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You searched for: Journal name Genes & genomics Remove constraint Journal name: Genes & genomics Publication year rev 7982-2018 Remove constraint Publication year rev: 7982-2018
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1. A case of interdigitating dendritic cell sarcoma studied by whole-exome sequencing

Author:
Ki Hwan Hong; Soyoung Song; Wonseok Shin; Keunsoo Kang; Chun-Sung Cho; Yong Tae Hong; Kyudong Han; Jeong Hwan Moon
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. A head transcriptome provides insights into odorant binding proteins of the bamboo grasshopper

Author:
Ran Li; Guo-Fang Jiang; Si-Yu Dong
Source:
Genes & genomics 2018 v.40 no.9 pp. 991-1000
ISSN:
1976-9571
Subject:
antennae; bamboos; binding proteins; databases; ecology; genes; genomics; grasshoppers; head; high-throughput nucleotide sequencing; odor compounds; pests; protocols; reverse transcriptase polymerase chain reaction; semiochemicals; tissue distribution; tissues; transcriptome; transcriptomics; China
Abstract:
... The bamboo grasshopper Ceracris kiangsu is a famous bamboo pest in China. The identification of genes involved in olfactory behavior of C. kiangsu is necessary for better understanding the molecular basis and expression profiles of behavior ecology. However, necessary genomic and transcriptomic data are lacking in the species, limiting control efficiency. The primary objective of this study was to ...
DOI:
10.1007/s13258-018-0706-0

3. A novel homozygous mutation in SZT2 gene in Saudi family with developmental delay, macrocephaly and epilepsy

Author:
Muhammad Imran Naseer; Mohammad Khalid Alwasiyah; Angham Abdulrahman Abdulkareem; Rayan Abdullah Bajammal; Carlos Trujillo; Muhammad Abu-Elmagd; Mohammad Alam Jafri; Adeel G. Chaudhary; Mohammad H. Al-Qahtani
Source:
Genes & genomics 2018 v.40 no.11 pp. 1149-1155
ISSN:
1976-9571
Subject:
chromosomes; databases; epilepsy; exons; frontal lobe; glutamic acid; homozygosity; humans; mice; mutation; phenotype; sequence analysis; siblings
Abstract:
... Epileptic encephalopathies are genetically heterogeneous disorders which leads to epilepsy and cause neurological disorders. Seizure threshold 2 (SZT2) gene located on chromosome 1p34.2 encodes protein mainly expressed predominantly in the parietal and frontal cortex and dorsal root ganglia in the brain. Previous studies in mice showed that mutation in this gene can confers low seizure threshold, ...
DOI:
10.1007/s13258-018-0673-5

4. A novel mutation in RDH5 gene causes retinitis pigmentosa in consanguineous Pakistani family

Author:
Neelam Sultan; Irfan Ali; Shazia Anwer Bukhari; Shahid Mahmood Baig; Muhammad Asif; Muhammad Qasim; Muhammad Imran Naseer; Mahmood Rasool
Source:
Genes & genomics 2018 v.40 no.5 pp. 553-559
ISSN:
1976-9571
Subject:
alanine; alleles; counseling; early diagnosis; exons; genotype-phenotype correlation; high-throughput nucleotide sequencing; homozygosity; loci; macular degeneration; missense mutation; mutants; patients; pedigree; phenotype; proteins; serine; Pakistan
Abstract:
... Retinitis pigmentosa (RP) is the most frequent genetically and clinically heterogeneous inherited retinal degeneration. To date, more than 80 genes have been identified that cause autosomal dominant, autosomal recessive and X linked RP. However, locus and allelic heterogeneity of RP has not been fully captured yet. This heterogeneity and lack of an accurate genotype phenotype correlation makes mol ...
DOI:
10.1007/s13258-018-0657-5

5. An efficient and tunable parameter to improve variant calling for whole genome and exome sequencing data

Author:
Yong Ju Ahn; Kesavan Markkandan; In-Pyo Baek; Seyoung Mun; Wooseok Lee; Heui-Soo Kim; Kyudong Han
Source:
Genes & genomics 2018 v.40 no.1 pp. 39-47
ISSN:
1976-9571
Subject:
genome; genomics; high-throughput nucleotide sequencing; human genetics; South Korea
Abstract:
... Next generation sequencing (NGS) has traditionally been performed in various fields including agricultural to clinical and there are so many sequencing platforms available in order to obtain accurate and consistent results. However, these platforms showed amplification bias when facilitating variant calls in personal genomes. Here, we sequenced whole genomes and whole exomes from ten Korean indivi ...
DOI:
10.1007/s13258-017-0608-6

6. Analyses of karyotype by G-banding and high-resolution microarrays in a gender dysphoria population

Author:
Rosa Fernández; Antonio Guillamón; Esther Gómez-Gil; Isabel Esteva; Mari Cruz Almaraz; Joselyn Cortés-Cortés; Beatriz Lamas; Estefanía Lema; Eduardo Pásaro
Source:
Genes & genomics 2018 v.40 no.5 pp. 465-473
ISSN:
1976-9571
Subject:
aneuploidy; chromosome banding; chromosomes; copy number variation; etiology; gender; genes; karyotyping; microarray technology; Spain
Abstract:
... Gender Dysphoria is characterized by a marked incongruence between the cerebral sex and biological sex. To investigate the possible influence of karyotype on the etiology of Gender Dysphoria we carried out the cytogenetic analysis of karyotypes in 444 male-to-females (MtFs) and 273 female-to-males (FtMs) that attended the Gender Identity Units of Barcelona and Málaga (Spain) between 2000 and 2016. ...
DOI:
10.1007/s13258-017-0646-0

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

Author:
K. N. Kalubi; P. Michael; A. Omri
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

8. Analysis of sulphur and chlorine induced DNA cytosine methylation alterations in fresh corn (Zea mays L. saccharata and rugosa) leaf tissues by methylation sensitive amplification polymorphism (MSAP) approach

Author:
Tinashe Zenda; Songtao Liu; Daxuan Yao; Huijun Duan
Source:
Genes & genomics 2018 v.40 no.9 pp. 913-925
ISSN:
1976-9571
Subject:
DNA; DNA methylation; Zea mays; abiotic stress; chlorine; corn; crops; cultivars; cytosine; demethylation; filling period; genome; hybrids; leaves; loci; oligodeoxyribonucleotides; photosynthates; soil fertility; stress response; sulfur; tissues
Abstract:
... DNA (cytosine) methylation mechanism is another way through which plants respond to various cues including soil fertility amendments and abiotic stresses, and the mechanism has been used to infer some physiological, biochemical or adaptation processes. Despite numerous studies on global DNA methylation profiling in various crop species, however, researches on fresh corn (Zea mays L. saccharata or ...
DOI:
10.1007/s13258-018-0685-1

9. Analysis of synonymous codon usage bias in helicase gene from Autographa californica multiple nucleopolyhedrovirus

Author:
Hongju Wang; Tao Meng; Wenqiang Wei
Source:
Genes & genomics 2018 v.40 no.7 pp. 767-780
ISSN:
1976-9571
Subject:
Autographa californica multiple nucleopolyhedrovirus; DNA helicases; DNA replication; Escherichia coli; amino acid composition; amino acids; cluster analysis; codons; evolution; host range; humans; mice; mutation; yeasts
Abstract:
... The helicase gene of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is not only involved in viral DNA replication, but also plays a role in viral host range. To identify the codon usage bias of helicase of AcMNPV, the codon usage bias of helicase was especially studies in AcMNPV and 41 reference strains of baculoviruses by calculating the codon adaptation index (CAI), effective numb ...
DOI:
10.1007/s13258-018-0689-x

10. Association analysis of the SNP (rs345476947) in the FUT2 gene with the production and reproductive traits in pigs

Author:
Haifei Wang; Sen Wu; Jiayun Wu; Shouyong Sun; Shenglong Wu; Wenbin Bao
Source:
Genes & genomics 2018 v.40 no.2 pp. 199-206
ISSN:
1976-9571
Subject:
neonates; duodenum; lymph; eyes; gene expression; spleen; genotype; Large White; introns; selection methods; messenger RNA; muscles; reproductive traits; kidneys; sows; backfat; single nucleotide polymorphism; quantitative polymerase chain reaction; liver; fat thickness; genetic variation; piglets; birth weight
Abstract:
... The FUT2 gene was considered as an important candidate for pathogenic infections, while the potential associations between this gene and the production and reproductive traits of pigs have not been explored. In this study, we detected the genetic variants of porcine FUT2 gene and analyzed the associations of the polymorphisms with FUT2 mRNA expression and production and reproductive traits (age at ...
DOI:
10.1007/s13258-017-0623-7

11. Association between STAT4 polymorphisms and risk of primary biliary cholangitis: a meta-analysis

Author:
Li Zhang; Chunming Gao; Chuanmiao Liu; Jiasheng Chen; Kuihua Xu
Source:
Genes & genomics 2018 v.40 no.10 pp. 1101-1109
ISSN:
1976-9571
Subject:
confidence interval; genetic models; genotype; liver diseases; meta-analysis; odds ratio; risk; signal transduction; transactivators
Abstract:
... Primary biliary cholangitis (PBC) is a chronic autoimmune liver disease. Several studies reported that SATA4 (signal transducer and activator of transcription 4) polymorphisms were significantly associated with PBC susceptibility. In order to derive a more comprehensive estimation of the association between STAT4 and PBC risk, this meta-analysis was conducted. Thirteen eligible studies from 8 arti ...
DOI:
10.1007/s13258-018-0717-x

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

Author:
Yang Yang; Zhaojun Lan; Hu Shu; Huiqiang Zhou; Xiaolu Jiang; Liping Hou; Pinghua Gu
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

13. Association between the length of the MUC8-minisatellite 5 region and susceptibility to chronic obstructive pulmonary disease (COPD)

Author:
Se-Ra Lee; Won-Tae Kim; Tae Nam Kim; Jong Kil Nam; Woo Jin Kim; Sun-Hee Leem
Source:
Genes & genomics 2018 v.40 no.1 pp. 123-127
ISSN:
1976-9571
Subject:
alleles; asthma; case-control studies; confidence interval; epithelial cells; heterozygosity; humans; minisatellite repeats; mucins; mucus; risk factors
Abstract:
... In asthma and chronic obstructive pulmonary disease (COPD), mucins display disease-related alterations caused by airway mucus obstruction. MUC5AC, MUC5B and MUC8 are known as the major secretory mucins in human airway epithelial cells. Analysis of mucin genes has identified the presence of several features with a variable number of tandem repeats (VNTR; minisatellites) in the central region of eac ...
DOI:
10.1007/s13258-017-0630-8

14. Association of rs1057035polymorphism in microRNA biogenesis pathway gene (DICER1) with azoospermia among Iranian population

