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Epigenetic Mechanisms of Paternal Stress in Offspring Development and Diseases Int. J. Genom. (IF 2.414) Pub Date : 2021-01-19 Xingyun Xu; Zhigang Miao; Miao Sun; Bo Wan
The major biological function of the sperm cell is to transmit the paternal genetic and epigenetic information to the embryo as well as the following offspring. Sperm has a unique epigenome. An increasing body of epidemiological study supports that paternal stress induced by environmental exposures and lifestyle can modulate the sperm epigenome (including histone modification, DNA methylation, and
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QTL Mapping of Traits Associated with Dual Resistance to the African Stem Borer (Busseola fusca) and Spotted Stem Borer (Chilo partellus) in Sorghum (Sorghum bicolor) Int. J. Genom. (IF 2.414) Pub Date : 2021-01-18 Phyllis W. Muturi; Mary Mgonja; Patrick Rubaihayo; James K. Mwololo
Sorghum (Sorghum bicolor (L.) Moench) is an important food crop in semi-arid tropics. The crop grain yield ranges from 0.5 t/ha to 0.8 t/ha compared to potential yields of 10 t/ha. The African stem borer Busseola fusca Fuller (Noctuidae) and the spotted stem borer Chilo partellus Swinhoe (Crambidae), are among the most economically important insect pests of sorghum. The two borers can cause 15% - 80%
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LAPTM5 Plays a Key Role in the Diagnosis and Prognosis of Testicular Germ Cell Tumors Int. J. Genom. (IF 2.414) Pub Date : 2021-01-13 Xiunan Li; Yu Su; Jiayao Zhang; Ye Zhu; Yingkun Xu; Guangzhen Wu
Objective. Testicular germ cell tumors (TGCT) are a serious malignant tumor with low early diagnosis rates and high mortality. Methods. To investigate novel biomarkers to predict the diagnosis and prognosis of this cancer, bioinformatics analysis was used as an accurate, efficient, and economical method. Results. Our study detected 39 upregulated and 589 downregulated differentially expressed genes
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Genome-Wide Characterization of RNA Editing Sites in Primary Gastric Adenocarcinoma through RNA-seq Data Analysis Int. J. Genom. (IF 2.414) Pub Date : 2020-12-18 Javad Behroozi; Shirin Shahbazi; Mohammad Reza Bakhtiarizadeh; Habibollah Mahmoodzadeh
RNA editing is a posttranscriptional nucleotide modification in humans. Of the various types of RNA editing, the adenosine to inosine substitution is the most widespread in higher eukaryotes, which is mediated by the ADAR family enzymes. Inosine is recognized by the biological machinery as guanosine; therefore, editing could have substantial functional effects throughout the genome. RNA editing could
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A Novel Four-Gene Prognostic Signature as a Risk Biomarker in Cervical Cancer Int. J. Genom. (IF 2.414) Pub Date : 2020-12-16 Jun Wang; Hua Zheng; Yatian Han; Geng Wang; Yanbin Li
Background. Cervical cancer (CC) is a major malignancy affecting women worldwide, with limited treatment options for patients with advanced disease. The aim of this study was to identify novel prognostic biomarkers for CC. Methods. RNA-Seq data from four Gene Expression Omnibus datasets (GSE5787, GSE6791, GSE26511, and GSE63514) were used to identify differentially expressed genes (DEGs) between CC
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Molecular Characterization and Evolution Analysis of Two Forms of TLR5 and TLR13 Genes Base on Larimichthys crocea Genome Data Int. J. Genom. (IF 2.414) Pub Date : 2020-12-09 Lihua Jiang; Liyi Pei; Ping Wang; Liqin Liu; Gong Li; Binjian Liu; Zhenming Lǚ; Tabata Hiromasa; Hao Pan; Atsushi Ogura
TLRs (Toll-like receptors) are essential in host defense against pathogens. There are two types of TLR5, namely, membrane form of TLR5 (TLR5M) and soluble form of TLR5 (TLR5S), both of which perform a crucial role in flagellin response. TLR13 is a TLR that localizes to endosomes and recognizes nucleic acids released by internal microorganisms, including viruses, bacteria, and fungi. Here, the full-length
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Identification of Differentially Expressed Drought-Responsive Genes in Guar [Cyamopsis tetragonoloba (L.) Taub] Int. J. Genom. (IF 2.414) Pub Date : 2020-12-04 Aref Alshameri; Fahad Al-Qurainy; Abdel-Rhman Gaafar; Salim Khan; Mohammad Nadeem; Saleh Alansi; Hassan O. Shaikhaldein; Abdalrhaman M. Salih
Drought remains one of the most serious environmental stresses because of the continuous reduction in soil moisture, which requires the improvement of crops with features such as drought tolerance. Guar [Cyamopsis tetragonoloba (L.) Taub], a forage and industrial crop, is a nonthirsty plant. However, the information on the transcriptome changes that occur under drought stress in guar is very limited;
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Characterization of an IncR Plasmid with Two Copies of ISCR-Linked qnrB6 from ST968 Klebsiella pneumoniae Int. J. Genom. (IF 2.414) Pub Date : 2020-11-24 Changrui Qian; Xinyi Zhu; Junwan Lu; Kai Shen; Qianqian Chen; Wangxiao Zhou; Hongmao Liu; Wei Lu; Danying Zhou; Zhewei Sun; Xi Lin; Kewei Li; Qiyu Bao; Teng Xu; Shunfei Lu
