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You searched for: 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

21. Harnessing epigenetic variability for crop improvement: current status and future prospects

Author:
Eun Yu Kim; Kyung Do Kim; Jungnam Cho
Source:
Genes & genomics 2022 v.44 no.3 pp. 259-266
ISSN:
1976-9571
Subject:
CRISPR-Cas systems; DNA methylation; artificial selection; epigenetics; epigenome; genes; genetic variation; genomics; tissue culture
Abstract:
... BACKGROUND: The epigenetic mechanisms play critical roles in a vast diversity of biological processes of plants, including development and response to environmental challenges. Particularly, DNA methylation is a stable epigenetic signature that supplements the genetics-based view of complex life phenomena. In crop breeding, the decrease in genetic diversity due to artificial selection of conventio ...
DOI:
10.1007/s13258-021-01189-7

22. Identification and clinical characterization of Charcot-Marie-Tooth disease type 1C patients with LITAF p.G112S mutation

Author:
Jaehong Park; Hyun Su Kim; Hye Mi Kwon; Jiah kim; Soo Hyun Nam; Na Young Jung; Ah Jin Lee; Young Hee Jung; Sang Beom Kim; Ki Wha Chung; Byung-Ok Choi
Source:
Genes & genomics 2022 v.44 no.8 pp. 1007-1016
ISSN:
1976-9571
Subject:
calves; electrophysiology; genes; genomics; genotype-phenotype correlation; mutation; peripheral nervous system diseases
Abstract:
... BACKGROUND: Charcot-Marie-Tooth disease type 1C (CMT1C) is a rare subtype associated with LITAF gene mutations. Until now, only a few studies have reported the clinical features of CMT1C. OBJECTIVE: This study was performed to find CMT1C patients with mutation of LITAF in a Korean CMT cohort and to characterize their clinical features. METHODS: In total, 1,143 unrelated Korean families with CMT we ...
DOI:
10.1007/s13258-022-01253-w

23. Identification and differential expression of microRNAs in Madin–Darby canine kidney cells with high and low tumorigenicities

Author:
Jiamin Wang; Lixia Liu; Di Yang; Li Zhang; Ayimuguli Abudureyimu; Zilin Qiao; Zhongren Ma
Source:
Genes & genomics 2022 v.44 no.2 pp. 187-196
ISSN:
1976-9571
Subject:
carcinogenesis; cell lines; dogs; gene expression regulation; genomics; kidneys; microRNA; neoplasms; phenotype; prediction; sequence analysis; vaccines
Abstract:
... BACKGROUND: Madin–Darby canine kidney (MDCK) cells are widely used for vaccine production, however, the safety of MDCK cells needs to be considered seriously because of high tumorigenicity. Micro RNAs (miRNAs) that are involved in the tumorigenicity of MDCK cells have been never been reported. OBJECTIVE: To reveal the role of miRNA in the tumorigenic phenotype of MDCK cell line. METHODS: The miRNA ...
DOI:
10.1007/s13258-021-01177-x

24. Identification of MicroRNAs as potential biomarkers for detecting ischemic stroke

Author:
Kexin Li; Li Shen; Pingping Zheng; Yanjun Wang; Lijuan Wang; Xiaoli Meng; Yaogai Lv; Zhiqiang Xue; Xin Guo; Anning Zhang; Pan Pan; Chunli Bi; Yang Chen; Tianyu Feng; Bo Li; Lina Jin; Yan Yao
Source:
Genes & genomics 2022 v.44 no.1 pp. 9-17
ISSN:
1976-9571
Subject:
DNA repair; biomarkers; brain; databases; gene expression regulation; genomics; ischemia; lysosomes; microRNA; pathogenesis; prediction; spliceosomes; stroke
Abstract:
... BACKGROUND: Increasing epidemic of ischemic stroke (IS) makes it urgent to understand the pathogenesis and regulatory mechanism, previous studies have described microRNAs (miRNAs) is part of the brain's response to ischemia. OBJECTIVE: The aim of this study was to screen potential biomarkers for the prediction and novel treatment of IS. METHODS: Differentially expressed miRNAs were screened from t ...
DOI:
10.1007/s13258-021-01060-9

25. Identification of yield-related genes through genome-wide association: case study of weeping forsythia, an emerging medicinal crop

Author:
Yong Li; Qiong Wu; Hong-Li Liu; Nan-Cai Pei; Yan-Xia He; Jine Quan
Source:
Genes & genomics 2022 v.44 no.2 pp. 145-154
ISSN:
1976-9571
Subject:
agricultural research; alpha-mannosidase; auxins; case studies; fruit weight; fruit yield; fruiting; fruits; genes; genetic variation; genome-wide association study; genomics; kinship; transcription factors
Abstract:
... KEY MESSAGE: This study identified candidate genes related to fruit yield for an emerging medicinal crop, weeping forsythia. BACKGROUND: The genetic basis of crop yield is an agricultural research hotspot. Identifying the genes related to yield traits is the key to increase the yield. Weeping forsythia is an emerging medicinal crop that currently lacks excellent varieties. The genes related to fru ...
DOI:
10.1007/s13258-021-01186-w

26. Impact of VEGFA promoter polymorphisms on esophageal cancer risk in North-West Indians: a case-control study

Author:
Kamlesh Guleria; Simranjot Kaur; Deepanshi Mahajan; Vasudha Sambyal; Meena Sudan; Manjit Singh Uppal
Source:
Genes & genomics 2022 v.44 no.8 pp. 923-936
ISSN:
1976-9571
Subject:
DNA; alleles; angiogenesis; blood; case-control studies; chloroform; endothelial cells; esophageal neoplasms; females; genomics; genotyping; haplotypes; mitogens; phenol; polymerase chain reaction; risk; vascular endothelial growth factors
Abstract:
... BACKGROUND: Angiogenesis play a critical role in the development and progression of tumors in solid tumors. Vascular endothelial growth factor (VEGF) is one of the most important endothelial cell mitogen which plays a critical role in normal physiological and tumor angiogenesis. OBJECTIVES: The objective of this case-control study was to investigate the association of VEGF-2578C/A, -2549 I/D, and ...
DOI:
10.1007/s13258-022-01269-2

27. Inhibition of BETs prevents heat shock-induced cell death via upregulating HSPs in SV40 large T antigen transfected cells

Author:
Nan Zhou; Ye Zhang; Gongyun Lei; Yifan Chen; Ting Lin; Qin Liu; Yinshuang Zhao; Jiahui Mao; Yongying Jiang; Renfang Mao
Source:
Genes & genomics 2022 v.44 no.10 pp. 1259-1269
ISSN:
1976-9571
Subject:
Western blotting; antigens; cell death; death; gene expression; genomics; heat; heat shock response; heat stress; humans; viruses
Abstract:
... BACKGROUND: Heat shock response is a protected mechanism against environmental changes for the organism, which must be tightly regulated. Bromodomain and extra terminal-containing protein family (BETs) regulate numerous gene expression in many physiological and pathological conditions, including viral infection. SV40 is considered as a highly human disease-associated virus. OBJECTIVE: We aimed to ...
DOI:
10.1007/s13258-022-01228-x

28. Inhibition of FOSL2 aggravates the apoptosis of ovarian cancer cells by promoting the formation of inflammasomes

Author:
Jie Li; Li Zhou; Hongye Jiang; Lin Lin; Yinguang Li
Source:
Genes & genomics 2022 v.44 no.1 pp. 29-38
ISSN:
1976-9571
Subject:
Western blotting; antigens; apoptosis; carcinogenesis; caspase-1; cysteine; enzyme-linked immunosorbent assay; females; fluorescence; genomics; inflammasomes; interleukin-18; lactate dehydrogenase; ovarian neoplasms; plasmids; quantitative polymerase chain reaction; transfection
Abstract:
... BACKGROUND: Ovarian cancer is a common gynecological malignancy among female patients and poses a serious threat to women’s health. Although it has been established that Fos-like antigen 2 (FOSL2) is linked to ovarian cancer (OC), its exact role in the development of OC remains unknown. OBJECTIVE: This article aims to investigate the role of FOSL2 in ovarian cancer development. METHODS: FOSL2 expr ...
DOI:
10.1007/s13258-021-01152-6

29. Iron metabolism protein transferrin receptor 1 involves in cervical cancer progression by affecting gene expression and alternative splicing in HeLa cells

Author:
Nan Huang; Yaxun Wei; Yi Cheng; Xiaolong Wang; Qi Wang; Dong Chen; Wenjing Li
Source:
Genes & genomics 2022 v.44 no.6 pp. 637-650
ISSN:
1976-9571
Subject:
DNA repair; cancer therapy; cell death; cell physiology; databases; gene expression; genomics; homeostasis; immunity; iron absorption; metabolism; neoplasm cells; neoplasm progression; prognosis; sequence analysis; small interfering RNA; transcription (genetics); transcriptome; transferrin receptors; uterine cervical neoplasms; virus replication
Abstract:
... BACKGROUND: Transferrin receptor 1 (TfR1), encoded by TFRC, is a key regulator of iron homeostasis and plays important roles in many diseases, including cancers. OBJECTIVE: To decipher the underlying molecular functions of TfR1 based on its influence on transcriptome profile in cancer cells. METHODS: In this study, we first identified the expression pattern and prognostic influence of TFRC in cerv ...
DOI:
10.1007/s13258-021-01205-w

30. LKB1 on POMC neurons affect the formation of diet-induced obesity by regulating the expression of HDAC1

Author:
Yan Zhang; Zhaoxia Wu; Pengjiao Xi; Haomin Wang; Wenjuan Zhu; Derun Tian
Source:
Genes & genomics 2022 v.44 no.4 pp. 467-475
ISSN:
1976-9571
Subject:
adipogenesis; computer software; food intake; genomics; high fat diet; histone deacetylase; hypothalamus; lipid content; liver; neurons; nutritional intervention; obesity; proteomics; public health; serine; threonine
Abstract:
... BACKGROUND: Obesity is considered a major public health issue worldwide. Liver Kinase B1 (LKB1) is a serine/threonine kinase, peripheral LKB1 is involved in obesity by regulating adipogenesis, but the role of central LKB1 in the development of obesity remains unclear. OBJECTIVE: This study aims to explore the main role of LKB1 in POMC neurons on obesity, and reveal the underlying mechanism of cent ...
DOI:
10.1007/s13258-021-01206-9

