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Knockdown of circPUM1 impedes cell growth, metastasis and glycolysis of papillary thyroid cancer via enhancing MAPK1 expression by serving as the sponge of miR-21-5p Genes Genom. (IF 1.188) Pub Date : 2021-01-22 Yanqi Li, Jun Qin, Zhaocai He, Guang Cui, Kun Zhang, Buqiang Wu
Background Circular RNAs (circRNAs) are a crucial class of regulatory RNAs in cancer procession, including papillary thyroid cancer (PTC). Circ-Pumilio 1 (circPUM1) is a novel circRNA with the oncogenic function in ovarian cancer and lung cancer. However, the role of circPUM1 in PTC is undiscovered. Objective This study was performed to investigate the biological function and molecular mechanism of
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Massively parallel sequencing of 25 short tandem repeat loci including the SE33 marker in Koreans Genes Genom. (IF 1.188) Pub Date : 2021-01-22 Ja Hyun Lee, Jeongyong Kim, Hyojeong Kim, Hyo Sook Kim, Eungsoo Kim
Background Massively parallel sequencing (MPS) technology has recently been introduced in research, clinical diagnostics, and forensics. MPS enables determination of the genotypes of multiple short tandem repeat (STR) markers and to determine nucleotide sequence variations, additionally. Objective To improve STR analysis and a paternity index, a new, smaller-sized STR panel was designed that includes
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Aberrant methylation of the 16q23.1 tumor suppressor gene ADAMTS18 promotes tumorigenesis and progression of clear cell renal cell carcinoma Genes Genom. (IF 1.188) Pub Date : 2021-01-19 Ben Xu, Yi-ji Peng, Bing-lei Ma, Si-da Cheng
Background The 16q23.1 tumor suppressor gene (TSG) of ADAMTS18 has been identified to be aberrant methylated in clear cell renal cell carcinoma (ccRCC), and there still exists an unclear situation between its methylation and the progression of ccRCC. Objective To analyze the biological function and mechanism of ADAMTS18 gene in the tumorigenesis and progression of ccRCC. Methods We examined ADAMTS18
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Identification of three novel mutations in PCNT in vietnamese patients with microcephalic osteodysplastic primordial dwarfism type II Genes Genom. (IF 1.188) Pub Date : 2021-01-18 Thu Hien Nguyen, Ngoc-Lan Nguyen, Chi Dung Vu, Can Thi Bich Ngoc, Ngoc Khanh Nguyen, Huy Hoang Nguyen
Background Primordial dwarfism (PD) is a group of genetically heterogeneous disorders related to developmental disabilities occurring in the uterus and prolongs during all stages of life, resulting in short stature, facial deformities and abnormal brain. Objective To determine the exact cause of the disease in two Vietnamese patients priory diagnosed with PD by severe pre-and postnatal growth retardation
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Suppression of HELLS by miR-451a represses mTOR pathway to hinder aggressiveness of SCLC Genes Genom. (IF 1.188) Pub Date : 2021-01-18 Jiyun Cui, Jing Wang, Yuyao Shen, Dianjie Lin
Background Uncovering molecular pathogenesis and mechanisms of small cell lung cancer (SCLC) will contribute to SCLC therapy. Multiple studies demonstrated that miR-451a acts as an anti-tumor miRNA in non-small cell lung cancer. However, the mechanism of miR-451a in SCLC was ambiguous. Objective We aimed to explore the function of miR-451a in SCLC and decipher the underlying mechanisms. Methods TargetScan
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Genetic characterization and association mapping in near-isogenic lines of waxy maize using seed characteristics and SSR markers Genes Genom. (IF 1.188) Pub Date : 2021-01-12 Hae Ri Kim, Kyu Jin Sa, Min Nam-Gung, Ki Jin Park, Si-Hwan Ryu, Chang Yeun Mo, Ju Kyong Lee
Background Association mapping has been advocated as the method of choice for identifying loci involved in the inheritance of complex traits in crop species. This method involves identifying markers with significant differences in allele frequency between individuals with a phenotype of interest and a set of unrelated control individuals. Objective The purpose of our study is not only to investigate
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A fast and powerful aggregated Cauchy association test for joint analysis of multiple phenotypes Genes Genom. (IF 1.188) Pub Date : 2021-01-11 Lili Chen, Yajing Zhou
Background Pleiotropy is a widespread phenomenon in complex human diseases. Jointly analyzing multiple phenotypes can improve power performance of detecting genetic variants and uncover the underlying genetic mechanism. Objective This study aims to detect the association between genetic variants in a genomic region and multiple phenotypes. Methods We develop the aggregated Cauchy association test to
