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You searched for: Subject "gene ontology" Remove constraint Subject: "gene ontology"
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1. Analysis of the long noncoding RNA profiles of RD and SH-SY5Y cells infected with coxsackievirus B5, using RNA sequencing

Author:
Peiying Teng; Heng Yang; Jing Li; Fan Yang; Wei Chen
Source:
Archives of virology 2022 v.167 no.2 pp. 367-376
ISSN:
0304-8608
Subject:
gene ontology,   etc   ; humans; mouth; non-coding RNA; virus replication;     Show all 5 Subjects
Abstract:
... Hand, foot, and mouth disease caused by coxsackievirus B5 (CV-B5) is a considerable threat to infant health, especially with regard to neurological damage. Long noncoding RNAs (lncRNAs) are known to play pivotal roles in virus-host interactions. However, the roles of lncRNAs in CV-B5-host interactions have not yet been elucidated. In the current study, we used RNA sequencing to determine the expre ...
DOI:
10.1007/s00705-021-05313-6

2. Whole-genome sequencing and functional analysis of a novel chitin-degrading strain Rhodococcus sp. 11-3

Author:
Yu Xiao; Haiqiang Lu; Yang Liu; Yaxin Sang; Jilu Sun
Source:
Journal of bioscience and bioengineering 2022 pp. -
ISSN:
1389-1723
Subject:
gene ontology,   etc   ; chitin; chitin deacetylase; chitinase; genes; nucleotide sequences;     Show all 6 Subjects
Abstract:
... Chitin is the second most abundant polysaccharide in nature. Therefore, how to utilize the resource is an important issue. Rhodococcus sp. 11–3 is a strain with high chitin deacetylase (CDA) activity. In the present study, we used a combined Illumina and PacBio sequencing strategy to assemble the whole genome sequence of this strain. The genome of Rhodococcus sp. 11–3 was 5,627,661 bp in size and ...
DOI:
10.1016/j.jbiosc.2022.04.010

3. Comprehensive analysis of the LncRNAs, MiRNAs, and MRNAs acting within the competing endogenous RNA network of LGG

Author:
Yiming Ding; Hanjie Liu; Chuanbao Zhang; Zhaoshi Bao; Shuqing Yu
Source:
Genetica 2022 v.150 no.1 pp. 41-50
ISSN:
0016-6707
Subject:
gene ontology,   etc   ; glioma; messenger RNA; microRNA; non-coding RNA; pathogenesis;     Show all 6 Subjects
Abstract:
... Messenger RNA (mRNA) and long noncoding RNA (lncRNA) targets interact via competitive microRNA (miRNA) binding. However, the roles of cancer-specific lncRNAs in the competing endogenous RNA (ceRNA) networks of low-grade glioma (LGG) remain unclear. This study obtained RNA sequencing data for normal solid tissue and LGG primary tumour tissue from The Cancer Genome Atlas database. We used a computat ...
DOI:
10.1007/s10709-021-00145-3

4. Genomic landscape, polymorphism and possible LINE-associated delivery of G-quadruplex motifs in the bovine genes

Author:
Georgios C. Stefos; Georgios Theodorou; Ioannis Politis
Source:
Genomics 2022 v.114 no.2 pp. 110272
ISSN:
0888-7543
Subject:
gene ontology,   etc   ; DNA; cattle; genetic variation; genomics; humans; introns; telomeres;     Show all 8 Subjects
Abstract:
... G-Quadruplex structures are non-B DNA structures that occur in regions carrying short runs of guanines. They are implicated in several biological processes including transcription, translation, replication and telomere maintenance as well as in several pathological conditions like cancer and thus have gained the attention of the scientific community. The rise of the –omics era significantly affect ...
DOI:
10.1016/j.ygeno.2022.110272

5. Effect of Peroxyl Radical-Induced Oxidation on Functional and Structural Characteristics of Walnut Protein Isolates Revealed by High-Resolution Mass Spectrometry

Author:
Xuechun Zhang; Xi Yang; Yunqian Li; Zhenxing Wang; Xuemei He; Jian Sun
Source:
Foods 2022 v.11 no.3 pp. -
ISSN:
2304-8158
Subject:
gene ontology,   etc   ; amino acids; crosslinking; disulfides; food allergens; hydrophobicity; mass spectrometry; oils; oxidation; walnuts;     Show all 10 Subjects
Abstract:
... The present study aims to investigate the structural and functional properties of oxidated walnut protein isolates (WPI) by 2,2′-azobis (2-amidinopropane) dihydrochloride (AAPH). The oxidation degree, changes in structural characteristics, processing properties, and protein modifications of WPI were measured. The results showed that oxidation significantly induced structural changes, mainly reflec ...
DOI:
10.3390/foods11030385

