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International Journal of Genomics | Page 2

Elisa Frullanti, Filomena T Papa, Elisa Grillo, Angus Clarke, Bruria Ben-Zeev, Mercedes Pineda, Nadia Bahi-Buisson, Thierry Bienvenu, Judith Armstrong, Ana Roche Martinez, Francesca Mari, Andreea Nissenkorn, Caterina Lo Rizzo, Edvige Veneselli, Silvia Russo, Aglaia Vignoli, Giorgio Pini, Milena Djuric, Anne-Marie Bisgaard, Kirstine Ravn, Vlatka Mejaski Bosnjak, Joussef Hayek, Rajni Khajuria, Barbara Montomoli, Francesca Cogliati, Maria Pintaudi, Kinga Hadzsiev, Dana Craiu, Victoria Voinova, Aleksandra Djukic, Laurent Villard, Alessandra Renieri
Rett spectrum disorder is a progressive neurological disease and the most common genetic cause of intellectual disability in females. MECP2 is the major causative gene. In addition, CDKL5 and FOXG1 mutations have been reported in Rett patients, especially with the atypical presentation. Each gene and different mutations within each gene contribute to variability in clinical presentation, and several groups worldwide performed genotype-phenotype correlation studies using cohorts of patients with classic and atypical forms of Rett spectrum disorder...
2019: International Journal of Genomics
Dongdong Zhang, Sujuan Gao, Ping Yang, Jie Yang, Songguang Yang, Keqiang Wu
As part of chromatin-remodeling complexes (CRCs), sucrose nonfermenting 2 (Snf2) family proteins alter chromatin structure and nucleosome position by utilizing the energy of ATP, which allows other regulatory proteins to access DNA. Plant genomes encode a large number of Snf2 proteins, and some of them have been shown to be the key regulators at different developmental stages in Arabidopsis . Yet, little is known about the functions of Snf2 proteins in tomato ( Solanum lycopersicum ). In this study, 45 Snf2s were identified by the homologous search using representative sequences from yeast ( S...
2019: International Journal of Genomics
Tieshan Feng, Ping Lin, Jiao Gong, Dong Cheng, Xi Yang, Quan Zhang, Tingcai Cheng
Bacillus bombyseptieus is a pathogen of Bombyx mori ; it can cause bacterial septicemia in silkworm. One of the components of the parasporal crystal toxin of B. bombyseptieus , α -toxin, plays an important role in the process of infection in silkworm. In this study, we investigated the immune response of silkworm induced by α -toxin by using RNA-seq. We compared the changes in gene expression in the midgut, fatbody, and hemocytes of silkworm and in the B. mori embryonic cell line (BmE) after treatment with α -toxin and identified 952 differentially expressed genes and 353 differentially expressed long noncoding RNAs (lncRNAs)...
2019: International Journal of Genomics
Alexander Vaiserman, Oleh Lushchak
Type 2 diabetes (T2D) is commonly regarded as a disease originating from lifestyle-related factors and typically occurring after the age of 40. There is, however, consistent experimental and epidemiological data evidencing that the risk for developing T2D may largely depend on conditions early in life. In particular, intrauterine growth restriction (IUGR) induced by poor or unbalanced nutrient intake can impair fetal growth and also cause fetal adipose tissue and pancreatic β -cell dysfunction. On account of these processes, persisting adaptive changes can occur in the glucose-insulin metabolism...
2019: International Journal of Genomics
Leila Bazrkar-Khatibani, Barat-Ali Fakheri, Maryam Hosseini-Chaleshtori, Anumalla Mahender, Nafiseh Mahdinejad, Jauhar Ali
Rice grain shape and nutritional quality traits have high economic value for commercial production of rice and largely determine the market price, besides influencing the global food demand for high-quality rice. In order to understand the genetic components of grain appearance traits in paddy, brown, and head rice, 15 traits were evaluated by using 157 recombinant inbred lines (RILs) derived from a cross between two Iranian rice cultivars Ali-Kazemi (A) and Kadous (K). A significant variation was observed and showed transgressive segregation among the RILs...
2019: International Journal of Genomics
Xiaoxuan Hu, Chenyu Hao, Zong-Ming Cheng, Yan Zhong
Superoxide dismutase (SOD) is an essential enzyme of the plant antioxidant system that responds to oxidative damage caused by adverse conditions. However, little is known about the SOD gene family in Vitis vinifera (Vv). In the present study, ten SOD genes, including 6 copper/zinc SODs, 2 iron SODs, and 2 manganese SODs, were identified in the grapevine genome where they were unevenly distributed on 12 chromosomes. Ten VvSOD genes were divided into three main groups based on phylogenetic analysis, subcellular localization, and the distribution of conserved protein motifs...