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Screening druggable targets and predicting therapeutic drugs for COVID-19 via integrated bioinformatics analysis Genes Genom. (IF 1.188) Pub Date : 2021-01-11 Siyou Tan, Wenyan Chen, Hongxian Xiang, Gaoyin Kong, Lianhong Zou, Lai Wei
Background Since the outbreak of coronavirus disease 2019 (COVID-19) in China, numerous research institutions have invested in the development of anti-COVID-19 vaccines and screening for efficacious drugs to manage the virus. Objective To explore the potential targets and therapeutic drugs for the prevention and treatment of COVID-19 through data mining and bioinformatics. Methods We integrated and
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Metagenomics analysis of the gut microbiome in healthy and bacterial pneumonia forest musk deer Genes Genom. (IF 1.188) Pub Date : 2021-01-11 Wei Zhao, Ziwei Ren, Yan Luo, Jianguo Cheng, Jie Wang, Yin Wang, Zexiao Yang, Xueping Yao, Zhijun Zhong, Wei Yang, Xi Wu
Background The forest musk deer (FMD, Moschus berezovskii) is an threatened species in China. Bacterial pneumonia was found to seriously restrict the development of FMD captive breeding. Historical evidence has demonstrated the relationship between immune system and intestinal Lactobacillus in FMD. Objective We sought to elucidate the differences in the gut microbiota of healthy and bacterial pneumonia
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MicroRNA 452 regulates ASB8 , NOL8 , and CDR2 expression in colorectal cancer cells Genes Genom. (IF 1.188) Pub Date : 2021-01-04 Ji-Su Mo, Soo-Cheon Chae
Background MicroRNAs play important roles in the pathogenesis of human diseases by regulating target gene expression in specific cells or tissues. Previously, we identified microRNA 452 (MIR452), which was specifically up-regulated in early stage human colorectal cancer (CRC) tissue. Objective The current study aims to identify and verify the target genes of MIR452 associated with CRC. Methods A luciferase
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Inhibition of oxidative stress induced-cytotoxicity by coptisine in V79-4 Chinese hamster lung fibroblasts through the induction of Nrf-2 mediated HO-1 expression Genes Genom. (IF 1.188) Pub Date : 2020-11-25 Hyeon-Gyun Jo, Cheol Park, Hyesook Lee, Gi-Young Kim, Young-Sam Keum, Jin Won Hyun, Taeg Kyu Kwon, Yung Hyun Choi, Su Hyun Hong
Background Coptisine is a natural alkaloid compound and is known to have multiple beneficial effects including antioxidant activity. However, whether it can protect lung fibroblasts from oxidative damage has not been studied yet. Objectives To investigate the potential inhibitory effect of coptisine against oxidative stress in V79-4 lung fibroblast cells. Methods V79-4 cells were treated with H2O2
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Diagnostic and therapeutic biomarkers for Alzheimer’s disease in human-derived platelets Genes Genom. (IF 1.188) Pub Date : 2020-11-12 Jae-Woong Min, Jina Lee, Hui-Jin Mun, Dae Hoon Kim, Byeong-Gyu Park, Bora Yoon, Jin-Hyeob Ryu, Hyun-Jeong Cho
Background Diagnosis of current Alzheimer’s disease (AD) is difficult even for medical specialists, and there is no clear biomarker. Also, aging is highly related to the onset of AD. Objectives The purpose of this study is to screen miRNA as an aging-considered biomarker for AD treatment and diagnosis. Methods The patient group for this study was divided into a young normal, old normal, or AD group
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The FvCYP714C2 gene plays an important role in gibberellin synthesis in the woodland strawberry Genes Genom. (IF 1.188) Pub Date : 2020-11-10 Xiaofan Guo, Zhibing Xie, Yang Zhang, Shouming Wang
Background Fragaria vesca, the woodland strawberry, is a diploid relative of the cultivated strawberry. A GA-deficient mutant was found in ethyl methanesulfonate (EMS)-mutagenized lines of the Fragaria vesca accession ‘Yellow Wonder’. Objective CYP714C2 was found to be differentially expressed using RNA-seq analysis. It is necessary to identify the function of this gene. Methods In order to identify
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SsPsaH , a H subunit of the photosystem I reaction center of Suaeda salsa , confers the capacity of osmotic adjustment in tobacco Genes Genom. (IF 1.188) Pub Date : 2020-11-05 Xiaoyan Hao, Jianping Li, Shengqi Gao, Zumuremu Tuerxun, Xiaochun Chang, Wenran Hu, Guo Chen, Quansheng Huang
Background Abiotic stress effects agricultural production, so research on improving stress tolerance of crop is important. Suaeda salsa is a halophyte with high salt and drought tolerance and ability to desalinate saline soil and improve soil quality. Objective To discover and utilize of salt and drought tolerance-related genes, we further investigated the mechanisms of salt and drought tolerance.
