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You searched for: Journal Genes & genomics Remove constraint Journal: Genes & genomics Publication Year 2018 Remove constraint Publication Year: 2018 Subject genes Remove constraint Subject: genes
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1. A case of interdigitating dendritic cell sarcoma studied by whole-exome sequencing

Author:
Hong, Ki Hwan; Song, Soyoung; Shin, Wonseok; Kang, Keunsoo; Cho, Chun-Sung; Hong, Yong Tae; Han, Kyudong; Moon, Jeong Hwan
Source:
Genes & genomics 2018 v.40 no.12 pp. 1279-1285
ISSN:
1976-9571
Subject:
DNA; DNA-directed DNA polymerase; bioinformatics; blood; case studies; dendritic cells; etiology; gene ontology; genes; genetic factors; immunohistochemistry; neoplasm cells; pathogenesis; patients; sarcoma; single nucleotide polymorphism
Abstract:
... Interdigitating dendritic cell sarcoma (IDCS) is an aggressive neoplasm and is an extremely rare disease, with a challenging diagnosis. Etiology of IDCS is also unknown and most studies with only case reports. In our case, immunohistochemistry showed that the tumor cells were positive for S100, CD45, and CD68, but negative for CD1a and CD21. This study aimed to investigate the causative factors of ...
DOI:
10.1007/s13258-018-0724-y

2. Bordetella bronchiseptica bateriophage suppresses B. bronchiseptica-induced inflammation in swine nasal turbinate cells

Author:
Park, Ga Young; Lee, Hye Min; Yu, Hyun Jin; Son, Jee Soo; Park, Sang Joon; Song, Kyoung Seob
Source:
Genes & genomics 2018 v.40 no.12 pp. 1383-1388
ISSN:
1976-9571
Subject:
Bordetella bronchiseptica; antibiotics; bacteria; bacterial infections; bacteriophages; chemokines; disease control; dose response; gene expression; genes; immune response; inflammation; interleukin-1beta; interleukin-6; mucins; nose; quantitative polymerase chain reaction; respiratory tract diseases; secretion; swine; swine diseases; therapeutics
Abstract:
... The development of therapeutic bacteriophages will provide several benefits based on an understanding the basic physiological dynamics of phage and bacteria interactions for therapeutic use in light of the results of antibiotic abuse. However, studies on bacteriophage therapeutics against microbes are very limited, because of lack of phage stability and an incomplete understanding of the physiolog ...
DOI:
10.1007/s13258-018-0755-4

3. Functional analysis of a homologue of the FLORICAULA/LEAFY gene in litchi (Litchi chinensis Sonn.) revealing its significance in early flowering process

Author:
Ding, Feng; Zhang, Shuwei; Chen, Houbin; Peng, Hongxiang; Lu, Jiang; He, Xinhua; Pan, Jiechun
Source:
Genes & genomics 2018 v.40 no.12 pp. 1259-1267
ISSN:
1976-9571
Subject:
Litchi chinensis; amino acids; complementary DNA; flower buds; flowering; fluorescent proteins; genes; heterologous gene expression; nucleotide sequences; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; sequence analysis; tobacco; transcription factors; transcriptome; transgenic plants
Abstract:
... Litchi (Litchi chinensis Sonn.) is an important subtropical fruit crop with high commercial value due to its high nutritional values and favorable tastes. However, irregular bearing attributed to unstable flowering is a major ongoing problem for litchi producers. Previous studies indicate that low-temperature is a key factor in litchi floral induction. In order to reveal the genetic and molecular ...
DOI:
10.1007/s13258-018-0739-4

4. Genome-wide analysis of Hanwoo and Chikso populations using the BovineSNP50 genotyping array

Author:
Song, Jun-Seok; Seong, Ha-Seung; Choi, Bong-Hwan; Lee, Chang-Woo; Hwang, Nam-Hyun; Lim, Dajeong; Lee, Joon-Hee; Kim, Jin Soo; Kim, Jeong-Dae; Park, Yeon-Soo; Choi, Jung-Woo; Kim, Jong-Bok
Source:
Genes & genomics 2018 v.40 no.12 pp. 1373-1382
ISSN:
1976-9571
Subject:
cattle; cattle breeds; data collection; genes; genetic relationships; genetic variation; genome-wide association study; genomics; genotyping; heterozygosity; inbreeding; inbreeding coefficient; linkage disequilibrium; meat; principal component analysis; quality control; reproductive traits; single nucleotide polymorphism
Abstract:
... Hanwoo and Chikso are classified as Korean native cattle breeds that are currently registered with the Food and Agriculture Organization. However, there is still a lack of genomic studies to compare Hanwoo to Chikso populations. The objective of this study was to perform genome-wide analysis of Hanwoo and Chikso populations, investigating the genetic relationships between these two populations. We ...
DOI:
10.1007/s13258-018-0733-x