31. LncSNHG3 promotes hepatocellular carcinoma epithelial mesenchymal transition progression through the miR-152-3p/JAK1 pathway

Author:
Hong Li; Yu Wu; Runmei Wang; Junmei Guo; Qin Yu; Lihe Zhang; Haiping Zhao; Hao Yang
Source:
Genes & genomics 2022 v.44 no.1 pp. 133-144
ISSN:
1976-9571
Subject:
RNA; apoptosis; bioluminescence assay; epithelium; genomics; hepatoma; oncogenes; precipitin tests; xenotransplantation
Abstract:
... BACKGROUND: The dysregulation of LncRNAs is related to the malignant progression of many cancers. OBJECTIVE: The study aimed to investigate the expression and the biological role of LncSNHG3 in hepatocellular carcinoma (HCC). METHODS: The TCGA data of the LncSNHG3 in HCC were analyzed. The expression in HCC cell lines was detected by qRT-PCR. Proliferation, migration, and invasion of HepG2 and Huh ...
DOI:
10.1007/s13258-021-01185-x

32. Mesenchymal stem cell-derived exosome mir-342-3p inhibits metastasis and chemo-resistance of breast cancer through regulating ID4

Author:
Shuyao Yu; Yuhui Zhou; Ligang Niu; Yan Qiao; Yu Yan
Source:
Genes & genomics 2022 v.44 no.5 pp. 539-550
ISSN:
1976-9571
Subject:
breast neoplasms; cancer therapy; exosomes; genomics; lymph nodes; metastasis; microRNA; neoplasm cells; reporter genes; transfection
Abstract:
... BACKGROUND: The mesenchymal stem cell-derived exosome (MSCs-exo) carrying microRNAs have been proved to regulate tumor biological activities. Clarifying molecular mechanism and identifying predictive microRNAs will be of great value in anti-tumor therapy improvement. OBJECTIVE: We aimed to investigate the regulatory role of microRNA-342-3p (miR-342-3p) in MSCs-exo on breast cancer. METHODS: Breast ...
DOI:
10.1007/s13258-021-01200-1

33. MiR-1299 functions as a tumor suppressor to inhibit the proliferation and metastasis of gastric cancer by targeting ARF6

Author:
Yang Qiu; Yonggang Yuan; Ping Luo
Source:
Genes & genomics 2022 v.44 no.2 pp. 237-245
ISSN:
1976-9571
Subject:
apoptosis; carcinogenesis; cell growth; cell proliferation; genomics; luciferase; metastasis; microRNA; stomach neoplasms
Abstract:
... BACKGROUND: MiRNAs belong to non-coding RNAs that are involved in cancer development. Acting as a mediator, they could regulate the expression level of numerous gens. However, the expression and function of miR-1299 in gastric cancer (GC) are not clear. OBJECTIVE: To explore the role of miR-1299 in the process of GC. METHODS: We detected the levels of miR-1299 in clinical samples of GC and investi ...
DOI:
10.1007/s13258-021-01124-w

34. MiR-200c-3p inhibits LPS-induced M1 polarization of BV2 cells by targeting RIP2

Author:
Lei Zhao; Xiaosong Liu; Jiankai Yang; Xiaoliang Wang; Xiaomeng Liu; Jianliang Wu; Chen Li; Donggang Xu; Yuhua Hu
Source:
Genes & genomics 2022 v.44 no.4 pp. 477-486
ISSN:
1976-9571
Subject:
bioluminescence assay; dose response; genomics; inducible nitric oxide synthase; interleukin-6; lipopolysaccharides; major histocompatibility complex; microRNA; neuroglia; phenotype; phosphorylation; quantitative polymerase chain reaction; therapeutics; transcription factor NF-kappa B
Abstract:
... BACKGROUND: Microglia are important immune cells, which can be induced by lipopolysaccharide (LPS) into M1 phenotype that express pro-inflammatory cytokines. Some studies have shown that microRNAs play critical roles in microglial activation. OBJECTIVE: This study was designed to investigate the role of miR-200c-3p in regulating inflammatory responses of LPS-treated BV2 cells. METHODS: The express ...
DOI:
10.1007/s13258-021-01210-z

35. Mir-326 potentiates radiosensitivity of cervical squamous cell carcinoma through downregulating SMO expression in the Hedgehog signaling pathway

Author:
Junqin Zhang; Yaxing Li; Yanan Ren; Hua Han; Jie Li
Source:
Genes & genomics 2022 v.44 no.8 pp. 981-991
ISSN:
1976-9571
Subject:
Erinaceidae; bioinformatics; bioluminescence assay; drug resistance; genomics; mutation; radiation resistance; radiotherapy; squamous cell carcinoma; uterine cervical neoplasms
Abstract:
... BACKGROUND: Radiotherapy resistance affects the therapeutic effect of cervical squamous cell carcinoma (CSCC). Smoothened (Smo) is an anticancer target of the Hedgehog (Hh) pathway and its mutation is related to drug resistance. OBJECTIVE: To explore the roles of miR-326 and Smoothened (SMO) on radiation resistance in patients with cervical carcinoma. METHODS: Expression of miR-326 and SMO in cerv ...
DOI:
10.1007/s13258-022-01276-3

36. NEDD4L suppresses PD-L1 expression and enhances anti-tumor immune response in A549 cells

Author:
Bin Zhong; Jie Zheng; Huilan Wen; Xinhui Liao; Xingxiang Chen; Yunwei Rao; Ping Yuan
Source:
Genes & genomics 2022 v.44 no.9 pp. 1071-1079
ISSN:
1976-9571
Subject:
genomics; immune response; interleukin-2; lung neoplasms; models; patients; prognosis; protein content; public health; ubiquitin-protein ligase; ubiquitination; xenotransplantation
Abstract:
... BACKGROUND: Non-small cell lung cancer (NSCLC) poses a salient threat to public health. E3 ubiquitin ligase commonly functions as an anti-tumor role. OBJECTIVE: This study probed the effect of E3 ligase NEDD4L on A549 cells. METHODS: NEDD4L expression in NSCLC and its correlation with NSCLC patient’s prognosis were predicted and verified. PD-L1 protein level was measured, and the correlation betwe ...
DOI:
10.1007/s13258-022-01238-9

37. Neferine increases sensitivities to multiple anticancer drugs via downregulation of Bcl-2 expression in renal cancer cells

Author:
Eun-Ae Kim; Ji Hoon Jang; Eon-Gi Sung; In-Hwan Song; Joo-Young Kim; Ho-Yong Sohn; Tae-Jin Lee
Source:
Genes & genomics 2022 v.44 no.2 pp. 165-173
ISSN:
1976-9571
Subject:
Nelumbo nucifera; acetylcysteine; alkaloids; apoptosis; cell cycle checkpoints; cisplatin; cytotoxicity; flow cytometry; genomics; humans; kidney neoplasms; reactive oxygen species; reverse transcriptase polymerase chain reaction; therapeutics; transcription (genetics)
Abstract:
... BACKGROUND: Neferine is the major alkaloid extracted from a seed embryo of Nelumbo nucifera and shows cytotoxic effects in various human cancer cells. However, no detailed studies have been reported on its antitumor efficacy of a combinational treatment in human renal cancer cells. OBJECTIVE: This study evaluated the antitumor effects of a combination therapy of neferine and various drugs on renal ...
DOI:
10.1007/s13258-021-01201-0

38. Novel blood-based hypomethylation of SH3BP5 is associated with very early-stage lung adenocarcinoma

Author:
Rong Qiao; Runbo Zhong; Chunlan Liu; Feifei Di; Zheng Zhang; Ling Wang; Tian Xu; Yue Wang; Liping Dai; Wanjian Gu; Baohui Han; Rongxi Yang
Source:
Genes & genomics 2022 v.44 no.4 pp. 445-453
ISSN:
1976-9571
Subject:
DNA methylation; adenocarcinoma; blood; genes; genomics; lung neoplasms; lungs; mass spectrometry; odds ratio; quantitative analysis; regression analysis; risk
Abstract:
... BACKGROUND: Early detection is essential to improve the survival of lung cancer (LC). The quantitative measurement of specific DNA methylation changes in the peripheral blood could provide an efficient strategy for the detection of early cancer. OBJECTIVE: We applied a candidate approach and assess the association between blood-based SH3BP5 methylation and the risk of lung adenocarcinoma (LUAD) in ...
DOI:
10.1007/s13258-021-01190-0

39. PKC-β modulates Ca2+ mobilization through Stim1 phosphorylation

Author:
Hye-Jin Song; In-Sook Jeon; Seung Ryul Kim; Kwan Sik Park; Jae-Won Soh; Kwang Youl Lee; Jae-Cheon Shin; Hak-Kyo Lee; Joong-Kook Choi
Source:
Genes & genomics 2022 v.44 no.5 pp. 571-582
ISSN:
1976-9571
Subject:
cAMP-dependent protein kinase; calcium; calcium channels; cell proliferation; diacylglycerols; endoplasmic reticulum; genomics; mitogen-activated protein kinase; phosphorylation; plasma membrane
Abstract:
... BACKGROUND: Calcium ions play a pivotal role in cell proliferation, differentiation, and migration. Under basal conditions, the calcium level is tightly regulated; however, cellular activation by growth factors increase the ion level through calcium pumps in the plasma membrane and endoplasmic reticulum for calcium signaling. Orai1 is a major calcium channel in the cell membrane of non-excitable c ...
DOI:
10.1007/s13258-022-01230-3

40. Phylogeography of the Korean endemic Coreoleuciscus (Cypriniformes: Gobionidae): the genetic evidence of colonization through Eurasian continent to the Korean Peninsula during Late Plio-Pleistocene