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Genome-wide investigation of a Korean synthetic breed, Woori-Heukdon using the Illumina PorcineSNP60K BeadChip Genes Genom. (IF 1.188) Pub Date : 2020-11-03 Yong-Min Kim, Ha-Seung Seong, Jung-Jae Lee, Da-Hye Son, Jin-Su Kim, Soo-Jin Sa, Young-Sin Kim, Tae-Jeong Choi, Kyu-Ho Cho, Joon-Ki Hong, Jung-Woo Choi, Eun-Seok Cho
Background Woori-Heukdon (KWH) is a Korean synthetic pig breed generated using Chookjin-Duroc (KCD), Chookjin-Chamdon (KCC), and their crossbreds. Currently, there is a severe lack of studies investigating the Korean breed populations including wild boars (KWB) throughout the genome. Objective This study was performed to investigate the genetic characteristics of Korean pig populations at the genome-wide
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Molecular subtypes of triple-negative breast cancer: understanding of subtype categories and clinical implication Genes Genom. (IF 1.188) Pub Date : 2020-11-03 Yong-Moon Lee, Man Hwan Oh, Jai-Hyang Go, Kyudong Han, Song-Yi Choi
Background Triple-negative breast cancer (TNBC) is a heterogeneous entity that encompasses several subtypes with distinct molecular characteristics. The patients with TNBCs show unpredictable response to the chemotherapy, and further there is the lack of effective agents. Thus, many studies have been underway to discover targeted therapy suitable for patients with specific genetic alterations in each
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Assessment of genetic diversity and population structure among a collection of Korean Perilla germplasms based on SSR markers Genes Genom. (IF 1.188) Pub Date : 2020-10-28 Jun Seok Oh, Kyu Jin Sa, Do Yoon Hyun, Gyu-Taek Cho, Ju Kyong Lee
Background Information on the genetic variation of genetic resource collections is very important for both the conservation and utilization of crop germplasms in genebanks. Var. frutescens of Perilla crop is extensively cultivated in South Korea as both an oil crop and a vegetable crop. Objectives We used SSR markers to evaluate the genetic diversity, genetic relationships, and population structure
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Proteostasis-associated aging: lessons from a Drosophila model Genes Genom. (IF 1.188) Pub Date : 2020-10-27 Garbin Yu, Seogang Hyun
As cells age, they lose their ability to properly fold proteins, maintain protein folding, and eliminate misfolded proteins, which leads to the accumulation of abnormal protein aggregates and loss of protein homeostasis (proteostasis). Loss of proteostasis can accelerate aging and the onset of neurodegenerative diseases such as Alzheimer’s disease and Parkinson’s disease. Mechanisms exist to prevent
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Natural variation in glycine-rich region of Brassica oleracea cold shock domain protein 5 ( BoCSDP5 ) is associated with low temperature tolerance Genes Genom. (IF 1.188) Pub Date : 2020-10-22 Hayoung Song, HyeRan Kim, Byung-Ho Hwang, Hankuil Yi, Yoonkang Hur
Background Low temperature (LT) or cold stress is a major environmental stress that seriously affects plant growth and development, limiting crop productivity. Cold shock domain proteins (CSDPs), which are present in most living organism, are involved in RNA metabolisms influencing abiotic stress tolerance. Objective The aims of this study are to identify target gene for LT-tolerance, like CSDPs, characterize
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Identification of differentially expressed genes in mouse embryonic stem cell under hypoxia Genes Genom. (IF 1.188) Pub Date : 2020-10-22 Su Jung Hwang, Hyo-Jong Lee
Background Under hypoxia, mouse embryonic stem cells (mESCs) lose the ability to self-renew and begin to differentiate through down-regulation of LIFR-STAT3 pathway via hypoxia-inducible factor-1α (HIF-1α). However, it remains largely unknown what kinds of factors are involved in hypoxia-induced differentiation of mESCs. Purpose This study aims to identify the differentially expressed genes (DEGs)
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CRISPR: a journey of gene-editing based medicine Genes Genom. (IF 1.188) Pub Date : 2020-10-22 Zhabiz Golkar
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) is one of the hallmark of biological tools, contemplated as a valid and hopeful alternatives to genome editing. Advancements in CRISPR-based technologies have empowered scientists with an editing kit that allows them to employ their knowledge for deleting, replacing and lately “Gene Surgery”, and provides unique control over genes in
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LncRNA A2M-AS1 lessens the injury of cardiomyocytes caused by hypoxia and reoxygenation via regulating IL1R2 Genes Genom. (IF 1.188) Pub Date : 2020-10-14 Xue-Lian Song, Fei-Fei Zhang, Wen-Jing Wang, Xin-Ning Li, Yi Dang, Ying-Xiao Li, Qian Yang, Mei-Jing Shi, Xiao-Yong Qi
Background Myocardial ischemia and reperfusion injury (MI/RI) is a complex pathophysiological process, which can lead to severe myocardial injury. The long noncoding RNA alpha-2-macroglobulin antisense RNA 1 (A2M-AS1) has been revealed to be abnormally expressed in MI, However, its function in MI and the potential mechanism are still unclear. Objective To evaluate the functional role of A2M-AS1 in
