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You searched for: Journal Genomics Remove constraint Journal: Genomics Publication Year 2021 Remove constraint Publication Year: 2021 Source 2021 v.113 no.3 Remove constraint Source: 2021 v.113 no.3
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1. Aberrant methylation modifications reflect specific drug responses in small cell lung cancer

Author:
Chen, Peixin; Guo, Haoyue; Liu, Yu; Chen, Bin; Zhao, Sha; Wu, Shengyu; Li, Wei; Wang, Lei; Jia, Keyi; Wang, Hao; Jiang, Minlin; Tang, Xuzhen; Qi, Hui; Dai, Chunlei; Ye, Junyan; He, Yayi
Source:
Genomics 2021 v.113 no.3 pp. 1114-1126
ISSN:
0888-7543
Subject:
DNA methylation; drug therapy; drugs; genomics; lung neoplasms; microRNA; precipitin tests; transcription initiation site
Abstract:
... In the study, Methylated DNA immunoprecipitation sequencing, RNA sequencing, and whole-exome sequencing were employed to clinical small cell lung cancer (SCLC) patients. Then, we verified the therapeutic predictive effects of differentially methylated genes (DMGs) in 62 SCLC cell lines. Of 4552 DMGs between chemo-sensitive and chemo-insensitive group, coding genes constituted the largest percentag ...
DOI:
10.1016/j.ygeno.2020.12.045

2. A comprehensive transcriptome analysis of contrasting rice cultivars highlights the role of auxin and ABA responsive genes in heat stress response

Author:
Sharma, Eshan; Borah, Pratikshya; Kaur, Amarjot; Bhatnagar, Akanksha; Mohapatra, Trilochan; Kapoor, Sanjay; Khurana, Jitendra P.
Source:
Genomics 2021 v.113 no.3 pp. 1247-1261
ISSN:
0888-7543
Subject:
ambient temperature; auxins; climate change; cold; cultivars; genes; genomics; heat; heat shock response; heat tolerance; microarray technology; red rice; transcriptome; transcriptomics; wheat
Abstract:
... Sensing a change in ambient temperature is key to survival among all living organisms. Temperature fluctuations due to climate change are a matter of grave concern since it adversely affects growth and eventually the yield of crop plants, including two of the major cereals, i.e., rice and wheat. Thus, to understand the response of rice seedlings to elevated temperatures, we performed microarray-ba ...
DOI:
10.1016/j.ygeno.2021.03.007

3. A computational approach to identify CRISPR-Cas loci in the complete genomes of the lichen-associated Burkholderia sp. PAMC28687 and PAMC26561

Author:
Shrestha, Prasansah; Han, So-Ra; Lee, Jun Hyuck; Park, Hyun; Oh, Tae-Jin
Source:
Genomics 2021 v.113 no.3 pp. 881-888
ISSN:
0888-7543
Subject:
Burkholderia; CRISPR-Cas systems; RNA; computer software; databases; genomics; plasmids; Antarctic region
Abstract:
... The genus Burkholderia and its strains PAMC28687 and PAMC26561 are lichen-associated bacteria isolated from the Antarctic region. Our study is the first to provide the genome sequence of the Burkholderia sp. PAMC26561 strain. The genus Burkholderia includes bacteria that are pathogenic to plants, animals, and humans. Computational analysis of complete genomes of strains from the uncategorized Burk ...
DOI:
10.1016/j.ygeno.2021.01.019

4. ASDB: A comprehensive omics database for Anopheles sinensis

Author:
Zhang, Yu-Juan; Lan, Yang; Chen, Bin
Source:
Genomics 2021 v.113 no.3 pp. 976-982
ISSN:
0888-7543
Subject:
Anopheles sinensis; amino acid sequences; databases; filariasis; genes; genetic variation; humans; malaria; metagenomics; microRNA; non-coding RNA; nucleotide sequences; sequence alignment; transcriptome; China; South East Asia
Abstract:
... Anopheles sinensis is a key disease vector for human malaria and parasitic diseases such as malayan filariasis, and it is considered to be one of the most important malaria vectors in China and Southeast Asia. As high-throughput sequencing and assembly technology are widely used in An. sinensis, a lot of omics data have been generated, and abundant genome, mRNA transcriptome, miRNA transcriptome a ...
DOI:
10.1016/j.ygeno.2021.02.005