6. Genetic evidence for facial variation being a composite phenotype of cranial variation and facial soft tissue thickness

Author:
Wei Qian; Manfei Zhang; Kaiwen Wan; Yunxia Xie; Siyuan Du; Jiarui Li; Xiongzheng Mu; Jiange Qiu; Xiangyang Xue; Xiahai Zhuang; Yingzhi Wu; Fan Liu; Sijia Wang
Source:
Journal of genetics and genomics 2022 pp. -
ISSN:
1673-8527
Subject:
gene ontology,   etc   ; Chinese people; computer software; face; genomics; models; morphogenesis; osteoblasts; phenotype; skull; variance;     Show all 11 Subjects
Abstract:
... Facial and cranial variation represent a multidimensional set of highly correlated and heritable phenotypes. Little is known about the genetic basis explaining this correlation. We develop a software package ALoSFL for simultaneous localization of facial and cranial landmarks from head computed tomography (CT) images, apply it in the analysis of head CT images of 777 Han Chinese women, and obtain ...
DOI:
10.1016/j.jgg.2022.02.020

7. Global MicroRNA Expression Profiling of Buffalo (Bubalus bubalis) Embryos at Different Developmental Stages Produced by Somatic Cell Nuclear Transfer and In-Vitro Fertilization Using RNA Sequencing

Author:
Pallavi Goel; Shivani Malpotra; Songyukta Shyam; Deepak Kumar; Manoj Kumar Singh; Prabhat Palta
Source:
Genes 2022 v.13 no.3 pp. -
ISSN:
2073-4425
Subject:
gene ontology,   etc   ; Bubalus bubalis; apoptosis; blastocyst; embryogenesis; in vitro fertilization; microRNA; progeny; somatic cells;     Show all 9 Subjects
Abstract:
... Despite the success of cloning technology in the production of offspring across several species, its application on a wide scale is severely limited by the very low offspring rate obtained with cloned embryos. The expression profile of microRNAs (miRNAs) in cloned embryos throughout embryonic development is reported to deviate from regular patterns. The present study is aimed at determining the dy ...
DOI:
10.3390/genes13030453

8. The Arabidopsis gene co‐expression network

Author:
David J. Burks; Soham Sengupta; Ronika De; Ron Mittler; Rajeev K. Azad
Source:
Plant direct 2022 v.6 no.4 pp. e396
ISSN:
2475-4455
Subject:
gene ontology,   etc   ; Arabidopsis thaliana; data collection; gene expression; genes; genomics; sequence analysis; transcription (genetics);     Show all 8 Subjects
Abstract:
... Identifying genes that interact to confer a biological function to an organism is one of the main goals of functional genomics. High‐throughput technologies for assessment and quantification of genome‐wide gene expression patterns have enabled systems‐level analyses to infer pathways or networks of genes involved in different functions under many different conditions. Here, we leveraged the public ...
DOI:
10.1002/pld3.396

9. UPIMAPI, reCOGnizer and KEGGCharter: Bioinformatics tools for functional annotation and visualization of (meta)-omics datasets

Author:
João C. Sequeira; Miguel Rocha; M. Madalena Alves; Andreia F. Salvador
Source:
Computational and Structural Biotechnology Journal 2022 v.20 pp. 1798-1810
ISSN:
2001-0370
Subject:
gene ontology,   etc   ; bioinformatics; biotechnology; computer software; data collection; gene expression regulation; metagenomics; taxonomy; transcriptomics;     Show all 9 Subjects
Abstract:
... Omics and meta-omics technologies are powerful approaches to explore microorganisms’ functions, but the sheer size and complexity of omics datasets often turn the analysis into a challenging task. Software developed for omics and meta-omics analyses, together with knowledgebases encompassing information on genes, proteins, taxonomic and functional annotation, among other types of information, are ...
DOI:
10.1016/j.csbj.2022.03.042

10. Genome-wide characterization of graft-transmissible mRNA-coding P450 genes of cucumber (Cucumis sativus L.)

Author:
Tao Wang; Xiaohong Lu; Chenggang Xiang; Xiaojun Li; Wenqian Liu; Qing Wang; Zixi Liu; Lihong Gao; Wenna Zhang
Source:
Horticultural plant journal 2022 pp. -
ISSN:
2468-0141
Subject:
gene ontology,   etc   ; Arabidopsis; Cucumis sativus; cucumbers; cytochrome P-450; data collection; horticultural crops; phylogeny; pumpkins;     Show all 9 Subjects
Abstract:
... P450 (cytochrome P450) is a supergene family, which is involved in various metabolic pathways in plants. Based on previous study, we found some of cucumber P450 mRNAs were systemic mobile in cucumber/pumpkin grafts. However, the reason that why P450 mRNAs were endorsed as signaling, and what specific motif (s) did they harbored is not clear yet. Here, we first identified 221 CsaP450 genes in cucum ...
DOI:
10.1016/j.hpj.2022.03.004