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Correlation between DNA methylation and Thymic Stromal Lymphopoietin expression in asthmatic airway epithelial cells Genes Genom. (IF 1.188) Pub Date : 2020-10-10 Yan-Li Li, Xi-Qian Xing, Yi Xiao, Yan-Hong Liu, Yu-Shan Zhou, Min Zhuang, Chao-Qian Li
Background The overexpression of TSLP and DNA methylation in asthma were both risk factors the relationship was not clear. Objective This study aimed to investigate the relationship between methylation status of TSLP promoter and mRNA/protein expression in asthmatic airway epithelial cells. Methods Human bronchial epithelial cells were cultured in vitro and divided into: Control group, treated with
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Association of XPD Lys751Gln gene polymorphism with susceptibility and clinical outcome of colorectal cancer in Pakistani population: a case–control pharmacogenetic study Genes Genom. (IF 1.188) Pub Date : 2020-10-06 Sumera Gul, Abad Khan, Abida Raza, Ismail Khan, Shumaila Ehtisham
Background XPD Lys751Gln polymorphism may modulate inter-individual variation in repair capacity of DNA, which may enhance a person’s susceptibility to develop colorectal cancer (CRC). The analysis of XPD Lys751Gln polymorphism may provide important information for identifying high-risk individuals and for selecting the most appropriate treatment for poor prognostic CRC patients. Objective The overall
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AbaR is a LuxR type regulator essential for motility and the formation of biofilm and pellicle in Acinetobacter baumannii Genes Genom. (IF 1.188) Pub Date : 2020-10-06 Man Hwan Oh, Kyudong Han
Background Acinetobacter baumannii is a major opportunistic pathogen causing nosocomial infections. Acinetobacter baumannii possesses a quorum sensing system consisting of abaI, encoding an autoinducer synthase, and abaR, encoding a putative LuxR type regulator. AbaI is required for motility and biofilm formation in A. baumannii. However, the functions of AbaR on the expression of abaI, motility, and
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LINC00657 knockdown suppresses hepatocellular carcinoma progression by sponging miR-424 to regulate PD-L1 expression Genes Genom. (IF 1.188) Pub Date : 2020-09-29 Xinling Cao, Guanping Zhang, Tao Li, Chengming Zhou, Lei Bai, Jinming Zhao, Turgunjan Tursun
Background Hepatocellular carcinoma (HCC) is the sixth most commonly diagnosed malignant tumor and the fourth leading cause of cancer-related deaths worldwide. As a novel non-coding RNA, LINC00657 was firstly identified as an oncogenic role in breast cancer. However, few research focus on the effect of LINC00657 on the progression of HCC. Objectives The purpose of this study was to investigate the
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Differential expression profile of microRNA in yak skeletal muscle and adipose tissue during development Genes Genom. (IF 1.188) Pub Date : 2020-09-29 Hui Ji, Hui Wang, Qiumei Ji, Winbo Ji, Xiaolin Luo, Jiabo Wang, Zhixin Chai, Jinwei Xin, Xin Cai, Zhijuan Wu, Jikun Wang, Jincheng Zhong
Background miRNAs play an important role in regulating normal animal development. Muscle tissue and fat metabolism are important for maintaining energy balance in animals. Yak has important agricultural and economic importance as it provides milk, meat, and hair. It is used for transportation as well. However, the miRNA expression profiles of their muscle and adipose tissue are currently unknown. Objective
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Identification of differentially expressed miRNAs after Lactobacillus reuteri treatment in the ileum mucosa of piglets Genes Genom. (IF 1.188) Pub Date : 2020-09-26 Qi Wang, Qian Sun, Jing Wang, Xiaoyu Qiu, Renli Qi, Jinxiu Huang
Background Lactobacillus reuteri I5007 possesses many excellent probiotic characteristics in piglets. miRNA plays important role in host-microbiota interactions, but the mechanism by which L. reuteri I5007 regulates intestinal function through its influence on miRNA expression is unknown. Objective This study analyzed the miRNA expression patterns in the ileum mucosa tissue of piglets by L. reuteri
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Protective mechanism of fdft1 in steroid hormone synthesis pathway in SD rats with acute hypoxic injury Genes Genom. (IF 1.188) Pub Date : 2020-09-26 Xue Lin, Haiyan Wang, Xiaoyan Pu
Background The acute hypoxic injury caused by the plain population entering the plateau in a short period of time has become the main cause of endangering the health of the people who rush into the plateau. Objective The study aimed to identify the key genes which participate in resisting the acute hypoxic injury in SD Rats by transcriptomic profile analysis. Methods 48 Sprague Dawley (SD) male rats
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NGS_SNPAnalyzer: a desktop software supporting genome projects by identifying and visualizing sequence variations from next-generation sequencing data Genes Genom. (IF 1.188) Pub Date : 2020-09-26 Dong-Jun Lee, Taesoo Kwon, Chang-Kug Kim, Young-Joo Seol, Dong-Suk Park, Tae-Ho Lee, Byung-Ohg Ahn