Author:
Sahar Moghbelinejad; Reza Najafipour; Abdolmabood Momeni
Source:
Genes & genomics 2018 v.40 no.1 pp. 17-24
ISSN:
1976-9571
Subject:
alleles; biogenesis; blood; gene expression; genotype; male fertility; men; microRNA; quantitative polymerase chain reaction; single nucleotide polymorphism; spermatogenesis; testes
Abstract:
... Since genes involved in microRNA biogenesis pathways have a main role in impaired spermatogenesis, in this research, we evaluated different genotypes frequency of seven single-nucleotide polymorphisms in DICER1 and DROSHA genes. Different genotypes frequency of DICER1 (rs12323635, rs1057035, rs13078 and rs3742330) and DROSHA (rs10719, rs642321 and rs2291102) were determined by sequencing method in ...
DOI:
10.1007/s13258-017-0605-9

15. Associations of HSP90AA2 gene polymorphisms with disease susceptibility, glucocorticoids efficacy and health-related quality of life in Chinese systemic lupus erythematosus patients

Author:
Man Zhang; Su-Su Li; Qiao-Mei Xie; Jian-Hua Xu; Xiu-Xiu Sun; Fa-Ming Pan; Sheng-Qian Xu; Sheng-Xiu Liu; Jin-Hui Tao; Shuang Liu; Jing Cai; Pei-Ling Chen; Long Qian; Chun-Huai Wang; Chun-Mei Liang; Hai-Liang Huang; Hai-Feng Pan; Hong Su; Yan-Feng Zou
Source:
Genes & genomics 2018 v.40 no.10 pp. 1069-1079
ISSN:
1976-9571
Subject:
alleles; case-control studies; disease susceptibility; genotyping; glucocorticoids; haplotypes; lupus erythematosus; mental health; models; patients; quality of life; questionnaires; risk; single nucleotide polymorphism; therapeutics
Abstract:
... Although the current glucocorticoids (GCs) treatment for systemic lupus erythematosus (SLE) is effective to a certain extent, the difference in therapeutic effect between patients is still a widespread problem. Some patients can have repeated attacks that greatly diminish their quality of life. This study was conducted to investigate the relationship between HSP90AA2 polymorphisms and disease susc ...
DOI:
10.1007/s13258-018-0714-0

16. BAG3 mutation in a patient with atypical phenotypes of myofibrillar myopathy and Charcot–Marie–Tooth disease

Author:
Seung Ju Kim; Soo Hyun Nam; Sumaira Kanwal; Da Eun Nam; Da Hye Yoo; Jong-Hee Chae; Yeon-Lim Suh; Ki Wha Chung; Byung-Ok Choi
Source:
Genes & genomics 2018 v.40 no.12 pp. 1269-1277
ISSN:
1976-9571
Subject:
atrophy; biopsy; blood serum; cardiomyopathy; creatine kinase; electrophysiology; females; gait; heterozygosity; magnetic resonance imaging; muscles; muscular diseases; mutation; patients; peripheral nervous system diseases; phenotype; sequence analysis
Abstract:
... Bcl2-associated athanogene 3 (BAG3) mutations have been reported to cause the myofibrillar myopathy (MFM) which shows progressive limb muscle weakness, respiratory failure, and cardiomyopathy. Myopathy patients with BAG3 mutation are very rare. We described a patient showing atypical phenotypes. We aimed to find the genetic cause of Korean patients with sensory motor polyneuropathy, myopathy and r ...
DOI:
10.1007/s13258-018-0721-1

17. BMP3 promoter hypermethylation in plasma-derived cell-free DNA in colorectal cancer patients

Author:
Parisa Rokni; Afsaneh Mojtabanezhad Shariatpanahi; Ebrahim Sakhinia; Mohammad Amin Kerachian
Source:
Genes & genomics 2018 v.40 no.4 pp. 423-428
ISSN:
1976-9571
Subject:
DNA; DNA methylation; biomarkers; biopsy; bisulfites; blood serum; bone morphogenetic proteins; colorectal neoplasms; melting; patients; tumor suppressor genes
Abstract:
... Detecting cfDNA in plasma or serum could serve as a ‘liquid biopsy’, for circulating tumor DNA with aberrant methylation patterns offer a possible method for early detection of several cancers which could avoid the need for tumor tissue biopsies. Bone Morphogenetic Protein 3 (BMP3) was identified as a candidate tumor suppressor gene putatively down-regulated in colorectal cancer (CRC). In this stu ...
DOI:
10.1007/s13258-017-0644-2

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

Author:
Ga Young Park; Hye Min Lee; Hyun Jin Yu; Jee Soo Son; Sang Joon Park; Kyoung Seob Song
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

19. Characterization and comparative expression analysis of CUL1 genes in rice

Author:
Sang-Hoon Kim; Og-Geum Woo; Hyunsoo Jang; Jae-Hoon Lee
Source:
Genes & genomics 2018 v.40 no.3 pp. 233-241
ISSN:
1976-9571
Subject:
Oryza sativa; abiotic stress; abscisic acid; amino acids; gene expression regulation; genes; hormones; rice; scaffolding proteins; seeds; ubiquitin-protein ligase
Abstract:
... Cullin-RING E3 ubiquitin ligase (CRL) complex is known as the largest family of E3 ligases. The most widely characterized CRL, SCF complex (CRL1), utilizes CUL1 as a scaffold protein to assemble the complex components. To better understand CRL1-mediated cellular processes in rice, three CUL1 genes (OsCUL1s) were isolated in Oryza sativa. Although all OsCUL1 proteins exhibited high levels of amino ...
DOI:
10.1007/s13258-017-0622-8

20. Characterization and development of EST-SSR markers to study the genetic diversity and populations analysis of Jerusalem artichoke (Helianthus tuberosus L.)

Author:
Shipeng Yang; Qiwen Zhong; Jie Tian; Lihui Wang; Mengliang Zhao; Li Li; Xuemei Sun
Source:
Genes & genomics 2018 v.40 no.10 pp. 1023-1032
ISSN:
1976-9571
Subject:
Helianthus annuus; Helianthus tuberosus; Jerusalem artichokes; alleles; biofuels; breeding; cluster analysis; computer software; expressed sequence tags; feeds; genetic distance; genetic heterogeneity; genetic markers; genetic similarity; genotype; germplasm; loci; microsatellite repeats; new variety; oligodeoxyribonucleotides; provenance; sugars; unigenes
Abstract:
... In recent years, Jerusalem artichoke has received widespread attention as a novel source of sugar, biofuel, and animal feed. Currently, only few gDNA-SSRs derived from sunflower were verified in the Jerusalem artichoke; therefore, it is particularly important to develop SSR primer markers that belonged to Jerusalem artichoke resources. Using EST data to develop EST-SSR markers is simple and effect ...
DOI:
10.1007/s13258-018-0708-y

21. Characterization and functional analysis of a MYB gene (GbMYBFL) related to flavonoid accumulation in Ginkgo biloba

Author:
Weiwei Zhang; Feng Xu; Shuiyuan Cheng; Yongling Liao
Source:
Genes & genomics 2018 v.40 no.1 pp. 49-61
ISSN:
1976-9571
Subject:
anthocyanins; quantitative polymerase chain reaction; transcription factors; biosynthesis; fruits; gene overexpression; stems; roots; bioinformatics; female flowers; metabolites; transcription (genetics); binding sites; leaves; exons; promoter regions; introns; callus; Ginkgo biloba
Abstract:
... Flavonoids are a group of metabolites in Ginkgo biloba thought to provide health benefits. R2R3-MYB transcription factors (TFs) play key roles in the transcriptional regulation of the flavonoid biosynthesis in plants. In this study, an R2R3-MYB transcription factor gene, GbMYBFL, was isolated from G. biloba and characterized. Results of bioinformatic analysis indicated that GbMYBFL is more closely ...
DOI:
10.1007/s13258-017-0609-5

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

Author:
Renyi Zhang; Xue Wang
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

23. Characterization of GA20ox genes in tall and dwarf types coconut (Cocos nucifera L.)

Author:
Tippawan Boonkaew; Chareerat Mongkolsiriwatana; Ananya Vongvanrungruang; Kornsorn Srikulnath; Surin Peyachoknagul
Source:
Genes & genomics 2018 v.40 no.7 pp. 735-745
ISSN:
1976-9571
Subject:
Cocos nucifera; Elaeis guineensis; Magnoliopsida; active sites; amino acid sequences; arginine; aspartic acid; binding sites; biosynthesis; coconuts; enzymes; exons; gibberellins; histidine; introns; iron; leaves; molecular cloning; mutation; phenotype; promoter regions; proteins; serine; vascular plants
Abstract:
... Coconuts (Cocos nucifera L.) are divided by the height into tall and dwarf types. In many plants the short phenotype was emerged by mutation of the GA20ox gene encoding the enzyme involved in gibberellin (GA) biosynthesis. Two CnGA20ox genes, CnGA20ox1 and CnGA20ox2, were cloned from tall and dwarf types coconut. The sequences, gene structures and expressions were compared. The structure of each g ...
DOI:
10.1007/s13258-018-0682-4

24. Characterization of the dynamic change of microRNA expression in mice hypothalamus during the time of female puberty

Author:
Gideon Omariba; Li Tong; Maochun Wang; Kai Li; Yuxun Zhou; Junhua Xiao
Source:
Genes & genomics 2018 v.40 no.3 pp. 295-304
ISSN:
1976-9571
Subject:
Primates; bioinformatics; cerebral cortex; data collection; females; gene expression; gene expression regulation; genes; hypothalamus; juveniles; mice; microRNA; neoplasms; puberty; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; signal transduction
Abstract:
... Puberty onset is a milestone in sexual development. A tumor suppress gene (TSG) network had been reported to be involved in the regulation of female puberty onset. The observations in rodents and primates showed a potential link between microRNAs and puberty onset. To figure out what miRNAs play roles in this important biological process, profilings of microRNAs in the hypothalamus of female mice ...
DOI:
10.1007/s13258-017-0633-5

25. Combined analysis and miRNA expression profiles of the flowering related genes in common wild rice (oryza rufipogon Griff.)

