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Molecular Genetics and Genomics: MGG

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https://www.readbyqxmd.com/read/28913654/discriminating-cirrnas-from-other-lncrnas-using-a-hierarchical-extreme-learning-machine-h-elm-algorithm-with-feature-selection
#1
Lei Chen, Yu-Hang Zhang, Guohua Huang, Xiaoyong Pan, ShaoPeng Wang, Tao Huang, Yu-Dong Cai
As non-coding RNAs, circular RNAs (cirRNAs) and long non-coding RNAs (lncRNAs) have attracted an increasing amount of attention. They have been confirmed to participate in many biological processes, including playing roles in transcriptional regulation, regulating protein-coding genes, and binding to RNA-associated proteins. Until now, the differences between these two types of non-coding RNAs have not been fully uncovered. It is still quite difficult to detect cirRNAs from other lncRNAs using simple techniques...
September 14, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28913560/deregulation-of-obesity-relevant-genes-is-associated-with-progression-in-bmi-and-the-amount-of-adipose-tissue-in-pigs
#2
Caroline M Junker Mentzel, Tainã Figueiredo Cardoso, Christian Bressen Pipper, Mette Juul Jacobsen, Claus Bøttcher Jørgensen, Susanna Cirera, Merete Fredholm
The aim of this study was to elucidate the relative impact of three phenotypes often used to characterize obesity on perturbation of molecular pathways involved in obesity. The three obesity-related phenotypes are (1) body mass index (BMI), (2) amount of subcutaneous adipose tissue (SATa), and (3) amount of retroperitoneal adipose tissue (RPATa). Although it is generally accepted that increasing amount of RPATa is 'unhealthy', a direct comparison of the relative impact of the three obesity-related phenotypes on gene expression has, to our knowledge, not been performed previously...
September 14, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28900732/plant-stand-p-loop-ntpases-a-current-perspective-of-genome-distribution-evolution-and-function-plant-stand-p-loop-ntpases-genomic-organization-evolution-and-molecular-mechanism-models-contribute-broadly-to-plant-pathogen-defense
#3
REVIEW
Preeti Arya, Vishal Acharya
STAND P-loop NTPase is the common weapon used by plant and other organisms from all three kingdoms of life to defend themselves against pathogen invasion. The purpose of this study is to review comprehensively the latest finding of plant STAND P-loop NTPase related to their genomic distribution, evolution, and their mechanism of action. Earlier, the plant STAND P-loop NTPase known to be comprised of only NBS-LRRs/AP-ATPase/NB-ARC ATPase. However, recent finding suggests that genome of early green plants comprised of two types of STAND P-loop NTPases: (1) mammalian NACHT NTPases and (2) NBS-LRRs...
September 12, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28894972/gene-regulation-of-mammalian-long-non-coding-rna
#4
REVIEW
Heeyoun Bunch
RNA polymerase II (Pol II) transcribes two classes of RNAs, protein-coding and non-protein-coding (ncRNA) genes. ncRNAs are also synthesized by RNA polymerases I and III (Pol I and III). In humans, the number of ncRNA genes exceeds more than twice that of protein-coding genes. However, the history of studying Pol II-synthesized ncRNA is relatively short. Since early 2000s, important biological and pathological functions of these ncRNA genes have begun to be discovered and intensively studied. And transcription mechanisms of long non-coding RNA (lncRNA) have been recently reported...
September 11, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28894953/significant-genetic-association-of-a-functional-tfpi-variant-with-circulating-fibrinogen-levels-and-coronary-artery-disease
#5
Duraid Hamid Naji, Chengcheng Tan, Fabin Han, Yuanyuan Zhao, Junhan Wang, Dan Wang, Jingjing Fa, Sisi Li, Shanshan Chen, Qiuyun Chen, Chengqi Xu, Qing K Wang
The tissue factor pathway inhibitor (TFPI) gene encodes a protease inhibitor with a critical role in regulation of blood coagulation. Some genomic variants in TFPI were previously associated with plasma TFPI levels, however, it remains to be further determined whether TFPI variants are associated with other coagulation factors. In this study, we carried out a large population-based study with 2313 study subjects for blood coagulation data, including fibrinogen levels, prothrombin time (PT), activated partial thromboplastin time (APTT), and thrombin time (TT)...