Author:
Hyung-Bae Jeon; Ha Youn Song; Ho Young Suk; In-Chul Bang
Source:
Genes & genomics 2022 v.44 no.6 pp. 709-719
ISSN:
1976-9571
Subject:
Cypriniformes; ancestry; drainage; freshwater; freshwater fish; genetic variation; genomics; indigenous species; mitochondria; phylogeny; phylogeography; rheophilic species; rivers; Korean Peninsula
Abstract:
... BACKGROUND: Freshwater endemism is thought to have been formed through the vicariance of connected water systems or the process by which ancestral populations colonized specific areas. The Korean Peninsula is well recognized for its high level of freshwater endemism with about 40% of freshwater fish species being endemic. OBJECTIVE: In this study, we attempted to reconstruct the process of speciat ...
DOI:
10.1007/s13258-022-01243-y

41. Physiological characteristics and miRNA sequencing of two root zones with contrasting ammonium assimilation patterns in Populus

Author:
Jing Zhou; Jiang ting Wu
Source:
Genes & genomics 2022 v.44 no.1 pp. 39-51
ISSN:
1976-9571
Subject:
Populus; ammonium; genomics; microRNA; plantlets; rhizosphere
Abstract:
... BACKGROUND: The net ammonium fluxes differ among the different root zones of Populus, but the physiological and microRNA regulatory mechanisms are unclear. OBJECTIVE: To elucidate the physiological and miRNA regulatory mechanisms, we investigated the two root zones displaying significant differences in net NH₄⁺ effluxes of P. × canescens. METHODS: Populus plantlets were cultivated with 500 μM NH₄C ...
DOI:
10.1007/s13258-021-01156-2

42. Population genetic analysis reveals secondary contact between Eriocheir sinensis and E. japonica in South Korea

Author:
Jibom Jung; Xugan Wu; Taeseo Park; Seok-hyun Lee; Hee-seung Hwang; Juwon Jung; Jongwoo Jung
Source:
Genes & genomics 2022 v.44 no.5 pp. 593-602
ISSN:
1976-9571
Subject:
Bayesian theory; Eriocheir japonica; Eriocheir sinensis; Japan; Russia; fisheries; genetic analysis; genetic relationships; genetic variation; genomics; habitats; haplotypes; life history; mitochondrial DNA; population genetics; rivers; salinity; secondary contact; temperature; variance; water currents; China; South Korea; Taiwan
Abstract:
... BACKGROUND: The Chinese mitten crab (Eriocheir sinensis) and the Japanese mitten crab (E. japonica) of the family Varunidae, which are also critical fishery species in their native habitats, including China, Japan, and South Korea, exhibit a rare migration life history for the decapod life cycle. Eriocheir sinensis and E. japonica in South Korea may have originated from speciation or secondary con ...
DOI:
10.1007/s13258-021-01198-6

43. Preliminary study of genome-wide association identified novel susceptibility genes for thyroid-related hormones in Chinese population

Author:
Liang Huang; Fenghua Bai; Yutian Zhang; Shanshan Zhang; Tianbo Jin; Xingwei Wei; Xiaoli Zhou; Mei Lin; Yufei Xie; Chanyi He; Qi Lin; Tian Xie; Yipeng Ding
Source:
Genes & genomics 2022 v.44 no.8 pp. 1031-1038
ISSN:
1976-9571
Subject:
Chinese people; blood serum; genomics; genotyping; loci; metabolism
Abstract:
... BACKGROUND: Thyroid hormones are critical regulators of metabolism, development and growth in mammals. However, the genetic association of thyroid-related hormones in the Chinese Han population is not fully understood. OBJECTIVE: We aimed to identify the genetic loci associated with circulating thyroid-related hormones concentrations in the healthy Chinese Han population. METHODS: Genotyping was p ...
DOI:
10.1007/s13258-021-01165-1

44. Prospects and challenges of epigenomics in crop improvement

Author:
Yuhong Huang; Yang Liu; Chang Liu; James A. Birchler; Fangpu Han
Source:
Genes & genomics 2022 v.44 no.3 pp. 251-257
ISSN:
1976-9571
Subject:
chromatin; corn; disease resistance; epigenetics; epigenome; genomics; growth and development; multiomics; rice; wheat
Abstract:
... BACKGROUND: The advent of high-throughput epigenome mapping techniques has ushered in a new era of multiomics with powerful tools now available to map and record genomic output at different levels. Integrating the different components of the epigenome from these multiomics measures allows investigations of cis-regulatory elements on a genome-scale. Mapping of chromatin state, chromatin accessibili ...
DOI:
10.1007/s13258-021-01187-9

45. Protective effect of berberine chloride against cisplatin-induced ototoxicity

Author:
Jong-Heun Kim; Jeong-In Baek; In-Kyu Lee; Un-Kyung Kim; Ye-Ri Kim; Kyu-Yup Lee
Source:
Genes & genomics 2022 v.44 no.1 pp. 1-7
ISSN:
1976-9571
Subject:
DNA fragmentation; antioxidant activity; apoptosis; berberine; caspase-3; cell viability; chlorides; cisplatin; colitis; dementia; diabetes; fluorescent antibody technique; genomics; mice; mitochondria; mitochondrial membrane; ototoxicity; oxidative stress; protective effect; reactive oxygen species; therapeutics
Abstract:
... BACKGROUND: Cisplatin (CP) is an effective anticancer drug broadly used for various types of cancers, but it has shown ototoxicity that results from oxidative stress. Berberine has been reported for its anti-oxidative stress suggesting its therapeutic potential for many diseases such as colitis, diabetes, and vascular dementia. OBJECTIVE: Organ of Corti of postnatal day 3 mouse cochlear explants w ...
DOI:
10.1007/s13258-021-01157-1

46. Protocadherin alpha 3 inhibits lung squamous cell carcinoma metastasis and epithelial-mesenchymal transition

Author:
Yu Tao; Liu Fei; Liu Chang; Liu Yongyu; Jia Jianhui; Liu Yanan; Ren Yi
Source:
Genes & genomics 2022 v.44 no.2 pp. 211-218
ISSN:
1976-9571
Subject:
Western blotting; biomarkers; cadherins; cell cycle; cell proliferation; epithelium; fibronectins; genomics; lungs; metastasis; plasmids; prognosis; squamous cell carcinoma; therapeutics; transfection; vimentin
Abstract:
... BACKGROUND: Lung squamous cell carcinoma (LUSC) is associated with poor clinical prognosis and lacks available targeted therapy. Given that the major threat of cancer is metastasis, delineation of the molecular mechanism underlying it would help devise therapeutic strategies. OBJECTIVE: To investigate the functional role of protocadherin alpha 3 (PCDHA3) in LUSC, as well as investigate the underly ...
DOI:
10.1007/s13258-021-01113-z

47. RBBP4 plays a vital role in the malignant progression of triple-negative breast cancer by regulating epithelial-mesenchymal transition

Author:
Zitong Zheng; Xu Yao; Yi Liu
Source:
Genes & genomics 2022 v.44 no.10 pp. 1301-1309
ISSN:
1976-9571
Subject:
biomarkers; breast neoplasms; carcinogenesis; genomics; models; xenotransplantation
Abstract:
... BACKGROUND: Mounting findings have revealed the increasingly appreciated functional importance of Retinoblastoma binding protein (RBBP) family members in tumorigenesis. However, the biological function of RBBP4 in breast cancer, especially in the most malignant and aggressive subtype, i.e., triple-negative breast cancer (TNBC), remains to be elucidated. OBJECTIVE: The present study was aimed at el ...
DOI:
10.1007/s13258-022-01262-9

48. RPTOR methylation in the peripheral blood and breast cancer in the Chinese population

Author:
Yifei Yin; Shuifang Lei; Lixi Li; Xiaoqin Yang; Qiming Yin; Tian Xu; Wenjie Zhou; Hong Li; Wanjian Gu; Fei Ma; Rongxi Yang; Zhengdong Zhang
Source:
Genes & genomics 2022 v.44 no.4 pp. 435-443
ISSN:
1976-9571
Subject:
DNA; DNA methylation; blood; breast neoplasms; females; genomics; mass spectrometry; postmenopause; regression analysis; risk factors
Abstract:
... BACKGROUND: Altered regulatory-associated protein of mTOR, complex 1 (RPTOR) methylation levels in peripheral blood was originally discovered as breast cancer (BC)-associated risk factor in Caucasians. OBJECTIVE: To explore the relationship between RPTOR methylation and BC in the Chinese population, we conducted two independent case–control studies. METHODS: Peripheral blood samples were collected ...
DOI:
10.1007/s13258-021-01182-0

49. Rapid identification of SARS-CoV-2 in the point-of-care using digital PCR-based Dr. PCR™ Di20K COVID-19 Detection Kit without viral RNA extraction

Author:
Wonseok Shin; Cherl-Joon Lee; Yong-Moon Lee; Young-Bong Choi; Seyoung Mun; Kyudong Han
Source:
Genes & genomics 2022 v.44 no.5 pp. 617-628
ISSN:
1976-9571
Subject:
COVID-19 infection; RNA; Severe acute respiratory syndrome coronavirus 2; biosafety; diagnostic sensitivity; genomics; pandemic; polymerase chain reaction
Abstract:
... BACKGROUND: Since COVID-19 was declared the pandemic by the WHO, it has continued to spread. There is a need for rapid, efficient, and accurate diagnostic kits and techniques to control its spread. OBJECTIVE: The diagnostic capability of the qRT-PCR-based Real-Q 2019-nCoV Detection Kit and dPCR-based Dr. PCR™ Di20K COVID-19 Detection Kit was compared and evaluated. METHODS: Diagnostic tests for CO ...
DOI:
10.1007/s13258-022-01242-z

50. Relative contributions of the host genome, microbiome, and environment to the metabolic profile

Author:
Kangjin Kim; Yunhwan Lee; Sungho Won
Source:
Genes & genomics 2022 v.44 no.9 pp. 1081-1089
ISSN:
1976-9571
Subject:
cardiovascular diseases; glucose; heritability; high density lipoprotein cholesterol; lifestyle; metabolic syndrome; metagenomics; microbiome; models; phenotype; phenotypic variation; prediction; risk factors; sample size; statistical analysis; waist circumference; waist-to-hip ratio
Abstract:
... BACKGROUND: Metabolic syndrome is as a well-known risk factor for cardiovascular disease, which is associated with both genetic and environmental factors. Recently, the microbiome composition has been shown to affect the development of metabolic syndrome. Thus, it is expected that the complex interplay among host genetics, the microbiome, and environmental factors could affect metabolic syndrome. ...
DOI:
10.1007/s13258-022-01277-2