5. Identification of pathways and genes associated with cerebral palsy

Author:
Zhu, Qingwen; Ni, Yufei; Wang, Jing; Yin, Honggang; Zhang, Qin; Zhang, Lingli; Bian, Wenjun; Liang, Bo; Kong, Lingyin; Xuan, Liming; Lu, Naru
Source:
Genes & genomics 2018 v.40 no.12 pp. 1339-1349
ISSN:
1976-9571
Subject:
axons; cerebral palsy; children; genes; genetic factors; genetic heterogeneity; high-throughput nucleotide sequencing; pathogenesis; protein-protein interactions; risk factors; synapse
Abstract:
... Cerebral palsy (CP) is a non-progressive neurological disease, of which susceptibility is linked to genetic and environmental risk factors. More and more studies have shown that CP might be caused by multiple genetic factors, similar to other neurodevelopmental disorders. Due to the high genetic heterogeneity of CP, we focused on investigating related molecular pathways. Ten children with CP were ...
DOI:
10.1007/s13258-018-0729-6

6. Locating QTLs controlling overwintering seedling rate in perennial glutinous rice 89-1 (Oryza sativa L.)

Author:
Deng, Xiaoshu; Gan, Lu; Liu, Yan; Luo, Ancai; Jin, Liang; Chen, Jiao; Tang, Ruyu; Lei, Lixia; Tang, Jianghong; Zhang, Jiani; Zhao, Zhengwu
Source:
Genes & genomics 2018 v.40 no.12 pp. 1351-1361
ISSN:
1976-9571
Subject:
Oryza sativa; buds; cell membranes; chromosome mapping; cold; cold stress; cold tolerance; gene ontology; genes; glutinous rice; inbred lines; loci; membrane proteins; microsatellite repeats; overwintering; phenotypic variation; quantitative trait loci; seedlings; stress response
Abstract:
... A new cold tolerant germplasm resource named glutinous rice 89-1 (Gr89-1, Oryza sativa L.) can overwinter using axillary buds, with these buds being ratooned the following year. The overwintering seedling rate (OSR) is an important factor for evaluating cold tolerance. Many quantitative trait loci (QTLs) controlling cold tolerance at different growth stages in rice have been identified, with some ...
DOI:
10.1007/s13258-018-0731-z

7. Sequence-based 5-mers highly correlated to epigenetic modifications in genes interactions

Author:
Salimi, Dariush; Moeini, Ali; Masoudi-Nejad, Ali
Source:
Genes & genomics 2018 v.40 no.12 pp. 1363-1371
ISSN:
1976-9571
Subject:
DNA; epigenetics; gene expression; gene interaction; gene regulatory networks; genes; humans; muscles; peroxisome proliferator-activated receptors; prioritization; signal transduction
Abstract:
... One of the main concerns in biology is extracting sophisticated features from DNA sequence for gene interaction determination, receiving a great deal of researchers’ attention. The epigenetic modifications along with their patterns have been intensely recognized as dominant features affecting on gene expression. However, studying sequenced-based features highly correlated to this key element has r ...
DOI:
10.1007/s13258-018-0730-0

8. Transcriptome profiling and identification of functional genes involved in H2S response in grapevine tissue cultured plantlets

Author:
Ma, Qian; Yang, Jingli
Source:
Genes & genomics 2018 v.40 no.12 pp. 1287-1300
ISSN:
1976-9571
Subject:
Vitis vinifera; amino acids; biochemical pathways; biosynthesis; carbon metabolism; cultivars; drought; ferritin; flowers; fruits; gene expression regulation; genes; gluconeogenesis; glycolysis; heat; heavy metals; hydrogen sulfide; osmotic stress; plant hormones; plantlets; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; root growth; secondary metabolites; seed germination; shelf life; signal transduction; stomatal movement; tissue culture; transcription (genetics); transcription factors; transcriptomics
Abstract:
... Hydrogen sulfide (H₂S), a small bioactive gas, has been proved functioning in plant growth and development as well as alleviation of abiotic stresses, which including promoting seed germination, accelerating embryonic root growth, regulating flower senescence, inducing stomatal closure, and defending drought, heat, heavy metals and osmotic stresses etc. However, the molecular functioning mechanism ...
DOI:
10.1007/s13258-018-0723-z

