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You searched for: Journal Genes & genomics Remove constraint Journal: Genes & genomics Journal name Genes & genomics Remove constraint Journal name: Genes & genomics
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1. Analysis of evolutionary and genetic patterns in structural genes of primate lentiviruses

Author:
Myeongji Cho; Xianglan Min; Hyeon S. Son
Source:
Genes & genomics 2022 v.44 no.7 pp. 773-791
ISSN:
1976-9571
Subject:
Puma; Simian immunodeficiency virus; anemia; cattle; codon usage; disease transmission; encephalitis; genomics; goats; horses; humans; immunotherapy; mutation; natural selection; selection pressure; sheep; vaccine development; vaccines; viruses
Abstract:
... BACKGROUND: Primate lentiviruses (HIV1, HIV2, and Simian immunodeficiency virus [SIV]) cause immune deficiency, encephalitis, and infectious anemia in mammals such as cattle, cat, goat, sheep, horse, and puma. OBJECTIVE: This study was designed and conducted with the main purpose of confirming the overall codon usage pattern of primate lentiviruses and exploring the evolutionary and genetic charac ...
DOI:
10.1007/s13258-022-01257-6

2. CDK1 promotes the proliferation of melanocytes in Rex rabbits

Author:
Yingying Dai; Shuaishuai Hu; Shaocheng Bai; Jiali Li; Naisu Yang; Pin Zhai; Bohao Zhao; Yang Chen; Xinsheng Wu
Source:
Genes & genomics 2022 v.44 no.10 pp. 1191-1199
ISSN:
1976-9571
Subject:
apoptosis; color; cyclin-dependent kinase; fur; gene expression; genes; genomics; melanin; melanocytes; melanogenesis; rabbits
Abstract:
... BACKGROUND: The fur color constitutes one of the most important economic characteristics of fur animals and is determined by the content of melanin. A previous study has shown that the cyclin-dependent kinase 1 (CDK1) is a member of the protein kinase family, involved in forming the color of the fur in Rex rabbits. However, its effect on the melanocytes remains unclear. OBJECTIVE: This study aimed ...
DOI:
10.1007/s13258-022-01283-4

3. Centromere protein N promotes lung adenocarcinoma progression by activating PI3K/AKT signaling pathway

Author:
Yi Zheng; Hui You; Jingzhu Duan; Biyu Chen; Chenlin Wu; Peipei Chen; Meifang Wang
Source:
Genes & genomics 2022 v.44 no.9 pp. 1039-1049
ISSN:
1976-9571
Subject:
Western blotting; adenocarcinoma; apoptosis; caspase-3; cell viability; centromeres; databases; flow cytometry; genomics; immunohistochemistry; lungs; neoplasm progression; phosphatidylinositol 3-kinase; phosphorylation; prognosis; protein synthesis; snails; xenotransplantation
Abstract:
... BACKGROUND: As an important member of centromere family, centromere associated protein N (CENPN) was abnormally expressed in varied malignant tumors. OBJECTIVE: This paper aimed to analyze the expression and related mechanism of CENPN in lung adenocarcinoma (LUAD). METHODS: The expression of CENPN in LUAD was analyzed by Gene Expression Profiling Interactive Analysis (GEPIA) database. The mRNA exp ...
DOI:
10.1007/s13258-021-01215-8

4. Characterization of the complete mitogenome of the endangered freshwater fish Gobiobotia naktongensis from the Geum River in South Korea: evidence of stream connection with the Paleo-Huanghe

Author:
Keun-Sik Kim; Dong-Won Kang; Keun-Yong Kim; Jung Soo Heo; Ha-Yoon Song; Ju-Duk Yoon
Source:
Genes & genomics 2022 v.44 no.8 pp. 945-956
ISSN:
1976-9571
Subject:
Geum; Gobiobotia; conspecificity; freshwater fish; genomics; mitochondrial genome; phylogeny; population size; ribosomal RNA; rivers; streams; transfer RNA; China; South Korea
Abstract:
... BACKGROUND: The freshwater fish Gobiobotia naktongensis (Teleostei, Cypriniformes, and Gobionidae) is an endangered class I species whose population size has been greatly reduced. OBJECTIVE: To successfully protect and restore the highly endangered freshwater fish G. naktongensis from the Geum River in South Korea. METHODS: The mitogenome was characterized using the primer walking method with phyl ...
DOI:
10.1007/s13258-022-01265-6