To characterize the molecular structure of IncR plasmid-related sequences, comparative genomic analysis was conducted using 261 IncR plasmid backbone-related sequences. Among the sequences, 257 were IncR plasmids including the multidrug-resistance IncR plasmid pR50-74 from Klebsiella pneumoniae strain R50 of this work, and the other four were from bacterial chromosomes. The IncR plasmids were derived
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Vaginal Microbiota Diversity of Patients with Embryonic Miscarriage by Using 16S rDNA High-Throughput Sequencing Int. J. Genom. (IF 2.414) Pub Date : 2020-11-23 Linfen Xu; Lingna Huang; Chengying Lian; Huili Xue; Yanfang Lu; Xiujuan Chen; Yong Xia
Embryonic miscarriage severely affects the life quality and physical and mental state of pregnant women. However, the detailed mechanism underlying embryonic miscarriage is not fully understood. This study is aimed at analyzing embryonic miscarriage. We collected samples from 25 normal pregnant women and 25 embryonic miscarriage patients of similar age to analyze microbiota isolated from the vagina
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Construction and Validation of Predictive Model to Identify Critical Genes Associated with Advanced Kidney Disease Int. J. Genom. (IF 2.414) Pub Date : 2020-11-12 Guangda Xin; Guangyu Zhou; Wenlong Zhang; Xiaofei Zhang
Background. Chronic kidney disease (CKD) is characterized by progressive renal function loss, which may finally lead to end-stage renal disease (ESRD). The study is aimed at identifying crucial genes related to CKD progressive and constructing a disease prediction model to investigate risk factors. Methods. GSE97709 and GSE37171 datasets were downloaded from the GEO database including peripheral blood
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Identification and Expression Analysis of Sugar Transporter Gene Family in Aspergillus oryzae Int. J. Genom. (IF 2.414) Pub Date : 2020-11-07 Gongbo Lv; Chunmiao Jiang; Tiantian Liang; Yayi Tu; Xiaojie Cheng; Bin Zeng; Bin He
Sugar transporter (SUT) genes are associated with multiple physiological and biochemical processes in filamentous fungi, such as the response to various stresses. However, limited systematic analysis and functional information of SUT gene family have been available on Aspergillus oryzae (A. oryzae). To investigate the potential roles of SUTs in A. oryzae, we performed an integrative analysis of the
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Differential Expression of miR-136 in Gestational Diabetes Mellitus Mediates the High-Glucose-Induced Trophoblast Cell Injury through Targeting E2F1 Int. J. Genom. (IF 2.414) Pub Date : 2020-10-23 Chunxia Zhang; Li Wang; Jinfeng Chen; Fei Song; Yuzhen Guo
Background. Gestational diabetes mellitus (GDM) seriously affects the health of mothers and infants. The high-glucose-induced inhibition in trophoblast cell viability is an important event in GDM pathogenesis. This study evaluated the expression and clinical significance of miR-136 in GDM patients, and the biological function and related mechanisms of miR-136 in the regulation of trophoblast cell proliferation
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Exploring Host Genetic Polymorphisms Involved in SARS-CoV Infection Outcomes: Implications for Personalized Medicine in COVID-19 Int. J. Genom. (IF 2.414) Pub Date : 2020-10-22 Omar Ramos-Lopez; Lidia Daimiel; Ana Ramírez de Molina; Diego Martínez-Urbistondo; Juan A. Vargas; J. Alfredo Martínez
Objective. To systematically explore genetic polymorphisms associated with the clinical outcomes in SARS-CoV infection in humans. Methods. This comprehensive literature search comprised available English papers published in PubMed/Medline and SCOPUS databases following the PRISMA-P guidelines and PICO/AXIS criteria. Results. Twenty-nine polymorphisms located in 21 genes were identified as associated
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Two Variants in the NOTCH4 and HLA-C Genes Contribute to Familial Clustering of Psoriasis Int. J. Genom. (IF 2.414) Pub Date : 2020-10-20 Minglong Cai; He Huang; Zhulin Hu; Tao Yuan; Weiran Li; Yaoguang Liu; Lijun Zheng; Yan Zhang; Yujun Sheng; Xuejun Zhang
Psoriasis is a multifactorial immune-mediated skin disease with a strong genetic background. Previous studies reported that psoriasis with a family history (PFH) and sporadic psoriasis (SP) have a distinct manifestation and genetic predisposition. However, the genetic heterogeneity of PFH and SP in the major histocompatibility complex (MHC) region has not been fully elucidated. To explore genetic variants
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Dysregulated Expression and Methylation Analysis Identified TLX1NB as a Novel Recurrence Marker in Low-Grade Gliomas Int. J. Genom. (IF 2.414) Pub Date : 2020-10-12 Hongzhou Duan; Zuozhen Yang; Chen Li; Jiayong Zhang; Shengli Shen; Changwei Yuan; Yingjin Wang