Background Sequence variations such as single nucleotide polymorphisms are markers for genetic diseases and breeding. Therefore, identifying sequence variations is one of the main objectives of several genome projects. Although most genome project consortiums provide standard operation procedures for sequence variation detection methods, there may be differences in the results because of human selection
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Suppression of long non-coding RNA PCAT19 inhibits glioma cell proliferation and invasion, and increases cell apoptosis through regulation of MELK targeted by miR-142-5p Genes Genom. (IF 1.188) Pub Date : 2020-09-26 Yu-hua Xie, Jiao Hu
Background Glioma has the chief type of primary brain tumors worldwide. The glioma may be controlled by regulators including some lncRNAs, miRNAs, and proteins. Objective Our study aims to discover the underlying mechanism for lncPCAT19/miR-142-5p/MELK axis in glioma progression. Methods The clinical samples were from patients with gliomas in our Hospital. Hematoxylin–eosin staining (H&E) was applied
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Genetic diversity and population structure of the endangered fish Pseudobagrus brevicorpus (Bagridae) using a newly developed 12-microsatellite marker. Genes Genom. (IF 1.188) Pub Date : 2020-09-21 Yeong Ho Kwak,Kang Rae Kim,Moo Sang Kim,In Chul Bang
Background Pseudobagrus brevicorpus is an endangered species in Korea. The development of genetic markers and genetic information regarding the populations of this species are needed to establish conservation strategies. Objective As part of the conservation of P. brevicorpus, a 12-microsatellite marker was developed using next-generation sequencing (NGS) to provide current genetic population information
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Characterization and functional analysis of Krtap11-1 during hair follicle development in Angora rabbits (Oryctolagus cuniculus). Genes Genom. (IF 1.188) Pub Date : 2020-09-21 Shuang Liang,Zhiyuan Bao,Bohao Zhao,Tong Zhou,Jiali Li,Ming Liu,Shuaishuai Hu,Naisu Yang,Yang Chen,Xinsheng Wu
Background Keratin-associated protein (KAP), the structural protein molecule of hair fibers, plays a key role in determining the physical properties of hair. Studies of Krtap11-1 have focused only on its localization. Functional studies of Krtap11-1 in hair follicle development have so far not been reported. Objective This study aimed to provide evidence for the role of Krtap11-1 in skin and hair development
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Transcriptomic analysis of the effect of (E)-3-(3,5-dimethoxyphenyl)-1-(2-methoxyphenyl) prop-2-en-1-one (DPP23) on reactive oxygen species generation in MIA PaCa-2 pancreatic cancer cells. Genes Genom. (IF 1.188) Pub Date : 2020-09-19 Hongnam Sim,Euitaek Jung,Da Hyun Lee,Ji Hye Choi,Young Han Lee,Soon Young Shin
Background Reactive oxygen species (ROS) generation specifically in cancer cells may be a promising strategy for their selective killing. The synthetic chalcone derivative (E)-3-(3,5-dimethoxyphenyl)-1-(2-methoxyphenyl)prop-2-en-1-one (DPP23) exerts antitumor activity through ROS-mediated apoptosis in cancer cells but not in healthy cells. However, the mechanism underlying ROS generation by DPP23 remains
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Comparative analysis of the down syndrome hippocampal non-coding RNA transcriptomes using a mouse model. Genes Genom. (IF 1.188) Pub Date : 2020-09-18 Zhaowei Cai,Zhilan Xiao,Yufang Wang,Huazhen Liu,Kangdi Zhang,Xiaoning Zhen,Xiaoling Jiang
Background Down syndrome (DS), caused by trisomy 21, is the most common human chromosomal disorder. Hippocampal abnormalities have been believed to be responsible for the DS developmental cognitive deficits. Cumulative evidences indicated that non-coding RNAs (ncRNAs) participated in brain development and function. Currently, few was known whether dysregulated ncRNAs existed in DS whether the dysregulated
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Genome-wide identification of microRNAs and phased siRNAs in soybean roots under long-term salt stress. Genes Genom. (IF 1.188) Pub Date : 2020-09-16 Qian Wang,Yingxia Yang,Guoqing Lu,Xianjun Sun,Youren Feng,Shuangyong Yan,Huiyuan Zhang,Qiyan Jiang,Hui Zhang,Zheng Hu,Rui Chen
Background Salinity stress, as the key limiting factor for agricultural productivity, can activate a series of molecular responses and alter gene expression in plants. Endogenous regulatory small RNAs, such as microRNAs (miRNAs) and phased siRNAs (phasiRNAs), play crucial roles during stress adaptation and prevent the injury from environmental circumstances. Objective To identify long-term salt stress
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Remarkably low genetic diversity and shallow population structure detected of the spiny eel (Sinobdella sinensis) in Eastern China. Genes Genom. (IF 1.188) Pub Date : 2020-09-16 Sheng Yuan,Meijian Liu,Ziming Zhao