Author:
Jiao Wang; Yan Long; Jingwen Zhang; Mande Xue; Gege Huang; Ke Huang; Qianhua Yuan; Xinwu Pei
Source:
Genes & genomics 2018 v.40 no.8 pp. 835-845
ISSN:
1976-9571
Subject:
Oryza rufipogon; Oryza sativa; RNA libraries; agronomic traits; cold tolerance; drought; flowering; gene expression; genes; genomics; high-throughput nucleotide sequencing; leaves; meristems; messenger RNA; microRNA; proteins; quantitative trait loci; salinity; transcriptome; wild rice
Abstract:
... Common wild rice (Oryza rufipogon Griff.) is the most closely related ancestral species to Asian cultivated rice (Oryza sativa L.). It contains various valuable traits with regard to tolerance to cold, drought and salinity, flowering diversity and many quantitative trait loci with agronomic important traits. Flowering is one of the most important agronomic traits. However, flowering-related transc ...
DOI:
10.1007/s13258-018-0688-y
PubMed:
30047109
PubMed Central:
PMC6060991

26. Comparative genomic analysis of Lactobacillus plantarum GB-LP4 and identification of evolutionarily divergent genes in high-osmolarity environment

Author:
Jaehoon Jung; Kwondo Kim; DongAhn Yoo; Chanho Lee; Jungsun Kang; Kyungjin Cho; Dae-Kyung Kang; Woori Kwak; Sook Hee Yoon; Hawsun Sohn; Heebal Kim; Seoae Cho
Source:
Genes & genomics 2018 v.40 no.2 pp. 217-223
ISSN:
1976-9571
Subject:
Lactobacillus plantarum; fermentation; fermented vegetables; genes; genetic variation; genome assembly; genomics; homeostasis; osmolarity; osmotic pressure; pH; probiotics
Abstract:
... Lactobacillus plantarum is one of the widely-used probiotics and there have been a large number of advanced researches on the effectiveness of this species. However, the difference between previously reported plantarum strains, and the source of genomic variation among the strains were not clearly specified. In order to understand further on the molecular basis of L. plantarum on Korean traditiona ...
DOI:
10.1007/s13258-017-0555-2
PubMed:
29568414
PubMed Central:
PMC5846872

27. Comparative genomics of 151 plant-associated bacteria reveal putative mechanisms underlying specific interactions between bacteria and plant hosts

Author:
Hongsheng Cai; Yan Bai; Changhong Guo
Source:
Genes & genomics 2018 v.40 no.8 pp. 857-864
ISSN:
1976-9571
Subject:
amino acid metabolism; beneficial microorganisms; chemotaxis; enzymes; genes; genomics; host plants; host specificity; human diseases; information processing; nitrogen-fixing bacteria; plant growth; polyketides; principal component analysis; terpenoids; transcription factors; transporters; vitamins
Abstract:
... Although much work has explored how microbes can benefit plant growth, the mechanisms underlying this intriguing process remain largely unknown, especially considering the diversity of bacteria that surrounds plants. The objective of the present study was to identify bacterial genes contributing to plant–microbe associations, beneficial effects, and host specificities. For this purpose, comparativ ...
DOI:
10.1007/s13258-018-0693-1

28. Comparison of leaf transcriptomes of cassava “Xinxuan 048” diploid and autotetraploid plants

Author:
Ling Yin; Junjie Qu; Huiwen Zhou; Xiaohong Shang; Hui Fang; Jiang Lu; Huabing Yan
Source:
Genes & genomics 2018 v.40 no.9 pp. 927-935
ISSN:
1976-9571
Subject:
autotetraploidy; brassinosteroids; breeding; cassava; chlorophyll; colchicine; diploidy; gene expression regulation; genes; genotype; gibberellins; internode length; leaves; photosynthesis; plant height; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; sequence analysis; stress response; stress tolerance; transcriptome
Abstract:
... Polyploidy breeding of cassava has been used to improve cassava traits over the past years. We previously reported in vitro induction of tetraploids in the cassava variety “Xinxuan 048” using colchicine. Significant differences in morphology and anatomy were found between the diploid and tetraploid plants. However, very little is known about the transcriptome difference between them. In this study ...
DOI:
10.1007/s13258-018-0692-2

29. Comparison of methods for library construction and short read annotation of shellfish viral metagenomes

Author:
Hong-Ying Wei; Sheng Huang; Jiang-Yong Wang; Fang Gao; Jing-Zhe Jiang
Source:
Genes & genomics 2018 v.40 no.3 pp. 281-288
ISSN:
1976-9571
Subject:
Azumapecten farreri; Crassostrea hongkongensis; RNA; Ruditapes philippinarum; coasts; complementary DNA; databases; genome; high-throughput nucleotide sequencing; metagenomics; molluscs; shellfish; transcriptome; viruses; China
Abstract:
... The emergence and widespread use of high-throughput sequencing technologies have promoted metagenomic studies on environmental or animal samples. Library construction for metagenome sequencing and annotation of the produced sequence reads are important steps in such studies and influence the quality of metagenomic data. In this study, we collected some marine mollusk samples, such as Crassostrea h ...
DOI:
10.1007/s13258-017-0629-1

30. Comparison of stomach microRNA transcriptomes of Tibetan and Yorkshire pigs by deep sequencing

Author:
Wen-kui Sun; Yanyue Li; Chi Cheng; Yi-hui Chen; Kai Zeng; Xiaohui Chen; Yiren Gu; Rui Liu; Xuebin Lv; Rong Gao
Source:
Genes & genomics 2018 v.40 no.9 pp. 937-943
ISSN:
1976-9571
Subject:
Tibetan (swine breed); digestion; gene expression regulation; genes; glycerol; high-throughput nucleotide sequencing; hybridization; lipid metabolism; microRNA; phospholipase A2; phospholipids; purebreds; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; stomach; swine; transcriptome
Abstract:
... MiRNAs regulate the expression of target genes in diverse cellular processes and hence play important roles in different physiological processes, yet little is known about the stomach microRNAome (miRNAome) of the Tibetan pig. The objective of this experiment was to investigate differentially expressed stomach miRNAs participating in digestion. Firstly, we isolated total RNA by Trizol reagent from ...
DOI:
10.1007/s13258-018-0696-y

31. Complete genome sequence of the sesame pathogen Ralstonia solanacearum strain SEPPX 05

Author:
Xinshen Li; Xiaomei Huang; Gongyou Chen; Lifang Zou; Lingen Wei; Juling Hua
Source:
Genes & genomics 2018 v.40 no.6 pp. 657-668
ISSN:
1976-9571
Subject:
Ralstonia solanacearum; bacteria; bacterial wilt; biodiversity; chromosomes; damping off; genes; industry; nucleotide sequences; phylogeny; phylotype; plant pathogens; plasmids; secretion; temperate zones
Abstract:
... Ralstonia solanacearum is a soil-borne phytopathogen associated with bacterial wilt disease of sesame. R. solanacearum is the predominant agent causing damping-off from tropical to temperate regions. Because bacterial wilt has decreased the sesame industry yield, we sequenced the SEPPX05 genome using PacBio and Illumina HiSeq 2500 systems and revealed that R. solanacearum strain SEPPX05 carries a ...
DOI:
10.1007/s13258-018-0667-3

32. Complete genome sequence of uropathogenic Escherichia coli isolate UPEC 26-1

Author:
Bindu Subhadra; Dong Ho Kim; Jaeseok Kim; Kyungho Woo; Kyung Mok Sohn; Hwa-Jung Kim; Kyudong Han; Man Hwan Oh; Chul Hee Choi
Source:
Genes & genomics 2018 v.40 no.6 pp. 643-655
ISSN:
1976-9571
Subject:
biofilm; chromosomes; control methods; disease prevention; genomic islands; multiple drug resistance; non-coding RNA; pathogenesis; patients; pseudogenes; ribosomal RNA; sequence analysis; transfer RNA; urinary tract diseases; urine; uropathogenic Escherichia coli; virulence; Korean Peninsula
Abstract:
... Urinary tract infections (UTIs) are among the most common infections in humans, predominantly caused by uropathogenic Escherichia coli (UPEC). The diverse genomes of UPEC strains mostly impede disease prevention and control measures. In this study, we comparatively analyzed the whole genome sequence of a highly virulent UPEC strain, namely UPEC 26-1, which was isolated from urine sample of a patie ...
DOI:
10.1007/s13258-018-0665-5

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

Author:
Liqiang Zhong; Minghua Wang; Daming Li; Shengkai Tang; Tongqing Zhang; Wenji Bian; Xiaohui Chen
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

34. Correction to: Development of 21 polymorphic microsatellite markers for the black-banded sea krait, Laticauda semifasciata (Elapidae: Laticaudinae), and cross-species amplification for two other congeneric species

Author:
Young Se Hyun; Il-Hun Kim; Ha Yeun Song; Daesik Park; Mamoru Toda; Tein-Shun Tsai; Hye Suck An
Source:
Genes & genomics 2018 v.40 no.7 pp. 799
ISSN:
1976-9571
Subject:
Laticauda; genetic markers; microsatellite repeats; polymerase chain reaction
Abstract:
... Unfortunately, one of the co-author’s family name has been incorrectly published in the original online publication. The correct family name should be Tsai. ...
DOI:
10.1007/s13258-018-0671-7

35. Correction to: Targeted next-generation sequencing for identifying genes related to horse temperament

Author:
Soyoung Song; Dong‑Yep Oh; Gil‑Jae Cho; Dong Hee Kim; Yong‑Soo Park; Kyudong Han
Source:
Genes & genomics 2018 v.40 no.7 pp. 797
ISSN:
1976-9571
Subject:
genes; high-throughput nucleotide sequencing; horses; temperament
Abstract:
... There is a minor spelling error in one of corresponding authors’ name in this article. Young-Soo Park should be Yong-Soo Park. Also, in Conflict of interest, “Young-Soo Park declares that he has no conflict of interest.” should be “Yong-Soo Park declares that he has no conflict of interest.” The author’s name is now updated in the author group, affiliation section and in conflict of interest in th ...
DOI:
10.1007/s13258-017-0627-3

36. Correlation of IGF1R expression with ABCG2 and CD44 expressions in human osteosarcoma

Author:
Cheung-Kue Kim; Sunju Oh; Sook-Ja Kim; Sun-Hee Leem; Jeonghoon Heo; So-Hak Chung
Source:
Genes & genomics 2018 v.40 no.4 pp. 381-388
ISSN:
1976-9571
Subject:
antineoplastic agents; females; humans; insulin; males; metastasis; osteosarcoma; patients; prognosis; proteins; tissues
Abstract:
... Osteosarcoma is the most common type of malignant bone tumors. Insulin Growth Factor 1 receptor (IGFR1) has been known as a prognostic factor for metastasis of osteosarcoma. ABC subfamily G member2 (ABCG2) is related to resistance to anti-cancer drug, and CD44 has a role in tumor growth and metastasis. The purpose of this study is to investigate the relationship among expression patterns of IGF1R, ...
DOI:
10.1007/s13258-017-0639-z

37. De novo assembly, characterization and annotation for the transcriptome of Sphaeroma terebrans and microsatellite marker discovery

Author:
Chong Han; Qiang Li; Xiufeng Li; Zhipeng Zhang; Jianrong Huang
Source:
Genes & genomics 2018 v.40 no.2 pp. 167-176
ISSN:
1976-9571
Subject:
transcriptomics; microsatellite repeats; gene ontology; polymerase chain reaction; data collection; unigenes; transcriptome; genomics; genetic variation; hybridization probes; genetic markers; China
Abstract:
... Sphaeroma terebrans, an economically and ecologically important marine wood-boring isopod, is mainly distributed in tropical and subtropical mangroves. Nevertheless, available genomic and transcriptomic information for this isopod is extremely deficient. Here, we first performed the assembly of S. terebrans transcriptome by Illumina sequencing. A total of 51,092 high-quality unigenes with an avera ...
DOI:
10.1007/s13258-017-0618-4