2019: International Journal of Genomics
Na Li, Yang Wang, Jing Lu, Chuan Liu
The ALOG domain genes, named after the Arabidopsis LSH1 and Oryza G1 (ALOG) proteins, have frequently been reported as key developmental regulators in rice and Arabidopsis . However, the investigation of the ALOG gene family is limited. Here, we conducted a genome-wide investigation of the ALOG gene family in rice and six other species. In total, eighty-four ALOG domain genes were identified from the seven species, of which fourteen ALOG domain genes ( OsG1 / G1Ls ) were identified in the rice genome. The fourteen OsG1 / G1Ls were unevenly distributed on eight chromosomes, and we found that eight segmental duplications contributed to the expansion of OsG1 / G1Ls in the rice genome...
2019: International Journal of Genomics
Emanuele Bosi, Flavia Mascagni
Organisms change to adapt to the environment in which they live, evolving with coresiding individuals. Classic Darwinism postulates the primal importance of antagonistic interactions and selfishness as a major driver of evolution, promoting an increase of genomic and organism complexities. Recently, advancements in evolutionary ecology reshaped this notion, showing how leakiness in biological functions favours the adaptive genome reduction, leading to the emergence of codependence patterns. Microbial communities are complex entities exerting a gargantuan influence on the environment and the biology of the eukaryotic hosts they are associated with...
2019: International Journal of Genomics
Huan Wang, Hongling Wei, Lei Tang, Junkai Lu, Changkao Mu, Chunlin Wang
Scylla paramamosain is a commercially important species distributed along the coast of southern China and other Indo-Pacific countries. Sudden salinity drop exceeding the adjustment capability of S. paramamosain can result in damage or even mortality. In our previous study, we had analyzed the mechanism of adapting sudden drop in salinity from the level of transcriptomics and proteomics, respectively. This study performed a correlation analysis of RNA sequencing transcriptomics and iTRAQ proteomics in order to investigate the adaptation mechanisms to sudden salinity drop from 23‰ to 3‰...
2019: International Journal of Genomics
Yu-Hua Fu, Chenglong Yang, Qiuyi Meng, Fanzhi Liu, Gang Shen, Mingqiang Zhou, Maohong Ao
Coix lacryma-jobi L. is an important minor cereal with a high nutritional and medicinal value in Asian countries. The hilly region of South China is the secondary center of diversity of Coix lacryma-jobi L. In the present study, we took a sample of 139 Coix lacryma-jobi L. genotypes from four geographical regions in Southwest China and analyzed the genetic diversity and population structure using AFLP markers. Six primer combinations detected a total of 743 (89.52%) polymorphic loci. The percentage of polymorphic bands within the four geographical populations ranged from 56...
2019: International Journal of Genomics
Qun-Feng Lu, De-Min Cao, Li-Li Su, Song-Bo Li, Guang-Bin Ye, Xiao-Ying Zhu, Ju-Ping Wang
N. gonorrhoeae and N. meningitidis , the only two human pathogens of Neisseria , are closely related species. But the niches they survived in and their pathogenic characteristics are distinctly different. However, the genetic basis of these differences has not yet been fully elucidated. In this study, comparative genomics analysis was performed based on 15 N. gonorrhoeae , 75 N. meningitidis , and 7 nonpathogenic Neisseria genomes. Core-pangenome analysis found 1111 conserved gene families among them, and each of these species groups had opening pangenome...
2019: International Journal of Genomics
Nathalie Grova, Henri Schroeder, Jean-Luc Olivier, Jonathan D Turner
The incidence of neurodevelopmental and neurodegenerative diseases worldwide has dramatically increased over the last decades. Although the aetiology remains uncertain, evidence is now growing that exposure to persistent organic pollutants during sensitive neurodevelopmental periods such as early life may be a strong risk factor, predisposing the individual to disease development later in life. Epidemiological studies have associated environmentally persistent organic pollutant exposure to brain disorders including neuropathies, cognitive, motor, and sensory impairments; neurodevelopmental disorders such as autism spectrum disorder (ASD) and attention-deficit hyperactivity disorder (ADHD); and neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis (ALS)...
2019: International Journal of Genomics
Yanming Cao, Bin Wang, Ding Wang, Dongxiang Zhan, Caiyuan Mai, Peng Wang, Qiushi Wei, Yamei Liu, Haibin Wang, Wei He, Liangliang Xu
Purpose: SOST gene is one of the key factors in regulating bone absorption. Although there are reports showing diverse transcription factors, epigenetic modification could be responsible for regulating SOST gene expression. There is still little exploration on promoter methylation status of SOST gene in osteoporotic bone tissues. The aim of this study is to investigate the involvement of CpG methylation in regulation of SOST expression in patients with primary osteoporosis. Methods: The diagnosis of osteoporosis was established on the basis of dual energy X-ray absorptiometry to measure BMD...
