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International Journal of Genomics

Giovanny Soca-Chafre, Angelica Montiel-Dávalos, Inti Alberto De La Rosa-Velázquez, Claudia Haydeé Saraí Caro-Sánchez, Adriana Peña-Nieves, Oscar Arrieta
Lung cancer (LC) is the first cause of cancer-related deaths worldwide. Elucidating the pathogenesis of LC will give information on key elements of tumor initiation and development while helping to design novel targeted therapies. LC is an heterogeneous disease that has the second highest mutation rate surpassed only by melanoma, since 90% of LC occurs in tobacco smokers. However, only a small percent of smokers develops LC, indicating an inherent genomic instability. Additionally, LC in never smokers suggests other molecular mechanisms not causally linked to tobacco carcinogens...
2019: International Journal of Genomics
Sidra Habib, Muhammad Waseem, Ning Li, Lu Yang, Zhengguo Li
Abiotic stresses remain the key environmental issues that reduce plant development and therefore affect crop production. Transcription factors, such as the GRAS family, are involved in various functions of abiotic stresses and plant growth. The GRAS family of tomato ( Solanum lycopersicum ), SlGRAS7 , is described in this study. We produced overexpressing SlGARS7 plants to learn more about the GRAS transcription factors. Plants overexpressing SlGARS7 ( SlGRAS7 -OE) showed multiple phenotypes related to many behaviors, including plant height, root and shoot length, and flowering time...
2019: International Journal of Genomics
I N Vasilyeva, V G Bespalov, J D Von, A L Semenov, G V Tochilnikov, V A Romanov, I K Alvovsky, D A Baranenko
The purpose of this work was to study changes in the level of cell-free DNA (cfDNA) in the blood of young and old rats in the normal state and with induced benign prostatic hyperplasia (BPH). Male Wistar rats were divided into 4 groups-young (3 months), old (20 months), intact, or with testosterone-induced BPH. Groups with BPH were subjected to surgical castration and administration of testosterone esters at a dose of 25 mg/kg for a total of 7 injections for 20 days. In intact animals, the level of cfDNA in old rats (2...
2019: International Journal of Genomics
Kai Chen, Zhonghuan Tian, Fatang Jiang, Yunjiang Cheng, Chao-An Long
Kloeckera apiculata plays an important role in the inhibition of citrus postharvest blue and green mould diseases. This study was based on the previous genome sequencing of K. apiculata strain 34-9. After homologous comparison, scaffold 27 was defined as the mitochondrial (mt) sequence of K. apiculata 34-9. The comparison showed a high level of sequence identity between scaffold 27 and the known mtDNA of Hanseniaspora uvarum . The genome sequence of H. vineae T02/19AF showed several short and discontinuous fragments homologous to the mtDNA of H...
2019: International Journal of Genomics
Peng Shang, Wenting Li, Gang Liu, Jian Zhang, Mengrou Li, Lvcao Wu, Kejun Wang, Yangzom Chamba
Tibetan pigs from the Tibetan Plateau are characterized with a significant phenotypic difference relative to lowland pigs. In this study, a significant difference of the fatness and fatty acid composition traits was observed between the Tibetan and Yorkshire pigs. To uncover the involved mechanism, the expression profile of long noncoding RNAs (lncRNAs) and genes was compared between them. After serial filtered steps, 1,964 lncRNAs were obtained through our computational pipeline. In total, 63 and 715 lncRNAs and genes were identified to be differentially expressed...
2019: International Journal of Genomics
T Ząbek, E Semik-Gurgul, T Szmatoła, A Gurgul, A Fornal, M Bugno-Poniewierska
Horses are one of the longest-living species of farm animals. Advanced age is often associated with a decrease in body condition, dysfunction of immune system, and late-onset disorders. Due to this, the search for new solutions in the prevention and treatment of pathological conditions of the advanced age of horses is desirable. That is why the identification of aging-related changes in the horse genome is interesting in this respect. In the recent years, the research on aging includes studies of age-related epigenetic effects observed on the DNA methylation level...
2019: International Journal of Genomics
Qing Qiu, Ping Wang, Hui Kang, Yu Wang, Kejian Tian, Hongliang Huo
In this study, we isolated a new estrogen-degrading bacterium from a soil sample collected near a pharmaceutical factory in Beijing, China. Morphological observations, physiological and biochemical analyses, and sequence analysis showed that the strain was in the genus Acinetobacter , and it was named DSSKY-A-001. The estrogen degradation rate and growth density of strain DSSKY-A-001 were determined by high-performance liquid chromatography and a growth assay using a microplate reader, respectively. The estrogen degradation rate was 76% on the third day and 90% on the sixth day of culture...
2019: International Journal of Genomics
Xinyu Kuang, Qian Zhou, Zhuying Li, Yujie Hu, Yulin Kang, Wenyan Huang
This study is aimed at exploring the mechanism by which the -254C>G single nucleotide polymorphism (SNP) on the transient receptor potential cation channel 6 ( TRPC6 ) gene promoter could increase its activation in steroid-resistant nephrotic syndrome children of China. Plasmids containing the TRPC6 promoter region (with the -254C or G allele) were constructed and then transfected into human embryonic kidney (HEK) 293T cells and human podocytes. Luciferase assays were used to test the promoter activity in both cell lines with or without tumor necrosis factor- α (TNF- α ) treatment, and chromatin immunoprecipitation-polymerase chain reaction (ChIP-PCR) analysis was used to verify the transcription factor that could bind to this mutant sequence...