September 11, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28884289/dispersals-of-the-siberian-y-chromosome-haplogroup-q-in-eurasia
#6
Yun-Zhi Huang, Horolma Pamjav, Pavel Flegontov, Vlastimil Stenzl, Shao-Qing Wen, Xin-Zhu Tong, Chuan-Chao Wang, Ling-Xiang Wang, Lan-Hai Wei, Jing-Yi Gao, Li Jin, Hui Li
The human Y-chromosome has proven to be a powerful tool for tracing the paternal history of human populations and genealogical ancestors. The human Y-chromosome haplogroup Q is the most frequent haplogroup in the Americas. Previous studies have traced the origin of haplogroup Q to the region around Central Asia and Southern Siberia. Although the diversity of haplogroup Q in the Americas has been studied in detail, investigations on the diffusion of haplogroup Q in Eurasia and Africa are still limited. In this study, we collected 39 samples from China and Russia, investigated 432 samples from previous studies of haplogroup Q, and analyzed the single nucleotide polymorphism (SNP) subclades Q1a1a1-M120, Q1a2a1-L54, Q1a1b-M25, Q1a2-M346, Q1a2a1a2-L804, Q1a2b2-F1161, Q1b1a-M378, and Q1b1a1-L245...
September 7, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28879530/correlation-analyses-revealed-global-microrna-mrna-expression-associations-in-human-peripheral-blood-mononuclear-cells
#7
Lan Wang, Jiang Zhu, Fei-Yan Deng, Long-Fei Wu, Xing-Bo Mo, Xiao-Wei Zhu, Wei Xia, Fang-Fei Xie, Pei He, Peng-Fei Bing, Ying-Hua Qiu, Xiang Lin, Xin Lu, Lei Zhang, Neng-Jun Yi, Yong-Hong Zhang, Shu-Feng Lei
MicroRNAs (miRNAs) can regulate gene expression through binding to complementary sites in the 3'-untranslated regions of target mRNAs, which will lead to existence of correlation in expression between miRNA and mRNA. However, the miRNA-mRNA correlation patterns are complex and remain largely unclear yet. To establish the global correlation patterns in human peripheral blood mononuclear cells (PBMCs), multiple miRNA-mRNA correlation analyses and expression quantitative trait locus (eQTL) analysis were conducted in this study...
September 6, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28879498/locating-qtls-controlling-overwintering-trait-in-chinese-perennial-dongxiang-wild-rice
#8
Yongshu Liang, Jian Zheng, Chao Yan, Xingxin Li, Shifeng Liu, Junjie Zhou, Xiaojian Qin, Wenbin Nan, Yongqing Yang, Hanma Zhang
Overwintering (OW) is the process by which rice passes through the winter season and germinates in the following spring. OW is also a typical quantitative inheritance trait. Currently, the molecular genetic basis of OW trait in Chinese perennial Dongxiang wild rice (DXWR) still remains to be known. In this study, a linkage map consisting of 139 simple sequence repeat (SSR) markers was constructed using an F2 population derived from a cross between DXWR and 93-11. This map covered the rice genome by approximately 1778...
September 6, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28866851/systematic-transcriptome-wide-analysis-of-mrna-mirna-interactions-reveals-the-involvement-of-mir-142-5p-and-its-target-foxo3-in-skeletal-muscle-growth-in-chickens
#9
Zhenhui Li, Bahareldin Ali Abdalla, Ming Zheng, Xiaomei He, Bolin Cai, Peigong Han, Hongjia Ouyang, Biao Chen, Qinghua Nie, Xiquan Zhang
The goal of this study was to perform a systematic transcriptome-wide analysis of mRNA-miRNA interactions and to identify candidates involved in the interplay between miRNAs and mRNAs that regulate chicken muscle growth. We used our previously published mRNA (GSE72424) and miRNA (GSE62971) deep sequencing data from two-tailed samples [i.e., the highest (h) and lowest (l) body weights] of Recessive White Rock (WRR) and Xinghua (XH) chickens to conduct integrative analyses of the miRNA-mRNA interactions involved in chicken skeletal muscle growth...
September 2, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28864888/molecular-cloning-of-a-cc-nbs-lrr-gene-from-vitis-quinquangularis-and-its-expression-pattern-in-response-to-downy-mildew-pathogen-infection
#10
Shuwei Zhang, Feng Ding, Hongxiang Peng, Yu Huang, Jiang Lu
Downy mildew, caused by Plasmopara viticola, can result in a substantial decrease in grapevine productivity. Vitis vinifera is a widely cultivated grapevine species, which is susceptible to this disease. Repeated pesticide applications are harmful for both the environment and human health. Thus, it is essential to develop varieties/cultivars that are resistant to downy mildew and other diseases. In our previous studies, we investigated the natural resistance of the Chinese wild grapevine V. quinquangularis accession 'PS' against P...