Low-grade gliomas (LGGs) are the most common CNS tumors, and the main therapy for LGGs is complete surgical resection, due to its curative effect. However, LGG recurrence occurs frequently. Biomarkers play a crucial role in evaluating the recurrence and prognosis of LGGs. Numerous studies have focused on LGG prognosis. However, the multiomics research investigating the roles played by gene methylation
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Whole Genome 5-Methylcytosine Level Quantification in Cirrhotic HCV-Infected Egyptian Patients with and without Hepatocellular Carcinoma Int. J. Genom. (IF 2.414) Pub Date : 2020-10-05 Ahmed M. Awad; Wafaa S. Ragab; Nourhan Degheidy; Said Ahmed Ooda
DNA methylation is an epigenetic mechanism used by cells to control gene expression. DNA methylation is a commonly used epigenetic signaling tool that can hold genes in the “off” position. Chronic infection with hepatitis C virus (HCV) is considered a major risk for chronic liver impairment. It is the most common leading cause of HCC. The present work is aimed at studying whole genome 5-methylcytosine
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Exploring Heat-Response Mechanisms of MicroRNAs Based on Microarray Data of Rice Post-meiosis Panicle Int. J. Genom. (IF 2.414) Pub Date : 2020-09-18 Yan Peng; Xianwen Zhang; Yuewu Liu; Xinbo Chen
To explore heat response mechanisms of mircoRNAs (miRNAs) in rice post-meiosis panicle, microarray analysis was performed on RNA isolated from rice post-meiosis panicles which were treated at 40°C for 0 min, 10 min, 20 min, 60 min, and 2 h. By integrating paired differentially expressed (DE) miRNAs and mRNA expression profiles, we found that the expression levels of 29 DE-miRNA families were negatively
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Clinical Evaluation of the Diagnostic Role of MicroRNA-155 in Breast Cancer. Int. J. Genom. (IF 2.414) Pub Date : 2020-09-08 Fatemeh Hosseini Mojahed,Amir Hossein Aalami,Vahid Pouresmaeil,Amir Amirabadi,Mahdi Qasemi Rad,Amirhossein Sahebkar
Aim. Biochemical markers, including microRNAs (miRs), may facilitate the diagnosis and prognosis of breast cancer. This study was aimed at assessing serum miR-155 expression in patients with breast cancer and receptors. Methods. This case-control study was conducted on 36 patients with breast cancer and 36 healthy individuals. After RNA extraction from the patient’s serum, cDNA was synthesized. The
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The Complete Chloroplast Genome of Arabidopsis thaliana Isolated in Korea (Brassicaceae): An Investigation of Intraspecific Variations of the Chloroplast Genome of Korean A. thaliana. Int. J. Genom. (IF 2.414) Pub Date : 2020-09-07 Jongsun Park,Hong Xi,Yongsung Kim
Arabidopsis thaliana (L.) Heynh. is a model organism of plant molecular biology. More than 1,700 whole genome sequences have been sequenced, but no Korean isolate genomes have been sequenced thus far despite the fact that many A. thaliana isolated in Japan and China have been sequenced. To understand the genetic background of Korean natural A. thaliana (named as 180404IB4), we presented its complete
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The Necessity of Prenatal Diagnosis by CMA for the Women with NIPS-Positive Results. Int. J. Genom. (IF 2.414) Pub Date : 2020-09-01 Jun Xu,Ying Xue,Jing Wang,Qin Zhou,Bin Zhang,Bin Yu,Ting Wang
Objective. To retrospectively analyze the results of prenatal diagnoses of noninvasive prenatal screening- (NIPS) positive pregnant women and discuss whether there is a need for chromosomal microarray analysis (CMA). Methods. The study recruited 1,019 NIPS-positive women from two prenatal diagnostic centers. Based on clinical advice, they opted for traditional karyotype analysis or CMA. Single nucleotide
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Global Transcriptome and Correlation Analysis Reveal Cultivar-Specific Molecular Signatures Associated with Fruit Development and Fatty Acid Determination in Camellia oleifera Abel. Int. J. Genom. (IF 2.414) Pub Date : 2020-09-01 Shaofeng Peng,Jia Lu,Zhen Zhang,Li Ma,Caixia Liu,Yongzhong Chen
Background. Oil-tea Camellia is a very important edible oil plant widely distributed in southern China. Tea oil extracted from the oil-tea Camellia seeds is beneficial to health and is considered as a health edible oil. We attempt to identify genes related to fatty acid biosynthesis in an oil-tea Camellia seed kernel, generated a comprehensive transcriptome analysis of the seed kernel at different
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Characterization and Comparative Analysis of RWP-RK Proteins from Arachis duranensis, Arachis ipaensis, and Arachis hypogaea. Int. J. Genom. (IF 2.414) Pub Date : 2020-08-28 Chenyang Liu,Dongliang Yuan,Tong Liu,Mengge Xing,Wenying Xu,Huiying Zhang,Hanqi Jin,Chunmei Cai,Shuai Li
RWP-RK proteins are important factors involved in nitrate response and gametophyte development in plants, and the functions of RWP-RK proteins have been analyzed in many species. However, the characterization of peanut RWP-RK proteins is limited. In this study, we identified 16, 19, and 32 RWP-RK members from Arachis duranensis, Arachis ipaensis, and Arachis hypogaea, respectively, and investigated
