Genes, Vol. 13, Pages 190: Functional Innovation through Gene Duplication Followed by Frameshift Mutation
i Innan In his influential book “Evolution by Gene Duplication”, Ohno postulated that frameshift mutation could lead to a new function after duplication, but frameshift mutation is generally thought to be deleterious, and thus drew little attention in functional innovation in duplicate evolution. To this end, we here report an exhaustive survey of the genomes of human, mouse, zebrafish, and fruit fly. We identified 80 duplicate genes that involved frameshift mutations after duplication. The frameshift mutation preferentially located close to the C-terminus in most cases (55/88), which indica...
Source: Genes - January 21, 2022 Category: Genetics & Stem Cells Authors: Baocheng Guo Ming Zou Takahiro Sakamoto Hideki Innan Tags: Brief Report Source Type: research

Genes, Vol. 13, Pages 183: Evolutionary Genetic Signatures of Selection on Bone-Related Variation within Human and Chimpanzee Populations
Verrelli Bone strength and the incidence and severity of skeletal disorders vary significantly among human populations, due in part to underlying genetic differentiation. While clinical models predict that this variation is largely deleterious, natural population variation unrelated to disease can go unnoticed, altering our perception of how natural selection has shaped bone morphologies over deep and recent time periods. Here, we conduct the first comparative population-based genetic analysis of the main bone structural protein gene, collagen type I α 1 (COL1A1), in clinical and 1000 Genomes Project dat...
Source: Genes - January 21, 2022 Category: Genetics & Stem Cells Authors: Daryn A. Stover Genevieve Housman Anne C. Stone Michael S. Rosenberg Brian C. Verrelli Tags: Article Source Type: research

Genes, Vol. 13, Pages 184: Increase in Ribosomal Fidelity Benefits Salmonella upon Bile Salt Exposure
ing Translational fidelity is maintained by multiple quality control steps in all three domains of life. Increased translational errors (mistranslation) occur due to genetic mutations and external stresses. Severe mistranslation is generally harmful, but moderate levels of mistranslation may be favored under certain conditions. To date, little is known about the link between translational fidelity and host–pathogen interactions. Salmonella enterica can survive in the gall bladder during systemic or chronic infections due to bile resistance. Here we show that increased translational fidelity contributes to...
Source: Genes - January 21, 2022 Category: Genetics & Stem Cells Authors: Zhihui Lyu Jiqiang Ling Tags: Article Source Type: research

Genes, Vol. 13, Pages 185: Combining Fine Mapping, Whole-Genome Re-Sequencing, and RNA-Seq Unravels Candidate Genes for a Soybean Mutant with Short Petioles and Weakened Pulvini
hang Zhao A short petiole is an important agronomic trait for the development of plant ideotypes with high yields. However, the genetic basis underlying this trait remains unclear. Here, we identified and characterized a novel soybean mutant with short petioles and weakened pulvini, designated as short petioles and weakened pulvini (spwp). Compared with the wild type (WT), the spwp mutant displayed shortened petioles, owing to the longitudinally decreased cell length, and exhibited a smaller pulvinus structure due to a reduction in motor cell proliferation and expansion. Genetic analysis showed that the phenotype of...
Source: Genes - January 21, 2022 Category: Genetics & Stem Cells Authors: Kong Xu Xu Sharmin Zhang Zhao Tags: Article Source Type: research

Genes, Vol. 13, Pages 186: Identification of Novel Gene Variants for Autism Spectrum Disorders in the Lebanese Population Using Whole-Exome Sequencing
res Hleihel In our previous study, in which array CGH was used on 19 Lebanese ASD subjects and their parents, we identified rare copy number variants (CNVs) in 14 subjects. The five remaining subjects did not show any CNVs related to autism spectrum disorders (ASD). In the present complementary study, we applied whole-exome sequencing (WES), which allows the identification of rare genetic variations such as single nucleotide variations and small insertions/deletions, to the five negative CNV subjects. After stringent filtering of initial data on the five families, three novel genes potentially related to neurodevelo...
Source: Genes - January 21, 2022 Category: Genetics & Stem Cells Authors: Gerges Bitar Laumonnier Marouillat Nemer Andres Hleihel Tags: Article Source Type: research

Genes, Vol. 13, Pages 187: Quantitative Real-Time Analysis of Differentially Expressed Genes in Peripheral Blood Samples of Hypertension Patients
This study was designed to explore possible differentially expressed genes (DEGs) that contribute to the pathophysiology of hypertension. To identify the DEGs of HTN, we investigated 22 publicly available cDNA Affymetrix datasets using an integrated system-level framework. Gene Ontology (GO), pathway enrichment, and transcriptional factors were analyzed to reveal biological information. From 50 DEGs, we ranked 7 hypertension-related genes (p-value < 0.05): ADM, ANGPTL4, USP8, EDN, NFIL3, MSR1, and CEBPD. The enriched terms revealed significant functional roles of HIF-1-α transcription; endothelin; ...
Source: Genes - January 21, 2022 Category: Genetics & Stem Cells Authors: Ali Khan Muhammad Hassan Tags: Article Source Type: research

Genes, Vol. 13, Pages 188: An Assessment of GPX1 (rs1050450), DIO2 (rs225014) and SEPP1 (rs7579) Gene Polymorphisms in Women with Endometrial Cancer
Conclusion: Carriers of the DIO2 (rs225014) polymorphism may be predisposed to the development of endometrial cancer. Further research confirming this relationship is recommended. (Source: Genes)
Source: Genes - January 21, 2022 Category: Genetics & Stem Cells Authors: Janowska Potocka Paszek Skrzypa Żulewicz Kluz Januszek Baszuk Gronwald Lubi ński Zawlik Kluz Tags: Article Source Type: research