51. SmGDB: genome database of Salvia miltiorrhiza, an important TCM Plant

Author:
Changhao Zhou; Caicai Lin; Piyi Xing; Xingfeng Li; Zhenqiao Song
Source:
Genes & genomics 2022 v.44 no.6 pp. 699-707
ISSN:
1976-9571
Subject:
Salvia miltiorrhiza; bioinformatics; computer software; databases; genomics; metabolism; multigene family; nucleotide sequences; sequence analysis
Abstract:
... BACKGROUND: Salvia miltiorrhiza is an important traditional Chinese medicinal (TCM) plant and a model plant in the genetic study of TCM. A series of omics related to Danshen have been published. Integrating, managing, storing, and sharing data has become an urgent problem to be solved in S. miltiorrhiza genetic studies. OBJECTIVES: The genome database is the link for the exchange, acquisition, and ...
DOI:
10.1007/s13258-022-01251-y

52. Transcriptome analysis reveals putative pathogenesis genes in Alternaria panax during infecting Panax notoginseng leaves

Author:
Taif Shah; Diqiu Liu; XiuMing Cui
Source:
Genes & genomics 2022 v.44 no.7 pp. 855-866
ISSN:
1976-9571
Subject:
Alternaria panax; Panax notoginseng; biosynthesis; catalytic activity; cell walls; cytochrome P-450; databases; etiological agents; gene expression regulation; genomics; ligases; nonribosomal peptides; pathogenesis; pathogenicity; starch; sucrose; transcriptome; transcriptomics; unigenes
Abstract:
... BACKGROUND: Alternaria panax is the causative agent of black spot disease in Panax notoginseng, which causes significant yield loss. However, the molecular mechanisms underlying its pathogenicity remain mostly unknown. OBJECTIVE: We sequenced the transcriptome of A. panax during infecting P. notoginseng leaves using next-generation RNA-seq to understand the molecular aspects of black spot disease. ...
DOI:
10.1007/s13258-022-01241-0

53. Transcriptomic analysis reveal the responses of dendritic cells to VDBP

Author:
Biwei Cao; Tao Wen; Meng Wei; Yuan Xiong; Wan Liu; Li Zhu; Jing Zhou
Source:
Genes & genomics 2022 v.44 no.10 pp. 1271-1282
ISSN:
1976-9571
Subject:
RNA; antigens; apoptosis; cell cycle; cell lines; cell-mediated immunity; flow cytometry; gene expression regulation; gene overexpression; genes; genomics; innate immunity; sequence analysis; transcriptomics; viability
Abstract:
... BACKGROUND: Vitamin D binding protein (VDBP) is an essential plasma carrier protein, which plays possible roles in reproductive health, disease and so on. However, the effects of VDBP on immunity have not been fully studied and the pertinent literatures remain very limited. OBJECTIVE: In this study, we introduced the exogenous VDBP into DC2.4 and established a stable DC2.4/VDBP cell line to explor ...
DOI:
10.1007/s13258-022-01234-z

54. Transethnic meta-analysis of exome-wide variants identifies new loci associated with male-specific metabolic syndrome

Author:
Ho-Sun Lee; Boram Kim; Taesung Park
Source:
Genes & genomics 2022 v.44 no.5 pp. 629-636
ISSN:
1976-9571
Subject:
cholesteryl ester transfer protein; genes; genomics; genotype; humans; meta-analysis; metabolic syndrome; regression analysis
Abstract:
... BACKGROUND: Metabolic syndrome (MetS) is a group of very common human conditions promoting strong understand the impact of rare variants, beyond exome-wide association studies, to potentially discover causative variants, across different ethnic populations. OBJECTIVE: We performed transethnic, exome-wide MetS association studies on MetS in men. METHODS: We analyzed genotype data of 5302 European s ...
DOI:
10.1007/s13258-021-01214-9

55. Tripartite Motif Containing 3 inhibits the aggressive behaviors of papillary thyroid carcinoma and indicates lower recurrence risk

Author:
Yubao Song; Zefeng Gao; Zhifeng Yan; Caihong Zheng
Source:
Genes & genomics 2022 v.44 no.4 pp. 455-465
ISSN:
1976-9571
Subject:
biomarkers; cadherins; carcinoma; cell proliferation; cyclins; genomics; lymph nodes; metastasis; multivariate analysis; prognosis; risk; therapeutics; thyroid neoplasms; vimentin
Abstract:
... BACKGROUND: Tripartite Motif Containing 3 (TRIM3) has been reported to be downregulated in several malignancies. However, its prognostic significance in thyroid cancer remains unknown. OBJECTIVE: Here we aimed to investigate TRIM3’s expression and its involvement in papillary thyroid carcinoma (PTC). METHODS: Clinicopathological analyses were performed in patients with PTC. Expression of TRIM3 pro ...
DOI:
10.1007/s13258-021-01197-7

56. Ubiquitin specific peptidase 47 promotes proliferation of lung squamous cell carcinoma

Author:
Lin Yu; Jiayu Fu; Chunjian Shen
Source:
Genes & genomics 2022 v.44 no.6 pp. 721-731
ISSN:
1976-9571
Subject:
beta catenin; breast neoplasms; chi-square distribution; colorectal neoplasms; genomics; hospitals; immunohistochemistry; lungs; prognosis; resection; squamous cell carcinoma; ubiquitin; xenotransplantation
Abstract:
... BACKGROUND: Ubiquitin specific peptidase 47 (USP47) is a kind of deubiquitinase, which has been reported to play oncogenic roles in several malignancies including colorectal cancer and breast cancer. OBJECTIVE: Here we aimed to investigate the clinical significance of USP47 in lung squamous cell carcinoma (LUSC). METHODS: We retrospectively enrolled a cohort of LUSC patients who underwent surgical ...
DOI:
10.1007/s13258-022-01233-0

57. VDR mediated HSD3B1 to regulate lipid metabolism and promoted testosterone synthesis in mouse Leydig cells

Author:
Zhen Xue; Jianan Zhuang; Hao Bai; Ling Wang; Hongzhao Lu; Shanshan Wang; Wenxian Zeng; Tao Zhang
Source:
Genes & genomics 2022 v.44 no.5 pp. 583-592
ISSN:
1976-9571
Subject:
Western blotting; bioluminescence assay; blood serum; cell culture; enzyme-linked immunosorbent assay; enzymes; genomics; lipid metabolism; mice; osteoporosis; proteome; quantitative polymerase chain reaction; testosterone; transcription (genetics)
Abstract:
... BACKGROUND: The vitamin D receptor (VDR) mediates the pleiotropic biological actions that include osteoporosis, immune responses and androgen synthesis wherein the VDR transcriptionally regulates expression of the genes involved in this complex process. 3β-Hydroxysteroid dehydrogenase-1 (HSD3B1) is an absolutely necessary enzyme for androgen synthesis. OBJECTIVE: The purpose of the present study w ...
DOI:
10.1007/s13258-022-01232-1

58. Whole-genome sequencing revealed different demographic histories among the Korean endemic hill pigeon (Columba rupestris), rock pigeon (Columba livia var. domestica) and oriental turtle dove (Streptopelia orientalis)

Author:
Jung A. Kim; Beom-Soon Choi; Nam-Soo Kim; Seung-Gu Kang; Jin-Young Park; Yong-Gu Yeo; Ju-Hee Bae; Ju-Hee Lee; Taeyoung Um; Ik-Young Choi; Junghwa An
Source:
Genes & genomics 2022 v.44 no.10 pp. 1231-1242
ISSN:
1976-9571
Subject:
Columba livia; Columba rupestris; Streptopelia orientalis; color; copy number variation; effective population size; endangered species; genome; genomics; pigeons; plumage; population dynamics; sequence alignment; turtles; Korean Peninsula
Abstract:
... BACKGROUND: The family Columbidae is known as the pigeon family and contains approximately 351 species and 50 genera. Compared to the wealth of biological and genomic information on these Columba livia var. domesteca, information on Columba rupestris and Streptopelia orientalis has been rather limited. The C. rupestris population size is decreasing in Korea. OBJECTIVES: Whole-genome sequencing and ...
DOI:
10.1007/s13258-022-01288-z

59. The association study between CYP20A1, CYP4F2, CYP2D6 gene polymorphisms and coronary heart disease risk in the Han population in southern China

Author:
Tiebiao Liang; Anshan Liang; Xianbo Zhang; Qi Wang; Haiqing Wu; Jun He; Tianbo Jin
Source:
Genes & genomics 2022 v.44 no.9 pp. 1125-1135
ISSN:
1976-9571
Subject:
coronary disease; drug therapy; experimental design; genes; genomics; human health; humans; pharmacokinetics; regression analysis; risk; China
Abstract:
... BACKGROUND: Coronary heart disease (CHD) is a disease that seriously harms human health. Genetic factors seriously affect the CHD susceptibility. The CYP20A1, CYP4F2 and CYP2D6 are important drug metabolism enzymes in the human body. OBJECTIVE: We aimed to explore the association between CYP20A1, CYP4F2, CYP2D6 single nucleotide polymorphisms (SNPs) and CHD risk in the Chinese Southern Han populat ...
DOI:
10.1007/s13258-021-01125-9

60. The inflammatory signature in monocytes of Sjögren’s syndrome and systemic lupus erythematosus, revealed by the integrated Reactome and drug target analysis