Background The spiny eel (Sinobdella sinensis) is a small subtropical fish endemic to China, Vietnam, and Laos. It has disappeared in many rivers and lakes due to anthropogenic stressors. Objective The aim of this study was to investigate the genetic diversity and population structure and to provide pertinent information of the evolutionary history and conservation of S. sinensis. Methods Mitochondrial
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Identifying genes for resistant starch, slowly digestible starch, and rapidly digestible starch in rice using genome-wide association studies. Genes Genom. (IF 1.188) Pub Date : 2020-09-08 Ning Zhang,Maike Wang,Ji Fu,Yi Shen,Yi Ding,Dianxing Wu,Xiaoli Shu,Wenjian Song
Background The digestibility of starch is important for the nutritive value of staple food. Although several genes are responsible for resistant starch (RS) and slowly digestible starch (SDS), gaps persist concerning the molecular basis of RS and SDS formation due to the complex genetic mechanisms of starch digestibility. Objectives The objective of this study was to identify new genes for starch digestibility
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Cellular and molecular mechanisms of DEET toxicity and disease-carrying insect vectors: a review. Genes Genom. (IF 1.188) Pub Date : 2020-09-05 Bhanu Shrestha,Youngseok Lee
Background Several insects such as mosquitoes, flies, ticks, fleas, lice, and mites are known to serve as vectors for a vast number of pathogens. Many such vectors are hematophagous, and therefore introduce pathogens directly into the host’s bloodstream. Importantly, the capacity of these vectors to spread disease can lead to serious global health crises. Furthermore, crop damage can be exacerbated
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Frequency spectra characterization of noncoding human genomic sequences. Genes Genom. (IF 1.188) Pub Date : 2020-08-31 O Paredes,Rebeca Romo-Vázquez,Israel Román-Godínez,Hugo Vélez-Pérez,Ricardo A Salido-Ruiz,J Alejandro Morales
Background Noncoding sequences have been demonstrated to possess regulatory functions. Its classification is challenging because they do not show well-defined nucleotide patterns that can correlate with their biological functions. Genomic signal processing techniques like Fourier transform have been employed to characterize coding and noncoding sequences. This transformation in a systematic whole-genome
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A comprehensive analysis of chimpanzee (Pan Troglodytes)-specific AluYb8 element. Genes Genom. (IF 1.188) Pub Date : 2020-08-29 Songmi Kim,Dong Hee Kim,Hiroo Imai,Yong-Moon Lee,Kyudong Han
Background Alu elements are most abundant retrotransposons with > 1.2 million copies in the primate genome. AluYb8 subfamily was diverged from AluY lineage, and has accumulated eight diagnostic mutations and 7-bp duplication during primate evolution. A total of 1851 AluYb copies are present in the human genome, and most of them are human-specific. On the other hand, only a few AluYb8 copies were identified
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Trans-cinnamaldehyde protects C2C12 myoblasts from DNA damage, mitochondrial dysfunction and apoptosis caused by oxidative stress through inhibiting ROS production. Genes Genom. (IF 1.188) Pub Date : 2020-08-27 Yung Hyun Choi
Background Oxidative stress-induced myoblast damage is one of the major causes of skeletal muscle loss associated with inhibition of myogenic differentiation and muscle dysfunction. Trans-cinnamaldehyde (tCA), the most common essential oil constituent in cinnamon, is known to possess strong anti-oxidant activity. However, it has not been determined whether tCA can protect myoblasts from oxidative damage
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High-throughput sequencing analysis of differences in intestinal microflora between ulcerative colitis patients with different glucocorticoid response types. Genes Genom. (IF 1.188) Pub Date : 2020-08-25 Yunzhen Zhu,Juan Luo,Zhaoqing Yang,Yinglei Miao
Background Previous investigations reported that the imbalance of intestinal microflora may be the initiation and promotion factor in the pathogenesis of inflammatory bowel disease such as ulcerative colitis (UC). Glucocorticoid is a very important class of regulatory molecules in the body. The response of different individuals to glucocorticoids can be divided into glucocorticoid sensitive, glucocorticoid
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Tuberculosis risk is associated with genetic polymorphisms in the LRP2, CUBN, and VDR genes. Genes Genom. (IF 1.188) Pub Date : 2020-08-17 Sung-Soo Kim,Sang In Lee,Hyun-Seok Jin,Sangjung Park
Background Vitamin D (Vit. D) is used extensively during tuberculosis treatment. Low levels of serum Vit. D increase the risk of active tuberculosis development. Altered expression of the proteins involved in Vit. D metabolism impairs cathelicidin production, thereby increasing the host susceptibility to tuberculosis. Objective We are trying to investigate whether single nucleotide polymorphisms (SNPs)
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Ovarian transcriptome profiles associated with sexual maturation in Pacific abalone (Haliotis discus hannai). Genes Genom. (IF 1.188) Pub Date : 2020-08-17 Mi Ae Kim,Tae Ha Kim,Sora Lee,Bo-Hye Nam,Jung Sick Lee,Wonhee Jang,Young Chang Sohn