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The Analysis of Estrogen-Degrading and Functional Metabolism Genes in Rhodococcus equi DSSKP-R-001. Int. J. Genom. (IF 2.414) Pub Date : 2020-08-26 Kejian Tian,Fanxing Meng,Qi Meng,Yan Gao,Lili Zhang,Le Wang,Yuqing Wang,Xue Li,Hongliang Huo
Estrogen contamination is recognized as one of the most serious environmental problems, causing widespread concern worldwide. Environmental estrogens are mainly derived from human and vertebrate excretion, drugs, and agricultural activities. The use of microorganisms is currently the most economical and effective method for biodegradation of environmental estrogens. Rhodococcus equi DSSKP-R-001 (R-001)
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Comparative Metabolomics Study Revealed Difference in Central Carbon Metabolism between Sika Deer and Red Deer Antler. Int. J. Genom. (IF 2.414) Pub Date : 2020-08-26 Hang Su,Chonghui Yang,Chenrong Jin,He Zhang,Chengcheng Yin,Yang Yang,Haoyuan Chen,Li Jing,Bin Qi,Daqing Zhao,Xueyuan Bai,Li Liu
The antler regeneration has been well studied for the past two decades and adopted in the regenerative medicine model for studying on developmental biology. Despite our growing knowledge of functional molecules regulating antler regeneration, we still do not know whether antler from different deer species possess the exact same mechanism or not. Our previous comparative study between sika deer and
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Mutations in the ARAP3 Gene in Three Families with Primary Lymphedema Negative for Mutations in Known Lymphedema-Associated Genes. Int. J. Genom. (IF 2.414) Pub Date : 2020-08-25 Maurizio Ricci,Rita Compagna,Bruno Amato,Sercan Kenanoglu,Dominika Veselenyiova,Danjela Kurti,Mirko Baglivo,Syed Hussain Basha,Roberta Serrani,Giacinto Abele Donato Miggiano,Barbara Aquilanti,Giuseppina Matera,Giuseppe Marceddu,Valeria Velluti,Lucilla Gagliardi,Munis Dundar,Juraj Krajcovic,Matteo Bertelli
Background. ARAP3 is a small GTPase-activating protein regulator, which has important functions in lymphatic vessel organogenesis and modulation of cell adhesion and migration. Mutations in the ARAP3 gene are associated with impaired lymphatic vessel formation. Objective. The aim of our study was to determine the genotypes of lymphedema patients in relation to variants in the ARAP3 gene in order to
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Goat Genomic Resources: The Search for Genes Associated with Its Economic Traits. Int. J. Genom. (IF 2.414) Pub Date : 2020-08-21 A M A M Zonaed Siddiki,Gous Miah,Md Sirazul Islam,Mahadia Kumkum,Meheadi Hasan Rumi,Abdul Baten,Mohammad Alamgir Hossain
Goat plays a crucial role in human livelihoods, being a major source of meat, milk, fiber, and hides, particularly under adverse climatic conditions. The goat genomics related to the candidate gene approach is now being used to recognize molecular mechanisms that have different expressions of growth, reproductive, milk, wool, and disease resistance. The appropriate literature on this topic has been
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Identification of CPT1A as a Prognostic Biomarker and Potential Therapeutic Target for Kidney Renal Clear Cell Carcinoma and Establishment of a Risk Signature of CPT1A-Related Genes Int. J. Genom. (IF 2.414) Pub Date : 2020-08-18 Yingkun Xu; Guangzhen Wu; Xue Ma; Jianyi Li; Ningke Ruan; Zhiyu Zhang; Yalei Cao; Yougen Chen; Qi Zhang; Qinghua Xia
This study is aimed at investigating the expression, clinical significance, and biological role of CPT1A in kidney renal clear cell carcinoma (KIRC). We used the TCGA database and clinical pathology of tissue specimens to study the expression of CPT1A in KIRC. The expression of CPT1A in the kidney cancer tissue was significantly lower than that in the normal tissue. Survival curves demonstrated that
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Genetic Diversity of Orobanche crenata Populations in Ethiopia Using Microsatellite Markers. Int. J. Genom. (IF 2.414) Pub Date : 2020-08-13 Gashaw Belay,Kassahun Tesfaye,Aladdin Hamwieh,Seid Ahmed,Tiegist Dejene,José Oscar Lustosa de Oliveira Júnior
Orobanche crenata is a parasitic weed that causes considerable yield losses on food legumes in Ethiopia and the Mediterranean region. Understanding the genetic diversity of Orobanche crenata using molecular techniques generate useful information in managing the weed through resistance breeding. This study aimed at assessing the genetic diversity of O. crenata populations collected from major faba bean
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Transcriptome Analysis Reveals Complex Defensive Mechanisms in Salt-Tolerant and Salt-Sensitive Shrub Willow Genotypes under Salinity Stress. Int. J. Genom. (IF 2.414) Pub Date : 2020-07-28 Dezong Sui,Baosong Wang
Salinity stress is one of the most devastating abiotic stresses limiting plant growth and productivity. As a moderately salt-tolerant crop, shrub willow (Salix spp.) is widely distributed over the world and can provide multiple bioenergy product and environmental benefits. To delve into the salt tolerance mechanism and screen out salt-tolerant genes, two shrub willow cultivars (a salt-sensitive genotype