5. Bioinformatic tools for DNA methylation and histone modification: A survey

Author:
Chenarani, Nasibeh; Emamjomeh, Abbasali; Allahverdi, Abdollah; Mirmostafa, SeyedAli; Afsharinia, Mohammad Hossein; Zahiri, Javad
Source:
Genomics 2021 v.113 no.3 pp. 1098-1113
ISSN:
0888-7543
Subject:
DNA methylation; bioinformatics; chromatin; epigenetics; genomics; histone code; histones; prediction; surveys
Abstract:
... Epigenetic inheritance occurs due to different mechanisms such as chromatin and histone modifications, DNA methylation and processes mediated by non-coding RNAs. It leads to changes in gene expressions and the emergence of new traits in different organisms in many diseases such as cancer. Recent advances in experimental methods led to the identification of epigenetic target sites in various organi ...
DOI:
10.1016/j.ygeno.2021.03.004

6. Bone marrow mesenchymal stem cells-derived exosomal microRNA-19b-1-5p reduces proliferation and raises apoptosis of bladder cancer cells via targeting ABL2

Author:
Fu, Dewang; Liu, Ben; Jiang, Huamao; Li, Zhaowei; Fan, Chenghui; Zang, Li'e
Source:
Genomics 2021 v.113 no.3 pp. 1338-1348
ISSN:
0888-7543
Subject:
apoptosis; bone marrow; cell communication; coculture; exosomes; genomics; microRNA; tyrosine; urinary bladder neoplasms
Abstract:
... Exosomes are involved in intercellular communication via specialized molecular cargo, such as microRNAs (miRNAs). However, the mechanisms underlying exosomal miR-19b-1-5p in bladder cancer remain largely unknown, thus, we aim to investigate the effect of exosomal miR-19b-1-5p on bladder cancer with the involvement of non-receptor protein tyrosine kinase Arg (ABL2).miR-19b-1-5p and ABL2 expression ...
DOI:
10.1016/j.ygeno.2021.03.011

7. CircRNA expression profile and functional analysis in retinal ischemia-reperfusion injury

Author:
Yao, Mu-Di; Zhu, Yan; Zhang, Qiu-Yang; Zhang, Hui-Ying; Li, Xiu-Miao; Jiang, Qin; Yan, Biao
Source:
Genomics 2021 v.113 no.3 pp. 1482-1490
ISSN:
0888-7543
Subject:
animal models; apoptosis; cataract; ganglia; genes; genomics; glaucoma; humans; microarray technology; neurodegenerative diseases; pathogenesis
Abstract:
... Retinal ischemia-reperfusion (I/R) is involved in the pathogenesis of many vision-threatening diseases. circRNAs act as key players in gene regulation and human diseases. However, the global circRNA expression profile in retinal I/R injury has not been fully uncovered. Herein, we established a murine model of retinal I/R injury and performed circRNA microarrays to identify I/R-related circRNAs. 12 ...
DOI:
10.1016/j.ygeno.2021.03.026

8. Coding and non-coding nucleotides': The future of stroke gene therapeutics

Author:
Chavda, Vishal; Madhwani, Kajal
Source:
Genomics 2021 v.113 no.3 pp. 1291-1307
ISSN:
0888-7543
Subject:
anticoagulants; death; gene therapy; genes; genomics; heart diseases; microRNA; morbidity; mortality; neuroprotective effect; nucleotides; stroke
Abstract:
... Stroke is the foremost cause of death ranked after heart disease and cancer. It is the fatal life-threatening event that requires immediate medical admissions to overcome following morbidity and mortality. The therapeutic advances in stroke therapy have been manipulated with diverse paths for last 5 years. Recent research and clinical trials have investigated a variety of anti-stroke agents includ ...
DOI:
10.1016/j.ygeno.2021.03.003

9. Comparative analysis of mitochondrial genomes of Nirvanini and Evacanthini (Hemiptera: Cicadellidae) reveals an explicit evolutionary relationship