Author:
Kyung Eun Lee; Seyoung Mun; Song-mi Kim; Wonseok Shin; Won Jung; Joon Paek; Jungnam Lee; Erin Hudson; Wesley H. Reeves; Kyudong Han; Seunghee Cha
Source:
Genes & genomics 2022 v.44 no.10 pp. 1215-1229
ISSN:
1976-9571
Subject:
complement; cytokines; drugs; gene expression regulation; gene ontology; genomics; inflammation; lupus erythematosus; macrophages; monocytes; pathogenesis; prostaglandin synthase; sequence analysis; therapeutics; transcriptomics; viruses
Abstract:
... BACKGROUND: The innate immune regulation, especially by the type I IFN signature in the CD14+ monocytes, is known to be critical in the pathogenesis of autoimmune Sjögren’s syndrome (SjS) and systemic lupus erythematosus (SLE). OBJECTIVE: Since patients with one condition can be overlapped with another, this study is to identify shared differentially expressed genes (DEGs) in SjS and SLE compared ...
DOI:
10.1007/s13258-022-01308-y

61. The long non-coding RNA UPAT promotes gastric cancer cell progression via UHRF1

Author:
Chaoyong Liu; De Hao; Minghua Ai; Yan Zhang; Jie Li; Chao Xu
Source:
Genes & genomics 2022 v.44 no.10 pp. 1283-1300
ISSN:
1976-9571
Subject:
RING finger domains; Western blotting; apoptosis; caspase-3; cell cycle; cell proliferation; cell viability; cyclins; flow cytometry; neoplasm cells; non-coding RNA; stomach neoplasms
Abstract:
... BACKGROUND: LncRNA ubiquitin-like with PHD and RING finger domains 1 (UHRF1) protein associated transcript (UPAT) regulates the progression of many cancers. However, its role in gastric cancer (GC) is less frequently reported. OBJECTIVE: In the context of the promoting effect of lncRNA on modulating GC progression, detailed insights into the role and underlying mechanism of UPAT in GC are the foot ...
DOI:
10.1007/s13258-022-01235-y

62. microRNA profiles of serum exosomes derived from children with nonalcoholic fatty liver

Author:
Jian-Wei Zhang; Hai-Tao Pan
Source:
Genes & genomics 2022 v.44 no.7 pp. 879-888
ISSN:
1976-9571
Subject:
alcohol drinking; biomarkers; blood serum; chronic diseases; electron microscopy; exosomes; fatty liver; genomics; liver; microRNA; obesity; patients
Abstract:
... BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) is a chronic disease caused by excessive fat accumulation in the liver in addition to alcohol consumption and other pathological factors. The incidence of NAFLD is rapidly growing, currently affecting 25% of the world population. Exosomes are extracellular vesicles containing a variety of biological molecules, including microRNAs (miRNAs). OBJEC ...
DOI:
10.1007/s13258-021-01150-8

63. missForest with feature selection using binary particle swarm optimization improves the imputation accuracy of continuous data

Author:
Heejin Jin; Surin Jung; Sungho Won
Source:
Genes & genomics 2022 v.44 no.6 pp. 651-658
ISSN:
1976-9571
Subject:
algorithms; data collection; genomics
Abstract:
... BACKGROUND: Missing data are a common problem in large-scale datasets and its appropriate handling is crucial for data analyses. Missingness can be categorized as (1) missing completely at random (MCAR), (2) missing at random (MAR), and (3) missing not at random (MNAR). Different missingness mechanisms require different imputation strategies. Multiple imputation, an approach for averaging outcomes ...
DOI:
10.1007/s13258-022-01247-8

64. A novel NPHS2 mutation (c.865A > G) identified in a Chinese family with steroid-resistant nephrotic syndrome alters subcellular localization of nephrin

Author:
Na Wu; Yingchuan Zhu; Wenhao Jiang; Yue Song; Lan Yin; Yilu Lu; Dachang Tao; Yunqiang Liu; Yongxin Ma
Source:
Genes & genomics 2022 v.44 no.5 pp. 551-559
ISSN:
1976-9571
Subject:
amino acid substitution; diaphragm; fluorescent antibody technique; genes; genomics; heterozygosity; immunoblotting; mutants; nephrotic syndrome; plasma membrane; precipitin tests
Abstract:
... BACKGROUND: NPHS2 is the causative gene of nephrotic syndrome type 2 (MIM 600995) which often clinically manifests as steroid-resistant nephrotic syndrome (SRNS). The NPHS2 gene encodes a slit diaphragm (SD) associated protein podocin. OBJECTIVE: This study reported a novel disease-causing mutation of NPHS2 in a Chinese family with SRNS. We also investigated the pathogenic mechanism of the variant ...
DOI:
10.1007/s13258-022-01220-5

65. ox-LDL regulates proliferation and apoptosis in VSMCs by controlling the miR-183-5p/FOXO1

Author:
Mingqiang Fan; Yinglong Huang; Kunsheng Li; Xiangxiang Yang; Jing Bai; Qiaoke Si; Zhengfei Peng; Chunwen Jia; Qiangnu Zhang; Ding Tao
Source:
Genes & genomics 2022 v.44 no.6 pp. 671-681
ISSN:
1976-9571
Subject:
Western blotting; aorta; apoptosis; atherosclerosis; bioluminescence assay; blood serum; flow cytometry; genomics; low density lipoprotein; microRNA; oxidation; smooth muscle; transcriptome
Abstract:
... BACKGROUND: microRNA–mRNA axes that are involved in oxidized low-density lipoprotein (ox-LDL)-induced vascular smooth muscle cells (VSMCs) proliferation/apoptosis imbalance need to be further investigated. OBJECTIVE: To investigate the functional role of miR-183-5p/FOXO1 in VSMCs and its interaction with ox-LDL. METHODS: RNA sequencing was used to detect transcriptome changes of VSMCs treated with ...
DOI:
10.1007/s13258-022-01236-x

66. The relationship between polymorphism of insulin-like growth factor I gene and susceptibility to type 2 diabetes in Uygur population, Xinjiang, China

Author:
Tingting Wang; Gulixiati Maimaitituersun; Haonan Shi; Cheng Chen; Qi Ma; Yinxia Su; Hua Yao; Jia Zhu
Source:
Genes & genomics 2022 v.44 no.4 pp. 499-508
ISSN:
1976-9571
Subject:
alleles; gene interaction; genomics; genotype; genotyping; loci; models; noninsulin-dependent diabetes mellitus; pathogenesis; risk; single nucleotide polymorphism; China
Abstract:
... BACKGROUND: Type 2 diabetes (T2DM) susceptibility varies among different populations and is affected by gene single nucleotide polymorphism (SNP). Insulin-like growth factor (IGF)-1 gene, which has many SNP loci, is involved in T2DM pathogenesis. However, the relationship of IGF-1 gene polymorphism with T2DM in Uyghur population is less studied. OBJECTIVE: To investigate the relationship between T ...
DOI:
10.1007/s13258-021-01209-6

67. Aberrant methylation of the 16q23.1 tumor suppressor gene ADAMTS18 promotes tumorigenesis and progression of clear cell renal cell carcinoma

Author:
Ben Xu; Yi-ji Peng; Bing-lei Ma; Si-da Cheng
Source:
Genes & genomics 2021 v.43 no.2 pp. 123-131
ISSN:
1976-9571
Subject:
carcinogenesis; cell viability; flow cytometry; genomics; immunohistochemistry; methylation; renal cell carcinoma; reverse transcriptase polymerase chain reaction; tumor suppressor genes
Abstract:
... BACKGROUND: The 16q23.1 tumor suppressor gene (TSG) of ADAMTS18 has been identified to be aberrant methylated in clear cell renal cell carcinoma (ccRCC), and there still exists an unclear situation between its methylation and the progression of ccRCC. OBJECTIVE: To analyze the biological function and mechanism of ADAMTS18 gene in the tumorigenesis and progression of ccRCC. METHODS: We examined ADA ...
DOI:
10.1007/s13258-021-01036-9

68. Alleles disrupting LBD37-like gene by an 136 bp insertion show different distributions between green and purple cabbages (Brassica oleracea var. capitata)

Author:
Ju Young Ahn; Yi Hyun Jung; Hayoung Song; Hankuil Yi; Yoonkang Hur
Source:
Genes & genomics 2021 v.43 no.6 pp. 679-688
ISSN:
1976-9571
Subject:
Arabidopsis thaliana; Brassica oleracea var. capitata; DNA; alleles; anthocyanins; biosynthesis; cabbage; exons; genomics; heterozygosity; homozygosity; nitrogen; reverse transcription
Abstract:
... BACKGROUND: In Arabidopsis thaliana (Arabidopsis), clade IIb lateral organ boundary domain (LBD) 37, 38, and 39 proteins negatively regulate anthocyanin biosynthesis and affect nitrogen responses. OBJECTIVE: To investigate the possible role of LBD genes in anthocyanin accumulations among green and purple cabbages (Brassica oleracea var. capitata), we determined sequence variations and expression l ...
DOI:
10.1007/s13258-021-01087-y

69. Analysis of protein determinants of host‐specific infection properties of polyomaviruses using machine learning

Author:
Myeongji Cho; Hayeon Kim; Hyeon S. Son
Source:
Genes & genomics 2021 v.43 no.4 pp. 407-420
ISSN:
1976-9571
Subject:
Polyomaviridae; amino acid composition; amino acids; birds; coat proteins; data collection; fish; genomics; host range; host specificity; hosts; hydrophobicity; mammals; neoplasm antigens; phylogeny; solvents; van der Waals forces
Abstract:
... BACKGROUND: The large tumor antigen (LT-Ag) and major capsid protein VP1 are known to play important roles in determining the host-specific infection properties of polyomaviruses (PyVs). OBJECTIVE: The objective of this study was to investigate the physicochemical properties of amino acids of LT-Ag and VP1 that have important effects on host specificity, as well as classification techniques used t ...
DOI:
10.1007/s13258-021-01059-2

70. Association of a novel antisense lncRNA TP73-AS1 polymorphisms and expression with colorectal cancer susceptibility and prognosis