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Integrated Bioinformatic Analysis Identifies Networks and Promising Biomarkers for Hepatitis B Virus-Related Hepatocellular Carcinoma. Int. J. Genom. (IF 2.414) Pub Date : 2020-07-28 Yun Ji,Yue Yin,Weizhen Zhang
Chronic infection with hepatitis B virus (HBV) has long been recognized as a dominant hazard factor for hepatocellular carcinoma (HCC) and accounts for at least half of HCC instances globally. However, the underlying molecular mechanism of HBV-linked HCC has not been completely elucidated. Here, three microarray datasets, totally containing 170 tumoral samples and 181 adjacent normal tissues from the
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Genome-Wide Association Study towards Genomic Predictive Power for High Production and Quality of Milk in American Alpine Goats. Int. J. Genom. (IF 2.414) Pub Date : 2020-07-27 Y Tilahun,T A Gipson,T Alexander,M L McCallum,P R Hoyt
This paper reports an exploratory study based on quantitative genomic analysis in dairy traits of American Alpine goats. The dairy traits are quality-determining components in goat milk, cheese, ice cream, etc. Alpine goat phenotypes for quality components have been routinely recorded for many years and deposited in the Council on Dairy Cattle Breeding (CDCB) repository. The data collected were used
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Genome-Wide Identification and Analysis of Variants in Domestic and Wild Bactrian Camels Using Whole-Genome Sequencing Data. Int. J. Genom. (IF 2.414) Pub Date : 2020-07-16 Nemat Hedayat-Evrigh,Reza Khalkhali-Evrigh,Mohammad Reza Bakhtiarizadeh
The population size of Bactrian camels is smaller than dromedary, and they are distributed in cold and mountain regions and are also at the risk of extinction in some countries such as Iran. To identify and investigate the genome-wide variations, whole-genome sequencing of two Iranian Bactrian camels were performed with 37.4- and 42.6-fold coverage for the first time. Along with Iranian Bactrian camels
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Identification of Prognostic Immune-Related Genes by Integrating mRNA Expression and Methylation in Lung Adenocarcinoma. Int. J. Genom. (IF 2.414) Pub Date : 2020-07-09 Jie Zhu,Min Wang,Daixing Hu
Background. There is plenty of evidence showing that immune-related genes (IRGs) and epigenetic modifications play important roles in the biological process of cancer. The purpose of this study is to establish novel IRG prognostic markers by integrating mRNA expression and methylation in lung adenocarcinoma (LUAD). Methods and Results. The transcriptome profiling data and the RNA-seq data of LUAD with
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Delineation of the Germline and Somatic Mutation Interaction Landscape in Triple-Negative and Non-Triple-Negative Breast Cancer. Int. J. Genom. (IF 2.414) Pub Date : 2020-07-07 Jiande Wu,Tarun K K Mamidi,Lu Zhang,Chindo Hicks
Background. Breast cancer development and progression involve both germline and somatic mutations. High-throughput genotyping and next-generation sequencing technologies have enabled discovery of genetic risk variants and acquired somatic mutations driving the disease. However, the possible oncogenic interactions between germline genetic risk variants and somatic mutations in triple-negative breast
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Genomic Analysis of the SUMO-Conjugating Enzyme and Genes under Abiotic Stress in Potato (Solanum tuberosum L.). Int. J. Genom. (IF 2.414) Pub Date : 2020-06-26 Shantwana Ghimire,Xun Tang,Ning Zhang,Weigang Liu,Xuehong Qi,Xue Fu,Huaijun Si
SUMO-conjugating enzymes (SCE) and SUMO (Small Ubiquitin-Like Modifiers) genes are important components of SUMOylation. SCE has a crucial role during the SUMOylation process which acts as a catalyst to transfer SUMO to the target protein. Comprehensive studies on SCE and SUMO have been performed in some plants, but studies on these genes remain limited in potato. This study is aimed at exploring the
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Identification of Heat-Responsive Genes in Guar [Cyamopsis tetragonoloba (L.) Taub]. Int. J. Genom. (IF 2.414) Pub Date : 2020-06-20 Aref Alshameri,Fahad Al-Qurainy,Abdel-Rhman Gaafar,Salim Khan,Mohammad Nadeem,Saleh Alansi
The threat of heat stress on crop production increased dramatically due to global warming leading to the rise on the demand of heat-tolerant crops and understanding their tolerance. The leguminous forage crop Guar [Cyamopsis tetragonoloba (L.) Taub] is a high-temperature tolerant plant with numerous works on its tolerance at morph-physiological levels but lack on molecular thermotolerance level. In
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Identification of a Robust Five-Gene Risk Model in Prostate Cancer: A Robust Likelihood-Based Survival Analysis. Int. J. Genom. (IF 2.414) Pub Date : 2020-06-01 Yutao Wang,Jiaxing Lin,Kexin Yan,Jianfeng Wang