Genes, Vol. 13, Pages 189: Identification and Functional Analysis of the Regulatory Elements in the pHSPA6 Promoter
g Pang Tang Xie Functional and expressional research of heat shock protein A6 (HSPA6) suggests that the gene is of great value for neurodegenerative diseases, biosensors, cancer, etc. Based on the important value of pigs in agriculture and biomedicine and to advance knowledge of this little-studied HSPA member, the stress-sensitive sites in porcine HSPA6 (pHSPA6) were investigated following different stresses. Here, two heat shock elements (HSEs) and a conserved region (CR) were identified in the pHSPA6 promoter by a CRISPR/Cas9-mediated precise gene editing strategy. Gene expression data showed that sequence ...
Source: Genes - January 21, 2022 Category: Genetics & Stem Cells Authors: Jiao Bai Qi Wu Hu Li Yang Zhao Ouyang Pang Tang Xie Tags: Article Source Type: research

Genes, Vol. 13, Pages 182: Population Structure and Diversity in European Honey Bees (Apis mellifera L.) & mdash;An Empirical Comparison of Pool and Individual Whole-Genome Sequencing
Conclusions: If costs are not the limiting factor, we recommend using ind-seq, as population genetic structure can be inferred similarly well, with the advantage gained from individual genetic information. Not least, it also significantly reduces the effort required for the collection of numerous samples and their further processing in the laboratory. (Source: Genes)
Source: Genes - January 21, 2022 Category: Genetics & Stem Cells Authors: Chao Chen Melanie Parejo Jamal Momeni Jorge Langa Rasmus O. Nielsen Wei Shi SMARTBEES WP3 DIVERSITY CONTRIBUTORS SMARTBEES WP3 DIVERSITY CONTRIBUTORS Rikke Vingborg Per Kryger Maria Bouga Andone Estonba Marina Meixner Tags: Article Source Type: research

Genes, Vol. 13, Pages 178: Epigenomic Modifications in Modern and Ancient Genomes
alkowiak Thalmann Epigenetic changes have been identified as a major driver of fundamental metabolic pathways. More specifically, the importance of epigenetic regulatory mechanisms for biological processes like speciation and embryogenesis has been well documented and revealed the direct link between epigenetic modifications and various diseases. In this review, we focus on epigenetic changes in animals with special attention on human DNA methylation utilizing ancient and modern genomes. Acknowledging the latest developments in ancient DNA research, we further discuss paleoepigenomic approaches as the only means to ...
Source: Genes - January 20, 2022 Category: Genetics & Stem Cells Authors: Niiranen Leciej Edlund Bernhardsson Fraser Quinto Herzig Jakobsson Walkowiak Thalmann Tags: Review Source Type: research

Genes, Vol. 13, Pages 179: cDNA Characterization and Expression of Selenium-Dependent CqGPx3 Isoforms in the Crayfish Cherax quadricarinatus under High Temperature and Hypoxia
We report the presence and differential expression of GPx3 isoforms in crustacean tissues in normal conditions and under stress for high temperature and hypoxia. The two isoforms are tissue specific and condition specific, which could indicate an important role of CqGPx3a in the central nervous system and CqGPx3b in exposed tissues, both involved in different responses to environmental stressors. (Source: Genes)
Source: Genes - January 20, 2022 Category: Genetics & Stem Cells Authors: Laura E. Hern ández-Aguirre Yazmin I. Fuentes-Sidas Lizandro R. Rivera-Rangel N éstor Gutiérrez-Méndez Gloria Yepiz-Plascencia David Ch ávez-Flores Francisco J. Zavala-D íaz de la Serna Mar ía del R. Peralta-Pérez Antonio Garc ía-Triana Tags: Article Source Type: research

Genes, Vol. 13, Pages 180: Regulation of Replication Stress in Alternative Lengthening of Telomeres by Fanconi Anaemia Protein
ing Jia Fanconi anaemia (FA)-related proteins function in interstrand crosslink (ICL) repair pathways and multiple damage repair pathways. Recent studies have found that FA proteins are involved in the regulation of replication stress (RS) in alternative lengthening of telomeres (ALT). Since ALT cells often exhibit high-frequency ATRX mutations and high levels of telomeric secondary structure, high levels of DNA damage and replicative stress exist in ALT cells. Persistent replication stress is required to maintain the activity of ALT mechanistically, while excessive replication stress causes ALT cell death. FA proteins...
Source: Genes - January 20, 2022 Category: Genetics & Stem Cells Authors: Duda Li Kailong Hou Ke Zhang Shuting Jia Tags: Review Source Type: research

Genes, Vol. 13, Pages 181: Genome-Wide Association Study of Root System Architecture in Maize
Chen Pan Roots are important plant organs for the absorption of water and nutrients. To date, there have been few genome-wide association studies of maize root system architecture (RSA) in the field. The genetic basis of maize RSA is poorly understood, and the maize RSA-related genes that have been cloned are very limited. Here, 421 maize inbred lines of an association panel were planted to measure the root systems at the maturity stage, and a genome-wide association study was performed. There was a strong correlation among eight RSA traits, and the RSA traits were highly correlated with the aboveground plant arc...
Source: Genes - January 20, 2022 Category: Genetics & Stem Cells Authors: Wu Ren Zhao Li Sun Chen Pan Tags: Article Source Type: research

Genes, Vol. 13, Pages 169: LMNA Mutation in a Family with a Strong History of Sudden Cardiac Death
We report a family with heterozygous deletion of exons 3–6 of the LMNA gene. The main presentation of affected family members was characterized by ventricular and supraventricular arrhythmias, atrioventricular (AV) block and sudden cardiac death (SCD) but also by severe dilative cardiomyopathy (DCM). We report on two siblings, a 36-year-old female and her 40-year-old brother, who suffer from heart failure with mildly reduced ejection fraction, AV conduction delays and premature ventricular complexes. Their 65-year-old mother underwent heart transplantation at the age of 55 due to advanced heart failure. Origi...
Source: Genes - January 19, 2022 Category: Genetics & Stem Cells Authors: Laura Keil Filip Berisha Dorit Knappe Christian Kubisch Moneef Shoukier Paulus Kirchhof Larissa Fabritz Yorck Hellenbroich Rixa Woitschach Christina Magnussen Tags: Case Report Source Type: research