Author:
Jiayao Fan; Huiqing Xu; Bing Liu; Fangyuan Jing; Qingfang He; Shasha Zheng; Haining Shi; Lefei Jiao; Chunhong Fan
Source:
Genes & genomics 2022 v.44 no.7 pp. 889-897
ISSN:
1976-9571
Subject:
bioinformatics; carcinogenesis; case-control studies; cell proliferation; colorectal neoplasms; confidence interval; gender; genomics; hazard ratio; heterozygosity; metastasis; models; non-coding RNA; odds ratio; prognosis; risk
Abstract:
... BACKGROUND: TP73-AS1 is a novel antisense long noncoding RNA and plays an important role in cell proliferation and cancer development. However, the link between TP73-AS1 and colorectal cancer (CRC) has not yet been reported. OBJECTIVE: To explore the association of genetic variants in TP73-AS1 and its expression with CRC susceptibility and prognosis. METHODS: A case–control study (including 507 CR ...
DOI:
10.1007/s13258-021-01161-5

71. Association of genetic variants of RNF213 with ischemic stroke risk in Koreans

Author:
Young Seok Park; Hyeon Woo Park; Han Sung Park; Chang Soo Ryu; Jeong Yong Lee; Eun Ju Ko; Jung Hoon Sung; Jinkwon Kim; Ok Joon Kim; Nam Keun Kim
Source:
Genes & genomics 2021 v.43 no.4 pp. 389-397
ISSN:
1976-9571
Subject:
alleles; databases; genomics; haplotypes; humans; restriction fragment length polymorphism; risk; stroke
Abstract:
... BACKGROUND: Large artery disease (LAD), cardioembolism (CE), and small vessel disease (SVD) are well-established causes of ischemic stroke. Although a founder variant of RNF213 has been regarded a genetic susceptibility for Moyamoya disease (MMD) and certain types of intracranial atherosclerotic stenosis (ICAS), correlations between RNF213 variants and ischemic stroke with SVD remain largely unkno ...
DOI:
10.1007/s13258-020-01022-7

72. Autophagy induced by H. pylori VacA regulated the survival mechanism of the SGC7901 human gastric cancer cell line

Author:
Juan Luo; Luyan Bai; Jun Tao; Yu Wen; Mingke Li; Yunzhen Zhu; Sufeng Luo; Guangyu Pu; Lanqing Ma
Source:
Genes & genomics 2021 v.43 no.10 pp. 1223-1230
ISSN:
1976-9571
Subject:
Helicobacter pylori; Western blotting; acetylcysteine; apoptosis; autophagy; cytotoxins; gene expression; genomics; humans; mitochondria; neoplasm cells; reactive oxygen species; stomach neoplasms; virulence
Abstract:
... BACKGROUND: Vacuolating cytotoxin (VacA) is an important virulence factor of Helicobacter pylori (H. pylori). It was previously believed that VacA can trigger the cascade of apoptosis on mitochondria to lead to cell apoptosis. Recently, it was found that VacA can induce autophagy. However, the molecular mechanism by which VacA induces autophagy is largely unknown. OBJECTIVE: We aimed to explore th ...
DOI:
10.1007/s13258-021-01151-7

73. BAIAP2L2 facilitates the malignancy of prostate cancer (PCa) via VEGF and apoptosis signaling pathways

Author:
Yuanzi Song; Guishan Zhuang; Jiazhen Li; Mingqing Zhang
Source:
Genes & genomics 2021 v.43 no.4 pp. 421-432
ISSN:
1976-9571
Subject:
RNA; Western blotting; angiogenesis; apoptosis; biomarkers; carcinogenesis; cell proliferation; databases; genes; genomics; males; prognosis; prostatic neoplasms; regression analysis
Abstract:
... BACKGROUND: Prostate cancer (PCa) is the second most common type of male cancer in western. Despite key roles of brain-specific angiogenesis inhibitor 1-associated protein like 2 (BAIAP2L2) in several cancers, the function of BAIAP2L2 in PCa is never reported. OBJECTIVE: We aimed to investigate the role of BAIAP2L2 in the progression of PCa and decipher the underlying mechanisms. METHODS: RNA sequ ...
DOI:
10.1007/s13258-021-01061-8

74. Baicalin attenuates adriamycin-induced nephrotic syndrome by regulating fibrosis procession and inflammatory reaction

Author:
Ning Tan; Chen-Xia Sun; Hui-Jun Zhu; De-Yu Li; Sheng-Guang Huang; Shou-Di He
Source:
Genes & genomics 2021 v.43 no.9 pp. 1011-1021
ISSN:
1976-9571
Subject:
apoptosis; baicalin; blood platelets; blood serum; creatinine; doxorubicin; fibrosis; gene expression; gene expression regulation; genomics; inflammation; kidneys; models; nephrotic syndrome; oxygen; protein content; rats; therapeutics; transcriptome
Abstract:
... BACKGROUND: Baicalin has anti-inflammatory, antibacterial, blood platelet aggregation-inhibiting, free oxygen radical-clearing, and endotoxin-decreasing properties. However, its molecular mechanism involved in the treatment of Adriamycin-induced nephrotic syndrome (NS) is still unclear. OBJECTIVE: This study aimed to explore the effects of baicalin on Adriamycin-induced nephrotic syndrome (NS) and ...
DOI:
10.1007/s13258-021-01107-x

75. Berberine protects against palmitate induced beta cell injury via promoting mitophagy

Author:
Mo Li; Jiang She; Louyan Ma; Li Ma; Xiaorui Ma; Jiajia Zhai
Source:
Genes & genomics 2022 v.44 no.7 pp. 867-878
ISSN:
1976-9571
Subject:
antioxidants; apoptosis; berberine; cell lines; cell viability; diabetes mellitus; genomics; insulin secretion; islets of Langerhans; membrane potential; mitochondria; mitochondrial membrane; mitophagy; models; oxidative stress; palmitates; protective effect; rodents; therapeutics
Abstract:
... BACKGROUND: Destruction of pancreatic beta cells is the most typical characteristic of diabetes. OBJECTIVE: We aimed to evaluate the effect of berberine (BBR), a bioactive isoquinoline derivative alkaloid, on beta cell injury. METHODS: Rodent pancreatic beta cell line INS-1 was treated with 0.5 mM palmitate (PA) for 24 h to establish an in vitro beta cell injury model. RESULTS: BBR at 5 µM promote ...
DOI:
10.1007/s13258-022-01250-z

76. Bulk segregant analysis identifies SSR markers associated with leaf- and seed-related traits in Perilla crop (Perilla frutescens L.)

Author:
Su Eun Lim; Kyu Jin Sa; Ju Kyong Lee
Source:
Genes & genomics 2021 v.43 no.4 pp. 323-332
ISSN:
1976-9571
Subject:
Perilla frutescens; chromosome mapping; color; computer software; crop quality; genes; genomics; hardness; leaves; marker-assisted selection; microsatellite repeats; phenotype; seed coat; seed size
Abstract:
... BACKGROUND: Bulk segregant analysis (BSA) is another method of identifying significant molecular markers linked to the target gene or region for specific traits. BSA is easier and less expensive than other methods; it does not require genetic map construction and needs fewer markers than the number needed to construct a genetic map for QTL mapping. OBJECTIVES: The purpose of our study was to ident ...
DOI:
10.1007/s13258-021-01056-5

77. CALM1 rs3179089 polymorphism might contribute to coronary artery disease susceptibility in Chinese male: a case–control study

Author:
Jingyan Huang; Siyun Huang; Jinhong Li; Minhua Li; Lin Gong; Tongshun Li; Lian Gu
Source:
Genes & genomics 2022 v.44 no.4 pp. 415-423
ISSN:
1976-9571
Subject:
blood coagulation; blood glucose; blood lipids; blood serum; calmodulin; case-control studies; coronary artery disease; diastolic blood pressure; disease susceptibility; gene expression; genomics; genotype; genotyping; low density lipoprotein cholesterol; males; models; risk; systolic blood pressure
Abstract:
... BACKGROUND: Calmodulin 1 (CALM1) mutations are involved in the development of coronary artery disease (CAD). However, the relationship of CALM1 rs3179089 polymorphism with CAD is unknown. OBJECTIVE: This study aimed to identify the relationship of CALM1 rs3179089 polymorphism with CAD susceptibility, CALM1 expression, blood pressure, blood glucose, blood coagulation and serum lipid levels of CAD p ...
DOI:
10.1007/s13258-021-01144-6

78. CHMP1A suppresses the growth of renal cell carcinoma cells via regulation of the PI3K/mTOR/p53 signaling pathway

Author:
Youping Wu; Yueguo Wu; Cong Xu; Wei Sun; Zhenqiang You; Yin Wang; Sheng Zhang
Source:
Genes & genomics 2022 v.44 no.7 pp. 823-832
ISSN:
1976-9571
Subject:
apoptosis; cell growth; genes; genomics; neoplasm cells; renal cell carcinoma
Abstract:
... BACKGROUND: CHMP1A, a member of the ESCRT-III complex family, has been indicated as a brand-new inhibitor gene of tumors. Our previous research has revealed that CHMP1A plays a vital role in the development and progression of renal cell carcinoma (RCC). OBJECTIVE: To investigate the potential target pathway of the regulation of the tumor cell growth by CHMP1A. METHODS: The effect of CHMP1A on mTOR ...
DOI:
10.1007/s13258-022-01237-w

79. Characteristics of circRNAs expression profiles in the piglets intestine induced by oxidative stress

Author:
Zhi-xin Li; Wei Chen; Ming Qin; Li-xue Wang; Yong-qing Zeng
Source:
Genes & genomics 2022 v.44 no.4 pp. 425-433
ISSN:
1976-9571
Subject:
antioxidants; blood serum; diquat; enzymes; gene expression regulation; genomics; jejunum; microRNA; oxidative phosphorylation; oxidative stress; proteolysis; transcriptome
Abstract:
... BACKGROUD: Oxidative stress (OS) can affect the expression of key genes and destroy the intestinal structure. However, it is unclear how OS regulates the expression of circular RNAs (circRNAs), microRNAs (miRNAs) and mRNAs. OBJECTIVE: The aim of this study was to examine the expression of circRNAs, miRNAs and mRNAs exposed to OS. METHODS: Piglets were exposed to diquat (DQ), a herbicide, and the a ...
DOI:
10.1007/s13258-021-01154-4