11. 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:
gene ontology,   etc   ; DNA methylation; DNA methyltransferase; bisulfites; epigenetics; evolution; genes; genomics; heterozygosity; mercury; mutants; rice;     Show all 12 Subjects
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

12. Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds

Author:
Rosalia Di Gerlando; Salvatore Mastrangelo; Marco Tolone; Ilaria Rizzuto; Anna Maria Sutera; Angelo Moscarelli; Baldassare Portolano; Maria Teresa Sardina
Source:
Animals 2022 v.12 no.2 pp. -
ISSN:
2076-2615
Subject:
gene ontology,   etc   ; genes; genetic relationships; immune response; lipid metabolism; phenotypic variation; sheep; single nucleotide polymorphism;     Show all 8 Subjects
Abstract:
... Copy number variants (CNVs) are one of the major contributors to genetic diversity and phenotypic variation in livestock. The aim of this work is to identify CNVs and perform, for the first time, a CNV-based population genetics analysis with five Italian sheep breeds (Barbaresca, Comisana, Pinzirita, Sarda, and Valle del Belìce). We identified 10,207 CNVs with an average length of 1.81 Mb. The bre ...
DOI:
10.3390/ani12020217

13. Quantitative Real-Time Analysis of Differentially Expressed Genes in Peripheral Blood Samples of Hypertension Patients

Author:
Fawad Ali; Arifullah Khan; Syed Aun Muhammad; Syed Shams ul Hassan
Source:
Genes 2022 v.13 no.2 pp. -
ISSN:
2073-4425
Subject:
gene ontology,   etc   ; blood; data collection; gene expression regulation; hypertension; ligands; mortality; pathophysiology; therapeutics; transcription (genetics);     Show all 10 Subjects
Abstract:
... Hypertension (HTN) is considered one of the most important and well-established reasons for cardiovascular abnormalities, strokes, and premature mortality globally. This study was designed to explore possible differentially expressed genes (DEGs) that contribute to the pathophysiology of hypertension. To identify the DEGs of HTN, we investigated 22 publicly available cDNA Affymetrix datasets using ...
DOI:
10.3390/genes13020187

14. Genome Sequence Resource for Colletotrichum viniferum, the Cause of Grapevine Ripe Rot in China

Author:
Mengru Dou; Yu Hao; Jing Yang; Xiaojian Yuan; Xiao Yin; Yuntong Jiao; Jiahe Zhao; Tingting Chen; Yuejin Wang; Yan Xu
Source:
Molecular plant-microbe interactions 2022 v.35 no.1 pp. 90-93
ISSN:
1943-7706
Subject:
gene ontology,   etc   ; Colletotrichum; Vitis; cytochrome P-450; fungi; grapes; nucleotide sequences; pathogenesis; pathogenicity; secondary metabolites; China;     Show all 11 Subjects
Abstract:
... Grape ripe rot is an important disease that has seriously damaged the yield and quality of grape worldwide. The disease is caused by Colletotrichum viniferum, a hemibiotrophic fungus that belongs to the Glomerellaceae family of Sordariomycetes class. Here, we present the genome of C. viniferum CvYL2a from grape, based on Illumina HiSeq 2500 and PacBio RS II. The high-quality genome consists of 70 ...
DOI:
10.1094/MPMI-04-21-0077-A

15. Identification and characterization of heat-responsive miRNAs and their regulatory network in maize

Author:
Yang Zhao; Qiye Wei; Tianci Chen; Lijuan Xu; Jing Liu; Xingen Zhang; Guomin Han; Qing Ma
Source:
Plant growth regulation 2022 v.96 no.1 pp. 195-208
ISSN:
0167-6903
Subject:
gene ontology,   etc   ; Zea mays; corn; crop yield; heat shock response; heat stress; microRNA; plant growth; temperature;     Show all 9 Subjects
Abstract:
... MicroRNAs (miRNAs) are small non-coding RNAs that play essential functions in abiotic stress responses. High temperature is a serious stress that affects crop yield and quality; however, the regulatory mechanisms of heat-responsive miRNAs remain poorly understood in maize (Zea mays L.). Here, 340 miRNAs (215 known and 125 novel) were identified from maize seedlings under heat stress and control co ...
DOI:
10.1007/s10725-021-00769-7

16. Integrated analysis of microRNA and mRNA interactions in ovary of counter-season breeding and egg-ceased geese (Anser cygnoides)