Genes, Vol. 13, Pages 170: Identification of HIV Rapid Mutations Using Differences in Nucleotide Distribution over Time
. Yau Mutation is the driving force of species evolution, which may change the genetic information of organisms and obtain selective competitive advantages to adapt to environmental changes. It may change the structure or function of translated proteins, and cause abnormal cell operation, a variety of diseases and even cancer. Therefore, it is particularly important to identify gene regions with high mutations. Mutations will cause changes in nucleotide distribution, which can be characterized by natural vectors globally. Based on natural vectors, we propose a mathematical formula for measuring the difference in nucleo...
Source: Genes - January 19, 2022 Category: Genetics & Stem Cells Authors: Nan Sun Jie Yang Stephen S.-T. Yau Tags: Article Source Type: research

Genes, Vol. 13, Pages 171: Expression Profiles of miR-22-5p and miR-142-3p Indicate Hashimoto & rsquo;s Disease and Are related to Thyroid Antibodies
Genes, Vol. 13, Pages 171: Expression Profiles of miR-22-5p and miR-142-3p Indicate Hashimoto’s Disease and Are related to Thyroid Antibodies Genes doi: 10.3390/genes13020171 Authors: Olivia Trummer Ines Foessl Natascha Schweighofer Edi Arifi Christoph W. Haudum Sharmaine Reintar Stefan Pilz Verena Theiler-Schwetz Christian Trummer Andreas Zirlik Albrecht Schmidt Caterina Colantonio Ewald Kolesnik Nicolas Verheyen Thomas R. Pieber Barbara Obermayer-Pietsch Hashimoto’s thyroiditis (HT) is the most prevalent autoimmune disorder of the thyroid (AITD) and characteri...
Source: Genes - January 19, 2022 Category: Genetics & Stem Cells Authors: Olivia Trummer Ines Foessl Natascha Schweighofer Edi Arifi Christoph W. Haudum Sharmaine Reintar Stefan Pilz Verena Theiler-Schwetz Christian Trummer Andreas Zirlik Albrecht Schmidt Caterina Colantonio Ewald Kolesnik Nicolas Verheyen Thomas R. Pieber Barb Tags: Article Source Type: research

Genes, Vol. 13, Pages 173: Predicting Essential Proteins Based on Integration of Local Fuzzy Fractal Dimension and Subcellular Location Information
Kai Liu Essential proteins are indispensable to cells’ survival and development. Prediction and analysis of essential proteins are crucial for uncovering the mechanisms of cells. With the help of computer science and high-throughput technologies, forecasting essential proteins by protein–protein interaction (PPI) networks has become more efficient than traditional approaches (expensive experimental methods are generally used). Many computational algorithms were employed to predict the essential proteins; however, they have various restrictions. To improve the prediction accuracy, by introduc...
Source: Genes - January 19, 2022 Category: Genetics & Stem Cells Authors: Li Shen Jian Zhang Fang Wang Kai Liu Tags: Article Source Type: research

Genes, Vol. 13, Pages 172: Variation in Genotype and DNA Methylation Patterns Based on Alcohol Use and CVD in the Korean Genome and Epidemiology Study (KoGES)
Jeong-An Gim Alcohol consumption can increase the risk of chronic diseases, such as myocardial infarction, coronary artery disease, hyperlipidemia, and hypertension. We aimed to assess the association between genotype, DNA methylation patterns, alcohol consumption, and chronic diseases in Korean population. We analyzed 8840 subjects for genotypes and 446 for DNA methylation among the 9351 subjects from the Korean Genome and Epidemiology Study (KoGES). We further divided both groups into two sub-groups according to the presence/absence of chronic diseases. We selected genes whose methylation varied significantly with a...
Source: Genes - January 19, 2022 Category: Genetics & Stem Cells Authors: Myoungjee Jung Yeon-Soon Ahn Sei-Jin Chang Chun-Bae Kim Kyoung Sook Jeong Sang-Baek Koh Jeong-An Gim Tags: Article Source Type: research

Genes, Vol. 13, Pages 175: Selection of References for microRNA Quantification in Japanese Flounder (Paralichthys olivaceus) Normal Tissues and Edwardsiella tarda-Infected Livers
In this study, combined with miRNA-Seq analysis and literature search, 10 candidates (miR-34a-5p, miR-205-5p, miR-101a-3p, miR-22-3p, miR-23a-3p, miR-210-5p, miR-30c-5p, U6, 5S rRNA, and 18S rRNA) were chosen as potential references to test their expression stability among P. olivaceus tissues, and in livers of P. olivaceus infected with Edwardsiella tarda at different time points. The expression stability of these candidates was analyzed by qRT-PCR and evaluated with Delta CT, BestKeeper, geNorm, as well as NormFinder methods, and RefFinder was employed to estimate the comprehensive ranking according to the four methods. ...
Source: Genes - January 19, 2022 Category: Genetics & Stem Cells Authors: Saisai Liu Haofei Song Zeyu Liu Wei Lu Quanqi Zhang Jie Cheng Tags: Article Source Type: research

Genes, Vol. 13, Pages 174: Mucilaginibacter sp. Strain Metal(loid) and Antibiotic Resistance Isolated from Estuarine Soil Contaminated Mine Tailing from the Fund & atilde;o Dam
Genes, Vol. 13, Pages 174: Mucilaginibacter sp. Strain Metal(loid) and Antibiotic Resistance Isolated from Estuarine Soil Contaminated Mine Tailing from the Fundão Dam Genes doi: 10.3390/genes13020174 Authors: Ana L. S. Vasconcelos Fernando Dini Andreote Thaiane Defalco Endrews Delbaje Leticia Barrientos Armando C. F. Dias Fabricio Angelo Gabriel Angelo F. Bernardino Kattia Núñez-Montero In 2015 a mine dam with Mn-Fe-rich tailings collapsed releasing million tons of sediments over an estuary, in the Southwest of Brazil. The tailings have a high concentration of metals that c...
Source: Genes - January 19, 2022 Category: Genetics & Stem Cells Authors: Ana L. S. Vasconcelos Fernando Dini Andreote Thaiane Defalco Endrews Delbaje Leticia Barrientos Armando C. F. Dias Fabricio Angelo Gabriel Angelo F. Bernardino Kattia N úñez-Montero Tags: Communication Source Type: research