9. Analysis of gene expression in red maple (Acer rubrum) and trembling aspen (Populus tremuloides) populations from a mining region

Author:
Kalubi, K. N.; Michael, P.; Omri, A.
Source:
Genes & genomics 2018 v.40 no.11 pp. 1127-1136
ISSN:
1976-9571
Subject:
Acer rubrum; Populus tremuloides; complementary DNA; environmental factors; gene expression; gene expression regulation; genes; mining; nickel; plant adaptation; transcription (genetics); tubulin; Canada
Abstract:
... The Greater Sudbury Region has been known as one of the most ecologically disturbed areas in Canada for the past century. Plant adaptation to environmental stressors often results in modifications in gene expression at the transcriptional level. The main objective of the present study was to compare the expression of genes associated with nickel resistance in Acer rubrum and Populus tremuloides gr ...
DOI:
10.1007/s13258-018-0670-8

10. Association between expression levels and growth trait-related SNPs located in promoters of the MC4R and MSTN genes in Spinibarbus hollandi

Author:
Yang, Yang; Lan, Zhaojun; Shu, Hu; Zhou, Huiqiang; Jiang, Xiaolu; Hou, Liping; Gu, Pinghua
Source:
Genes & genomics 2018 v.40 no.11 pp. 1119-1125
ISSN:
1976-9571
Subject:
Spinibarbus; brain; fish; genes; genotype; growth performance; growth traits; marker-assisted selection; muscles; myostatin; single nucleotide polymorphism
Abstract:
... Melanocortin 4 receptor: (MC4R) and Myostatin (MSTN) are two important growth trait-related genes in animals. In this study, we showed that two SNPs, MC4R-719A>G and MSTN-519C>T, found in the promoters of the MC4R and MSTN genes, respectively, are both associated with growth traits in Spinibarbus hollandi. Furthermore, we observed that there were significant associations between the expression lev ...
DOI:
10.1007/s13258-018-0666-4

11. Complete mitochondrial genome of freshwater goby Rhinogobius cliffordpopei (Perciformes, Gobiidae): genome characterization and phylogenetic analysis

Author:
Zhong, Liqiang; Wang, Minghua; Li, Daming; Tang, Shengkai; Zhang, Tongqing; Bian, Wenji; Chen, Xiaohui
Source:
Genes & genomics 2018 v.40 no.11 pp. 1137-1148
ISSN:
1976-9571
Subject:
Perciformes; Rhinogobius; Tridentiger; fish; genes; invasive species; mitochondrial DNA; mitochondrial genome; monophyly; nucleotide sequences; ribosomal RNA; transfer RNA; China
Abstract:
... Freshwater gobies Rhinogobius cliffordpopei and R. giurinus are invasive species with particular concern because they have become dominant and were fierce competitors in the invaded areas in Yunnan-Guizhou Plateau (southwest of China). Information about genetic characteristics of R. giurinus have been published, but there were still no relevant reports about R. cliffordpopei. In present study, the ...
DOI:
10.1007/s13258-018-0669-1

12. Effect of 1-aminocyclopropane-1-carboxylic acid (ACC)-induced ethylene on cellulose synthase A (CesA) genes in flax (Linum usitatissimum L. ‘Nike’) seedlings

Author:
Lim, Hansol; Paek, Seung-Ho; Oh, Seung-Eun
Source:
Genes & genomics 2018 v.40 no.11 pp. 1237-1248
ISSN:
1976-9571
Subject:
1-aminocyclopropane-1-carboxylic acid; Linum usitatissimum; carboxylic acids; cell walls; cellulose microfibrils; cellulose synthase; ethylene; flax; gene expression; gene expression regulation; genes; hypocotyls; polymers; promoter regions; seedling growth; seedlings
Abstract:
... INTRODUCTION: Cellulose microfibril is a major cell wall polymer that plays an important role in the growth and development of plants. The gene cellulose synthase A (CesA), encoding cellulose synthases, is involved in the synthesis of cellulose microfibrils. However, the regulatory mechanism of CesA gene expression is not well understood, especially during the early developmental stages. OBJECTIVE ...
DOI:
10.1007/s13258-018-0720-2