Author:
Du, Yimin; Liang, Zonglei; Dietrich, Christopher H.; Dai, Wu
Source:
Genomics 2021 v.113 no.3 pp. 1378-1385
ISSN:
0888-7543
Subject:
Cicadellidae; codon usage; data collection; genetic variation; genomics; mitochondrial genome; monophyly
Abstract:
... Mitogenomes of five leafhopper species, Chudania hellerina and Concaveplana rufolineata in Nirvanini, Carinata rufipenna, Evacanthus danmainus and E. heimianus representing Evacanthini, were sequenced. The lengths of these five mitogenomes range from 15,044 (C. hellerina) to 15,680 bp (E. heimianus). All five mitogenomes exhibit similar base composition, gene size and codon usage of protein-coding ...
DOI:
10.1016/j.ygeno.2021.03.017

10. Comparative genomics analysis of two banana Fusarium wilt biocontrol endophytes Bacillus subtilis R31 and TR21 provides insights into their differences on phytobeneficial trait

Author:
Li, Chunji; Cheng, Ping; Zheng, Li; Li, Yongjian; Chen, Yanhong; Wen, Shuheng; Yu, Guohui
Source:
Genomics 2021 v.113 no.3 pp. 900-909
ISSN:
0888-7543
Subject:
Bacillus subtilis; Dendrobium; Fusarium wilt; Panama disease; antibiotics; bananas; biological control; endophytes; genomics; growth promotion; plant growth; rhizosphere; sporulation
Abstract:
... Fusarium wilt of banana is considered one of the most destructive plant diseases. Bacillus subtilis R31 and TR21, isolated from Dendrobium sp. leaves, exhibit different phytobeneficial effects on banana Fusarium wilt bio-controlling. Here, we performed genome sequencing and comparative genomics analysis of R31 and TR21 to enhance our understanding of the different phytobeneficial traits. These res ...
DOI:
10.1016/j.ygeno.2021.02.006

11. Comparative profile of exosomal microRNAs in postmenopausal women with various bone mineral densities by small RNA sequencing

Author:
Kong, Dece; Chen, Tianning; Zheng, Xinhui; Yang, Tieyi; Zhang, Yan; Shao, Jin
Source:
Genomics 2021 v.113 no.3 pp. 1514-1521
ISSN:
0888-7543
Subject:
bone density; exosomes; gene ontology; genomics; microRNA; osteopenia; osteoporosis; postmenopause; prediction; quantitative polymerase chain reaction
Abstract:
... To explore the role of plasma miRNAs in exosomes in early postmenopausal women. Small RNA sequencing was implemented to clarify the expression of miRNA in plasma exosomes obtained from 15 postmenopausal women, divided into groups of osteoporosis, osteopenia, and normal bone mass based on bone mineral density. Differentially expressed miRNAs (DEMs) were identified by comparing miRNA expression prof ...
DOI:
10.1016/j.ygeno.2021.03.028

12. Comparative proteomic analysis provides insight into the molecular mechanism of vegetative growth advantage in allotriploid Populus

Author:
Li, Jiang; Wang, Yi; Wei, Hairong; Kang, Xiangyang
Source:
Genomics 2021 v.113 no.3 pp. 1180-1192
ISSN:
0888-7543
Subject:
Calvin cycle; Populus; biomass; carbon dioxide fixation; diploidy; gene expression regulation; genomics; lumber; photorespiration; protein degradation; protein synthesis; proteomics; starch; sucrose; vegetative growth
Abstract:
... Though allotriploid poplar shows a salient vegetative growth advantage that impacts biomass and lumber yield, the proteomic data of Populus allotriploids have not been scrutinized for identifying the underlying molecular mechanisms. We conducted a large-scale label-free proteomics profiling of the 5th, 10th, and 25th leaves of allotriploids and diploids, and identified 4587 protein groups. Among 9 ...
DOI:
10.1016/j.ygeno.2021.03.002

13. Comparative transcriptome analyses for metribuzin tolerance provide insights into key genes and mechanisms restoring photosynthetic efficiency in bread wheat (Triticum aestivum L.)

