella Tags: Communication Source Type: research

Genes, Vol. 11, Pages 742: Interplay between Metabolism, Nutrition and Epigenetics in Shaping Brain DNA Methylation, Neural Function and Behavior
ini Gene expression in the brain is dramatically regulated by a variety of stimuli. While the role of neural activity has been extensively studied, less is known about the effects of metabolism and nutrition on transcriptional control mechanisms in the brain. Extracellular signals are integrated at the chromatin level through dynamic modifications of epigenetic marks, which in turn fine-tune gene transcription. In the last twenty years, it has become clear that epigenetics plays a crucial role in modulating central nervous system functions and finally behavior. Here, we will focus on the effect of metabolic signals in ...
Source: Genes - July 3, 2020 Category: Genetics & Stem Cells Authors: Tommaso Pizzorusso Paola Tognini Tags: Review Source Type: research

Genes, Vol. 11, Pages 743: Genetic Reconstruction and Forensic Analysis of Chinese Shandong and Yunnan Han Populations by Co-Analyzing Y Chromosomal STRs and SNPs
This study provides Y-STR haplotypes for 27 markers typed by the Yfiler™ Plus kit and Y-SNP haplogroups defined by 24 loci within the Y-SNP Pedigree Tagging System for Shandong Han (n = 305) and Yunnan Han (n = 565) populations. The genetic backgrounds of these two populations were explicitly characterized by the analysis of molecular variance (AMOVA) and multi-dimensional scaling (MDS) plots based on 27 Y-STRs. Then, population comparisons were conducted by observing Y-SNP allelic frequencies and Y-SNP haplogroups distribution, estimating forensic parameters, and depicting distribution spectrums of Y-STR all...
Source: Genes - July 3, 2020 Category: Genetics & Stem Cells Authors: Caiyong Yin Kaiyuan Su Ziwei He Dian Zhai Kejian Guo Xueyun Chen Li Jin Shilin Li Tags: Article Source Type: research

Genes, Vol. 11, Pages 744: Genomic Comparison of Insect Gut Symbionts from Divergent Burkholderia Subclades
chi Stink bugs of the superfamilies Coreoidea and Lygaeoidea establish gut symbioses with environmentally acquired bacteria of the genus Burkholderia sensu lato. In the genus Burkholderia, the stink bug-associated strains form a monophyletic clade, named stink bug-associated beneficial and environmental (SBE) clade (or Caballeronia). Recently, we revealed that members of the family Largidae of the superfamily Pyrrhocoroidea are associated with Burkholderia but not specifically with the SBE Burkholderia; largid bugs harbor symbionts that belong to a clade of plant-associated group of Burkholderia, called plant-associate...
Source: Genes - July 3, 2020 Category: Genetics & Stem Cells Authors: Kazutaka Takeshita Yoshitomo Kikuchi Tags: Article Source Type: research

Genes, Vol. 11, Pages 735: Knockout of Pi21 by CRISPR/Cas9 and iTRAQ-Based Proteomic Analysis of Mutants Revealed New Insights into M. oryzae Resistance in Elite Rice Line
Rongbai Li Rice blast (Magnaporthe oryzae) is a devastating disease affecting rice production globally. The development of cultivars with host resistance has been proved to be the best strategy for disease management. Several rice-resistance genes (R) have been recognized which induce resistance to blast in rice but R gene-mediated mechanisms resulting in defense response still need to be elucidated. Here, mutant lines generated through CRISPR/Cas9 based targeted mutagenesis to investigate the role of Pi21 against blast resistance and 17 mutant plants were obtained in T0 generation with the mutation rate of 66% incl...
Source: Genes - July 2, 2020 Category: Genetics & Stem Cells Authors: Gul Nawaz Babar Usman Haowen Peng Neng Zhao Ruizhi Yuan Yaoguang Liu Rongbai Li Tags: Article Source Type: research

