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International Journal of Genomics

Yuzhu Huo, Wangdan Xiong, Kunlong Su, Yu Li, Yawen Yang, Chunxiang Fu, Zhenying Wu, Zhen Sun
The plant-specific transcription factor TCPs play multiple roles in plant growth, development, and stress responses. However, a genome-wide analysis of TCP proteins and their roles in salt stress has not been declared in switchgrass ( Panicum virgatum L.). In this study, 42 PvTCP genes ( PvTCPs ) were identified from the switchgrass genome and 38 members can be anchored to its chromosomes unevenly. Nine PvTCPs were predicted to be microRNA319 ( miR319 ) targets. Furthermore, PvTCPs can be divided into three clades according to the phylogeny and conserved domains...
2019: International Journal of Genomics
Eliane Evanovich, Patricia Jeanne de Souza Mendonça Mattos, João Farias Guerreiro
Background: Lactobacillus plantarum is widely used in the manufacture of dairy products, fermented foods, and bacteriocins. The genomes of the strains contain multiple genes which may have been acquired by horizontal gene transfer. Many of these genes are important for the regulation, metabolism, and transport of various sugars; however, other genes may carry and spread virulence and antibiotic resistance determinants. In this way, monitoring these genomes is essential to the manufacture of food...
2019: International Journal of Genomics
Yongxiang Yu, Zheng Zhang, Yingeng Wang, Meijie Liao, Xiaojun Rong, Bin Li, Kai Wang, Jing Chen, Hao Zhang
Photobacterium damselae subsp. damselae (PDD) is a Gram-negative bacterium that can infect a variety of aquatic organisms and humans. Based on an epidemiological investigation conducted over the past 3 years, PDD is one of the most important pathogens causing septic skin ulcer in deep-sea cage-cultured Sebastes schlegelii in the Huang-Bohai Sea area and present throughout the year with high abundance. To further understand the pathogenicity of this species, the pathogenic properties and genome of PDD strain SSPD1601 were analyzed...
2019: International Journal of Genomics
Arnoud Boot, Jan Oosting, Saskia Doorn, Sarah Ouahoud, Marina Ventayol Garcia, Dina Ruano, Hans Morreau, Tom van Wezel
Allele-specific expression (ASE) is found in approximately 20-30% of human genes. During tumorigenesis, ASE changes due to somatic alterations that change the regulatory landscape. In colorectal cancer (CRC), many chromosomes show frequent gains or losses while homozygosity of chromosome 7 is rare. We hypothesized that genes essential to survival show allele-specific expression (ASE) on both alleles of chromosome 7. Using a panel of 21 recently established low-passage CRC cell lines, we performed ASE analysis by hybridizing DNA and cDNA to Infinium HumanExome-12 v1 BeadChips containing cSNPs in 392 chromosome 7 genes...
2019: International Journal of Genomics
Luzhao Pan, Jiaqiu Zheng, Jia Liu, Jun Guo, Fawan Liu, Lecheng Liu, Hongjian Wan
Acetylserotonin methyltransferase (ASMT) in plant species, one of the most important enzymes in melatonin biosynthesis, plays a rate-limiting role in the melatonin production. In this study, based on the whole genome sequence, we performed a systematic analysis for the ASMT gene family in pepper ( Capsicum annuum L.) and analyzed their expression profiles during growth and development, as well as abiotic stresses. The results showed that at least 16 CaASMT genes were identified in the pepper genome. Phylogenetic analyses of all the CaASMTs were divided into three groups (group I, group II, and group III) with a high bootstrap value...
2019: International Journal of Genomics
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
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