Genes, Vol. 13, Pages 176: Research on Frequent Itemset Mining of Imaging Genetics GWAS in Alzheimer & rsquo;s Disease
Genes, Vol. 13, Pages 176: Research on Frequent Itemset Mining of Imaging Genetics GWAS in Alzheimer’s Disease Genes doi: 10.3390/genes13020176 Authors: Hong Liang Luolong Cao Yue Gao Haoran Luo Xianglian Meng Ying Wang Jin Li Wenjie Liu As an efficient method, genome-wide association study (GWAS) is used to identify the association between genetic variation and pathological phenotypes, and many significant genetic variations founded by GWAS are closely associated with human diseases. However, it is not enough to mine only a single marker effect variation on complex biological phenotypes. Mi...
Source: Genes - January 19, 2022 Category: Genetics & Stem Cells Authors: Hong Liang Luolong Cao Yue Gao Haoran Luo Xianglian Meng Ying Wang Jin Li Wenjie Liu Tags: Article Source Type: research

Genes, Vol. 13, Pages 177: The Organization of the Pig T-Cell Receptor & gamma; (TRG) Locus Provides Insights into the Evolutionary Patterns of the TRG Genes across Cetartiodactyla
Genes, Vol. 13, Pages 177: The Organization of the Pig T-Cell Receptor γ (TRG) Locus Provides Insights into the Evolutionary Patterns of the TRG Genes across Cetartiodactyla Genes doi: 10.3390/genes13020177 Authors: Linguiti Giannico D’Addabbo Pala Caputi Jambrenghi Ciccarese Massari Antonacci The domestic pig (Sus scrofa) is a species representative of the Suina, one of the four suborders within Cetartiodactyla. In this paper, we reported our analysis of the pig TRG locus in comparison with the loci of species representative of the Ruminantia, Tylopoda, and Cetacea suborders. ...
Source: Genes - January 19, 2022 Category: Genetics & Stem Cells Authors: Linguiti Giannico D ’Addabbo Pala Caputi Jambrenghi Ciccarese Massari Antonacci Tags: Article Source Type: research

Genes, Vol. 13, Pages 164: The Interactive Effect of Genetic and Epigenetic Variations in FKBP5 and ApoE Genes on Anxiety and Brain EEG Parameters
eny I. Rogaev FKBP51 is a key stress-responsive regulator of the hypothalamic–pituitary–adrenal axis. To elucidate the contribution of rs1360780 FKBP5 C/T alleles to aging and longevity, we genotyped FKBP5 in a cohort of 800 non-demented and Alzheimer’s disease (AD) subjects of different age, taking into account the allele state of ApoE ε4, the major risk factor for AD. Furthermore, we searched for the association of FKBP5 with subcohorts of non-demented subjects evaluated for anxiety and resting-state quantitative EEG characteristics, associated with cognitive,...
Source: Genes - January 18, 2022 Category: Genetics & Stem Cells Authors: Irina L. Kuznetsova Natalya V. Ponomareva Ekaterina A. Alemastseva Andrey D. Manakhov Tatyana V. Andreeva Fedor E. Gusev Evgeny I. Rogaev Tags: Article Source Type: research

Genes, Vol. 13, Pages 165: Splicing Variants, Protein-Protein Interactions, and Drug Targeting in Hutchinson-Gilford Progeria Syndrome and Small Cell Lung Cancer
Joon Park Alternative splicing (AS) is a biological operation that enables a messenger RNA to encode protein variants (isoforms) that give one gene several functions or properties. This process provides one of the major sources of use for understanding the proteomic diversity of multicellular organisms. In combination with post-translational modifications, it contributes to generating a variety of protein–protein interactions (PPIs) that are essential to cellular homeostasis or proteostasis. However, cells exposed to many kinds of stresses (aging, genetic changes, carcinogens, etc.) sometimes derive cance...
Source: Genes - January 18, 2022 Category: Genetics & Stem Cells Authors: Bae-Hoon Kim Tae-Gyun Woo So-Mi Kang Soyoung Park Bum-Joon Park Tags: Review Source Type: research

Genes, Vol. 13, Pages 166: Stalling of Eukaryotic Translesion DNA Polymerases at DNA-Protein Cross-Links
Zharkov DNA-protein cross-links (DPCs) are extremely bulky adducts that interfere with replication. In human cells, they are processed by SPRTN, a protease activated by DNA polymerases stuck at DPCs. We have recently proposed the mechanism of the interaction of DNA polymerases with DPCs, involving a clash of protein surfaces followed by the distortion of the cross-linked protein. Here, we used a model DPC, located in the single-stranded template, the template strand of double-stranded DNA, or the displaced strand, to study the eukaryotic translesion DNA polymerases ζ (POLζ), ι (PO...
Source: Genes - January 18, 2022 Category: Genetics & Stem Cells Authors: Anna V. Yudkina Evgeniy S. Shilkin Alena V. Makarova Dmitry O. Zharkov Tags: Article Source Type: research

Genes, Vol. 13, Pages 167: The Special Features of Prenatal and Preimplantation Genetic Counseling in Arab Countries
We report that: (i) utilization of genetic counseling services varies across different Arab countries; (ii) many factors affect decision making and service utilization, especially religion; and (iii) parents are faced with an array of decisions in the prenatal setting, partly driven by increased utilization of prenatal diagnosis and preimplantation genetic testing in some countries. Our work is the first to highlight the different factors and decisions influencing genetic counseling in Arab countries. Understanding these factors is essential for improving genetic counseling services in the region and helping counselors fac...
Source: Genes - January 18, 2022 Category: Genetics & Stem Cells Authors: Shaza D. Malik Mashael Al-Shafai Atiyeh M. Abdallah Tags: Review Source Type: research