13. Genome-wide analyses of the Jeju, Thoroughbred, and Jeju crossbred horse populations using the high density SNP array

Author:
Kim, Nam Young; Seong, Ha-Seung; Kim, Dae Cheol; Park, Nam Geon; Yang, Byoung Chul; Son, Jun Kyu; Shin, Sang Min; Woo, Jae Hoon; Shin, Moon Cheol; Yoo, Ji Hyun; Choi, Jung-Woo
Source:
Genes & genomics 2018 v.40 no.11 pp. 1249-1258
ISSN:
1976-9571
Subject:
Thoroughbred; genes; genetic relationships; genetic similarity; genome-wide association study; genomics; heterozygosity; horses; inbreeding; linkage disequilibrium; loci; population structure; principal component analysis; single nucleotide polymorphism
Abstract:
... The Jeju horse is an indigenous Korean horse breed that is currently registered with the Food and Agriculture Organization of the United Nations. However, there is severe lack of genomic studies on Jeju horse. This study was conducted to investigate genetic characteristics of horses including Jeju horse, Thoroughbred and Jeju crossbred (Jeju × Thoroughbred) populations. We compared the genomes of ...
DOI:
10.1007/s13258-018-0722-0

14. Low pH stress responsive transcriptome of seedling roots in wheat (Triticum aestivum L.)

Author:
Hu, Haiyan; He, Jie; Zhao, Junjie; Ou, Xingqi; Li, Hongmin; Ru, Zhengang
Source:
Genes & genomics 2018 v.40 no.11 pp. 1199-1211
ISSN:
1976-9571
Subject:
Arabidopsis; Triticum aestivum; antioxidant activity; biosynthesis; complementary DNA; flavonoids; gene expression regulation; genes; immune system; jasmonic acid; microarray technology; nitrogen fertilizers; pH; rhizosphere; roots; seedlings; signal transduction; soil acidification; toxicity; transcription (genetics); transcription factors; transcriptome; transcriptomics; wheat; China
Abstract:
... Soil acidification is one of major problems limiting crop growth and especially becoming increasingly serious in China owing to excessive use of nitrogen fertilizer. Only the STOP1 of Arabidopsis was identified clearly sensitive to proton rhizotoxicity and the molecular mechanism for proton toxicity tolerance of plants is still poorly understood. The main objective of this study was to investigate ...
DOI:
10.1007/s13258-018-0680-6

15. Mitochondrial OXPHOS genes provides insights into genetics basis of hypoxia adaptation in anchialine cave shrimps

Author:
Guo, Huayun; Yang, Hao; Tao, Yitao; Tang, Dan; Wu, Qiong; Wang, Zhengfei; Tang, Boping
Source:
Genes & genomics 2018 v.40 no.11 pp. 1169-1180
ISSN:
1976-9571
Subject:
Crustacea; amino acid substitution; amino acids; caves; dissolved oxygen; energy metabolism; evolutionary adaptation; genes; habitats; hypoxia; mitochondria; mitochondrial genome; phylogeny; salinity; shrimp; temperature; temporal variation
Abstract:
... Cave shrimps from the genera Typhlatya, Stygiocaris and Typhlopatsa (TST complex) comprises twenty cave-adapted taxa, which mainly occur in the anchialine environment. Anchialine habitats may undergo drastic environmental fluctuations, including spatial and temporal changes in salinity, temperature, and dissolved oxygen content. Previous studies of crustaceans from anchialine caves suggest that th ...
DOI:
10.1007/s13258-018-0674-4

16. Molecular characterization and expression of suppressor of cytokine signaling (SOCS) 1, 2 and 3 under acute hypoxia and reoxygenation in pufferfish, Takifugu fasciatus

Author:
Wang, Dan; Wen, Xin; Zhang, Xinyu; Hu, Yadong; Li, Xinru; Zhu, Wenxu; Wang, Tao; Yin, Shaowu
Source:
Genes & genomics 2018 v.40 no.11 pp. 1225-1235
ISSN:
1976-9571
Subject:
Takifugu; Western blotting; brain; cytokines; fish; genes; hypoxia; innate immunity; liver; messenger RNA; protein content; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; tissue distribution
Abstract:
... Hypoxia seriously affects the innate immune system of fish. However, the roles of suppressor of cytokine signaling (SOCS), pivotal anti-inflammatory genes, in response to hypoxia/reoxygenation remain largely unexplored. The primary objective of this study was to elucidate the function of SOCS genes under acute hypoxia and reoxygenation in pufferfish (Takifugu fasciatus). In the present study, SOCS ...
DOI:
10.1007/s13258-018-0719-8