September 1, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28852881/itraq-based-proteomics-monitors-the-withering-dynamics-in-postharvest-leaves-of-tea-plant-camellia-sinensis
#11
Zhi-Jun Wu, Hong-Yu Ma, Jing Zhuang
Tea plant [Camellia sinensis (L.) O. Kuntze] is a typical leaf-type beverage crop. Many secondary metabolites, such as tea polyphenols, theanine, and caffeine that accumulated in tea leaves are beneficial to human health. The fresh leaves of tea plant are harvested and timely processed into tea products with different flavors. The withering of fresh tea leaves is the first step in tea processing and directly affects tea color, taste, and fragrance. To understand the molecular mechanism that influences tea quality during withering, we investigated the dynamic changes in the proteome of postharvest tea leaves in four withering stages (0, 1, 4, and 12 h treatments)...
August 29, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28849273/a-d-genome-originated-ty1-copia-type-retrotransposon-family-expanded-significantly-in-tetraploid-cottons
#12
Qian Li, Yue Zhang, Zhengsheng Zhang, Xianbi Li, Dan Yao, Yi Wang, Xufen Ouyang, Yaohua Li, Wu Song, Yuehua Xiao
Retrotransposons comprise of a major fraction of higher plant genomes, and their proliferation and elimination have profound effects on genome evolution and gene functions as well. Previously we found a D-genome-originated Ty1/Copia-type LTR (DOCL) retrotransposon in the chromosome A08 of upland cotton. To further characterize the DOCL retrotransposon family, a total of 342 DOCL retrotransposons were identified in the sequenced cotton genomes, including 73, 157, and 112 from Gossypium raimondii, G. hirsutum, and G...
August 28, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28840320/cre-lox-based-multiple-markerless-gene-disruption-in-the-genome-of-the-extreme-thermophile-thermus-thermophilus
#13
Yoichiro Togawa, Tatsuo Nunoshiba, Keiichiro Hiratsu
Markerless gene-disruption technology is particularly useful for effective genetic analyses of Thermus thermophilus (T. thermophilus), which have a limited number of selectable markers. In an attempt to develop a novel system for the markerless disruption of genes in T. thermophilus, we applied a Cre/lox system to construct a triple gene disruptant. To achieve this, we constructed two genetic tools, a loxP-htk-loxP cassette and cre-expressing plasmid, pSH-Cre, for gene disruption and removal of the selectable marker by Cre-mediated recombination...
August 24, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28836000/antcaller-an-accurate-variant-caller-incorporating-ancient-dna-damage
#14
Boyan Zhou, Shaoqing Wen, Lingxiang Wang, Li Jin, Hui Li, Hong Zhang
Ancient DNA obtained from ancient samples, such as sediments, bones, and teeth, is an important genetic resource that can be used to reconstruct an evolutional history of humans, animals, and plants. The application of high-throughput sequencing enables the research of ancient DNA to be conducted in a whole genome scale. However, post-mortem DNA damage mainly caused by deamination of cytosine to uracil (or methylated cytosine to thymine) may confound the variant calling and downstream analysis. In this article, we develop a Python program to implement a new variant caller, "AntCaller", which extracts the information on nucleotide substitutions from sequencing data and calculates the probability of each genotype based on a Bayesian rule...
August 23, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28821952/genome-wide-association-study-and-gene-set-analysis-for-understanding-candidate-genes-involved-in-salt-tolerance-at-the-rice-seedling-stage
#15
Jie Yu, Weiguo Zao, Qiang He, Tae-Sung Kim, Yong-Jin Park
Salt is the major factor limiting crop productivity in saline soils and is controlled by various genes. The development of salt-tolerant rice through molecular breeding methods is important to meet the needs of rice breeding. We used 295 accessions to perform a genome-wide association study (GWAS) of salt tolerance-related phenotypes in rice at the seedling stage and obtained 93 candidate genes with high association peaks across six phenotypes. We constructed a protein interaction network using the candidate genes identified here, and 33 genes were associated...