Genes, Vol. 13, Pages 168: Further Delineation of Developmental Delay with Gastrointestinal, Cardiovascular, Genitourinary, and Skeletal Abnormalities Caused by ZNF699 Gene Mutation
bert Smigiel Until 2021, the ZNF699 gene was not associated with any human genetic disease. There were only two studies exploring the associations between variants in ZNF699 and alcohol dependence. In 2021 Bertoli-Avella et al. reported 13 patients with a ZNF699 gene mutation. All patients presented global developmental delay and with systemic manifestations. A new phenotype was proposed and called DEGCAGS syndrome (OMIM 619488) (developmental delay with gastrointestinal, cardiovascular, genitourinary, and skeletal abnormalities). The DEGCAGS syndrome is inherited in the autosomal recessive mode. Here, we report a new ...
Source: Genes - January 18, 2022 Category: Genetics & Stem Cells Authors: Mateusz Biela Malgorzata Rydzanicz Agnieszka Jankowska Agnieszka Szlagatys-Sidorkiewicz Anna Rozensztrauch Rafa ł Płoski Robert Smigiel Tags: Case Report Source Type: research

Genes, Vol. 13, Pages 158: Inorganic Nitrogen Transport and Assimilation in Pea (Pisum sativum)
J. Miller The genome sequences of several legume species are now available allowing the comparison of the nitrogen (N) transporter inventories with non-legume species. A survey of the genes encoding inorganic N transporters and the sensing and assimilatory families in pea, revealed similar numbers of genes encoding the primary N assimilatory enzymes to those in other types of plants. Interestingly, we find that pea and Medicago truncatula have fewer members of the NRT2 nitrate transporter family. We suggest that this difference may result from a decreased dependency on soil nitrate acquisition, as legumes have the capa...
Source: Genes - January 17, 2022 Category: Genetics & Stem Cells Authors: Benguo Gu Yi Chen Fang Xie Jeremy D. Murray Anthony J. Miller Tags: Review Source Type: research

Genes, Vol. 13, Pages 159: Identification of AMH and AMHR2 Variants Led to the Diagnosis of Persistent M & uuml;llerian Duct Syndrome in Three Cases
In this study, we performed molecular genetic analysis of 11 unrelated cryptorchidism patients using whole-exome sequencing and classified the variants. Three of the 11 patients had biallelic mutations in AMH or AMHR2. Case 1 carried a homozygous 4-bp deletion; c.321_324del:p.Q109Lfs*29 in exon 1 of AMH (NM_000479 transcript), which is a frameshift mutation, leading to the loss of function of AMH. Case 2 carried compound heterozygous mutations; c.494_502del (p.I165_A168delinsT) in exon 4 and g.6147C>A of AMHR2 (NM_001164690 transcript). Case 3 carried compound heterozygous mutations; c.G1168A (p.E390K) in exon 9...
Source: Genes - January 17, 2022 Category: Genetics & Stem Cells Authors: Yang Liu Sida Wang Ruzhu Lan Jun Yang Tags: Article Source Type: research

Genes, Vol. 13, Pages 160: Selection and Validation of Reliable Reference Genes for Gene Expression Studies in Different Genotypes and TRV-Infected Fruits of Peach (Prunus persica L. Batsch) during Ripening
In this study, 10 reference genes were selected and gene expression was characterized by RT-qPCR across all samples, including different genotypes and TRV-infected fruits during ripening. Four statistical algorithms (geNorm, NormFinder, BestKeeper, and RefFinder) were used to calculate the stability of 10 reference genes. The geNorm analysis indicated that two suitable reference genes should be used for gene expression normalization. In general, the best combination of reference genes was CYP2 and Tua5 for TRV-infected fruits and CYP2 and Tub1 for different genotypes. In 18S, GADPH, and TEF2, there is an unacceptable varia...
Source: Genes - January 17, 2022 Category: Genetics & Stem Cells Authors: Ze Xu Jieyu Dai Weijing Su Haixia Wu Kamran Shah Libo Xing Juanjuan Ma Dong Zhang Caiping Zhao Tags: Article Source Type: research

Genes, Vol. 13, Pages 161: Indirect Genetic Effects of ADIPOQ Variants on Lipid Levels in a Sibling Study of a Rural Chinese Population
ang Chen Tao Wu Variations in lipid levels are the result of combinations of genetic and environmental factors. We aim to investigate the indirect effect between siblings of the three polymorphisms of ADIPOQ on serum lipid levels in rural Chinese populations. A total of 2571 sibling pairs were enrolled as study participants. A generalized estimating equation was used to accommodate a family-based design. We used stratified analysis to detect sex combination differences in the indirect genetic effect. We found a significant association between the number of altered risk alleles of rs182052 and ego lipid levels of TG (...
Source: Genes - January 17, 2022 Category: Genetics & Stem Cells Authors: Zechen Zhou Yujia Ma Xiaoyi Li Zeyu Yan Kexin Ding Han Xiao Yiqun Wu Dafang Chen Tao Wu Tags: Article Source Type: research

Genes, Vol. 13, Pages 162: Evaluation of Different Cleaning Strategies for Removal of Contaminating DNA Molecules
In this study, the effects of ten different cleaning strategies were evaluated to compare their ability to remove contaminating DNA molecules. Cell-free DNA or blood was deposited on three surfaces (plastic, metal, and wood) and decontaminated with various treatments. The quantities of recovered DNA, obtained by swabbing the surfaces after cleaning using the different strategies, was analyzed by real-time PCR. Large differences in the DNA removal efficiencies were observed between different cleaning strategies, as well as between different surfaces. The most efficient cleaning strategies for cell-free DNA were the differen...
Source: Genes - January 17, 2022 Category: Genetics & Stem Cells Authors: Martina Nilsson Hanne De Maeyer Marie Allen Tags: Article Source Type: research