38. De novo transcriptome analysis of Rhododendron molle G. Don flowers by Illumina sequencing

Author:
Zheng Xiao; Jiale Su; Xiaobo Sun; Chang Li; Lisi He; Shangping Cheng; Xiaoqing Liu
Source:
Genes & genomics 2018 v.40 no.6 pp. 591-601
ISSN:
1976-9571
Subject:
Rhododendron; beta-carotene; biochemical pathways; biosynthesis; breeding; color; enzymes; flowering; gene ontology; genomics; high-throughput nucleotide sequencing; microsatellite repeats; phylogeny; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; transcriptome; transcriptomics; unigenes
Abstract:
... Rhododendron molle G. Don occupies an important phylogenetic node in the genus rhododendron with unique yellow flower and medicinal functions. However, only limited genetic resources and their genome information are available for the generation of rhododendron flowers. The next generation sequencing technologies enables generation of genomic resources in a short time and at a minimal cost, and the ...
DOI:
10.1007/s13258-018-0662-8

39. Deciphering signature of selection affecting beef quality traits in Angus cattle

Author:
Mengistie Taye; Joon Yoon; Tadelle Dessie; Seoae Cho; Sung Jong Oh; Hak-Kyo Lee; Heebal Kim
Source:
Genes & genomics 2018 v.40 no.1 pp. 63-75
ISSN:
1976-9571
Subject:
Angus; Jersey; artificial selection; beef cattle; beef quality; biochemical pathways; body size; color; data collection; dystocia; focal adhesions; gene ontology; genes; genetic disorders; genomics; insulin; phenotype; tight junctions
Abstract:
... Artificial selection towards a desired phenotype/trait has modified the genomes of livestock dramatically that generated breeds that greatly differ in morphology, production and environmental adaptation traits. Angus cattle are among the famous cattle breeds developed for superior beef quality. This paper aimed at exploring genomic regions under selection in Angus cattle that are associated with m ...
DOI:
10.1007/s13258-017-0610-z

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

Author:
Hong Gil Lee; Pil Joon Seo
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

41. Detection of favorable alleles for yield and yield components by association mapping in upland cotton

Author:
Chengguang Dong; Juan Wang; Quanjia Chen; Yu Yu; Baocheng Li
Source:
Genes & genomics 2018 v.40 no.7 pp. 725-734
ISSN:
1976-9571
Subject:
Gossypium hirsutum; alleles; chromosome mapping; genetic markers; genetic variation; linear models; linkage disequilibrium; loci; marker-assisted selection; microsatellite repeats; phenotype; phenotypic variation; population structure; prediction; quantitative trait loci; yield components; China
Abstract:
... Association mapping based on linkage disequilibrium provides a promising tool for dissecting the genetic basis underlying complex traits. To reveal the genetic variations of yield and yield components traits in upland cotton, 403 upland cotton accessions were collected and analyzed by 560 genome-wide simple sequence repeats (SSRs). A diverse panel consisting of 403 upland cotton accessions was gro ...
DOI:
10.1007/s13258-018-0678-0

42. Development of 21 polymorphic microsatellite markers for the black-banded sea krait, Laticauda semifasciata (Elapidae: Laticaudinae), and cross-species amplification for two other congeneric species

Author:
Young Se Hyun; Il-Hun Kim; Ha Yeun Song; Daesik Park; Mamoru Toda; Tein-Shun Tai; Hye Suck An
Source:
Genes & genomics 2018 v.40 no.4 pp. 447-454
ISSN:
1976-9571
Subject:
DNA primers; Laticauda; alleles; coastal water; cost effectiveness; founder effect; gene flow; genetic markers; genetic variation; heterozygosity; loci; microsatellite repeats; philopatry; polymerase chain reaction; sequence analysis; snakes
Abstract:
... The genus Laticauda (Reptilia: Elapidae), commonly known as sea kraits, is venomous marine amphibious snakes distributed throughout the south and southeast Asian islands and mostly found in coastal waters. To facilitate genetic studies, we have developed microsatellite loci for L. semifasciata using the 454 GS-FLX pyrosequencing technique. A total of 65,680 sequences containing a minimum of five r ...
DOI:
10.1007/s13258-017-0626-4

43. Development of genic-SSR markers and genetic diversity of Indian lettuce (Lactuca indica L.) in South Korea

Author:
Bal Kumari Oliya; Moon Young Kim; Suk-Ha Lee
Source:
Genes & genomics 2018 v.40 no.6 pp. 615-623
ISSN:
1976-9571
Subject:
Lactuca indica; Lactuca sativa; Lactuca serriola; alleles; genetic markers; genetic variation; germplasm; heterozygosity; lettuce; loci; microsatellite repeats; phylogeny; transcriptomics; variance; wild plants; South Korea
Abstract:
... Indian lettuce (Lactuca indica L.) is an undomesticated wild plant with high economic potential. We know little about the plant’s genome, such as its DNA markers, making genetic research using this plant difficult. In this study, 100 genic simple sequence repeat (SSR) primers with a 99–250 bp target amplicon were synthesized from L. indica transcriptomic sequences. These primers were examined in 8 ...
DOI:
10.1007/s13258-018-0660-x

44. Differential expression of photosynthesis-related genes in pentaploid interspecific hybrid and its decaploid of Fragaria spp.

Author:
Tao Wang; Dongya Huang; Baoyu Chen; Nini Mao; Yushan Qiao; Muxiang Ji
Source:
Genes & genomics 2018 v.40 no.3 pp. 321-331
ISSN:
1976-9571
Subject:
DNA methylation; Fragaria ananassa; Fragaria viridis; chloroplast genes; chromosomes; epigenetics; gene expression; gene expression regulation; genotype; hybrids; interspecific hybridization; messenger RNA; parents; pentaploidy; photosynthesis; regulator genes; strawberries; structural genes; transcriptome
Abstract:
... Polyploidization always induces a series of changes in genome, transcriptome and epigenetics, of which changes in gene expression are the immediate causes of genotype alterations of polyploid plants. In our previous study on strawberry polyploidization, genes related to photosynthesis were found to undergo changes in gene expression and DNA methylation. Therefore, we chose 11 genes that were close ...
DOI:
10.1007/s13258-018-0647-7

45. Differential expression of primary pair-rule genes during bidirectional regeneration in Perionyx excavatus

Author:
Yun-Sang Yu; Jin-Se Kim; Brenda Irene Medina Jiménez; Tae-Wuk Kim; Sung-Jin Cho
Source:
Genes & genomics 2018 v.40 no.7 pp. 747-753
ISSN:
1976-9571
Subject:
Perionyx excavatus; arthropods; earthworms; gene expression regulation; genes; head; reverse transcriptase polymerase chain reaction; tail; transcription (genetics)
Abstract:
... The earthworm Perionyx excavatus is a species highly capable of bidirectional regeneration. Pair-rule genes are thought to have an ancestral function in arthropod segmentation. However, orthologs in annelids (i.e. Capitella teleta) do not exhibit segmental expression in the ectoderm or mesoderm. Their role in regeneration is currently unclear. Here, we report the expression profile of primary pair ...
DOI:
10.1007/s13258-018-0683-3

46. Dominance effects of ion transport and ion transport regulator genes on the final weight and backfat thickness of Landrace pigs by dominance deviation analysis

Author:
Young-Sup Lee; Donghyun Shin; Ki-Duk Song
Source:
Genes & genomics 2018 v.40 no.12 pp. 1331-1338
ISSN:
1976-9571
Subject:
adipose tissue; backfat; fat thickness; gene ontology; genome-wide association study; landraces; models; overdominance; phenotype; regulator genes; single nucleotide polymorphism; swine
Abstract:
... Although there have been plenty of dominance deviation analysis, few studies have dealt with multiple phenotypes. Because researchers focused on multiple phenotypes (final weight and backfat thickness) of Landrace pigs, the classification of the genes was possible. With genome-wide association studies (GWASs), we analyzed the additive and dominance effects of the single nucleotide polymorphisms (S ...
DOI:
10.1007/s13258-018-0728-7

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

Author:
Hansol Lim; Seung-Ho Paek; Seung-Eun Oh
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

48. Evolutionary dynamics of transposable elements during silkworm domestication

Author:
Min-Jin Han; Hong-En Xu; Xiao-Min Xiong; Hua-Hao Zhang
Source:
Genes & genomics 2018 v.40 no.10 pp. 1041-1051
ISSN:
1976-9571
Subject:
Bombyx mandarina; Bombyx mori; animals; artificial selection; domestication; genes; models; population dynamics; selection pressure; silkworms; statistical analysis; transposons
Abstract:
... Although there are some documented examples on population dynamics of transposable elements (TEs) in model organisms, the evolutionary dynamics of TEs in domesticated species has not been systematically investigated. The objective of this study is to understand population dynamics of TEs during silkworm domestication. In this work, using transposon-display we examined the polymorphism of seven TE ...
DOI:
10.1007/s13258-018-0713-1

49. Extrapolation of significant genes and transcriptional regulatory networks involved in Zea mays in response in UV-B stress

Author:
Saurabh Gupta; Vikas Gupta; Vishal Singh; Pritish Kumar Varadwaj
Source:
Genes & genomics 2018 v.40 no.9 pp. 973-990
ISSN:
1976-9571
Subject:
Zea mays; biosynthesis; cell cycle; cell death; chromatin; corn; enzymes; flavonoids; gene ontology; gene regulatory networks; genes; genotype; leaves; memory; plant hormones; signal transduction; stress response; transcription (genetics); transcriptomics; ultraviolet radiation
Abstract:
... A wide range of plant species growth influenced when they exposed to solar UV-B radiation. Leaves of the plant are highly affected by UV-B radiation lead to the reduction in the growth of the plant. Current work demonstrates the comparative transcriptional changes and visible symptoms occurred in the maize leaf growth zone (GZ). Primary objective of this study was to identify differentially expres ...
DOI:
10.1007/s13258-018-0705-1