2019: International Journal of Genomics
Enéas Ricardo Konzen, Gustavo Henrique Recchia, Fernanda Cassieri, Danielle Gregorio Gomes Caldas, Jorge C Berny Mier Y Teran, Paul Gepts, Siu Mui Tsai
We analyzed the nucleotide variability and the expression profile of DREB genes from common bean, a crop of high economic and nutritional value throughout the world but constantly affected by abiotic stresses in cultivation areas. As DREB genes have been constantly associated with abiotic stress tolerance, we systematically categorized 54 putative PvDREB genes distributed in the common bean genome. It involved from AP2 domain location and amino acid conservation analysis (valine at the 14th position) to the identification of conserved motifs within peptide sequences representing six subgroups (A-1 to A-6) of PvDREB proteins...
2019: International Journal of Genomics
Qingzhen Wei, Liming Du, Wuhong Wang, Tianhua Hu, Haijiao Hu, Jinglei Wang, Karine David, Chonglai Bao
Eggplant ( Solanum melongena L.) is an economically and nutritionally important fruit crop of the Solanaceae family, which was domesticated in India and southern China. However, the genome regions subjected to selective sweeps in eggplant remain unknown. In the present study, we performed comparative transcriptome analysis of cultivated and wild eggplant species with emphasis on the selection pattern during domestication. In total, 44,073 ( S. sisymbriifolium ) to 58,677 ( S. melongena cultivar S58) unigenes were generated for the six eggplant accessions with total lengths of 36...
2019: International Journal of Genomics
Jieying Qian, Yong Liu, Chengtong Ma, Naixia Chao, Qicong Chen, Yangmei Zhang, Yu Luo, Danzhao Cai, Yaosheng Wu
Triterpenoid saponins are secondary metabolites synthesized through isoprenoid pathways in plants. Cucurbitaceae represent an important plant family in which many species contain cucurbitacins as secondary metabolites synthesized through isoprenoid and triterpenoid pathways. Squalene synthase ( SQS ) is required for the biosynthesis of isoprenoids, but the forces driving the evolution of SQS remain undetermined. In this study, 10 SQS cDNA sequences cloned from 10 species of Cucurbitaceae and 49 sequences of SQS downloaded from GenBank and UniProt databases were analyzed in a phylogenetic framework to identify the evolutionary forces for functional divergence...
2019: International Journal of Genomics
Shi-Weng Li, Meng-Yuan Liu, Rui-Qi Yang
The complete genome sequence of Bacillus subtilis strain DM2 isolated from petroleum-contaminated soil on the Tibetan Plateau was determined. The genome of strain DM2 consists of a circular chromosome of 4,238,631 bp for 4458 protein-coding genes and a plasmid of 84,240 bp coding for 103 genes. Thirty-four genomic islands coding for 330 proteins and 5 prophages are found in the genome. The DDH value shows that strain DM2 belongs to B. subtilis subsp . subtilis subspecies, but significant variations of the genome are also present...
2019: International Journal of Genomics
Alessandra Borgognone, Walter Sanseverino, Riccardo Aiese Cigliano, Raúl Castanera
Long noncoding RNAs have been thoroughly studied in plants, animals, and yeasts, where they play important roles as regulators of transcription. Nevertheless, almost nothing is known about their presence and characteristics in filamentous fungi, especially in basidiomycetes. In the present study, we have carried out an exhaustive annotation and characterization of lncRNAs in two lignin degrader basidiomycetes, Coniophora puteana and Serpula lacrymans. We identified 2,712 putative lncRNAs in the former and 2,242 in the latter, mainly originating from intergenic locations of transposon-sparse genomic regions...
2019: International Journal of Genomics
Tao Wang, Yiming Chen, Weibing Zhuang, Fengjiao Zhang, Xiaochun Shu, Zhong Wang, Qing Yang
Taxol is one of the most potent and effective anticancer drugs and is originally isolated from Taxus species. To investigate the specific regulatory mechanisms of taxol synthesis in Taxus wallichiana var. mairei , RNA-seq was conducted to reveal the differences in transcriptional levels between wild type (WT) and "Jinxishan" (JXS), a cultivar selected from a population of Taxus mairei that shows about 3-fold higher taxol content in the needles than WT. Our results indicated that high expressions of the genes taxadienol acetyltransferase ( TAT ), taxadiene 5-alpha hydroxylase ( T5H ), 5-alpha-taxadienol-10-beta-hydroxylase ( T10OH ), and 2-debenzoyl-7,13-diacetylbaccatin III-2-O-benzoyl-transferase ( DBBT ), which catalyze a series of key acetylation and hydroxylation steps, are the main cause of high taxol content in JXS...
2019: International Journal of Genomics
Zhouyiyuan Xue, Abdur Rahman Ansari, Xing Zhao, Kun Zang, Yu Liang, Lei Cui, Yafang Hu, Ranran Cheng, Xiaolong Zhang, Juming Zhong, Huazhen Liu
The thymus is a lobulated unique lymphoid immune organ that plays a critical role in the selection, development, proliferation, and differentiation of T cells. The thymus of developing chickens undergoes continued morphological alterations; however, the biomolecular and transcriptional dynamics of the postnatal thymus in avian species is not clear yet. Therefore, the thymuses from chickens at different stages of development (at weeks 0, 1, 5, 9, 18, and 27) were used in the present study. The RNA-seq method was used to study the gene expression patterns...
2019: 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
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