17. Profiling of glucose-induced transcription in Sulfolobus acidocaldarius DSM 639

Author:
Park, Jungwook; Lee, Areum; Lee, Hyun-Hee; Park, Inmyoung; Seo, Young-Su; Cha, Jaeho
Source:
Genes & genomics 2018 v.40 no.11 pp. 1157-1167
ISSN:
1976-9571
Subject:
Sulfolobus; amino acids; biosynthesis; carbon; carbon metabolism; electron transport chain; energy; gene expression regulation; gene ontology; genes; glucose; pyruvic acid; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; sequence analysis; sulfites; sulfur; transcription (genetics); transcriptomics
Abstract:
... Sulfolobus species can grow on a variety of organic compounds as carbon and energy sources. These species degrade glucose to pyruvate by the modified branched Entner–Doudoroff pathway. We attempted to determine the differentially expressed genes (DEGs) under sugar-limited and sugar-rich conditions. RNA sequencing (RNA-seq) was used to quantify the expression of the genes and identify those DEGs be ...
DOI:
10.1007/s13258-018-0675-3

18. Transcriptome profiling of rubber tree (Hevea brasiliensis) discovers candidate regulators of the cold stress response

Author:
Gong, Xiao-Xiao; Yan, Bing-Yu; Hu, Jin; Yang, Cui-Ping; Li, Yi-Jian; Liu, Jin-Ping; Liao, Wen-Bin
Source:
Genes & genomics 2018 v.40 no.11 pp. 1181-1197
ISSN:
1976-9571
Subject:
GRAS substances; Hevea brasiliensis; biosynthesis; cDNA libraries; cold; cold shock response; cold stress; cold treatment; complementary DNA; cutin; flavonoids; gene expression regulation; genes; pentoses; phenylalanine; plant hormones; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; rubber; sequence analysis; signal transduction; starch; sucrose; transcription (genetics); transcription factors; transcriptomics; tropical plants
Abstract:
... Tropical plant rubber tree (Hevea brasiliensis) is the sole source of commercial natural rubber and low-temperature stress is the most important limiting factor for its cultivation. To characterize the gene expression profiles of H. brasiliensis under the cold stress and discover the key cold stress-induced genes. Three cDNA libraries, CT (control), LT2 (cold treatment at 4 °C for 2 h) and LT24 (c ...
DOI:
10.1007/s13258-018-0681-5

19. Characterization and phylogenetic analysis of the complete mitogenome of a rare cavefish, Sinocyclocheilus multipunctatus (Cypriniformes: Cyprinidae)

Author:
Zhang, Renyi; Wang, Xue
Source:
Genes & genomics 2018 v.40 no.10 pp. 1033-1040
ISSN:
1976-9571
Subject:
Bayesian theory; Sinocyclocheilus; genes; mitochondrial DNA; mitochondrial genome; phylogeny; polymerase chain reaction; ribosomal RNA; statistical analysis; transfer RNA
Abstract:
... The genus Sinocyclocheilus is a representative group of cave creatures. However, genetic studies on Sinocyclocheilus are rare. The primary objective of this study was to explore the structure and feature of the complete mitochondrial genome of S. multipunctatus, and reconstruct the mitogenomic phylogeny of Sinocyclocheilus. The mitochondrial DNA of S. multipunctatus was amplified by overlapping PC ...
DOI:
10.1007/s13258-018-0711-3

20. Dependence and independence of the root clock on the shoot clock in Arabidopsis

Author:
Lee, Hong Gil; Seo, Pil Joon
Source:
Genes & genomics 2018 v.40 no.10 pp. 1063-1068
ISSN:
1976-9571
Subject:
Arabidopsis; circadian clocks; circadian rhythm; genes; messenger RNA; mutants; mutation; roots; shoots
Abstract:
... Temporal and spatial compartmentalization of biological processes is facilitated by tissue-specific uncoupled circadian clocks in plants. However, interactions among tissue-specific circadian clocks have not been well established. The primary objective of this study was to describe both organ-specific circadian behaviors and centralized actions of the root clock. We analyzed transcript accumulatio ...
DOI:
10.1007/s13258-018-0710-4