Background There is now abundant information on genes involved in molluscan oogenesis and their associations with ovarian development. However, few studies have investigated the ovarian transcriptome of Pacific abalone (Haliotis discus hannai). Objective The objective of this study was to identify genes related to ovarian development and maturation in Pacific abalone utilizing RNA-sequencing (RNA-seq)
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Genome-wide insights of Ethiopian indigenous sheep populations reveal the population structure related to tail morphology and phylogeography. Genes Genom. (IF 1.188) Pub Date : 2020-08-16 Agraw Amane,Gurja Belay,Yao Nasser,Martina Kyalo,Tadelle Dessie,Adebabay Kebede,Tesfaye Getachew,Jean-Baka Domelevo Entfellner,Zewdu Edea,Olivier Hanotte,Getinet Mekuriaw Tarekegn
Background Ethiopian sheep living in different climatic zones and having contrasting morphologies are a most promising subject of molecular-genetic research. Elucidating their genetic diversity and genetic structure is critical for designing appropriate breeding and conservation strategies. Objective The study was aimed to investigate genome-wide genetic diversity and population structure of eight
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GEN2VCF: a converter for human genome imputation output format to VCF format. Genes Genom. (IF 1.188) Pub Date : 2020-08-16 Dong Mun Shin,Mi Yeong Hwang,Bong-Jo Kim,Keun Ho Ryu,Young Jin Kim
Background For a genome-wide association study in humans, genotype imputation is an essential analysis tool for improving association mapping power. When IMPUTE software is used for imputation analysis, an imputation output (GEN format) should be converted to variant call format (VCF) with imputed genotype dosage for association analysis. However, the conversion requires multiple software packages
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Molecular characterization of Arabidopsis thaliana LSH1 and LSH2 genes. Genes Genom. (IF 1.188) Pub Date : 2020-08-16 Myungjin Lee,Xiangshu Dong,Hayong Song,Ju Yeon Yang,Soyun Kim,Yoonkang Hur
Background Arabidopsis thaliana genome encodes ten DUF640 (short for domain of unknown function 640)/ALOG (short for Arabidopsis LSH1 and Oryza G1) proteins, also known as light-dependent short hypocotyl (LSH) proteins. While some of the LSH genes regulate organ boundary determination and shade avoidance response, the function of most of these genes remains largely unknown. Objective In this study
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Analysis of KAP1 expression patterns and human endogenous retrovirus Env proteins in ovarian cancer. Genes Genom. (IF 1.188) Pub Date : 2020-08-12 Kyung-Yoon Jeon,Eun-Ji Ko,Young Lim Oh,Hongbae Kim,Wan Kyu Eo,Ari Kim,Han Gyu Sun,Mee Sun Ock,Ki Hyung Kim,Hee-Jae Cha
Background Human endogenous retroviruses (HERVs) constitute around 8% of the human genome and have important roles in human health and disease, including cancers. Previous studies showed that HERV envelope (Env) proteins are highly expressed in cancer tissues and co-related with cancer progression. KAP1 has been reported to play a key role in regulating retrotransposons, including HERV-K, through epigenetic
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Comparative genomics of canine Lactobacillus reuteri reveals adaptation to a shared environment with humans. Genes Genom. (IF 1.188) Pub Date : 2020-08-06 Seungwoo Son,Jae-Don Oh,Sung Ho Lee,Donghyun Shin,Yangseon Kim
Background Lactobacillus reuteri is a gram-positive, non-motile bacterial species that has been used as a representative microorganism model to describe the ecology and evolution of vertebrate gut symbionts. Objective Because the genetic features and evolutionary strategies of L. reuteri from the gastrointestinal tract of canines remain unknown, we tried to construct draft genome canine L. reuteri
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MiR-339 attenuates LPS-induced intestinal epithelial cells inflammatory responses and apoptosis by targeting TLR4. Genes Genom. (IF 1.188) Pub Date : 2020-08-05 Meiying Xie,Lina Zhang,Luoye Li,Minhuan Fan,Lianjie Hou
Background Intestinal epithelial cells are important for defending against pathogen infection. LPS is an endotoxin that is highly antigenic and cytotoxic produced by bacteria. LPS disrupts the intestine epithelium integrity and induced the intestinal epithelial cell inflammation and apoptosis. Our previous study has predicted the function of exosome miRNAs through bioinformatics analysis, and we found
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The SnRK2 family in pepper (Capsicum annuum L.): genome-wide identification and expression analyses during fruit development and under abiotic stress. Genes Genom. (IF 1.188) Pub Date : 2020-07-31 Zhiming Wu,Jiaowen Cheng,Fang Hu,Cheng Qin,Xiaowan Xu,Kailin Hu
Plant-specific SnRK2 (sucrose nonfermenting-1-related protein kinase 2) genes play crucial roles in the coordination of plant growth and development and responses to stress. However, comprehensive studies have not been performed for this gene family in pepper (Capsicum annuum), a very important Solanaceous vegetable worldwide. To fully understand the status of SnRK2s in chili pepper, a total of 9 putative