5. Coffin-Siris syndrome in two chinese patients with novel pathogenic variants of ARID1A and SMARCA4

Author:
Mingjie Liu; Linlin Wan; Chunrong Wang; Hongyu Yuan; Yun Peng; Na Wan; Zhichao Tang; Xinrong Yuan; Daji Chen; Zhe Long; Yuting Shi; Rong Qiu; Beisha Tang; Hong Jiang; Zhao Chen
Source:
Genes & genomics 2022 v.44 no.9 pp. 1061-1070
ISSN:
1976-9571
Subject:
DNA; blood; face; genetic analysis; genomics; genotype-phenotype correlation; guidelines; heterozygosity; pathogenicity; phenotype; China
Abstract:
... BACKGROUND: Coffin-Siris syndrome (CSS) is a rare congenital syndrome characterized by developmental delay, intellectual disability, microcephaly, coarse face and hypoplastic nail of the fifth digits. Heterozygous variants of different BAF complex-related genes were reported to cause CSS, including ARID1A and SMARCA4. So far, no CSS patients with ARID1A and SMARCA4 variants have been reported in C ...
DOI:
10.1007/s13258-022-01231-2

6. Comparative analysis of genome-based CAZyme cassette in Antarctic Microbacterium sp. PAMC28756 with 31 other Microbacterium species

Author:
Sushma Gupta; So-Ra Han; Byeollee Kim; Chang-Muk Lee; Tae-Jin Oh
Source:
Genes & genomics 2022 v.44 no.6 pp. 733-746
ISSN:
1976-9571
Subject:
Microbacterium; activated sludge; amylases; carbohydrate metabolism; carbon; cellulose; databases; energy; genomics; glyoxylate cycle; hemicellulose; lichens; polygalacturonase; Antarctic region
Abstract:
... BACKGROUND: The genus Microbacterium belongs to the family Microbacteriaceae and phylum Actinobacteria. A detailed study on the complete genome and systematic comparative analysis of carbohydrate-active enzyme (CAZyme) among the Microbacterium species would add knowledge on metabolic and environmental adaptation. Here we present the comparative genomic analysis of CAZyme using the complete genome ...
DOI:
10.1007/s13258-022-01254-9

7. Compound heterozygous mutations of NDUFV1 identified in a child with mitochondrial complex I deficiency

Author:
Xiaojun Tang; Wuhen Xu; Xiaozhen Song; Haiyun Ye; Xiang Ren; Yongchen Yang; Hong Zhang; Shengnan Wu; Xiaoping Lan
Source:
Genes & genomics 2022 v.44 no.6 pp. 691-698
ISSN:
1976-9571
Subject:
amino acid substitution; cardiomyopathy; childhood; children; computer simulation; databases; encephalopathy; genomics; heterozygosity; missense mutation; mitochondria; muscular diseases; patients; prediction; reproduction
Abstract:
... BACKGROUND: Mitochondrial complex I deficiency (MCID) is the most common biochemical defect identified in childhood with mitochondrial diseases, mainly including Leigh syndrome, encephalopathy, macrocephaly with progressive leukodystrophy, hypertrophic cardiomyopathy and myopathy. OBJECTIVE: To identify genetic cause in a patient with early onset autosomal recessive MCID. METHODS: Trio whole-exome ...
DOI:
10.1007/s13258-022-01260-x