Aim. In this paper, we aimed to develop and validate a risk prediction method using independent prognosis genes selected robustly in prostate cancer. Method. We considered 723 samples obtained from TCGA (the Cancer Genome Atlas), GSE46602, and GSE21032. Prostate cancer prognosis-related genes with were selected using Univariable Cox regression analysis. We then built the lowest AIC (Akaike information
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Association Study of Puberty-Related Candidate Genes in Chinese Female Population. Int. J. Genom. (IF 2.414) Pub Date : 2020-06-01 Gideon Omariba,Junhua Xiao
Puberty is a transition period where a child transforms to an adult. Puberty can be affected by various genetic factors and environmental influences. In mammals, the regulation of puberty is enhanced by the hypothalamic-pituitary-gonadal axis (HPG axis). A number of genes such as GnRH, Kiss1, and GPR54 have been reported as key regulators of puberty onset. In this study, we have conducted an association
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FcircSEC: An R Package for Full Length circRNA Sequence Extraction and Classification. Int. J. Genom. (IF 2.414) Pub Date : 2020-06-01 Md Tofazzal Hossain,Yin Peng,Shengzhong Feng,Yanjie Wei
Circular RNAs (circRNAs) are formed by joining the 3 and 5 ends of RNA molecules. Identification of circRNAs is an important part of circRNA research. The circRNA prediction methods can predict the circRNAs with start and end positions in the chromosome but cannot identify the full-length circRNA sequences. We present an R package FcircSEC (Full Length circRNA Sequence Extraction and Classification)
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From Microbial Genomics to Metagenomics. Int. J. Genom. (IF 2.414) Pub Date : 2020-05-31 Ravi Kant,Abhishek Kumar,Tarja Sironen
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Molecular Sex Identification in the Hardy Rubber Tree (Eucommia ulmoides Oliver) via ddRAD Markers. Int. J. Genom. (IF 2.414) Pub Date : 2020-05-16 Wencai Wang,Guoqian Yang,Xin Deng,Fengqing Shao,Yongquan Li,Wei Guo,Hong Liang,Xianzhi Zhang
Eucommia ulmoides, also known as the industrially and medicinally important hardy rubber tree, is the sole species of Eucommiaceae. Nevertheless, its dioecious property hinders sex recognition by traditional morphological observation at very early developmental stages, thus inhibiting breeding and economic cropping. In this study, double-digest restriction site-associated DNA sequencing (ddRAD-seq)
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Long Noncoding RNA HOTTIP Serves as an Independent Predictive Biomarker for the Prognosis of Patients with Clear Cell Renal Cell Carcinoma. Int. J. Genom. (IF 2.414) Pub Date : 2020-05-14 Zhanxin Liu,Zichun Wang,Xiaoxiong Wang,Meisong Lu,Guang Chen
Several studies have indicated that HOXA transcript at the distal tip (HOTTIP) play important roles in the tumorigenesis and development of various cancers. We aim to investigate the expression and prognostic value of HOTTIP in clear cell renal cell carcinoma (ccRCC). A systematic review of PubMed, Embase, Medline, and Web of Science databases was performed to select eligible literatures relevant to
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Mining the Prognostic Value of HNRNPAB and Its Function in Breast Carcinoma. Int. J. Genom. (IF 2.414) Pub Date : 2020-05-14 Yun Cao,Wei Zhang,Yi-Ting Jin,Qiang Zou
Heterogeneous nuclear ribonucleoproteins (HNRNPs) are crucial members in the pathogenesis and progression of numerous cancers. However, the expression pattern and clinical significance of HNRNPs in breast carcinoma (BC) remain to be investigated. In the present study, bioinformatic analysis identified HNRNPAB as the only commonly upregulated HNRNP in BC. Elevated expression of HNRNPAB was positively
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Diagnostic Value of miR-103 in Patients with Sepsis and Noninfectious SIRS and Its Regulatory Role in LPS-Induced Inflammatory Response by Targeting TLR4. Int. J. Genom. (IF 2.414) Pub Date : 2020-05-13 Min Yang,Li Zhao,Mingyan Sun
Background. Sepsis is a life-threatening condition and a systemic inflammatory response syndrome (SIRS) driven by infection. This study aimed at investigating the expression of microRNA-103 (miR-103) in sepsis patients, evaluating its diagnostic value, and exploring the regulatory effect of miR-103 on LPS-induced inflammation in monocytes. Methods. Expression of miR-103 was measured using quantitative
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Genome-Wide Analysis, Characterization, and Expression Profile of the Basic Leucine Zipper Transcription Factor Family in Pineapple. Int. J. Genom. (IF 2.414) Pub Date : 2020-05-11 Yanhui Liu,Mengnan Chai,Man Zhang,Qing He,Zhenxia Su,S V G N Priyadarshani,Liping Liu,Guanxi Dong,Yuan Qin
This study identified 57 basic leucine zipper (bZIP) genes from the pineapple genome, and the analysis of these bZIP genes was focused on the evolution and divergence after multiple duplication events in relation to the pineapple genome fusion. According to bioinformatics analysis of a phylogenetic tree, the bZIP gene family was divided into 11 subgroups in pineapple, Arabidopsis, and rice; gene structure