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Complete genome sequence of Sphingobium sp. strain PAMC 28499 reveals a potential for degrading pectin with comparative genomics approach. Genes Genom. (IF 1.188) Pub Date : 2020-07-31 So-Ra Han,Sung-Min Jang,Young Min Chi,Byeollee Kim,Sang-Hee Jung,Yung Mi Lee,Jun Uetake,Jun Hyuck Lee,Hyun Park,Tae-Jin Oh
Background Spingobium sp. PAMC 28499 is isolated from the glaciers of Uganda. Uganda is a unique region where hot areas and glaciers coexist, with a variety of living creatures surviving, but the survey on them is very poor. The genetic character and complete genome information of Sphingobium strains help with environmental studies and the development of better to enzyme industry. Objective In this
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Phylogenetic relationships between different raccoon dog (Nyctereutes procyonoides) populations based on four nuclear and Y genes. Genes Genom. (IF 1.188) Pub Date : 2020-07-28 YoonJee Hong,Hang Lee,Kyung Seok Kim,Mi-Sook Min
Background The raccoon dog (Nyctereutes procyonoides), endemic to East Asia, is classified as six subspecies according to their geographical distribution including a population introduced to Europe. Studies on phylogenetic relationship or population genetics in both native and introduced areas have been carried out recently. Lately, opinions that Japanese raccoon dogs should be classified as a different
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Identification of two rare mutations c.1318G>A and c.6438+2T>G in a Chinese DMD family as genetic markers. Genes Genom. (IF 1.188) Pub Date : 2020-07-28 Yingchuan Zhu,Lijun Yang,Tengjiao Ma,Yilu Lu,Dachang Tao,Yunqiang Liu,Yongxin Ma
Background Duchenne muscular dystrophy (DMD) is a fatal X-linked recessive disorder with no effective treatment, which underscores the importance of avoiding the birth of children with DMD by identifying pathogenic mutations and obtaining an accurate prenatal diagnosis. Objective The objective of this study was to analyze the genetic defect of a Chinese family where all male patients have died of DMD
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The impact of TNFSF14 on prognosis and immune microenvironment in clear cell renal cell carcinoma. Genes Genom. (IF 1.188) Pub Date : 2020-07-28 Fangshi Xu,Yibing Guan,Peng Zhang,Li Xue,Xiaojie Yang,Ke Gao,Tie Chong
Background TNFSF14 has been proven to play an important role in various types of tumors. However, its function in renal cell carcinoma (RCC) has not yet been fully elucidated. Objective In order to explore molecular mechanism of RCC, we evaluated the effect of TNFSF14 on RCC progression, prognosis and immune microenvironment. Methods Using TCGA database, the differential expression of TNFSF14 and its
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De novo assembly and characterization of transcriptome in the medicinal plant Euphorbia jolkini. Genes Genom. (IF 1.188) Pub Date : 2020-07-26 Neha Samir Roy,In-Hye Lee,Jung-A Kim,Rahul Vasudeo Ramekar,Kyong-Cheul Park,Nam-Il Park,Joo-Hong Yeo,Ik-Young Choi,Soonok Kim
Background Euphorbia jolkini, a medicinal herb that grows on the warm beaches in Japan and South Korea, is known to be used for traditional medicines to treat a variety of ailments, including bruises, stiffness, indigestion, toothache, and diabetes. Objective It is to analyze the whole transcriptome and identify the genes related to the phenylpropanoid biosynthesis in the medicinally important herb
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A novel compound heterozygous mutation of SLC12A3 gene in a pedigree with Gitelman syndrome and literature review. Genes Genom. (IF 1.188) Pub Date : 2020-07-25 Minglan Yang,Ying Dong,Jianqing Tian,Li Yan,Yawen Chen,Huiying Qiu,Wei Liu,Yaomin Hu
Background Gitelman syndrome (GS) is a tubulopathy characterized by hypokalemia, hypomagnesemia, hypocalciuria and metabolic alkalosis, which is caused by mutations in SLC12A3 gene. Objective The objective of this study was to investigate the mutation of SLC12A3 gene in a pedigree with GS and analyzed the clinical manifestations. Methods Next-generation sequencing and Sanger sequencing were performed
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Expression and evolution of the phospholipase C gene family in Brachypodium distachyon. Genes Genom. (IF 1.188) Pub Date : 2020-07-25 Xianguo Wang,Yang Liu,Zheng Li,Xiang Gao,Jian Dong,Mingming Yang
Background Phospholipase C (PLC) is an enzyme that hydrolyzes phospholipids and plays an important role in plant growth and development. The Brachypodium distachyon is a model plant of Gramineae, but the research on PLC gene family of Brachypodium has not been reported. Objective This study was performed to identify the PLC family gene in Brachypodium and to determine the expression profiles of PLCs
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Differential manifestation of ocular phenotypes in TALEN-mediated p19arf knockout FVB/N and C57BL/6J mouse lines. Genes Genom. (IF 1.188) Pub Date : 2020-07-25 Jin-Sung Park,Joo-Il Kim,Hyun-Jin Lim,Soo-Kyung Ryu,Euna Kwon,Kang-Min Han,Ki-Taek Nam,Han-Woong Lee,Byeong-Cheol Kang