8. DNA methylation and histone modifications induced by abiotic stressors in plants

Author:
Karolina Czajka; Melanie Mehes-Smith; Kabwe Nkongolo
Source:
Genes & genomics 2022 v.44 no.3 pp. 279-297
ISSN:
1976-9571
Subject:
DNA hypermethylation; DNA hypomethylation; abiotic stress; bisulfites; epigenetics; genomics; high performance liquid chromatography; histone code; histones; plant response
Abstract:
... BACKGROUND: A review of research shows that methylation in plants is more complex and sophisticated than in microorganisms and animals. Overall, studies on the effects of abiotic stress on epigenetic modifications in plants are still scarce and limited to few species. Epigenetic regulation of plant responses to environmental stresses has not been elucidated. This study summarizes key effects of ab ...
DOI:
10.1007/s13258-021-01191-z

9. Diversity in the composition of the accessory genome of Mexican Pseudomonas aeruginosa strains

Author:
Luis F. Espinosa-Camacho; Gabriela Delgado; Alejandro Cravioto; Rosario Morales-Espinosa
Source:
Genes & genomics 2022 v.44 no.1 pp. 53-77
ISSN:
1976-9571
Subject:
CRISPR-Cas systems; DNA; Pseudomonas aeruginosa; antibiotic resistance; antibiotics; bacteremia; bioinformatics; chromosome aberrations; chromosomes; cross infection; genetic variation; genomics; hospitals; multiple drug resistance; opportunistic pathogens; phenotype; pneumonia; virulence
Abstract:
... BACKGROUND: Pseudomonas aeruginosa is an important opportunistic pathogen especially in nosocomial infections due to its easy adaptation to different environments; this characteristic is due to the great genetic diversity that presents its genome. In addition, it is considered a pathogen of critical priority due to the high antimicrobial resistance. OBJECTIVES: The aim of this study was to charact ...
DOI:
10.1007/s13258-021-01155-3

10. Effect of human endogenous retrovirus-K env gene knockout on proliferation of ovarian cancer cells

Author:
Eun-Ji Ko; Eun Taeg Kim; Heungyeol Kim; Chul Min Lee; Suk Bong Koh; Wan Kyu Eo; Hongbae Kim; Young Lim Oh; Mee Sun Ock; Ki Hyung Kim; Hee-Jae Cha
Source:
Genes & genomics 2022 v.44 no.9 pp. 1091-1097
ISSN:
1976-9571
Subject:
CRISPR-Cas systems; RNA; Retroviridae; Western blotting; cell lines; cell proliferation; colorectal neoplasms; cyclins; gene targeting; genes; genomics; humans; neoplasm cells; ovarian neoplasms; pancreatic neoplasms; protein content; protein synthesis
Abstract:
... BACKGROUND: Among various human endogenous retroviruses (HERVs), the HERV-K (HML-2) group has been reported to be highly related to cancer. In pancreatic cancer cells, shRNA-mediated downregulation of HERV-K env RNA decreases cell proliferation and tumor growth through the RAS-ERK-RSK pathway; in colorectal cancer, CRISPR-Cas9 knockout (KO) of the HERV-K env gene affects tumorigenic characteristic ...
DOI:
10.1007/s13258-022-01280-7

11. Effects of Fdft 1 gene silencing and VD3 intervention on lung injury in hypoxia-stressed rats

Author:
Xiaoyan Pu; Xue Lin; Yinglian Qi; Yinglian Li; Tiantian Li; Yang Liu; Dengbang Wei
Source:
Genes & genomics 2022 v.44 no.10 pp. 1201-1213
ISSN:
1976-9571
Subject:
animal models; apoptosis; biosynthesis; cholecalciferol; edema; genes; genomics; hypertension; hypoxia; lungs; metabolites; mitochondria; oxygen; oxygen partial pressure; protective effect; pulmonary artery; synergism; water content
Abstract:
... BACKGROUND: Hypoxia can induce lung injury such as pulmonary arterial hypertension and pulmonary edema. And in the rat model of hypoxia-induced lung injury, the expression of Farnesyl diphosphate farnesyl transferase 1 (Fdft 1) was highly expressed and the steroid biosynthesis pathway was activated. However, the role of Fdft 1 and steroid biosynthesis pathway in hypoxia-induced lung injury remains ...
DOI:
10.1007/s13258-022-01284-3