50. Fine mapping and candidate gene analysis of the quantitative trait locus gw8.1 associated with grain length in rice

Author:
Yun-Joo Kang; Kyu-Chan Shim; Hyun-Sook Lee; Yun-A Jeon; Sun-Ha Kim; Ju-Won Kang; Yeo-Tae Yun; In-Kyu Park; Sang-Nag Ahn
Source:
Genes & genomics 2018 v.40 no.4 pp. 389-397
ISSN:
1976-9571
Subject:
Oryza rufipogon; RNA; cell growth; chromosomes; cultivars; gene expression; genes; heading; inflorescences; isogenic lines; leaves; mutation; quantitative trait loci; rice; scanning electron microscopy
Abstract:
... A quantitative trait locus (QTL) gw8.1 was detected in the population derived from a cross between the elite japonica cultivar, ‘Hwaseong’ and Oryza rufipogon (IRGC 105491). Near isogenic lines (NILs) harboring the O. rufipogon segment on chromosome 8 showed increased grain length and weight compared to those of the recurrent parent, Hwaseong. This QTL was mapped to a 175.3-kb region containing 28 ...
DOI:
10.1007/s13258-017-0640-6

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

Author:
Feng Ding; Shuwei Zhang; Houbin Chen; Hongxiang Peng; Jiang Lu; Xinhua He; Jiechun Pan
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

52. Functional conservation of Arabidopsis LNG1 in tobacco relating to leaf shape change by increasing longitudinal cell elongation by overexpression

Author:
Young Koung Lee; In-Jung Kim
Source:
Genes & genomics 2018 v.40 no.10 pp. 1053-1062
ISSN:
1976-9571
Subject:
Arabidopsis; cell growth; cell walls; genes; leaf blade; leaf length; leaf morphology; messenger RNA; petioles; phenotype; tobacco; transgenic plants
Abstract:
... The LONGIFOLIA1 (LNG1) gene of Arabidopsis regulates leaf shape by polar cell elongation independent of ROTUNDAFOLIA3 (ROT3). To expand our knowledge on the function of this gens in plant systems, Arabidopsis LNG1 (AtLNG1) was introduced both sense and antisense orientation under the control of 35S CaMV promoter into tobacco plants that lack AtLNG1 homolog. Resulting transgenic tobacco plants were ...
DOI:
10.1007/s13258-018-0712-2

53. Gene profiling involved in fate determination of salivary gland type in mouse embryogenesis

Author:
Nirpesh Adhikari; Sanjiv Neupane; Jiyeon Roh; Yam Prasad Aryal; Eui-Seon Lee; Jae-Kwang Jung; Hitoshi Yamamoto; Youngkyun Lee; Wern-Joo Sohn; Jae-Young Kim; Ji-Youn Kim
Source:
Genes & genomics 2018 v.40 no.10 pp. 1081-1089
ISSN:
1976-9571
Subject:
RNA; branching; buds; cell differentiation; data analysis; embryogenesis; enzymes; epithelium; gene expression; gene expression regulation; genes; loss-of-function mutation; mice; microarray technology; morphogenesis; parotid gland; reverse transcriptase polymerase chain reaction; saliva
Abstract:
... Salivary gland (SG) development involves dynamic epithelial-mesenchymal interactions resulting in the formation of highly branched epithelial structures that produce and secrete saliva. The SG epithelium differentiates into saliva-producing terminal buds, i.e., acini, and transporting ducts. Most studies on the salivary gland have focused on branching morphogenesis; however, acinar cell differenti ...
DOI:
10.1007/s13258-018-0715-z

54. Genetic analysis assessed by microsatellites for a diallel mating design of two geographical stocks of the blood clam Tegillarca granosa

Author:
Yinghui Dong; Hanhan Yao; Xiaolong Zhou; Zhihua Lin
Source:
Genes & genomics 2018 v.40 no.4 pp. 373-379
ISSN:
1976-9571
Subject:
Tegillarca granosa; clams; diallel analysis; genetic analysis; genetic distance; genetic improvement; genetic variation; heterozygosity; microsatellite repeats; progeny; reciprocal crosses
Abstract:
... To determine the potential for productive efficiency and genetic improvement in the blood clam Tegillarca granosa, four offspring populations (ZZ, ZK, KZ and KK) were produced from a diallel mating of two different geographical stocks (Z and K). The levels of genetic diversity and population structures of four populations were analyzed using 14 polymorphic microsatellites. The results showed that ...
DOI:
10.1007/s13258-017-0636-2

55. Genetic associations between ADHD and dopaminergic genes (DAT1 and DRD4) VNTRs in Korean children

Author:
Jun Ho Hong; In Wook Hwang; Myung Ho Lim; Ho Jang Kwon; Han Jun Jin
Source:
Genes & genomics 2018 v.40 no.12 pp. 1309-1317
ISSN:
1976-9571
Subject:
Koreans; alleles; children; etiology; exons; gene frequency; genotype; minisatellite repeats; odds ratio; polymerase chain reaction; tandem repeat sequences
Abstract:
... It is well known that dopaminergic genes affect the development of attention deficit hyperactivity disorder (ADHD) in various populations. Many studies have shown that variable number tandem repeats (VNTRs) located within the 3′-untranslated region of DAT1 and in exon 3 of DRD4 are associated with ADHD development; however, these results were inconsistent. Therefore, we investigated the genetic as ...
DOI:
10.1007/s13258-018-0726-9

56. Genetic characteristics of Y-chromosome short tandem repeat haplotypes from cigarette butt samples presumed to be smoked by North Korean men

Author:
Kyu-Sik Jeong; Heejin Shin; Sung-Jin Lee; Hyo-Sook Kim; Jang-Yong Kim; Myun-Soo Han; Yang-Han Lee; Ki-Won Park; Byung-Won Chun
Source:
Genes & genomics 2018 v.40 no.8 pp. 819-824
ISSN:
1976-9571
Subject:
DNA; DNA fingerprinting; Koreans; Y chromosome; cigarettes; databases; genetic polymorphism; genetic variation; haplotypes; loci; men; microsatellite repeats; multidimensional scaling; variance; North Korea; South Korea
Abstract:
... Korea has been divided into South Korea and North Korea for over 70 years. DNA profiles of the North Korean population have never been reported in the Y-chromosome STR Haplotype Reference Database (YHRD; https://yhrd.org). To investigate genetic features of Y-chromosome STR haplotypes of the North Korean population for the first time. Genomic DNA was isolated from 838 cigarette butts assumed to ha ...
DOI:
10.1007/s13258-018-0701-5

57. Genetic diversity and population structure among accessions of Perilla frutescens (L.) Britton in East Asia using new developed microsatellite markers

Author:
Kyu Jin Sa; Ik-Young Choi; Kyong-Cheul Park; Ju Kyong Lee
Source:
Genes & genomics 2018 v.40 no.12 pp. 1319-1329
ISSN:
1976-9571
Subject:
Perilla frutescens; RNA; alleles; breeding programs; chromosome mapping; cultivar identification; gene frequency; genetic markers; genetic relationships; genetic variation; loci; microsatellite repeats; oligodeoxyribonucleotides; population structure; quantitative trait loci; sequence analysis; transcriptomics; East Asia
Abstract:
... SSRs were successfully isolated from the Perilla crop in our current study, and used to analyze Perilla accessions from East Asia. Analyses of the clear genetic diversity and relationship for Perilla crop still remain insufficient. In this study, 40 new simple sequence repeat (SSR) primer sets were developed from RNA sequences using transcriptome analysis. These new SSR markers were applied to ana ...
DOI:
10.1007/s13258-018-0727-8

58. Genetic structure analysis of mantis shrimp Oratosquilla oratoria based on mitochondrial DNA control region sequence

Author:
Yang Zhang; Zhiqiang Han; Tianxiang Gao; Huilai Shi
Source:
Genes & genomics 2018 v.40 no.9 pp. 1001-1009
ISSN:
1976-9571
Subject:
coastal water; estuaries; freshwater; gene flow; genes; genetic relationships; genetic variation; geographical distribution; haplotypes; larvae; mitochondrial DNA; population growth; shrimp; sympatry; China; Japan; Yangtze River
Abstract:
... The genetic relationships of mantis shrimp Oratosquilla oratoria between the coastal waters of China and Japan were not well studied. To reveal the genetic differentiation and genetic structure among populations, we collected populations of mantis shrimp O. oratoria from the coastal waters of China and Japan to analyze the mtDNA control region variation. A total of 309 individuals of O. oratoria w ...
DOI:
10.1007/s13258-018-0707-z

59. Genetic structure of six cattle populations revealed by transcriptome-wide SNPs and gene expression

Author:
Wei Wang; Huai Wang; Hui Tang; Jia Gan; Changgeng Shi; Qing Lu; Donghui Fang; Jun Yi; Maozhong Fu
Source:
Genes & genomics 2018 v.40 no.7 pp. 715-724
ISSN:
1976-9571
Subject:
cattle; cattle breeds; chromosomes; gene expression; genes; genomics; marker-assisted selection; population structure; sequence analysis; single nucleotide polymorphism; transcriptomics; China
Abstract:
... There are abundant cattle breeds/populations in China, and the systematic discovery of genomic variants is essential for performing the marker assisted selection and conservation of genetic resources. In the present study, we employed whole transcriptome sequencing (RNA-Seq) technology for revealing genetic structure among six Chinese cattle populations according to transcriptome-wide SNPs and gen ...
DOI:
10.1007/s13258-018-0677-1
PubMed:
29934811
PubMed Central:
PMC6015124

60. Genetic variability comparison of cultured Israeli carp (Cyprinus carpio) from Korea using microsatellites

Author:
Jung Eun Kim; In Bon Goo; Ju-ae Hwang; Hyeong Su Kim; Hye-Sung Choi; Jeong-Ho Lee
Source:
Genes & genomics 2018 v.40 no.6 pp. 635-642
ISSN:
1976-9571
Subject:
Cyprinus carpio; alleles; aquaculture; breeding stock; carp; genetic markers; genetic variation; heterozygosity; immunity; loci; microsatellite repeats; monitoring; population structure; selection methods; surveys; survival rate; China; South Korea
Abstract:
... In aquaculture, cultured fish often undergo continuous cross-fertilization without any inflow of new broodstock. This lowers genetic diversity, leading to increased disease rates and decreased survival rates. To improve the mass production and easy culture of Israeli carp, it is essential to investigate the population structure and genetic diversity of these fish. However, such a survey has not ye ...
DOI:
10.1007/s13258-018-0663-7

61. Genetics of CRISPR arrays in Salmonella Typhimurium 14028 associated with foreign DNA decay

Author:
Jeong Nam Kim
Source:
Genes & genomics 2018 v.40 no.8 pp. 865-872
ISSN:
1976-9571
Subject:
CRISPR sequences; Salmonella Typhimurium; adaptive immunity; algorithms; bacteriophages; bioinformatics; gene editing; genes; loci; mutants; plasmids; prediction; prokaryotic cells
Abstract:
... Clustered regularly interspaced short palindromic repeats (CRISPRs) are a genetic locus of prokaryotes and contain highly conserved direct repeats, spacers, and CRISPR-associated genes. Spacers in CRISPRs are known as adaptive immune markers and reveal what types of phage or foreign DNA have been introduced in the past. The primary objective of this study was to analyze spacer sequences in CRISPR ...
DOI:
10.1007/s13258-018-0700-6