Genes, Vol. 13, Pages 163: Genetic Rescue of the Highly Inbred Norwegian Lundehund
Vik Stronen Augmenting the genetic diversity of small, inbred populations by the introduction of new individuals is often termed “genetic rescue”. An example is the Norwegian Lundehund, a small spitz dog with inbreeding-related health problems that is being crossed with three Nordic breeds, including the Norwegian Buhund. Conservation breeding decisions for the (typically) small number of outcrossed individuals are vital for managing the rescue process, and we genotyped the Lundehund (n = 12), the Buhund (n = 12), their crosses (F1, n = 7) and first-generation backcrosses to the Lundehund (F...
Source: Genes - January 17, 2022 Category: Genetics & Stem Cells Authors: Claudia Melis Cino Pertoldi William Basil Ludington Carol Beuchat Gunnar Qvigstad Astrid Vik Stronen Tags: Article Source Type: research

Genes, Vol. 13, Pages 156: Drought, Low Nitrogen Stress, and Ultraviolet-B Radiation Effects on Growth, Development, and Physiology of Sweetpotato Cultivars during Early Season
aja Reddy Drought, ultraviolet-B (UV-B), and nitrogen stress are significant constraints for sweetpotato productivity. Their impact on plant growth and development can be acute, resulting in low productivity. Identifying phenotypes that govern stress tolerance in sweetpotatoes is highly desirable to develop elite cultivars with better yield. Ten sweetpotato cultivars were grown under nonstress (100% replacement of evapotranspiration (ET)), drought-stress (50% replacement of ET), UV-B (10 kJ), and low-nitrogen (20% LN) conditions. Various shoot and root morphological, physiological, and gas-exchange traits were measured...
Source: Genes - January 16, 2022 Category: Genetics & Stem Cells Authors: Purushothaman Ramamoorthy Raju Bheemanahalli Stephen L. Meyers Mark W. Shankle Kambham Raja Reddy Tags: Article Source Type: research

Genes, Vol. 13, Pages 157: Genetic Distribution of Five Spinocerebellar Ataxia Microsatellite Loci in Mexican Native American Populations and Its Impact on Contemporary Mestizo Populations
uis Velázquez-Pérez Jonathan J. Magaña Spinocerebellar ataxias (SCAs) conform a heterogeneous group of neurodegenerative disorders with autosomal dominant inheritance. Five of the most frequent SCAs are caused by a CAG repeat expansion in the exons of specific genes. The SCAs incidence and the distribution of polymorphic CAG alleles vary among populations and ethnicities. Thus, characterization of the genetic architecture of ethnically diverse populations, which have undergone recent admixture and demographic events, could facilitate the identification of genetic risk factors. Owing to the great ...
Source: Genes - January 16, 2022 Category: Genetics & Stem Cells Authors: Roc ío Gómez Yessica S. Tapia-Guerrero Bulmaro Cisneros Lorena Orozco C ésar Cerecedo-Zapata Elvia Mendoza-Caamal Gerardo Leyva-G ómez Norberto Leyva-Garc ía Luis Vel ázquez-Pérez Jonathan J. Maga ña Tags: Article Source Type: research

Genes, Vol. 13, Pages 147: All Ways Lead to Rome & mdash;Meiotic Stabilization Can Take Many Routes in Nascent Polyploid Plants
Genes, Vol. 13, Pages 147: All Ways Lead to Rome—Meiotic Stabilization Can Take Many Routes in Nascent Polyploid Plants Genes doi: 10.3390/genes13010147 Authors: Adrián Gonzalo Newly formed polyploids often show extensive meiotic defects, resulting in aneuploid gametes, and thus reduced fertility. However, while many neopolyploids are meiotically unstable, polyploid lineages that survive in nature are generally stable and fertile; thus, those lineages that survive are those that are able to overcome these challenges. Several genes that promote polyploid stabilization are now known in plants, allowi...
Source: Genes - January 15, 2022 Category: Genetics & Stem Cells Authors: Adri án Gonzalo Tags: Review Source Type: research

Genes, Vol. 13, Pages 148: Methylphosphonate Degradation and Salt-Tolerance Genes of Two Novel Halophilic Marivita Metagenome-Assembled Genomes from Unrestored Solar Salterns
Tringe Aerobic bacteria that degrade methylphosphonates and produce methane as a byproduct have emerged as key players in marine carbon and phosphorus cycles. Here, we present two new draft genome sequences of the genus Marivita that were assembled from metagenomes from hypersaline former industrial salterns and compare them to five other Marivita reference genomes. Phylogenetic analyses suggest that both of these metagenome-assembled genomes (MAGs) represent new species in the genus. Average nucleotide identities to the closest taxon were <85%. The MAGs were assembled with SPAdes, binned with MetaBAT, and ...
Source: Genes - January 15, 2022 Category: Genetics & Stem Cells Authors: Clifton P. Bueno de Mesquita Jinglie Zhou Susanna Theroux Susannah G. Tringe Tags: Article Source Type: research

Genes, Vol. 13, Pages 149: Novel Pathogenic Variants in PJVK, the Gene Encoding Pejvakin, in Subjects with Autosomal Recessive Non-Syndromic Hearing Impairment and Auditory Neuropathy Spectrum Disorder
We report three novel DFNB59 cases, one from the AR-NSHI cohort and two from the ANSD cohort, with stable, severe to profound NSHI. Two of the subjects received unilateral cochlear implantation, with apparent good outcomes. Our study expands the spectrum of PJVK mutations, as we report four novel pathogenic variants: p.Leu224Arg, p.His294Ilefs*43, p.His294Asp and p.Phe317Serfs*20. We review the reported cases of DFNB59, summarize the clinical features of this rare subtype of AR-NSHI and discuss the involvement of PJVK in ANSD. (Source: Genes)
Source: Genes - January 15, 2022 Category: Genetics & Stem Cells Authors: Mar ía Domínguez-Ruiz Montserrat Rodr íguez-Ballesteros Marta Gand ía Elena G ómez-Rosas Manuela Villamar Pietro Scimemi Patrizia Mancini Nanna D. Rendtorff Miguel A. Moreno-Pelayo Lisbeth Tranebjaerg Carme Med à Rosamaria Santarelli Ignacio del Cas Tags: Article Source Type: research