12. Effects of TLR9/NF-κB on oxidative stress and inflammation in IPEC-J2 cells

Author:
Lixia Ma; Jinhong Geng; Wei Chen; Ming Qin; Lixue Wang; Yongqing Zeng
Source:
Genes & genomics 2022 v.44 no.10 pp. 1149-1158
ISSN:
1976-9571
Subject:
antioxidants; diquat; genomics; inflammation; malondialdehyde; models; oxidative stress; oxygen; secretion; superoxide dismutase
Abstract:
... BACKGROUND: Oxidative stress is one of the most important factors affecting large-scale breeding, especially the performance of pigs. Oxidative stress plays a role by affecting various genes in pigs, which can cause serious body damage, functional degradation and reduce production performance. OBJECTIVE: The purpose of this study was to investigate the effect of Toll like receptor 9 (TLR9) pathway ...
DOI:
10.1007/s13258-022-01271-8

13. Epigenetic control of abiotic stress signaling in plants

Author:
Sunglan Chung; Chian Kwon; Jae-Hoon Lee
Source:
Genes & genomics 2022 v.44 no.3 pp. 267-278
ISSN:
1976-9571
Subject:
DNA; DNA methylation; abiotic stress; acetylation; chromatin; cold; drought; epigenetics; genomics; heat; histones
Abstract:
... BACKGROUND: Although plants may be regularly exposed to various abiotic stresses, including drought, salt, cold, heat, heavy metals, and UV-B throughout their lives, it is not possible to actively escape from such stresses due to the immobile nature of plants. To overcome adverse environmental stresses, plants have developed adaptive systems that allow appropriate responses to diverse environmenta ...
DOI:
10.1007/s13258-021-01163-3

14. Epigenetic reorganization during early embryonic lineage specification

Author:
Haitong Fang; Zhuojuan Luo; Chengqi Lin
Source:
Genes & genomics 2022 v.44 no.3 pp. 379-387
ISSN:
1976-9571
Subject:
DNA methylation; blastocyst; chromatin; epigenetics; epigenome; gastrulation; gene expression; genomics; histone code; mice; transcription (genetics); transcription factors
Abstract:
... BACKGROUND: Dynamic chromatin reorganization occurs during two waves of cell lineage specification process, blastocyst formation and gastrulation, to generate distinct cell types. Epigenetic defects have been associated with severe developmental defects and diseases. How epigenetic remodeling coordinates the two lineage specification waves is becoming uncovered, benefiting from the development and ...
DOI:
10.1007/s13258-021-01213-w

15. Expression profiling of the mitogen-activated protein kinase gene family reveals their diverse response pattern in two different salt-tolerant Glycyrrhiza species

Author:
Aiping Cao; Ling Gao; Fei Wang; Xuechen Tong; Shuangquan Xie; Xifeng Chen; Tianxin Lu; Haitao Shen; Hailiang Liu; Xiang Jin; Hongbin Li
Source:
Genes & genomics 2022 v.44 no.7 pp. 757-771
ISSN:
1976-9571
Subject:
Glycyrrhiza uralensis; bioinformatics; genes; genomics; medicinal plants; metabolites; mitogen-activated protein kinase; pharmacodynamics; phylogeny; plant growth; plant hormones; regulatory sequences; salt stress; salt tolerance
Abstract:
... BACKGROUND: Mitogen-activated protein kinases (MPKs) play important role in response to environmental stress as crucial signal receptors or sensors. Our previous study indicated that salt stress acts as a positive factor to stimulate the production of pharmacodynamic metabolites in the medicinal plant Glycyrrhiza uralensis. Currently, little is known about the MPK gene family and their functions i ...
DOI:
10.1007/s13258-021-01216-7

16. GADD45A induces neuropathic pain by activating P53 apoptosis pathway in mice

Author:
Jing Li; Jia Chen
Source:
Genes & genomics 2022 v.44 no.9 pp. 1051-1060
ISSN:
1976-9571
Subject:
apoptosis; bioinformatics; biomarkers; etiology; fluorescent antibody technique; genomics; mice; nerve tissue; pain; phenotype; protein synthesis; spinal cord; therapeutics
Abstract:
... BACKGROUND: Neuropathic pain is a common condition with current heights of varying etiology. The therapeutic drugs are also poorly work and often limited by side effects such as dizziness. OBJECTIVE: This study aimed to explore the function mechanism of GADD45A in neuropathic pain. METHODS: The DEGs in neuropathic pain mouse model chip were screened by bioinformatics analysis. The expression of GA ...
DOI:
10.1007/s13258-022-01226-z