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

Author:
Nam Young Kim; Ha-Seung Seong; Dae Cheol Kim; Nam Geon Park; Byoung Chul Yang; Jun Kyu Son; Sang Min Shin; Jae Hoon Woo; Moon Cheol Shin; Ji Hyun Yoo; Jung-Woo Choi
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

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

Author:
Jun-Seok Song; Ha-Seung Seong; Bong-Hwan Choi; Chang-Woo Lee; Nam-Hyun Hwang; Dajeong Lim; Joon-Hee Lee; Jin Soo Kim; Jeong-Dae Kim; Yeon-Soo Park; Jung-Woo Choi; Jong-Bok Kim
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

64. Genome-wide identification and characterization of the RIO atypical kinase family in plants

Author:
Qingsong Gao; Shuhui Xu; Xiayuan Zhu; Lingling Wang; Zefeng Yang; Xiangxiang Zhao
Source:
Genes & genomics 2018 v.40 no.6 pp. 669-683
ISSN:
1976-9571
Subject:
Arabidopsis; Oryza sativa; Zea mays; actinomycin D; biogenesis; corn; eukaryotic cells; gene expression; genes; open reading frames; phosphotransferases (kinases); phylogeny; prediction; protein subunits; ribosomal proteins; ribosomes; rice
Abstract:
... Members of the right open reading frame (RIO) atypical kinase family are present in all three domains of life. In eukaryotes, three subfamilies have been identified: RIO1, RIO2, and RIO3. Studies have shown that the yeast and human RIO1 and RIO2 kinases are essential for the biogenesis of small ribosomal subunits. Thus far, RIO3 has been found only in multicellular eukaryotes. In this study, we sy ...
DOI:
10.1007/s13258-018-0658-4

65. Genome-wide identification and evolution of TC1/Mariner in the silkworm (Bombyx mori) genome

Author:
Li-Qin Xie; Ping-Lan Wang; Shen-Hua Jiang; Ze Zhang; Hua-Hao Zhang
Source:
Genes & genomics 2018 v.40 no.5 pp. 485-495
ISSN:
1976-9571
Subject:
Bombyx mori; active sites; expressed sequence tags; phylogeny; silkworms; transposons
Abstract:
... TC1/Mariner transposons belong to class II transposable elements (TEs) that use DNA-mediated “cut and paste” mechanism to transpose, and they have been identified in almost all organisms. Although silkworm (Bombyx mori) has a large amount of TC1/Mariner elements, the genome wide information of this superfamily in the silkworm is unknown. In this study, we have identified 2670 TC1/Mariner (Bmmar) e ...
DOI:
10.1007/s13258-018-0648-6

66. Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in cucumber (Cucumis sativus)

Author:
Yong Zhou; Lifang Hu; Lunwei Jiang; Shiqiang Liu
Source:
Genes & genomics 2018 v.40 no.6 pp. 579-589
ISSN:
1976-9571
Subject:
Arabidopsis; Cucumis sativus; RNA-binding proteins; abiotic stress; abscisic acid; chromosomes; cucumbers; drought; genes; growth and development; phylogeny; regulatory sequences; rice; stress response; transcriptome
Abstract:
... YTH domain-containing RNA-binding proteins are involved in post-transcriptional regulation and play important roles in the growth and development as well as abiotic stress responses of plants. However, YTH genes have not been previously studied in cucumber (Cucumis sativus). In this study, a total of five YTH genes (CsYTH1–CsYTH5) were identified in cucumber, which could be mapped on three out of ...
DOI:
10.1007/s13258-018-0659-3

67. Genome-wide identification and expression analysis of the BTB domain-containing protein gene family in tomato

Author:
Jinhua Li; Xiaoxing Su; Yinlei Wang; Wei Yang; Yu Pan; Chenggang Su; Xingguo Zhang
Source:
Genes & genomics 2018 v.40 no.1 pp. 1-15
ISSN:
1976-9571
Subject:
Kelch repeats; Solanum lycopersicum; abiotic stress; chromatin; crops; cytoskeleton; genes; hormones; hypocotyls; models; phylogeny; potassium channels; protein degradation; protein-protein interactions; tomatoes; transcription (genetics); zinc finger motif
Abstract:
... BTB (broad-complex, tramtrack, and bric-a-brac) family proteins are characterized by the presence of a protein–protein interaction BTB domain. BTB proteins have diverse functions, including transcriptional regulation, protein degradation, chromatin remodeling, and cytoskeletal regulation. However, little is known about this gene family in tomato (Solanum lycopersicum), the most important model pla ...
DOI:
10.1007/s13258-017-0604-x

68. Genome-wide identification of WRKY transcription factors in kiwifruit (Actinidia spp.) and analysis of WRKY expression in responses to biotic and abiotic stresses

Author:
Zhaobin Jing; Zhande Liu
Source:
Genes & genomics 2018 v.40 no.4 pp. 429-446
ISSN:
1976-9571
Subject:
Actinidia; Arabidopsis; abiotic stress; ancestry; genes; kiwifruit; phylogeny; stress response; transcription (genetics); transcription factors
Abstract:
... As one of the largest transcriptional factor families in plants, WRKY transcription factors play important roles in various biotic and abiotic stress responses. To date, WRKY genes in kiwifruit (Actinidia spp.) remain poorly understood. In our study, o total of 97 AcWRKY genes have been identified in the kiwifruit genome. An overview of these AcWRKY genes is analyzed, including the phylogenetic re ...
DOI:
10.1007/s13258-017-0645-1

69. Homeostatic balance of histone acetylation and deconstruction of repressive chromatin marker H3K9me3 during adipocyte differentiation of 3T3-L1 cells

Author:
Han-Heom Na; Keun-Cheol Kim
Source:
Genes & genomics 2018 v.40 no.12 pp. 1301-1308
ISSN:
1976-9571
Subject:
Western blotting; acetylation; adipocytes; adipogenesis; chromatin; enzymes; gene expression; histones; mice; models; phenotype; reverse transcriptase polymerase chain reaction; staining
Abstract:
... Background Adipocyte differentiation is completed by changing gene expression. Chromatin is closely related to gene expression. Therefore, its structure might be changed for adipocyte differentiation. Mouse 3T3-L1 preadipocytes have been used as a cell model to study molecular mechanisms of adipogenesis. Objective To examine changes of chromatin modification and expression of histone modifying enz ...
DOI:
10.1007/s13258-018-0725-x

70. Identification and characterization of a novel goose-type and chicken-type lysozyme genes in Chinese rare minnow (Gobiocypris rarus) with potent antimicrobial activity

Author:
Yingying Zhang; Hui Yang; Weijia Song; Dan Cui; Lixin Wang
Source:
Genes & genomics 2018 v.40 no.6 pp. 569-577
ISSN:
1976-9571
Subject:
Aeromonas hydrophila; Gobiocypris rarus; Gram-negative bacteria; Gram-positive bacteria; antibacterial properties; gene expression; gene expression regulation; genes; innate immunity; kidneys; liver; lysozyme; messenger RNA; minimum inhibitory concentration; minnows; pH; pathogens; polyinosinic-polycytidylic acid; proteins; quantitative polymerase chain reaction; temperature; viruses
Abstract:
... Lysozymes act as important innate immunity molecule against various pathogen infections. In the present study, a new c-type and g-type lysozymes were isolated from rare minnow Gobiocypris rarus. The deduced amino acid sequence of c-type lysozyme contained 145 residues and possessed conserved catalytic residues (Glu⁵³ and Asp⁷²). The deduced g-type lysozyme contained 185 residues and possessed thre ...
DOI:
10.1007/s13258-018-0656-6

71. Identification and genetic mapping for rht-DM, a dominant dwarfing gene in mutant semi-dwarf maize using QTL-seq approach

Author:
Qian Chen; Jun Song; Wen-Ping Du; Li-Yuan Xu; Yun Jiang; Jie Zhang; Xiao-Li Xiang; Gui-Rong Yu
Source:
Genes & genomics 2018 v.40 no.10 pp. 1091-1099
ISSN:
1976-9571
Subject:
breeding; chromosome mapping; chromosomes; corn; dominant genes; dwarfing; genetic analysis; inheritance (genetics); irradiation; lodging resistance; mutants; phenotype; quantitative trait loci; rain; single nucleotide polymorphism; wind
Abstract:
... Semi-dwarfism is an agronomically important trait in breeding for stable high yields and for resistance to damage by wind and rain (lodging resistance). Many QTLs and genes causing dwarf phenotype have been found in maize. However, because of the yield loss associated with these QTLs and genes, they have been difficult to use in breeding for dwarf stature in maize. Therefore, it is important to fi ...
DOI:
10.1007/s13258-018-0716-y

72. Identification of differentially expressed genes in longissimus dorsi muscle between Wei and Yorkshire pigs using RNA sequencing

Author:
Jingen Xu; Chonglong Wang; Erhui Jin; Youfang Gu; Shenghe Li; Qinggang Li
Source:
Genes & genomics 2018 v.40 no.4 pp. 413-421
ISSN:
1976-9571
Subject:
absorption; biosynthesis; cell differentiation; digestion; extracellular matrix; fatty acid metabolism; gene expression regulation; gene ontology; genes; genetic background; high-throughput nucleotide sequencing; intramuscular fat; longissimus muscle; meat quality; muscle development; phenotype; phospholipids; pork; quantitative polymerase chain reaction; skeletal muscle; swine; swine breeds; transcription (genetics); transcriptome; transcriptomics
Abstract:
... Intramuscular fat (IMF) content is an important trait closely related to meat quality, which is highly variable among pig breeds from diverse genetic backgrounds. High-throughput sequencing has become a powerful technique for analyzing the whole transcription profiles of organisms. In order to elucidate the molecular mechanism underlying porcine meat quality, we adopted RNA sequencing to detect tr ...
DOI:
10.1007/s13258-017-0643-3

73. Identification of drug target candidates of the swine pathogen Actinobacillus pleuropneumoniae by construction of protein–protein interaction network

Author:
Siqi Li; Zhipeng Su; Chengjun Zhang; Zhuofei Xu; Xiaoping Chang; Jiawen Zhu; Ran Xiao; Lu Li; Rui Zhou
Source:
Genes & genomics 2018 v.40 no.8 pp. 847-856
ISSN:
1976-9571
Subject:
Actinobacillus pleuropneumoniae; antibiotic resistance; bacteria; biochemical pathways; drugs; financial economics; pathogens; pleuropneumonia; protein-protein interactions; proteins; proteome; swine; topology
Abstract:
... Porcine pleuropneumonia caused by Actinobacillus pleuropneumoniae has led to severe economic losses in the pig industry worldwide. A. pleuropneumoniae displays various levels of antimicrobial resistance, leading to the dire need to identify new drug targets. Protein–protein interaction (PPI) network can aid the identification of drug targets by discovering essential proteins during the life of bac ...
DOI:
10.1007/s13258-018-0691-3