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Statistical Method Based on Bayes-Type Empirical Score Test for Assessing Genetic Association with Multilocus Genotype Data. Int. J. Genom. (IF 2.414) Pub Date : 2020-05-07 Yi Tian,Li Ma,Xiaohong Cai,Jiayan Zhu
Simultaneous testing of multiple genetic variants for association is widely recognized as a valuable complementary approach to single-marker tests. As such, principal component regression (PCR) has been found to have competitive power. We focus on exploring a robust test for an unknown genetic mode of all SNPs, an unknown Hardy-Weinberg equilibrium (HWE) in a population, and a large number of all SNPs
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Transcriptional Sequencing and Gene Expression Analysis of Various Genes in Fruit Development of Three Different Black Pepper (Piper nigrum L.) Varieties. Int. J. Genom. (IF 2.414) Pub Date : 2020-04-30 Choy Yuen Khew,Jennifer Ann Harikrishna,Wei Yee Wee,Ee Tiing Lau,Siaw San Hwang
Black pepper (Piper nigrum) is a vital spice crop with uses ranging from culinary to pharmacological applications. However, limited genetic information has constrained the understanding of the molecular regulation of flower and fruit development in black pepper. In this study, a comparison among three different black pepper varieties, Semengok Aman (SA), Kuching (KC), and Semengok 1 (S1), with varying
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Whole-Genome Sequencing of Mexican Strains of Anaplasma marginale: An Approach to the Causal Agent of Bovine Anaplasmosis. Int. J. Genom. (IF 2.414) Pub Date : 2020-04-14 Fernando Martínez-Ocampo,Rosa Estela Quiroz-Castañeda,Itzel Amaro-Estrada,Edgar Dantán-González,Jesús Francisco Preciado de la Torre,Sergio Rodríguez-Camarillo
Anaplasma marginale is the main etiologic agent of bovine anaplasmosis, and it is extensively distributed worldwide. We have previously reported the first genome sequence of a Mexican strain of A. marginale (Mex-01-001-01). In this work, we report the genomic analysis of one strain from Hidalgo (MEX-14-010-01), one from Morelos (MEX-17-017-01), and two strains from Veracruz (MEX-30-184-02 and MEX-30-193-01)
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An Integrated Approach Exploring the Synergistic Mechanism of Herbal Pairs in a Botanical Dietary Supplement: A Case Study of a Liver Protection Health Food. Int. J. Genom. (IF 2.414) Pub Date : 2020-04-11 Liang Chen,Chun Hu,Molly Hood,Juntao Kan,Xiaona Gan,Xue Zhang,Yi Zhang,Jun Du
Herbal pairs are used as a bridge between single herb and polyherbal formulas in Traditional Chinese Medicine (TCM) to provide rationale for complicated TCM formulas. The effectiveness and rationality of TCM herbal pairs have been widely applied as a strategy for dietary supplements. However, due to the complexity of the phytochemistry of individual and combinations of herbal materials, it is difficult
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Pharmacodynamics of Ceftiofur Selected by Genomic and Proteomic Approaches of Streptococcus parauberis Isolated from the Flounder, Paralichthys olivaceus. Int. J. Genom. (IF 2.414) Pub Date : 2020-03-31 Naila Boby,Muhammad Aleem Abbas,Eon-Bee Lee,Seung-Chun Park
We employed an integrative strategy to present subtractive and comparative metabolic and genomic-based findings of therapeutic targets against Streptococcus parauberis. For the first time, we not only identified potential targets based on genomic and proteomic database analyses but also recommend a new antimicrobial drug for the treatment of olive flounder (Paralichthys olivaceus) infected with S.
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Effect of Huangqin Tang on Colonic Gene Expression in Rats with Ulcerative Colitis. Int. J. Genom. (IF 2.414) Pub Date : 2020-03-27 Dunfang Wang,KaiFeng Shi,Yanli Wang,Dixin Zou,Shanshan Guo,Tao Li,Hangyu Xu,Xuran Ma,JiaXing Liu,HongXin Song,Weipeng Yang,Yu Li
In this study, we explored the pharmacological mechanisms of Huangqin Tang (HQT; a traditional Chinese medicine formula) in ulcerative colitis (UC) and provided evidence for potential roles HQT plays by gene expression profiling. The UC rat model was made via a compound method (trinitrobenzene sulfonic acid plus ethanol). After a ten-day treatment, microarray analysis was performed from the colon segment
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A Five-Genes-Based Prognostic Signature for Cervical Cancer Overall Survival Prediction. Int. J. Genom. (IF 2.414) Pub Date : 2020-03-26 Menghuang Zhao,Wenbin Huang,Shuangwei Zou,Qi Shen,Xueqiong Zhu
Aims. This study is aimed at identifying a prognostic signature for cervical cancer. Main Methods. The gene expression data and clinical information of cervical cancer and normal cervical tissues were acquired from The Cancer Genome Atlas and from three datasets of the Gene Expression Omnibus database. DESeq2 and Limma were employed to screen differentially expressed genes (DEGs). The overlapping DEGs