Author:
Bhoite, Roopali; Si, Ping; Siddique, Kadambot H.M.; Yan, Guijun
Source:
Genomics 2021 v.113 no.3 pp. 910-918
ISSN:
0888-7543
Subject:
; Triticum aestivum; chlorophyll; dose response; genomics; glucose; marker-assisted selection; metribuzin; photosystem II; sequence analysis; transcriptome; weed control; wheat
Abstract:
... Weeds are the biggest threat to cropping system sustainability in wheat. Metribuzin is a versatile herbicide for broad-spectrum weed management. Understanding key genes, mechanisms and functional markers are essential to develop higher metribuzin tolerant wheats. We identified Chuan Mai 25 (tolerant) and Ritchie (susceptible) as contrasting genotypes to metribuzin stress through dose-response anal ...
DOI:
10.1016/j.ygeno.2021.02.004

14. Comparative transcriptome analysis of the gills of Cardisoma armatum provides novel insights into the terrestrial adaptive related mechanism of air exposure stress

Author:
Wu, Lv; Tang, Dan; Shen, Chenchen; Bai, Yuze; Jiang, Kaiqin; Yu, Qian; Wang, Zhengfei
Source:
Genomics 2021 v.113 no.3 pp. 1193-1202
ISSN:
0888-7543
Subject:
Cardisoma; acid-base balance; air; energy metabolism; gene expression regulation; genomics; histology; immune response; lungs; osmotic pressure; oxygen; transcriptomics
Abstract:
... Cardisoma armatum is a typical member of the Gecarcinidae which show significant behavioral, morphological, physiological, and/or biochemical adaptations permitting extended activities on the land. The special gills (branchiostegal lung) of C. armatum play an important role in maintaining osmotic pressure balance and obtaining oxygen to adapt to the terrestrial environment. However, adaptive molec ...
DOI:
10.1016/j.ygeno.2021.03.010

15. Complete chloroplast genome sequencing of ten wild Fragaria species in China provides evidence for phylogenetic evolution of Fragaria

Author:
Sun, Jian; Sun, Rui; Liu, Huabo; Chang, Linlin; Li, Shuangtao; Zhao, Mizhen; Shennan, Carol; Lei, Jiajun; Dong, Jing; Zhong, Chuanfei; Xue, Li; Gao, Yongshun; Wang, Guixia; Zhang, Yuntao
Source:
Genomics 2021 v.113 no.3 pp. 1170-1179
ISSN:
0888-7543
Subject:
ancestry; chloroplast genome; genomics; glaciation; indigenous species; octaploidy; phylogeny; temperature; China
Abstract:
... Complete chloroplast genomes of ten wild Fragaria species native to China were sequenced. Phylogenetic analysis clustered Fragaria species into two clades: The south clade (F. iinumae, F. chinensis, F. pentaphylla, F. nilgerrensis, F. daltoniana, F. corymbosa, F. moupinensis, F. tibetica, F. nipponica, F. gracilis, and F. nubicola and north clade (F. viridis, F. orientalis, F. moschata, F. mandshu ...
DOI:
10.1016/j.ygeno.2021.01.027

16. Complete genome sequence and comparative genomic analysis of Enterococcus faecalis EF-2001, a probiotic bacterium

Author:
Panthee, Suresh; Paudel, Atmika; Hamamoto, Hiroshi; Ogasawara, Akihiko Ano; Iwasa, Toshihiro; Blom, Jochen; Sekimizu, Kazuhisa
Source:
Genomics 2021 v.113 no.3 pp. 1534-1542
ISSN:
0888-7543
Subject:
Enterococcus faecalis; bacteria; digestive system; drug resistance; genomics; humans; nucleotide sequences; pathogenesis; phylogeny; probiotics
Abstract:
... Enterococcus faecalis is a common human gut commensal bacterium. While some E. faecalis strains are probiotic, others are known to cause opportunistic infections, and clear distinction between these strains is difficult using traditional taxonomic approaches. In this study, we completed the genome sequencing of EF-2001, a probiotic strain, using our in-house hybrid assembly approach. Comparative a ...
DOI:
10.1016/j.ygeno.2021.03.021

17. Constructing a de novo transcriptome and a reference proteome for the bivalve Scrobicularia plana: Comparative analysis of different assembly strategies and proteomic analysis