17. Genetically predicted physical activity is associated with lower serum urate concentrations

Author:
Ying Guan; Jiahe Wei; Lifeng Meng; Yasong Li; Tianle Wang; Dingwan Chen; Qilin Qian
Source:
Genes & genomics 2022 v.44 no.7 pp. 843-853
ISSN:
1976-9571
Subject:
blood serum; confidence interval; genetic predisposition to disease; genomics; gout; physical activity; pleiotropy; risk
Abstract:
... BACKGROUND: Physical activity (PA) is considered to play an important role in the reduced gout risk. However, the epidemiology results are inconsistent and causality remains unclear. OBJECTIVE: To investigate the causal relationship of PA with serum urate concentrations and gout risk by a bidirectional Mendelian randomization (MR) approach. METHOD: Two genome-wide association studies (GWASs) from ...
DOI:
10.1007/s13258-022-01239-8

18. Genome-wide DNA methylation profiling in differentiating Crohn’s disease from intestinal tuberculosis

Author:
Hao Wu; Hongchun Liu; Haining Liu; Yanjie Chen; Taotao Liu; Xizhong Shen; Lili Liu
Source:
Genes & genomics 2022 v.44 no.5 pp. 603-615
ISSN:
1976-9571
Subject:
DNA; DNA methylation; biomarkers; blood; epigenetics; genome-wide association study; genomics; immune system; immunomodulators; intestines; pathogenesis; promoter regions; signal transduction; tuberculosis
Abstract:
... BACKGROUND: Differential diagnosis of Crohn’s disease (CD) and intestinal tuberculosis (ITB) is still difficult in clinical pratice. DNA methylation has been considered as a favorable area for biomarker exploration and identification. OBJECTIVE: The purpose of the current study was to evaluate DNA methylation changes between CD and ITB. METHODS: We performed a genome-wide association study to iden ...
DOI:
10.1007/s13258-022-01224-1

19. Genome-wide locus-specific DNA methylation repatterning may facilitate rapid evolution of mercury resistance in rice

Author:
Weixuan Cong; Ning Li; Jinbin Wang; Ying Kang; Yiling Miao; Chunming Xu; Ziqi Wang; Tongtong Liu; Lei Gong; Bao Liu; Xiufang Ou
Source:
Genes & genomics 2022 v.44 no.3 pp. 299-306
ISSN:
1976-9571
Subject:
DNA methylation; DNA methyltransferase; bisulfites; epigenetics; evolution; gene ontology; genes; genomics; heterozygosity; mercury; mutants; rice
Abstract:
... BACKGROUND: Albeit a relatively stable epigenetic modification, DNA methylation in plants can be repatterned and play important roles in response to biotic and abiotic stresses. However, whether DNA methylation dynamics may contribute to cope with mercury (Hg) stress in plants remains to be fully investigated. OBJECTIVE: To probe the potential roles of DNA methylation dynamics in coping with Hg st ...
DOI:
10.1007/s13258-021-01192-y

20. Genomic perspectives on epigenetics

Author:
Jung-Shin Lee; Nam-Soo Kim
Source:
Genes & genomics 2022 v.44 no.3 pp. 247-249
ISSN:
1976-9571
Subject:
epigenetics; genomics; intergenic DNA; molecular biology; phenotype
Abstract:
... For much of the twentieth century, it was accepted that genes dictate phenotypes. Nevertheless, genetics in combination with molecular biology and genomics has facilitated the explanation of some peculiar molecular phenomena. Most eukaryotic genomes are crammed with noncoding DNA, which was previously hypothesized to be selfish DNA, with only a small fraction of sequences encoding proteins. We now ...
DOI:
10.1007/s13258-022-01225-0