74. Identification of microRNAs involved in drought stress responses in early-maturing cotton by high-throughput sequencing

Author:
Zhanghui Dong; Jianhong Zhang; Qingzhu Zhu; Lifen Zhao; Shuxiang Sui; Zengshu Li; Yanli Zhang; Hu Wang; Dongliang Tian; Yankun Zhao
Source:
Genes & genomics 2018 v.40 no.3 pp. 305-314
ISSN:
1976-9571
Subject:
RNA libraries; cotton; drought tolerance; gene expression regulation; high-throughput nucleotide sequencing; microRNA; stress response; water stress
Abstract:
... Drought stress is one of the most important abiotic stresses. Cotton is classified as drought tolerant crop but the regulatory mechanism is unknown. MicroRNAs (miRNAs) have been implicated important roles in stress responses in many plants. However, the study of miRNAs in cotton responsive to drought stress is limited, especially in early-maturing cotton. In this study, we performed deep sequencin ...
DOI:
10.1007/s13258-017-0637-1

75. Identification of novel EST-SSR markers by transcriptome sequencing in ridgetail white prawn Exopalaemon carinicauda

Author:
Jiajia Wang; Qianqian Ge; Jitao Li; Haiyu Gao; Jian Li; Fazhen Zhao
Source:
Genes & genomics 2018 v.40 no.2 pp. 207-215
ISSN:
1976-9571
Subject:
transcriptomics; microsatellite repeats; loci; DNA primers; gene ontology; breeding; expressed sequence tags; mariculture; polymerase chain reaction; genomics; shrimp; genetic variation; genetic markers; China
Abstract:
... The ridgetail white prawn Exopalaemon carinicauda is one of the major commercial mariculture species in eastern China. However, only limited molecular markers are currently available due to the lack of genome information, which hinders its genetic and breeding studies. In this study, we identified new simple sequence repeats from transcriptome sequences by Illumina Hiseq 2500 platform. A total of ...
DOI:
10.1007/s13258-017-0571-2

76. Identification of pathways and genes associated with cerebral palsy

Author:
Qingwen Zhu; Yufei Ni; Jing Wang; Honggang Yin; Qin Zhang; Lingli Zhang; Wenjun Bian; Bo Liang; Lingyin Kong; Liming Xuan; Naru Lu
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

77. Identification of transposable elements fused in the exonic region of the olive flounder genome

Author:
Gyu-Hwi Nam; Jeong-An Gim; Anshuman Mishra; Kung Ahn; Suhkmann Kim; Do-Hyung Kim; Hee-Jae Cha; Yung Hyun Choi; Chan-Il Park; Heui-Soo Kim
Source:
Genes & genomics 2018 v.40 no.7 pp. 707-713
ISSN:
1976-9571
Subject:
DNA; Paralichthys olivaceus; exons; flounder; gene ontology; genomics; immunology; mortality; terminal repeat sequences; transcriptomics; transposons; East Asia
Abstract:
... Transposable elements (TEs) are mobile genetic sequences that comprise a large portion of vertebrate genomes. The olive flounder (Paralichthys olivaceus) is a valuable marine resource in East Asia. The scope of most genomic studies on the olive flounder is limited to its immunology as their focus is the prevention of mass mortality of this species. Thus, for a broader understanding of the species, ...
DOI:
10.1007/s13258-018-0676-2

78. Imprinted gene expression in maize starchy endosperm and aleurone tissues of reciprocal F1 hybrids at a defined developmental stage

Author:
Meishan Zhang; Ruili Lv; Wei Yang; Tiansi Fu; Bao Liu
Source:
Genes & genomics 2018 v.40 no.1 pp. 99-107
ISSN:
1976-9571
Subject:
pollination; Zea mays; alternative splicing; hybrids; triploidy; corn; gene expression; endosperm; inbred lines; seed coat; embryogenesis; introns
Abstract:
... Imprinted gene expression in flowering plants predominantly occurs in the triploid endosperm of developing seed. However, endosperm is composed of distinct tissue types. For example, the maize (Zea mays) endosperm is constituted by two major tissues, starchy endosperm and aleurone. Previous studies in imprinted gene expression have generally assumed that the different tissues constituting endosper ...
DOI:
10.1007/s13258-017-0613-9

79. In silico identification and computational characterization of endogenous small interfering RNAs from diverse grapevine tissues and stages

Author:
Xudong Zhu; Songtao Jiu; Xiaopeng Li; Kekun Zhang; Mengqi Wang; Chen Wang; Jinggui Fang
Source:
Genes & genomics 2018 v.40 no.8 pp. 801-817
ISSN:
1976-9571
Subject:
Vitis vinifera; auxins; disease resistance; gene ontology; genes; high-throughput nucleotide sequencing; metabolism; plant development; small interfering RNA; tissues
Abstract:
... Small interfering RNAs (siRNAs) are effectors of regulatory pathways underlying plant development, metabolism, and stress- and nutrient-signaling regulatory networks. The endogenous siRNAs are generally not conserved between plants; consequently, it is necessary and important to identify and characterize siRNAs from various plants. To address the nature and functions of siRNAs, and understand the ...
DOI:
10.1007/s13258-018-0679-z

80. In vivo evidence on the functional variation within fatty acid synthase gene associated with lipid metabolism in bovine longissimus dorsi muscle tissue

Author:
Dong-yep Oh; Insik Nam; Sehwan Hwang; Hongsik Kong; Honggu Lee; Jaejung Ha; Myunggi Baik; Man Hwan Oh; Songmi Kim; Kyudong Han; Yoonseok Lee
Source:
Genes & genomics 2018 v.40 no.3 pp. 289-294
ISSN:
1976-9571
Subject:
Wagyu; adipocytes; beef quality; binding sites; cattle; fatty acids; fatty-acid synthase; genes; genetic factors; hydrophilicity; hydrophobicity; intramuscular fat; lipogenesis; longissimus muscle; marbling; muscle tissues; single nucleotide polymorphism; site-directed mutagenesis; transcription factors
Abstract:
... In Korean cattle, intramuscular fat (IMF), or marbling, of the longissimus dorsi muscle (LM) cross section is one of the most important indicators of beef quality and are influenced by environmental and genetic factors. This study was to evaluate the effect of SNPs on the beef quality in Korean cattle for functional studies, such as site-directed mutagenesis based on bovine adipocytes. The fatty a ...
DOI:
10.1007/s13258-017-0634-4

81. LncRNA Gm2044 highly expresses in spermatocyte and inhibits Utf1 translation by interacting with Utf1 mRNA

Author:
Ke Hu; Leina Li; Yaping Liao; Meng Liang
Source:
Genes & genomics 2018 v.40 no.7 pp. 781-787
ISSN:
1976-9571
Subject:
Western blotting; bioinformatics; cell lines; cell proliferation; genes; male fertility; males; mechanism of action; messenger RNA; mice; microarray technology; non-coding RNA; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; spermatocytes; spermatogenesis; spermatogonia; spermatozoa; stem cells
Abstract:
... Spermatogenesis is a process which includes the following phases: spermatogonial stem cell proliferation and differentiation, spermatogonia, spermatocyte, spermatid and mature sperm. Spermatogenic failure is the important factor resulting in male infertility. Recent studies showed that long noncoding RNA (lncRNA) have been found to be involved in the regulation of male reproduction. However, lncRN ...
DOI:
10.1007/s13258-018-0690-4

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

Author:
Xiaoshu Deng; Lu Gan; Yan Liu; Ancai Luo; Liang Jin; Jiao Chen; Ruyu Tang; Lixia Lei; Jianghong Tang; Jiani Zhang; Zhengwu Zhao
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

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

Author:
Haiyan Hu; Jie He; Junjie Zhao; Xingqi Ou; Hongmin Li; Zhengang Ru
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

84. Microarray analysis after adipose derived mesenchymal stem cells injection in monosodium iodoacetate-induced osteoarthritis rats

Author:
Jae Chul Lee
Source:
Genes & genomics 2018 v.40 no.1 pp. 25-37
ISSN:
1976-9571
Subject:
DNA repair; bone resorption; cartilage; cell death; cell proliferation; gene expression regulation; genes; humans; immune response; inflammation; lipid metabolism; microarray technology; oligonucleotides; osteoarthritis; proteins; quality control; rats; stem cells
Abstract:
... Osteoarthritis (OA) is a degenerative joint disease characterized by abrasion, and ultimately, destruction of the articular cartilage and trabecular bone loss. OA is still considered a devastating disease, which requires an aggressive therapeutic approach. Despite the therapeutic potential of human adipose-derived mesenchymal stem cells (AD-MSCs), the molecular parameters needed to define the “ste ...
DOI:
10.1007/s13258-017-0607-7

85. Microsatellite DNA analysis reveals lower than expected genetic diversity in the threatened leopard cat (Prionailurus bengalensis) in South Korea

Author:
Byung June Ko; Junghwa An; Hong Seomun; Mu-Yeong Lee; Soo Hyung Eo
Source:
Genes & genomics 2018 v.40 no.5 pp. 521-530
ISSN:
1976-9571
Subject:
DNA; Naemorhedus caudatus; Nyctereutes procyonoides; Prionailurus bengalensis; alleles; conservation status; deer; extinction; genetic markers; genetic variation; habitats; heterozygosity; microsatellite repeats; population size; risk; threatened species; South Korea
Abstract:
... To optimize conservation efforts, it is necessary to determine the risk of extinction by collecting reliable population information for a given species. We developed eight novel, polymorphic microsatellite markers and used these markers in conjunction with twelve existing markers to measure genetic diversity of South Korean populations of leopard cat (Prionailurus bengalensis), a species for which ...
DOI:
10.1007/s13258-018-0654-8

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

Author:
Huayun Guo; Hao Yang; Yitao Tao; Dan Tang; Qiong Wu; Zhengfei Wang; Boping Tang
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

87. Molecular characterization and expression analysis of WRKY family genes in Dendrobium officinale

Author:
Tao Wang; Zheng Song; Li Wei; Lubin Li
Source:
Genes & genomics 2018 v.40 no.3 pp. 265-279
ISSN:
1976-9571
Subject:
seed germination; transcription factors; Dendrobium officinale; seeds; seedlings; cold stress; phylogeny; methyl jasmonate; transcription (genetics); stress tolerance; gene expression regulation; introns; fungi
Abstract:
... The WRKY family of transcription factors is one of the most important families of plant transcriptional regulators, and the members regulate multiple biological processes. However, there is limited information on WRKYs in Dendrobium officinale. In this study, 52 WRKY family genes of D. officinale were surveyed for the first time. Conserved domain, phylogenetic, exon–intron construction, and expres ...
DOI:
10.1007/s13258-017-0602-z