Genes, Vol. 11, Pages 736: Growth Trajectories in Genetic Subtypes of Prader –Willi Syndrome
This study aimed to investigate growth trajectories in PWS and associations between PWS subtype (deletion vs. non-deletion) and height, weight and body mass index (BMI). Growth data were available for 125 individuals with PWS (63 males, 62 females), of which 72 (57.6%) had the deletion subtype. There was a median of 28 observations per individual (range 2–85), producing 3565 data points distributed from birth to 18 years of age. Linear mixed models with cubic splines, subject-specific random effects and an autoregressive correlation structure were used to model the longitudinal growth data whilst accounting f...
Source: Genes - July 2, 2020 Category: Genetics & Stem Cells Authors: Daisy A. Shepherd Niels Vos Susan M. Reid David E. Godler Angela Guzys Margarita Moreno-Betancur David J. Amor Tags: Article Source Type: research

Genes, Vol. 11, Pages 737: Genetic Diversity, Population Structure, and Parentage Analysis of Croatian Grapevine Germplasm
We present what is the most comprehensive genetic analysis of all major Croatian national repositories, with a large number of microsatellite, or simple sequence repeat (SSR) markers, and it is also the first study to apply single nucleotide polymorphism (SNP) markers. After 212 accessions were fingerprinted, 95 were classified as unique to Croatian germplasm. Genetic diversity of Croatian germplasm is rather high considering its size. SNP markers proved useful for fingerprinting but less informative and practical than SSRs. Analysis of the genetic structure showed that Croatian germplasm is predominantly part of the Balka...
Source: Genes - July 2, 2020 Category: Genetics & Stem Cells Authors: Maja Žulj Mihaljević Edi Maleti ć Darko Preiner Goran Zduni ć Marijan Bubola Eva Zyprian Ivan Peji ć Tags: Article Source Type: research

Genes, Vol. 11, Pages 738: Experimental Approaches in Delineating mTOR Signaling
a Liu The mTOR signaling controls essential biological functions including proliferation, growth, metabolism, autophagy, ageing, and others. Hyperactivation of mTOR signaling leads to a plethora of human disorders; thus, mTOR is an attractive drug target. The discovery of mTOR signaling started from isolation of rapamycin in 1975 and cloning of TOR genes in 1993. In the past 27 years, numerous research groups have contributed significantly to advancing our understanding of mTOR signaling and mTOR biology. Notably, a variety of experimental approaches have been employed in these studies to identify key mTOR pathway memb...
Source: Genes - July 2, 2020 Category: Genetics & Stem Cells Authors: Jiayi Qian Siyuan Su Pengda Liu Tags: Review Source Type: research

Genes, Vol. 11, Pages 734: Purification and Characterization of Double-Stranded Nucleic Acid-Dependent ATPase Activities of Tagged Dicer-Related Helicase 1 and its Short Isoform in Caenorhabditis elegans
In this study, the secondary structure prediction by JPred4 revealed that DRH-1 and DRH-3 had distinct N-terminal regions and that a 200-amino acid N-terminal region of DRH-1 could form a structure very rich in α-helices. We investigated expressions and purifications of a codon-optimized DRH-1 with four different N-terminal tags, identifying poly-histidine (His)-small ubiquitin-like modifier (SUMO) as a suitable tag for DRH-1 preparation. Full-length (isoform a) and a N-terminal truncated (isoform b) of DRH-1 were purified as the His-SUMO-tagged fusion proteins. Finally, the nucleic acid-dependent ATPase acti...
Source: Genes - July 1, 2020 Category: Genetics & Stem Cells Authors: Taishi Kobayashi Takuro Murakami Yuu Hirose Toshihiko Eki Tags: Article Source Type: research

Genes, Vol. 11, Pages 728: Chasing the Apomictic Factors in the Ranunculus auricomus Complex: Exploring Gene Expression Patterns in Microdissected Sexual and Apomictic Ovules
F. Sharbel Apomixis, the asexual reproduction via seeds, is associated to polyploidy and hybridization. To identify possible signatures of apomixis, and possible candidate genes underlying the shift from sex to apomixis, microarray-based gene expression patterns of live microdissected ovules at four different developmental stages were compared between apomictic and sexual individuals of the Ranunculus auricomus complex. Following predictions from previous work on mechanisms underlying apomixis penetrance and expressivity in the genus, gene expression patterns were classified into three categories based on their relativ...
Source: Genes - June 30, 2020 Category: Genetics & Stem Cells Authors: Marco Pellino Diego Hojsgaard Elvira H örandl Timothy F. Sharbel Tags: Article Source Type: research