August 18, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28819830/identification-and-characterization-of-tyrosine-kinases-in-anole-lizard-indicate-the-conserved-tyrosine-kinase-repertoire-in-vertebrates
#16
Ake Liu, Funan He, Xun Gu
The tyrosine kinases (TKs) play principal roles in regulation of multicellular aspects of the organism and are implicated in many cancer types and congenital disorders. The anole lizard has recently been introduced as a model organism for laboratory-based studies of organismal function and field studies of ecology and evolution. However, the TK family of anole lizard has not been systematically identified and characterized yet. In this study, we identified 82 TK-encoding genes in the anole lizard genome and classified them into 28 subfamilies through phylogenetic analysis, with no member from ROS and STYK1 subfamilies identified...
August 17, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28785867/scmed7-a-sugarcane-mediator-subunit-gene-acts-as-a-regulator-of-plant-immunity-and-is-responsive-to-diverse-stress-and-hormone-treatments
#17
Xu Zhang, Yuting Yang, Jiake Zou, Yun Chen, Qibin Wu, Jinlong Guo, Youxiong Que, Liping Xu
The Mediator complex, is an essential component of the RNA polymerase II general transcriptional machinery in eukaryotes. Mediator subunit 7 (MED7), a key subunit in the central module of this complex, plays an important role in gene transcriptional regulation. The present study isolated the full-length cDNA of the MED7 gene of sugarcane, hereby designated as ScMED7, which was characterized to harbor a 525-bp open reading frame that is predicted to encode a 174-amino acid protein with a molecular mass of 19...
August 7, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28785866/whole-genome-comparative-analysis-of-four-georgian-grape-cultivars
#18
V Tabidze, I Pipia, M Gogniashvili, N Kunelauri, L Ujmajuridze, M Pirtskhalava, B Vishnepolsky, A G Hernandez, C J Fields, Tengiz Beridze
Grapevine is the one of the most important fruit species in the world. Comparative genome sequencing of grape cultivars is very important for the interpretation of the grape genome and understanding its evolution. The genomes of four Georgian grape cultivars-Chkhaveri, Saperavi, Meskhetian green, and Rkatsiteli, belonging to different haplogroups, were resequenced. The shotgun genomic libraries of grape cultivars were sequenced on an Illumina HiSeq. Pinot Noir nuclear, mitochondrial, and chloroplast DNA were used as reference...
August 7, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28766017/pmk-1-p38-mapk-promotes-cadmium-stress-resistance-the-expression-of-skn-1-nrf-and-daf-16-target-genes-and-protein-biosynthesis-in-caenorhabditis-elegans
#19
Alex Keshet, Ansgar Mertenskötter, Sarah A Winter, Vanessa Brinkmann, Ramona Dölling, Rüdiger J Paul
The mechanisms of cadmium (Cd) resistance are complex and not sufficiently understood. The present study, therefore, aimed at assessing the roles of important components of stress-signaling pathways and of ABC transporters under severe Cd stress in Caenorhabditis elegans. Survival assays on mutant and control animals revealed a significant promotion of Cd resistance by the PMK-1 p38 MAP kinase, the transcription factor DAF-16/FoxO, and the ABC transporter MRP-1. Transcriptome profiling by RNA-Seq on wild type and a pmk-1 mutant under control and Cd stress conditions revealed, inter alia, a PMK-1-dependent promotion of gene expression for the translational machinery...
August 1, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28748394/association-mapping-analysis-of-fiber-yield-and-quality-traits-in-upland-cotton-gossypium-hirsutum-l
#20
Mulugeta Seyoum Ademe, Shoupu He, Zhaoe Pan, Junling Sun, Qinglian Wang, Hongde Qin, Jinhai Liu, Hui Liu, Jun Yang, Dongyong Xu, Jinlong Yang, Zhiying Ma, Jinbiao Zhang, Zhikun Li, Zhongmin Cai, Xuelin Zhang, Xin Zhang, Aifen Huang, Xianda Yi, Guanyin Zhou, Lin Li, Haiyong Zhu, Baoyin Pang, Liru Wang, Yinhua Jia, Xiongming Du
Fiber yield and quality are the most important traits for Upland cotton (Gossypium hirsutum L.). Identifying high yield and good fiber quality genes are the prime concern of researchers in cotton breeding. Association mapping offers an alternative and powerful method for detecting those complex agronomic traits. In this study, 198 simple sequence repeats (SSRs) were used to screen markers associated with fiber yield and quality traits with 302 elite Upland cotton accessions that were evaluated in 12 locations representing the Yellow River and Yangtze River cotton growing regions of China...
July 26, 2017: Molecular Genetics and Genomics: MGG
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