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A Pooling Genome-Wide Association Study Identifies Susceptibility Loci and Signaling Pathways of Immune Thrombocytopenia in Chinese Han Population Int. J. Genom. (IF 2.414) Pub Date : 2020-03-11 Yanmei Xu; Jing Li; Wentao Yang; Xiaoli Tang; Bo Huang; Jing Liu; Jin Lin; Jing Zhang; Weiming Yang; Shuqi Li; Fan Sun; Libin Deng; Xiaozhong Wang
Immune thrombocytopenia (ITP) is an acquired bleeding disease due to immune-mediated destruction of antilogous platelets and ineffective thrombopoiesis. Although the etiology of ITP remains unknown, genetic variants are thought to predispose individuals to the disease. Several candidate gene analyses have identified several loci that increased ITP susceptibility, but no systematic genetic analysis
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The Association of OTX1 rs17850223 Polymorphisms in Han Chinese Patients with Idiopathic Epilepsy Int. J. Genom. (IF 2.414) Pub Date : 2020-03-10 Jin Lv; Chunsheng Qu; Zhenqiang Huang; Yingbiao Zhu; Wei Wang; Likang Lan
This study is aimed at investigating the association between orthodenticle homeobox 1 (OTX1) gene polymorphisms and idiopathic epilepsy in a cohort of Han Chinese patients. We carried out a case-control study on 147 patients with idiopathic epilepsy and 150 healthy controls. Genomic DNA was isolated from 1 ml of ethylene diamine tetraacetic acid (EDTA)-treated blood. The OTX1 coding sequence was divided
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Metabolite Profiling of Sorghum Seeds of Different Colors from Different Sweet Sorghum Cultivars Using a Widely Targeted Metabolomics Approach Int. J. Genom. (IF 2.414) Pub Date : 2020-03-04 Yaxing Zhou; Zhenguo Wang; Yan Li; Zhigang Li; Hui Liu; Wei Zhou
Sweet sorghum (Sorghum bicolor) is one of the most important cereal crops in the world with colorful seeds. To study the diversity and cultivar-specificity of phytochemicals in sweet sorghum seeds, widely targeted metabolomics was used to analyze the metabolic profiles of the white, red, and purple seeds from three sweet sorghum cultivars Z6, Z27, and HC4. We identified 651 metabolites that were divided
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Genomic Analysis of Bacillus megaterium NCT-2 Reveals Its Genetic Basis for the Bioremediation of Secondary Salinization Soil Int. J. Genom. (IF 2.414) Pub Date : 2020-02-29 Bin Wang; Dan Zhang; Shaohua Chu; Yuee Zhi; Xiaorui Liu; Pei Zhou
Bacillus megaterium NCT-2 is a nitrate-uptake bacterial, which shows high bioremediation capacity in secondary salinization soil, including nitrate-reducing capacity, phosphate solubilization, and salinity adaptation. To gain insights into the bioremediation capacity at the genetic level, the complete genome sequence was obtained by using a multiplatform strategy involving HiSeq and PacBio sequencing
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Comparative Transcriptome Analysis Reveals Molecular Defensive Mechanism of Arachis hypogaea in Response to Salt Stress Int. J. Genom. (IF 2.414) Pub Date : 2020-02-27 Hao Zhang; Xiaobo Zhao; Quanxi Sun; Caixia Yan; Juan Wang; Cuiling Yuan; Chunjuan Li; Shihua Shan; Fengzhen Liu
Abiotic stresses comprise all nonliving factors, such as soil salinity, drought, extreme temperatures, and metal toxicity, posing a serious threat to agriculture and affecting the plant production around the world. Peanut (Arachis hypogaea L.) is one of the most important crops for vegetable oil, proteins, minerals, and vitamins in the world. Therefore, it is of importance to understand the molecular
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Reevaluating the Mutation Classification in Genetic Studies of Bradycardia Using ACMG/AMP Variant Classification Framework Int. J. Genom. (IF 2.414) Pub Date : 2020-02-26 Liting Cheng; Xiaoyan Li; Lin Zhao; Zefeng Wang; Junmeng Zhang; Zhuo Liang; Yongquan Wu
Purpose. Next-generation sequencing (NGS) has become more accessible, leading to an increasing number of genetic studies of familial bradycardia being reported. However, most of the variants lack full evaluation. The relationship between genetic factors and bradycardia should be summarized and reevaluated. Methods. We summarized genetic studies published in the PubMed database from 2008/1/1 to 2019/9/1
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Comparative Genomics of Actinobacillus pleuropneumoniae Serotype 8 Reveals the Importance of Prophages in the Genetic Variability of the Species Int. J. Genom. (IF 2.414) Pub Date : 2020-02-19 Isabelle Gonçalves de Oliveira Prado; Giarlã Cunha da Silva; Josicelli Souza Crispim; Pedro Marcus Pereira Vidigal; Moysés Nascimento; Mateus Ferreira Santana; Denise Mara Soares Bazzolli
Actinobacillus pleuropneumoniae is the etiologic agent of porcine pleuropneumonia. Currently, there are 18 different serotypes; the serotype 8 is the most widely distributed in the United States, Canada, United Kingdom, and southeastern Brazil. In this study, genomes of seven A. pleuropneumoniae serotype 8 clinical isolates were compared to the other genomes of twelve serotypes. The analyses of serotype