80. Characterization of the B cell receptor repertoire of patients with acute coronary syndrome

Author:
Ruiqiang Weng; Sudong Liu; Xiaodong Gu; Zhixiong Zhong
Source:
Genes & genomics 2022 v.44 no.1 pp. 19-28
ISSN:
1976-9571
Subject:
B-lymphocytes; bioinformatics; disease severity; genomics; inflammation; myocardial infarction
Abstract:
... BACKGROUND: Acute coronary syndrome (ACS) is a complex cardiovascular disease whose development involves the dysregulation of adaptive immune responses. Though it has been proven that T cells associate with inflammation in the development of ACS, the function of B cells in disease remains unclear. OBJECTIVE: The aim of this study was to reveal the diversity of the B cell receptor (BCR) repertoire ...
DOI:
10.1007/s13258-021-01110-2

81. CircRNA_OTUD7A upregulates FOXP1 expression to facilitate the progression of diffuse large B-cell lymphoma via acting as a sponge of miR-431-5p

Author:
Wei Liu; Lei Lei; Xiaoying Liu; Suiyan Ye
Source:
Genes & genomics 2021 v.43 no.6 pp. 653-667
ISSN:
1976-9571
Subject:
B-cell lymphoma; Western blotting; apoptosis; bioluminescence assay; cell cycle checkpoints; cell proliferation; circular RNA; cyclins; flow cytometry; genomics; metastasis; microRNA; neoplasm progression; oncogenes; quantitative polymerase chain reaction; toxicity testing
Abstract:
... BACKGROUND: A growing number of studies have shown that circular RNA (circRNA) is an important regulator molecule in cancer progression, but it has been poorly studied in diffuse large b-cell lymphoma (DLBCL). OBJECTIVE: This study aimed to explore the role of circ_OTUD7A in DLBCL. METHODS: Relative expression levels of circ_OTUD7A, microRNA (miR)-431-5p and forkhead box P1 (FOXP1) were determined ...
DOI:
10.1007/s13258-021-01094-z

82. Comparative study of predicted miRNA between Indonesia and China (Wuhan) SARS-CoV-2: a bioinformatics analysis

Author:
Agus Rahmadi; Ismaily Fasyah; Digdo Sudigyo; Arif Budiarto; Bharuno Mahesworo; Alam Ahmad Hidayat; Bens Pardamean
Source:
Genes & genomics 2021 v.43 no.9 pp. 1079-1086
ISSN:
1976-9571
Subject:
COVID-19 infection; Severe acute respiratory syndrome coronavirus 2; bioinformatics; chi-square distribution; comparative study; gene ontology; genes; genomics; humans; immune system; inflammation; microRNA; pandemic; China; Indonesia
Abstract:
... BACKGROUND: Several reports on the discovery of SARS-CoV-2 mutations and variations in Indonesia COVID-19 cases led to genomic dysregulation with the first pandemic cases in Wuhan, China. MicroRNA (miRNA) plays an important role in this genetic regulation and contributes to the enhancement of viral RNA binding through the host mRNA. OBJECTIVE: This research is aimed to detect miRNA targets of SARS ...
DOI:
10.1007/s13258-021-01119-7

83. Comparing of backfat microRNAomes of Landrace and Neijiang pig by high-throughput sequencing

Author:
Yanyue Li
Source:
Genes & genomics 2021 v.43 no.5 pp. 543-551
ISSN:
1976-9571
Subject:
backfat; biomarkers; genes; genomics; landraces; lipid metabolism; lipids; luciferase; microRNA; swine
Abstract:
... BACKGROUND: MicroRNAs (miRNAs) could regulate the expression of target genes and play important roles in modulation of various metabolic processes. Nevertheless, little is known about the backfat microRNAome (miRNAome) of the Neijiang pig. OBJECTIVES: The primary objective of this study was to analyse miRNAomes of Landrace and Neijiang pig backfat (LPB and NPB resp.). Furthermore, investigating di ...
DOI:
10.1007/s13258-021-01078-z

84. Comprehensive analysis of TCR repertoire of COVID-19 patients in different infected stage

Author:
Guangyu Wang; Yongsi Wang; Shaofeng Jiang; Wentao Fan; Chune Mo; Weiwei Gong; Hui Chen; Dan He; Jinqing Huang; Minglin Ou; Xianliang Hou
Source:
Genes & genomics 2022 v.44 no.7 pp. 813-822
ISSN:
1976-9571
Subject:
COVID-19 infection; Severe acute respiratory syndrome coronavirus 2; T-lymphocytes; disease progression; genes; genomics; pandemic; pathogenesis; public health
Abstract:
... BACKGROUND: The current pandemic of coronavirus disease 2019 (COVID-19), transmitted person-to-person by the severe acute respiratory syndrome of coronavirus 2 (SARS-CoV-2), poses a threat to global public health. OBJECTIVE: In this study, we performed the comprehensive analysis of the T cell receptor (TCR) repertoire may contribute to a more in-depth understanding of the pathogenesis of COVID-19. ...
DOI:
10.1007/s13258-022-01261-w

85. Correlation between recurrence of anorectal condyloma acuminatum and human papilloma virus subtype

Author:
Jeong-ki Kim; Yong-Gum Park; Beom Gyu Kim
Source:
Genes & genomics 2022 v.44 no.3 pp. 389-394
ISSN:
1976-9571
Subject:
Human immunodeficiency virus; Papillomaviridae; genomics; histopathology; medical facilities; sexually transmitted diseases; surgery
Abstract:
... BACKGROUND: Anorectal condyloma is the representative venereal disease caused by human papilloma virus (HPV), which has more 180 subtypes. Although there are various known risk factors for recurrence, few studies have investigated the influence of HPV subtypes. OBJECTIVE: We aimed to investigate the correlation between the recurrence of anorectal condyloma and HPV subtypes. METHODS: We analyzed th ...
DOI:
10.1007/s13258-022-01221-4

86. Deduction and exploration of the evolution and function of vertebrate GFPT family

Author:
Si-ang Wei; Ran Xu; Yu-yao Ji; Zhi-wen Ding; Yun-zeng Zou
Source:
Genes & genomics 2022 v.44 no.2 pp. 175-185
ISSN:
1976-9571
Subject:
Danio rerio; Gallus gallus; National Center for Biotechnology Information; Plasmodium relictum; Rattus norvegicus; Rhincodon typus; Trachypithecus francoisi; Xenopus tropicalis; gene ontology; genes; genomics; hexosamines; humans; metabolism; models; nucleic acids; phosphorylation; phylogeny; therapeutics
Abstract:
... BACKGROUND: Glutamine-fructose-6-phosphate aminotransferase (GFPT) is a key factor in the hexosamine metabolism pathway. It regulates the downstream factor O-GlcNAc to change cell function and plays an important role in the metabolism and immune process of tissues and organs. However, the evolutionary relationship of GFPT family proteins in vertebrates has not been elucidated. OBJECTIVE: To deduce ...
DOI:
10.1007/s13258-021-01188-8

87. Defense responses of sulfur dioxygenase to sulfide stress in the razor clam Sinonovacula constricta

Author:
Caifang Chen; Yaoyao Shen; Weiliang Shen; Jing He; Zhihua Lin; Yinghui Dong
Source:
Genes & genomics 2021 v.43 no.5 pp. 513-522
ISSN:
1976-9571
Subject:
Veneroida; Western blotting; genomics; mitochondria; nucleotide sequences; oxidation; prediction; sulfides; sulfur
Abstract:
... BACKGROUND: Sulfide is a well-known toxicant widely distributed in the culture environment. As a representative burrowing benthic bivalve, the razor clam Sinonovacula constricta is highly sulfide tolerant. Mitochondrial sulfide oxidation is an important way for sulfide detoxification, where sulfur dioxygenase (SDO) is the second key enzyme. OBJECTIVE: To investigate the mechanism of sulfide tolera ...
DOI:
10.1007/s13258-021-01077-0

88. Dexmedetomidine targets miR-146a and participates in the progress of chronic obstructive pulmonary disease in vivo and in vitro

Author:
Na Li; Shuangfeng Li; Yehua Wu; Lu Xiong; Tiejun Li; Dandan Xing; Qiuchang Li; Duozhi Wu
Source:
Genes & genomics 2021 v.43 no.12 pp. 1371-1379
ISSN:
1976-9571
Subject:
Western blotting; animal models; apoptosis; blood serum; bronchoconstriction; cell proliferation; death; dexmedetomidine; epithelium; genomics; humans; interleukin-6; quantitative polymerase chain reaction; respiratory tract diseases
Abstract:
... BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a chronic lung disease and the third leading cause of death in the world. Dexmedetomidine has been reported to effectively inhibit histamine-induced bronchoconstriction. However, the molecular mechanism of dexmedetomidine in COPD has not been found. OBJECTIVE: To explore the role and mechanism of dexmedetomidine in COPD, and to provide th ...
DOI:
10.1007/s13258-020-01019-2

89. Differential expression and functional analysis of circRNA in the ovaries of Yili geese at different egg-laying stages

Author:
Xiao-yu Zhao; Ying-ping Wu; Hai-ying Li; Yan Cao; Zhi-yong Mei; Jia-hui Li
Source:
Genes & genomics 2022 v.44 no.10 pp. 1171-1180
ISSN:
1976-9571
Subject:
bioinformatics; biosynthesis; circular RNA; geese; gene expression regulation; genomics; glycerophospholipids; ovarian development; oviposition; phototransduction; vitamin A
Abstract:
... BACKGROUND: Ovarian development is regulated by genes that are expressed dynamically and stage-specifically. Circular RNA (circRNA) has been proven to play a significant role in the regulation of animal reproduction. OBJECTIVE: Studying the expression characteristics of circRNAs in goose ovaries at various egg-laying stages can provide a reference for the molecular regulation mechanism of ovary de ...
DOI:
10.1007/s13258-022-01290-5

90. Disheveled-associated activator of morphogenesis 2 promotes invasion of colorectal cancer by activating PAK1 and promoting MMP7 expression