Author:
Jin-Shan Ran; Ling-Qian Yin; Jing-Jing Li; Yan-Qiang Tang; Jian Huang; Peng Ren; Xian-Xian Zhang; Si-Ming Li; Yi-Ping Liu
Source:
Theriogenology 2022 v.186 pp. 146-154
ISSN:
0093-691X
Subject:
gene ontology,   etc   ; Anser cygnoides; apoptosis; atrophy; cell proliferation; gene expression regulation; genes; microRNA; ovarian development; oviposition;     Show all 10 Subjects
Abstract:
... Egg-ceasing is a phenomenon that occurs in most avian species and significantly reduces productivity. Although several factors are reported to regulate the reproduction progress, the underlying molecular mechanism of egg-ceasing remains obscure. Herein, we identified and explored the differentially expressed miRNAs and mRNAs involved in ovarian atrophy via high throughput sequencing. We identified ...
DOI:
10.1016/j.theriogenology.2022.04.007

17. Network pharmacology-based approach to evaluate the effect and predict the mechanism of Calculus bovis against oral ulcers

Author:
Tian Xu; Xue Yu; Jing Ji; Qi Shao; Ying Li; Ting Li; Hanfen Shi; Huiling Tian; Jiayang Sai; Chongyang Ma; Xueqian Wang; Fafeng Cheng; Qingguo Wang
Source:
Pharmacological research 2022 v.3 pp. 100098
ISSN:
2667-1425
Subject:
gene ontology,   etc   ; Oriental traditional medicine; apoptosis; computer software; models; pharmacology; protein-protein interactions; rats; research; therapeutics;     Show all 10 Subjects
Abstract:
... Calculus bovis (CB), a famous traditional Chinese medicine, is commonly used to treat various inflammatory diseases, including oral ulcers. However, the potential mechanisms of CB in the treatment of oral ulcers are still limited. The present study aimed to use a network pharmacology-based approach to understand the multi-compound, multi-target, multi-pathway effect of CB against oral ulcers. The ...
DOI:
10.1016/j.prmcm.2022.100098

18. Bioinformatics Prediction and Analysis of MicroRNAs and Their Targets as Biomarkers for Prostate Cancer: A Preliminary Study

Author:
Chipampe Patricia Lombe; Mervin Meyer; Ashley Pretorius
Source:
Molecular biotechnology 2022 v.64 no.4 pp. 401-412
ISSN:
1073-6085
Subject:
gene ontology,   etc   ; bioinformatics; biomarkers; biotechnology; data collection; gamma radiation; gene expression regulation; metastasis; microRNA; prediction; prostatic neoplasms;     Show all 11 Subjects
Abstract:
... Prostate cancer (PCa) is the second most common form of cancer in men around the world. Due to its heterogeneity, presentations range from aggressive lethal disease to indolent disease. There is a need to identify core biomarkers that are important for early detection and progression, allowing a more precise method for the treatment and management of Pca. We obtained metastatic prostate cancer ass ...
DOI:
10.1007/s12033-021-00414-8

19. Cellular protein HSC70 promotes fowl adenovirus serotype 4 replication in LMH cells via interacting with viral 100K protein

Author:
Shenyan Gao; Huayuan Chen; Xiaozhan Zhang; Jun Zhao; Zeng Wang
Source:
Poultry science 2022 pp. 101941
ISSN:
0032-5791
Subject:
gene ontology,   etc   ; etiological agents; pathogenicity; poultry industry; poultry science; precipitin tests; serotypes; tandem mass spectrometry; virus replication;     Show all 9 Subjects
Abstract:
... Fowl adenovirus serotype 4 (FAdV-4), the predominant causative agent of hepatitis-hydropericardium syndrome (HHS), has caused severe economic losses to poultry industry since 2015. Although fiber2 and hexon have been confirmed to be the virulence-related factors, the roles of nonstructural viral proteins in pathogenicity of FAdV-4 remain poorly understood. Here, a tandem mass spectrometry (MS) was ...
DOI:
10.1016/j.psj.2022.101941

20. Expression profile screening and bioinformatics analysis of CircRNA, LncRNA, and mRNA in HeLa cells infected with Chlamydia muridarum

Author:
Yuanjun Liu; Junqiu Xiang; Xinyue Hu; Huiping Wang; Yina Sun
Source:
Archives of microbiology 2022 v.204 no.6 pp. 352
ISSN:
0302-8933
Subject:
gene ontology,   etc   ; Chlamydia muridarum; Chlamydia trachomatis; Toll-like receptors; apoptosis; bioinformatics; catabolism; gene expression; microarray technology; microbiology;     Show all 10 Subjects
Abstract:
... We have previously shown that circRNAs in host cells are involved in the process of Chlamydia trachomatis infection. In this study we aimed to identify significantly altered circRNAs/lncRNAs/mRNAs in Chlamydia muridarum infected cells and investigate their biological functions in the interaction between Chlamydia muridarum and host cells. For this purpose, circRNA, lncRNA and mRNA expression profi ...
DOI:
10.1007/s00203-022-02941-7