Genes, Vol. 13, Pages 150: A Simulated Shift Work Schedule Does Not Increase DNA Double-Strand Break Repair by NHEJ in the Drosophila Rr3 System
der M. Yu Long-term shift work is widely believed to increase the risk of certain cancers, but conflicting findings between studies render this association unclear. Evidence of interplay between the circadian clock, cell cycle regulation, and DNA damage detection machinery suggests the possibility that circadian rhythm disruption consequent to shift work could alter the DNA double-strand break (DSB) repair pathway usage to favor mutagenic non-homologous end-joining (NHEJ) repair. To test this hypothesis, we compared relative usage of NHEJ and single-strand annealing (SSA) repair of a complementary ended chromosomal dou...
Source: Genes - January 15, 2022 Category: Genetics & Stem Cells Authors: Lydia Bergerson Caleb Fitzmaurice Tyler Knudtson Halle McCormick Alder M. Yu Tags: Article Source Type: research

Genes, Vol. 13, Pages 151: Changes in Expression of Specific mRNA Transcripts after Single- or Re-Irradiation in Mouse Testes
In this study, we examined the levels of mRNA transcripts encoding markers of 13 markers of germ cell differentiation and 28 Sertoli cell-specific products in single- and re-irradiated mice. Our results demonstrated that re-irradiation induced significantly decreased testicular weights with a significant decrease in germ cell differentiation mRNA species (Spo11, Tnp1, Gfra1, Oct4, Sycp3, Ddx4, Boll, Crem, Prm1, and Acrosin). In the 13 Sertoli cell-specific mRNA species decreased upon irradiation, six mRNA species (Claudin-11,Espn, Fshr, GATA1, Inhbb, and Wt1) showed significant differences between single- and re-irradiatio...
Source: Genes - January 15, 2022 Category: Genetics & Stem Cells Authors: Kenta Nagahori Ning Qu Miyuki Kuramasu Yuki Ogawa Daisuke Kiyoshima Kaori Suyama Shogo Hayashi Kou Sakabe Takayuki Yoshimoto Masahiro Itoh Tags: Article Source Type: research

Genes, Vol. 13, Pages 153: Establishing the Mutational Spectrum of Hungarian Patients with Familial Hypercholesterolemia
s Mariann Harangi István Balogh Familial hypercholesterolemia (FH) is one of the most common autosomal, dominantly inherited diseases affecting cholesterol metabolism, which, in the absence of treatment, leads to the development of cardiovascular complications. The disease is still underdiagnosed, even though an early diagnosis would be of great importance for the patient to receive proper treatment and to prevent further complications. No studies are available describing the genetic background of Hungarian FH patients. In this work, we present the clinical and molecular data of 44 unrelated individuals with...
Source: Genes - January 15, 2022 Category: Genetics & Stem Cells Authors: L ászló Madar Lilla Juh ász Zsuzsanna Sz űcs L óránt Kerkovits Mariann Harangi Istv án Balogh Tags: Article Source Type: research

Genes, Vol. 13, Pages 154: Genotype-Phenotype Comparison in POGZ-Related Neurodevelopmental Disorders by Using Clinical Scoring
hung Jolanda H. Schieving Jana Behunova Mateja Smogavec Franco Laccone Martina Witsch-Baumgartner Joachim Zobel Hans-Christoph Duba Denisa Weis POGZ-related disorders (also known as White-Sutton syndrome) encompass a wide range of neurocognitive abnormalities and other accompanying anomalies. Disease severity varies widely among POGZ patients and studies investigating genotype-phenotype association are scarce. Therefore, our aim was to collect data on previously unreported POGZ patients and perform a large-scale phenotype-genotype comparison from published data. Overall, 117 POGZ patients’...
Source: Genes - January 15, 2022 Category: Genetics & Stem Cells Authors: D óra Nagy Sarah Verheyen Kristen M. Wigby Artem Borovikov Artem Sharkov Valerie Slegesky Austin Larson Christina Fagerberg Charlotte Brasch-Andersen Maria Kib æk Ingrid Bader Rebecca Hernan Frances A. High Wendy K. Chung Jolanda H. Schieving Jana Behun Tags: Article Source Type: research

Genes, Vol. 13, Pages 155: Molecular Responses to Thermal and Osmotic Stress in Arctic Intertidal Mussels (Mytilus edulis): The Limits of Resilience
Melody S. Clark Increases in Arctic temperatures have accelerated melting of the Greenland icesheet, exposing intertidal organisms, such as the blue mussel Mytilus edulis, to high air temperatures and low salinities in summer. However, the interaction of these combined stressors is poorly described at the transcriptional level. Comparing expression profiles of M. edulis from experimentally warmed (30 °C and 33 °C) animals kept at control (23‰) and low salinities (15‰) revealed a significant lack of enrichment for Gene Ontology terms (GO), indicating that similar ...
Source: Genes - January 15, 2022 Category: Genetics & Stem Cells Authors: Nicholas J. Barrett Jakob Thyrring Elizabeth M. Harper Mikael K. Sejr Jesper G. S ørensen Lloyd S. Peck Melody S. Clark Tags: Article Source Type: research

Genes, Vol. 13, Pages 152: LncRNAs and the Angiogenic Switch in Cancer: Clinical Significance and Therapeutic Opportunities
amini Angiogenesis is one of the hallmarks of cancer, and the establishment of new blood vessels is vital to allow for a tumour to grow beyond 1–2 mm in size. The angiogenic switch is the term given to the point where the number or activity of the pro-angiogenic factors exceeds that of the anti-angiogenic factors, resulting in the angiogenic process proceeding, giving rise to new blood vessels accompanied by increased tumour growth, metastasis, and potential drug resistance. Long noncoding ribonucleic acids (lncRNAs) have been found to play a role in the angiogenic switch by regulating gene expression, tr...
Source: Genes - January 15, 2022 Category: Genetics & Stem Cells Authors: Peace Mabeta Rodney Hull Zodwa Dlamini Tags: Review Source Type: research