Author:
Aimei Chen; Zhiqiang Liu; Quanyan Wu; Hailin Li
Source:
Genes & genomics 2021 v.43 no.8 pp. 923-935
ISSN:
1976-9571
Subject:
biomarkers; cell proliferation; colorectal neoplasms; drugs; genomics; immunohistochemistry; morphogenesis; multivariate analysis; prognosis; risk factors
Abstract:
... BACKGROUND: Disheveled-associated activator of morphogenesis (DAAM) family, including DAAM1 and DAAM2, is key regulators in Wnt signaling pathway. Although the oncogenic role of Wnt signaling pathway in colorectal cancer (CRC) was investigated in several lines, the expression and function of DAAM in CRC are still obscure. OBJECTIVE: To investigate the expression and function of DAAM in CRC. METHOD ...
DOI:
10.1007/s13258-021-01111-1

91. Dysregulated lncRNA and mRNA may promote the progression of ischemic stroke via immune and inflammatory pathways: results from RNA sequencing and bioinformatics analysis

Author:
Yingshuang Wang; Feifei Feng; Pingping Zheng; Lijuan Wang; Yanjun Wang; Yaogai Lv; Li Shen; Kexin Li; Tianyu Feng; Yang Chen; Zhigang Liu; Yan Yao
Source:
Genes & genomics 2022 v.44 no.1 pp. 97-108
ISSN:
1976-9571
Subject:
antigens; bioinformatics; blood; epigenetics; gene expression regulation; genomics; herpes simplex; humans; inflammation; influenza; stroke; transcription (genetics)
Abstract:
... BACKGROUND: Long non-coding RNAs (lncRNAs) are widely involved in gene transcription regulation and which act as epigenetic modifiers in many diseases. OBJECTIVE: To determine whether lncRNAs are involved in ischemic stroke (IS), we analyzed the expression profile of lncRNAs and mRNAs in IS. METHODS: RNA sequencing was performed on the blood of three pairs of IS patients and healthy controls. Diff ...
DOI:
10.1007/s13258-021-01173-1

92. EGR1 promotes stemness and predicts a poor outcome of uterine cervical cancer by inducing SOX9 expression

Author:
Juanhong Zhao; Haixia Li; Miao Yuan
Source:
Genes & genomics 2021 v.43 no.5 pp. 459-470
ISSN:
1976-9571
Subject:
biomarkers; chi-square distribution; drugs; genomics; immunohistochemistry; transcription factors; uterine cervical neoplasms
Abstract:
... BACKGROUND: Early growth response-1 (EGR1) is a transcription factor involved in the progression of several cancer types. However, the expression and clinical significance of EGR1 in uterine cervical cancer (CC) have not been elucidated. OBJECTIVE: To investigate the expression, clinical significance and prognostic value of EGR1 in CC. METHODS: The expression of EGR1 was detected in 13 CCs and pai ...
DOI:
10.1007/s13258-021-01064-5

93. Effects of thymosin β4-derived peptides on migration and invasion of ovarian cancer cells

Author:
Hyung Joon Yoon; Young Lim Oh; Eun-Ji Ko; Ahyun Kang; Wan Kyu Eo; Ki Hyung Kim; Ji Young Lee; Ari Kim; Sungwook Chun; Hongbae Kim; Mee Sun Ock; Hee-Jae Cha
Source:
Genes & genomics 2021 v.43 no.8 pp. 987-993
ISSN:
1976-9571
Subject:
Western blotting; actin; cell movement; cell proliferation; genomics; metastasis; neoplasm cells; ovarian neoplasms; synthetic peptides; thymosin
Abstract:
... BACKGROUND: Thymosin β4 (Tβ4) is a highly conserved actin binding protein associated with the metastatic potential of tumor cells by stimulating cell migration. The role of Tβ4 and its derived fragment peptides in migration of ovarian cancer cells has not been studied. OBJECTIVE: To analyze the effects of Tβ4 and its derived fragment peptides on ovarian cancer cell migration and invasion, we appli ...
DOI:
10.1007/s13258-021-01127-7

94. Efficacy of reduced-size short tandem repeat PCR analysis for degraded DNA samples

Author:
Jeongyong Kim; Hyojeong Kim; Youn-Hyoung Nam; Ja Hyun Lee; Hyo Sook Kim; Eungsoo Kim
Source:
Genes & genomics 2021 v.43 no.7 pp. 749-758
ISSN:
1976-9571
Subject:
DNA; alleles; forensic sciences; genomics; humans; loci; microsatellite repeats; polymerase chain reaction
Abstract:
... BACKGROUND: Short tandem repeats (STR) typing is an essential analysis method for human identification in forensic field. When DNAs obtained from the field as evidences are severely degraded or in too small amounts, STR analysis often shows allele drop-out. OBJECTIVE: To improve STR analysis for degraded DNA or trace DNA, reduced-size STR (rSTR) polymerase chain reaction (PCR) system was devised b ...
DOI:
10.1007/s13258-021-01066-3

95. Emerging roles of centromeric RNAs in centromere formation and function

Author:
Qian Liu; Yang Liu; Qinghua Shi; Handong Su; Chunhui Wang; James A. Birchler; Fangpu Han
Source:
Genes & genomics 2021 v.43 no.3 pp. 217-226
ISSN:
1976-9571
Subject:
DNA; chromosome segregation; epigenetics; genomics; heterochromatin; humans; kinetochores; nucleotide sequences; yeasts
Abstract:
... BACKGROUND: Centromeres are specialized chromosomal domains involved in kinetochore formation and faithful chromosome segregation. Despite a high level of functional conservation, centromeres are not identified by DNA sequences, but by epigenetic means. Universally, centromeres are typically formed on highly repetitive DNA, which were previously considered to be silent. However, recent studies hav ...
DOI:
10.1007/s13258-021-01041-y

96. Epigenetic control of centromere: what can we learn from neocentromere?

Author:
Taekyung Kim
Source:
Genes & genomics 2022 v.44 no.3 pp. 317-325
ISSN:
1976-9571
Subject:
DNA; epigenetics; genomics; heterochromatin; humans; kinetochores; meiosis; mitosis
Abstract:
... BACKGROUND: The centromere is the special region on a chromosome, which serves as the site for assembly of kinetochore complex and is essential for maintaining genomic integrity. Neocentromeres are new centromeres that form on the non-centromeric regions of the chromosome when the natural centromere is disrupted or inactivated. Although neocentromeres lack the typical features found in centromeres ...
DOI:
10.1007/s13258-021-01193-x

97. Epigenetic inactivation of ACAT1 promotes epithelial-mesenchymal transition of clear cell renal cell carcinoma

Author:
Peipei Han; Shu Wu; Limei Li; Danping Li; Jun Zhao; Haishan Zhang; Yifang Wang; Xuemin Zhong; Zhe Zhang; Ping Li; Liudmila Matskova; Xiaoying Zhou
Source:
Genes & genomics 2022 v.44 no.4 pp. 487-497
ISSN:
1976-9571
Subject:
Internet; acetyl coenzyme A; biomarkers; cadherins; databases; epigenetics; epithelial cell adhesion molecule; genomics; histology; kidneys; meta-analysis; metastasis; methylation; microRNA; mitochondria; promoter regions; renal cell carcinoma; secretion; vimentin
Abstract:
... BACKGROUND: Acetyl-CoA acyltransferase 1 (ACAT1) is a key enzyme catalyzing the production of mitochondrial ketone bodies. We have shown that ACAT1 is down-regulated in kidney renal clear cell carcinoma (KIRC) previously. OBJECTIVE: To investigate the reasons for downregulation of ACAT1 in KIRC and explore the underlying mechanisms involved in metastatic inhibition regulated by ACAT1. METHODS: The ...
DOI:
10.1007/s13258-021-01211-y

98. Epigenome editing: targeted manipulation of epigenetic modifications in plants

Author:
Hosub Shin; Woo Lee Choi; Joo Young Lim; Jin Hoe Huh
Source:
Genes & genomics 2022 v.44 no.3 pp. 307-315
ISSN:
1976-9571
Subject:
DNA methylation; cell differentiation; chromatin; crops; disease resistance; epigenetics; epigenome; gene expression; genes; genomics; histones; meiosis; mitosis; nucleotide sequences; phenotype; stress tolerance; therapeutics
Abstract:
... BACKGROUND: Epigenetic modifications play important roles in diverse cellular processes such as X chromosome inactivation, cell differentiation, development and senescence. DNA methylation and histone modifications are major epigenetic modifications that regulate chromatin structure and gene expression without DNA sequence changes. Epigenetic alterations may induce phenotypic changes stable enough ...
DOI:
10.1007/s13258-021-01199-5

99. Epigenomic and transcriptomic analysis of chronic inflammatory diseases

Author:
Sabrina Ka Man Tam; Danny Chi Yeu Leung
Source:
Genes & genomics 2021 v.43 no.3 pp. 227-236
ISSN:
1976-9571
Subject:
epigenetics; epigenome; etiology; gene expression; genomics; inflammation; transcription (genetics); transcriptomics
Abstract:
... Chronic inflammatory diseases (CIDs) have complex pathologies that result from aberrant and persistent immune responses. However, the precise triggers and mechanisms remain elusive. An important aspect of CID research focuses on epigenetics modifications, which regulate gene expression and provide a dynamic transcriptional response to inflammation. In recent years, mounting evidence has demonstrat ...
DOI:
10.1007/s13258-021-01045-8

100. Establishment and validation of five autophagy-related signatures for predicting survival and immune microenvironment in glioma

Author:
Zijun Zhao; Yue Wu; Zairan Wang; Jiayi Xu; Yizheng Wang; Zongmao Zhao
Source:
Genes & genomics 2022 v.44 no.1 pp. 79-95
ISSN:
1976-9571
Subject:
DNA repair; RNA; at-risk population; autophagy; carcinogenesis; central nervous system; genomics; glioblastoma; hypoxia; immune response; immunosuppression; models; prognosis; protein-protein interactions; regression analysis; risk; therapeutics
Abstract:
... BACKGROUND: Gliomas, especially Glioblastoma multiforme, are the most frequent type of primary tumors in central nervous system. Increasing researches have revealed the relationship between autophagy and tumor, while the molecular mechanism of autophagy in glioma is still rarely reported. OBJECTIVE: Our research aims to conform the autophagy-related genes (ARGs) implicated in the development and p ...
DOI:
10.1007/s13258-021-01172-2