2019: International Journal of Genomics
Artur Gurgul, Klaudia Pawlina-Tyszko, Monika Bugno-Poniewierska, Tomasz Szmatoła, Igor Jasielczuk, Stefan Dobosz, Konrad Ocalewicz
[This corrects the article DOI: 10.1155/2018/5197126.].
2018: International Journal of Genomics
Chongyang Wu, Chaoqin Lin, Xinyi Zhu, Hongmao Liu, Wangxiao Zhou, Junwan Lu, Licheng Zhu, Qiyu Bao, Cong Cheng, Yunliang Hu
In this work, by high-throughput sequencing, antibiotic resistance genes, including class A ( bla CTX-M , bla Z , bla TEM , bla VEB , bla KLUC , and bla SFO ), class C ( bla SHV , bla DHA , bla MIR , bla AZECL-29 , and bla ACT ), and class D ( bla OXA ) β -lactamase genes, were identified among the pooled genomic DNA from 212 clinical Enterobacter cloacae isolates. Six bla MIR -positive E. cloacae strains were identified, and pulsed-field gel electrophoresis (PFGE) showed that these strains were not clonally related...
2018: International Journal of Genomics
Ningyang Li, Zhichang Qiu, Xiaoming Lu, Bingchao Shi, Xiudong Sun, Xiaozhen Tang, Xuguang Qiao
Green discoloration is one of the most important problems that cause low quality of product in the processing of garlic, which can be induced by low-temperature stress. But the mechanism of low temperature-induced green discoloration is poorly understood. In the present study, the control garlic and three low temperature-treated garlic samples (stored at 4°C with 10, 15, and 40 days, respectively) were used for genome-wide transcriptome profiling analysis. A total of 49280 garlic unigenes with an average length of 1337 bp were de novo assembled, 20231 of which were achieved for functional annotation...
2018: International Journal of Genomics
Shuang Zhao, Xuemei Zhang, Yanping Su, Yilan Chen, Yang Liu, Meng Sun, Guohui Qi
Walnut ( Juglans regia L.) is an important woody oilseed species cultivated throughout the world. In this study, comparative transcript profiling was performed using high-throughput RNA sequencing technology at the following three stages of walnut fat synthesis in the "Lvling" walnut cultivar: the initial developmental stage (L1), the fast developing stage (L2), and the last developing stage (L3). A total of 68.18 GB of data were obtained on the three developmental stages, and 92% to 94% of clean data were able to be located to the reference genome...
2018: International Journal of Genomics
Xing Huang, Bo Wang, Jingen Xi, Yajie Zhang, Chunping He, Jinlong Zheng, Jianming Gao, Helong Chen, Shiqing Zhang, Weihuai Wu, Yanqiong Liang, Kexian Yi
Agave species are an important family of crassulacean acid metabolism (CAM) plants with remarkable tolerance to heat and drought stresses ( Agave deserti ) in arid regions and multiple agricultural applications, such as spirit ( Agave tequilana ) and fiber ( Agave sisalana ) production. The agave genomes are commonly too large to sequence, which has significantly restricted our understanding to the molecular basis of stress tolerance and economic traits in agaves. In this study, we collected three transcriptome databases for comparison to reveal the phylogenic relationships and evolution patterns of the three agave species...
2018: International Journal of Genomics
Shang-Qian Xie, Yue Han, Xiao-Zhou Chen, Tai-Yu Cao, Kai-Kai Ji, Jie Zhu, Peng Ling, Chuan-Le Xiao
The accurate landscape of transcript isoforms plays an important role in the understanding of gene function and gene regulation. However, building complete transcripts is very challenging for short reads generated using next-generation sequencing. Fortunately, isoform sequencing (Iso-Seq) using single-molecule sequencing technologies, such as PacBio SMRT, provides long reads spanning entire transcript isoforms which do not require assembly. Therefore, we have developed ISOdb, a comprehensive resource database for hosting and carrying out an in-depth analysis of Iso-Seq datasets and visualising the full-length transcript isoforms...
2018: International Journal of Genomics
Omar Ramos-Lopez, Jose I Riezu-Boj, Fermin I Milagro, Marta Cuervo, Leticia Goni, J A Martinez
Background and Aim: Individual lipid phenotypes including circulating total cholesterol (TC), low-density lipoprotein cholesterol (LDL-c), high-density lipoprotein cholesterol (HDL-c), and triglycerides (TG) determinations are influenced by gene-environment interactions. The aim of this study was to predict blood lipid level (TC, LDL-c, HDL-c, and TG) variability using genetic and lifestyle data in subjects with excessive body weight-for-height. Methods: This cross-sectional study enrolled 304 unrelated overweight/obese adults of self-reported European ancestry...
2018: International Journal of Genomics
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