Genes, Vol. 13, Pages 139: OTP970 Is Required for RNA Editing of Chloroplast ndhB Transcripts in Arabidopsis thaliana
ang Honglei Jin RNA editing is essential for compensating for defects or mutations in haploid organelle genomes and is regulated by numerous trans-factors. Pentatricopeptide repeat (PPR) proteins are the prime factors that are involved in RNA editing; however, many have not yet been identified. Here, we screened the plastid-targeted PLS-DYW subfamily of PPR proteins belonging to Arabidopsis thaliana and identified ORGANELLE TRANSCRIPT PROCESSING 970 (OTP970) as a key player in RNA editing in plastids. A loss-of-function otp970 mutant was impaired in RNA editing of ndhB transcripts at site 149 (ndhB-C149). RNA-immunop...
Source: Genes - January 14, 2022 Category: Genetics & Stem Cells Authors: Mei Fu Xiaona Lin Yining Zhou Chunmei Zhang Bing Liu Dongru Feng Jinfa Wang Hongbin Wang Honglei Jin Tags: Article Source Type: research

Genes, Vol. 13, Pages 141: Review of the Forensic Applicability of Biostatistical Methods for Inferring Ancestry from Autosomal Genetic Markers
k The inference of ancestry has become a part of the services many forensic genetic laboratories provide. Interest in ancestry may be to provide investigative leads or identify the region of origin in cases of unidentified missing persons. There exist many biostatistical methods developed for the study of population structure in the area of population genetics. However, the challenges and questions are slightly different in the context of forensic genetics, where the origin of a specific sample is of interest compared to the understanding of population histories and genealogies. In this paper, the methodologies for mod...
Source: Genes - January 14, 2022 Category: Genetics & Stem Cells Authors: Torben Tvedebrink Tags: Review Source Type: research

Genes, Vol. 13, Pages 142: Effects of BPA, BPS, and BPF on Oxidative Stress and Antioxidant Enzyme Expression in Bovine Oocytes and Spermatozoa
Favetta Bisphenol A (BPA) and its analogs, bisphenol S (BPS) and bisphenol F (BPF), might impact fertility by altering oxidative stress pathways. Here, we hypothesize that bisphenols-induced oxidative stress is responsible for decreased gamete quality. In both female (cumulus-oocyte-complexes—COCs) and male (spermatozoa), oxidative stress was measured by CM-H2DCFDA assay and key ROS scavengers (SOD1, SOD2, GPX1, GPX4, CAT) were quantified at the mRNA and protein levels using qPCR and Western blot (COCs)/immunofluorescence (sperm). Either gamete was treated in five groups: control, vehicle, and 0.05 mg/mL ...
Source: Genes - January 14, 2022 Category: Genetics & Stem Cells Authors: Mimi Nguyen Reem Sabry Ola S. Davis Laura A. Favetta Tags: Article Source Type: research

Genes, Vol. 13, Pages 140: Cyanogenesis in the Sorghum Genus: From Genotype to Phenotype
In this study, leaves of wild species endemic in Australia are screened for the presence of the cyanogenic glucoside dhurrin. The direct measurement of dhurrin content and the potential for dhurrin-derived HCN release (HCNp) showed that all the tested Australian wild species were essentially phenotypically acyanogenic. The unexpected low dhurrin content may reflect the variable and generally nutrient-poor environments in which they are growing in nature. Genome sequencing of six CWR and PCR amplification of the CYP79A1 gene from additional species showed that a high conservation of key amino acids is required for correct p...
Source: Genes - January 14, 2022 Category: Genetics & Stem Cells Authors: Max Cowan Birger Lindberg M øller Sally Norton Camilla Knudsen Christoph Crocoll Agnelo Furtado Robert Henry Cecilia Blomstedt Roslyn M. Gleadow Tags: Article Source Type: research

Genes, Vol. 13, Pages 143: Genome-Wide Analysis in Drosophila Reveals the Genetic Basis of Variation in Age-Specific Physical Performance and Response to ACE Inhibition
adir Jeff Leips Despite impressive results in restoring physical performance in rodent models, treatment with renin–angiotensin system (RAS) inhibitors, such as Lisinopril, have highly mixed results in humans, likely, in part, due to genetic variation in human populations. To date, the genetic determinants of responses to drugs, such as RAS inhibitors, remain unknown. Given the complexity of the relationship between physical traits and genetic background, genomic studies which predict genotype- and age-specific responses to drug treatments in humans or vertebrate animals are difficult. Here, using 126 g...
Source: Genes - January 14, 2022 Category: Genetics & Stem Cells Authors: Mariann M. Gabrawy Nick Khosravian George S. Morcos Tatiana V. Morozova Meagan Jezek Jeremy D. Walston Wen Huang Peter M. Abadir Jeff Leips Tags: Article Source Type: research

Genes, Vol. 13, Pages 144: Influence of Haptoglobin Polymorphism on Stroke in Sickle Cell Disease Patients
vain Doré This review outlines the current clinical research investigating how the haptoglobin (Hp) genetic polymorphism and stroke occurrence are implicated in sickle cell disease (SCD) pathophysiology. Hp is a blood serum glycoprotein responsible for binding and removing toxic free hemoglobin from the vasculature. The role of Hp in patients with SCD is critical in combating blood toxicity, inflammation, oxidative stress, and even stroke. Ischemic stroke occurs when a blocked vessel decreases oxygen delivery in the blood to cerebral tissue and is commonly associated with SCD. Due to the malformed red blood cell...
Source: Genes - January 14, 2022 Category: Genetics & Stem Cells Authors: Olivia Edwards Alicia Burris Josh Lua Diana J. Wilkie Miriam O. Ezenwa Sylvain Dor é Tags: Review Source Type: research