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

Author:
Dan Wang; Xin Wen; Xinyu Zhang; Yadong Hu; Xinru Li; Wenxu Zhu; Tao Wang; Shaowu Yin
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

89. Molecular cloning and characterization of a novel salt-specific responsive WRKY transcription factor gene IlWRKY2 from the halophyte Iris lactea var. chinensis

Author:
Jun Tang; Qingquan Liu; Haiyan Yuan; Yongxia Zhang; Weilin Wang; Suzhen Huang
Source:
Genes & genomics 2018 v.40 no.8 pp. 893-903
ISSN:
1976-9571
Subject:
Elaeis guineensis; Iris lactea; Musa acuminata subsp. malaccensis; amino acid sequences; amino acids; complementary DNA; computer software; gene expression regulation; genes; halophytes; molecular cloning; open reading frames; ornamental value; phylogeny; quantitative polymerase chain reaction; salt stress; salt tolerance; sequence analysis; shoots; sodium chloride; transcription factors; zinc finger motif
Abstract:
... Iris lactea var. chinensis is a perennial herbaceous halophyte with high salt tolerance and ornamental value. Previous RNA sequencing analysis revealed a transcription factor gene IlWRKY2 expression was upregulated by salt stress. To obtain the full-length sequence, the basic characteristics of IlWRKY2 and its expression pattern under salt stress. Full-length cDNA of IlWRKY2 was cloned by 3′/5′ RA ...
DOI:
10.1007/s13258-018-0698-9

90. Multivariate genome-wide association studies on tenderness of Berkshire and Duroc pig breeds

Author:
Dongsung Jang; Joon Yoon; Mengistie Taye; Wonseok Lee; Taehyung Kwon; Seunghyun Shim; Heebal Kim
Source:
Genes & genomics 2018 v.40 no.7 pp. 701-705
ISSN:
1976-9571
Subject:
Duroc; breeding programs; genes; genetic variation; genome-wide association study; genomics; intramuscular fat; meat tenderness; pork; pork quality; single nucleotide polymorphism; statistical models; swine
Abstract:
... Genome-wide association studies (GWAS) have been steadily used for identification of genomic links to disease and various economical traits. Of those traits, a tenderness of pork is one of the most important factors in quality evaluation of consumers. In this study, we use two pig breed populations; Berkshire is known for its excellent meat quality and Duroc which is known for its high intramuscul ...
DOI:
10.1007/s13258-018-0672-6

91. Obese rats supplemented with bitter melon display marked shifts in the expression of genes controlling inflammatory response and lipid metabolism by RNA-Seq analysis of colonic mucosa

Author:
Juan Bai; Ying Zhu; Ying Dong
Source:
Genes & genomics 2018 v.40 no.6 pp. 561-567
ISSN:
1976-9571
Subject:
Momordica charantia; carbohydrates; cecum; colon; dietary supplements; digestion; ecology; gene expression; gene expression regulation; genes; high fat diet; inflammation; lipid metabolism; mucosa; obesity; phospholipase A2; protein kinase C; rats; reverse transcriptase polymerase chain reaction; sequence analysis; small intestine; stomach; transcriptomics
Abstract:
... Obesity is known to induce pathological changes in the gut and diets rich in complex carbohydrates that resist digestion in the small bowel can alter large bowel ecology. The purposes of this study were to identify the effects of bitter melon powder (BMP) on the global gene expression pattern in the colon mucosa of obese rats. Obese rats were fed a high-fat diet and treated without or with BMP for ...
DOI:
10.1007/s13258-017-0642-4

92. PSCArs2294008 T polymorphism increases the risk of bladder cancer in Bai, Dai, and Han ethnicity in China and a potential mechanism

Author:
Junfeng Yang; Wei Li; Zhuorui Zhang; Jie Shen; Ningnan Zhang; Min Yang; Maolin Yang; Yanhong Yu
Source:
Genes & genomics 2018 v.40 no.5 pp. 531-541
ISSN:
1976-9571
Subject:
alleles; cell cycle; cell proliferation; genotype; nationalities and ethnic groups; neoplasm cells; risk; tissues; urinary bladder neoplasms; China
Abstract:
... The aim of this study is to make a comparative evaluation on association of PSCArs2294008 C/T polymorphism with the risk of bladder cancer in Bai, Dai, and Han people in China. A potential mechanism of the T allele risk was also investigated. T allele increased the occurring risk of bladder cancer in Han (OR 1.34; 95% CI 1.17–1.69), Dai, (OR 1.33; 95% CI 1.12–1.70), and Bai (OR 1.14; 95% CI 1.08–1 ...
DOI:
10.1007/s13258-018-0653-9

93. Pelagic larval dispersal habits influence the population genetic structure of clam Gomphina aequilatera in China

Author:
Yingying Ye; Zeqin Fu; Yunfang Tian; Jiji Li; Baoying Guo; Zhenming Lv; Changwen Wu
Source:
Genes & genomics 2018 v.40 no.11 pp. 1213-1223
ISSN:
1976-9571
Subject:
clams; coasts; cytochrome-c oxidase; gene flow; genetic variation; larvae; larval development; mitochondria; plankton; population structure; ribosomal RNA; China
Abstract:
... Pelagic larval dispersal habits influence the population genetic structure of marine mollusk organisms via gene flow. The genetic information of the clam Gomphina aequilatera (short larval stage, 10 days) which is ecologically and economically important in the China coast is unknown. To determine the influence of planktonic larval duration on the genetic structure of G. aequilatera. Mitochondrial ...
DOI:
10.1007/s13258-018-0718-9

94. Performance evaluation method for read mapping tool in clinical panel sequencing

Author:
Hojun Lee; Ki-Wook Lee; Taeseob Lee; Donghyun Park; Jongsuk Chung; Chung Lee; Woong-Yang Park; Dae-Soon Son
Source:
Genes & genomics 2018 v.40 no.2 pp. 189-197
ISSN:
1976-9571
Subject:
bioinformatics; biopsy; clinical trials; genome; high-throughput nucleotide sequencing; liquids; system optimization
Abstract:
... In addition to the rapid advancement in Next-Generation Sequencing (NGS) technology, clinical panel sequencing is being used increasingly in clinical studies and tests. However, tools that are used in NGS data analysis have not been comparatively evaluated in performance for panel sequencing. This study aimed to evaluate the tools used in the alignment process, the first procedure in bioinformatic ...
DOI:
10.1007/s13258-017-0621-9
PubMed:
29568413
PubMed Central:
PMC5846869

95. Physiological and proteomic analysis of plant growth enhancement by the rhizobacteria Bacillus sp. JS

Author:
Ji Seong Kim; Jeong Eun Lee; Hualin Nie; Yong Jae Lee; Sun Tae Kim; Sun-Hyung Kim
Source:
Genes & genomics 2018 v.40 no.2 pp. 129-136
ISSN:
1976-9571
Subject:
Bacillus (bacteria); Lactuca sativa; Nicotiana tabacum; binding proteins; chlorophyll; lettuce; plant growth-promoting rhizobacteria; plant proteins; proteomics; rhizosphere bacteria; shoots; tobacco; two-dimensional gel electrophoresis
Abstract:
... In this study, the effects of the plant growth-promoting rhizobacterium (PGPR), Bacillus sp. JS on the growth of tobacco (Nicotiana tabacum ‘Xanthi’) and lettuce (Lactuca sativa ‘Crispa’), were evaluated by comparing various growth parameters between plants treated with the bacterium and those exposed to water or nutrient broth as control. In both tobacco and lettuce, fresh weight and length of sh ...
DOI:
10.1007/s13258-017-0615-7

96. Profiling and identification of pregnancy-associated circulating microRNAs in dairy cattle

Author:
Kesavan Markkandan; Kung Ahn; Dong Jin Lee; Tae Il. Kim; Changgwon Dang; Song-Eui Hong; Ho-Baek Yoon; Hyun-Joo Lim; Chang Pyo Hong
Source:
Genes & genomics 2018 v.40 no.10 pp. 1111-1117
ISSN:
1976-9571
Subject:
G-protein coupled receptors; Holstein; biomarkers; blood sampling; cell membranes; chromosomes; dairy cows; dairy industry; early diagnosis; exosomes; genes; high-throughput nucleotide sequencing; immune response; mammary development; microRNA; milk yield; physiological transport; pre-eclampsia; pregnancy; signal transduction
Abstract:
... Holstein is one among the dairy cattle which provide higher milk yields than most other cattle breeds. Lack of high-accuracy, reliable methods for early detection of cattle pregnancy reduces overall productivity and constitutes a high economic burden to the dairy industry. The circulating microRNAs (miRNAs) in exosomes could provide information and serve as potential biomarkers for livestock healt ...
DOI:
10.1007/s13258-018-0668-2

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

Author:
Jungwook Park; Areum Lee; Hyun-Hee Lee; Inmyoung Park; Young-Su Seo; Jaeho Cha
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

98. Retrotransposons in Betula nana, and interspecific relationships in the Betuloideae, based on inter-retrotransposon amplified polymorphism (IRAP) markers

Author:
Neha Samir Roy; Sung-Il Lee; Kabwe Nkongolo; Nam-Soo Kim
Source:
Genes & genomics 2018 v.40 no.5 pp. 511-519
ISSN:
1976-9571
Subject:
Alnus; Betula nana; databases; phylogeny; phylogeography; retrotransposons; sequence analysis; terminal repeat sequences
Abstract:
... The Betulaceae family comprises two subfamilies, Betuloideae and Corylaceae. The subfamily Betuloideae contains two genera, Alnus Mill. and Betula L. Twenty putative long terminal repeat (LTR) retrotransposons were mined from 171 scaffolds containing 5,208,995 bp of dwarf birch (Betula nana) genome sequences. Five retrotransposons were finally selected after filtering the retrotransposon canonical ...
DOI:
10.1007/s13258-018-0655-7

99. Selected microRNA-192 mutant indicates association with several function genes in bovine cells

Author:
Chen Zi; Dexin Zeng; Jiyong Zhou; Jianjun Dai; Luyan Jiang; Feng Xue; Yuan Jiang; Baoguang Li
Source:
Genes & genomics 2018 v.40 no.4 pp. 361-371
ISSN:
1976-9571
Subject:
Escherichia coli; carcinogenesis; cattle; cell differentiation; gene expression regulation; gene ontology; genes; infectious diseases; microRNA; mutants; neoplasms; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; sequence analysis
Abstract:
... MicroRNAs are implicated in many cellular processes such as cell differentiation and development, tumorigenesis, and immune regulation. In this study, miR192 was detected using quantitative real-time polymerase chain reaction (qRT-PCR) when MDBK cells were exposed to Escherichia coli. Cells with malfunction of bta-miR-192 were established using transcription activator-like effector nuclease (TALEN ...
DOI:
10.1007/s13258-017-0635-3

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

Author:
Dariush Salimi; Ali Moeini; Ali Masoudi-Nejad
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