Author:
Amil-Ruiz, Francisco; Herruzo-Ruiz, Ana María; Fuentes-Almagro, Carlos; Baena-Angulo, Casimiro; Jiménez-Pastor, José Manuel; Blasco, Julián; Alhama, José; Michán, Carmen
Source:
Genomics 2021 v.113 no.3 pp. 1543-1553
ISSN:
0888-7543
Subject:
Scrobicularia plana; algorithms; clams; data collection; databases; ecotoxicology; estuaries; genomics; peptides; pollutants; proteome; proteomics; transcriptome
Abstract:
... Scrobicularia plana is a coastal and estuarine bivalve widely used in ecotoxicological studies. However, the underlying molecular mechanisms for S. plana pollutant responses are hardly known due to the lack of molecular databases. Thus, in this study we present a holistic approach to assess a robust reference transcriptome and proteome of this clam. A mixture of control and metal-exposed individua ...
DOI:
10.1016/j.ygeno.2021.03.025

18. Cotton transcriptome analysis reveals novel biological pathways that eliminate reactive oxygen species (ROS) under sodium bicarbonate (NaHCO3) alkaline stress

Author:
Fan, Yapeng; Lu, Xuke; Chen, Xiugui; Wang, Junjuan; Wang, Delong; Wang, Shuai; Guo, Lixue; Rui, Cun; Zhang, Yuexin; Cui, Ruifeng; Malik, Waqar Afzal; Wang, Qinqin; Chen, Chao; Yu, John Z.; Ye, Wuwei
Source:
Genomics 2021 v.113 no.3 pp. 1157-1169
ISSN:
0888-7543
Subject:
amino acids; biosynthesis; cotton; gene expression; gene expression regulation; gene ontology; genetic improvement; genomics; pH; plant hormones; reactive oxygen species; secondary metabolites; signal transduction; sodium bicarbonate; toxicity; transcription (genetics); transcriptomics
Abstract:
... Alkaline stress is one of the abiotic stresses limiting cotton production. Though RNA-Seq analyses, have been conducted to investigate genome-wide gene expression in response to alkaline stress in plants, the response of sodium bicarbonate (NaHCO₃) stress-related genes in cotton has not been reported. To explore the mechanisms of cotton response to this alkaline stress, we used next-generation seq ...
DOI:
10.1016/j.ygeno.2021.02.022

19. De novo full length transcriptome analysis of Arachis glabrata provides insights into gene expression dynamics in response to biotic and abiotic stresses

Author:
Zhao, Chuanzhi; He, Liangqiong; Xia, Han; Zhou, Ximeng; Geng, Yun; Hou, Lei; Li, Pengcheng; Li, Guanghui; Zhao, Shuzhen; Ma, Changle; Tang, Ronghua; Pandey, Manish K.; Varshney, Rajeev K.; Wang, Xingjun
Source:
Genomics 2021 v.113 no.3 pp. 1579-1588
ISSN:
0888-7543
Subject:
Arachis glabrata; catechol oxidase; cold; drought; flowers; forage; forage crops; gene expression; gene expression regulation; genomics; leaf spot; leaves; peanuts; sequence analysis; transcriptome; transcriptomics
Abstract:
... The perennial ornamental peanut Arachis glabrata represents one of the most adaptable wild Arachis species. This study used PacBio combined with BGISEQ-500 RNA-seq technology to study the transcriptome and gene expression dynamics of A. glabrata. Of the total 109,747 unique transcripts obtained, >90,566 transcripts showed significant homology to known proteins and contained the complete coding seq ...
DOI:
10.1016/j.ygeno.2021.03.030

20. Differential alternative RNA splicing and transcription events between tumors from African American and White patients in The Cancer Genome Atlas

Author:
Al Abo, Muthana; Hyslop, Terry; Qin, Xiaodi; Owzar, Kouros; George, Daniel J.; Patierno, Steven R.; Freedman, Jennifer A.
Source:
Genomics 2021 v.113 no.3 pp. 1234-1246
ISSN:
0888-7543
Subject:
RNA; ancestry; biomarkers; data collection; genomics; introns; mortality; neoplasms; patients; therapeutics
Abstract:
... Individuals of African ancestry suffer disproportionally from higher incidence, aggressiveness, and mortality for particular cancers. This disparity likely results from an interplay among differences in multiple determinants of health, including differences in tumor biology. We used The Cancer Genome Atlas (TCGA) SpliceSeq and TCGA aggregate expression datasets and identified differential alternat ...
DOI:
10.1016/j.ygeno.2021.02.020