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1. Abiotic stress induced miRNA-TF-gene regulatory network: A structural perspective

Author:
Sharma, Rinku; Upadhyay, Shashankaditya; Bhat, Basharat; Singh, Garima; Bhattacharya, Sudeepto; Singh, Ashutosh
Source:
Genomics 2019
ISSN:
0888-7543
Subject:
transcriptome,   etc   ; Arabidopsis; cold; cold stress; cultivars; databases; drought; flooded conditions; genes; meta-analysis; microRNA; salt stress; transcription (genetics); transcription factors;     Show all 14 Subjects
Abstract:
... MicroRNAs (miRNAs) and transcription factors (TFs) are the largest families of trans-acting gene regulatory species, which are pivotal players in a complex regulatory network. Recently, extensive research on miRNAs and TFs in agriculture has identified these trans-acting regulatory species, as an effective tool for engineering new crop cultivars to increase yield and quality as well tolerance to e ...
DOI:
10.1016/j.ygeno.2019.03.004

2. A comparative in silico linear B-cell epitope prediction and characterization for South American and African Trypanosoma vivax strains

Author:
Guedes, Rafael Lucas Muniz; Rodrigues, Carla Monadeli Filgueira; Coatnoan, Nicolas; Cosson, Alain; Cadioli, Fabiano Antonio; Garcia, Herakles Antonio; Gerber, Alexandra Lehmkuhl; Machado, Rosangela Zacarias; Minoprio, Paola Marcella Camargo; Teixeira, Marta Maria Geraldes; de Vasconcelos, Ana Tereza Ribeiro
Source:
Genomics 2019 v.111 no.3 pp. 407-417
ISSN:
0888-7543
Subject:
transcriptome,   etc   ; B-lymphocytes; Trypanosoma vivax; diagnostic techniques; disease severity; epitopes; genome; parasites; prediction; recombinant antigens; virulence; Brazil; Nigeria; Venezuela;     Show all 14 Subjects
Abstract:
... Trypanosoma vivax is a parasite widespread across Africa and South America. Immunological methods using recombinant antigens have been developed aiming at specific and sensitive detection of infections caused by T. vivax. Here, we sequenced for the first time the transcriptome of a virulent T. vivax strain (Lins), isolated from an outbreak of severe disease in South America (Brazil) and performed ...
DOI:
10.1016/j.ygeno.2018.02.017

3. A comparative morphological and transcriptomic study on autotetraploid Stevia rebaudiana (bertoni) and its diploid

Author:
Xiang, Zeng-xu; Tang, Xing-li; Liu, Wei-hu; Song, Chang-nian
Source:
Plant physiology and biochemistry 2019 v.143 pp. 154-164
ISSN:
0981-9428
Subject:
transcriptome,   etc   ; Stevia rebaudiana; autotetraploidy; biosynthesis; databases; diploidy; flavonoids; gene expression regulation; genes; glycosides; leaves; messenger RNA; morphogenesis; phenotypic plasticity; photosynthesis; plant growth; sequence analysis; steviol; stevioside; transcriptomics;     Show all 20 Subjects
Abstract:
... Stevia rebaudiana is an important medical plant for producing steviol glycosides (SGs) or stevioside. Autotetraploids (4x = 44) show an increasing level of morphology, physiology and tolerances comparing to diploids (2x = 22). However, little information regarded on the comparative transcriptome analysis between diploid and autotetraploid S. rebaudiana was found. In this study, synthetic autotetra ...
DOI:
10.1016/j.plaphy.2019.09.003

4. A comparative transcriptomic study on developmental gonads provides novel insights into sex change in the protandrous black porgy (Acanthopagrus schlegelii)

Author:
Zhang, Kai; Xu, Jin; Zhang, Zhiwei; Huang, Yu; Ruan, Zhiqiang; Chen, Shuyin; Zhu, Fei; You, Xinxin; Jia, Chaofeng; Meng, Qian; Gu, Ruobo; Lin, Xueqiang; Xu, Junmin; Xu, Pao; Zhang, Zhiyong; Shi, Qiong
Source:
Genomics 2019 v.111 no.3 pp. 277-283
ISSN:
0888-7543
Subject:
transcriptome,   etc   ; Acanthopagrus schlegelii schlegelii; adults; animal ovaries; breeding; females; gene expression regulation; genes; genome assembly; genomics; males; marine fish; protandry; sex determination; sex reversal; testes; transcriptomics; China;     Show all 18 Subjects
Abstract:
... Protandrous black porgy (Acanthopagrus schlegelii) is a popular and valuable commercial marine fish in China and East Asian countries. Controlling and managing its breeding has been an imperative step towards obtaining a sustainable supply of this fish in aquaculture production systems. Therefore, study on the molecular mechanisms of sex change in black porgy has both scientific and commercial imp ...
DOI:
10.1016/j.ygeno.2018.11.006

5. A comparison of the transcriptomes between diploid and autotetraploid Paulownia fortunei under salt stress

Author:
Wang, Zhe; Zhao, Zhenli; Fan, Guoqiang; Dong, Yanpeng; Deng, Minjie; Xu, Enkai; Zhai, Xiaoqiao; Cao, Heping
Source:
Physiology and molecular biology of plants 2019 v.25 no.1 pp. 1-11
ISSN:
0971-5894
Subject:
transcriptome,   etc   ; Paulownia fortunei; autotetraploidy; databases; diploidy; gene expression regulation; growth and development; photosynthesis; plant development; plant growth; salt stress; salt tolerance; stress tolerance; trees; unigenes;     Show all 15 Subjects
Abstract:
... Paulownia is a tree species grown in many countries. Our previous study reveals that tetraploid Paulownia fortunei is more tolerant to salt stress than its corresponding diploid tree. To investigate the molecular mechanisms of salt stress tolerance in P. fortunei, the transcriptomes of normal and salt-stressed diploid and tetraploid were investigated. After assembling the clean reads, we obtained ...
DOI:
10.1007/s12298-018-0578-4

6. Activity changes in gill ion transporter enzymes in response to salinity and temperature in fathead minnows (Pimephales promelas)

Author:
Monroe, Ian; Wentworth, Simon; Thede, Katrina; Aravindabose, Varsha; Garvin, Jeffrey; Packer, Randall K.
Source:
Comparative biochemistry and physiology 2019 v.228 pp. 29-34
ISSN:
1095-6433
Subject:
transcriptome,   etc   ; Pimephales promelas; ammonia; ammonium; ecotoxicology; enzyme activity; genome; gills; glutamate dehydrogenase; ion channels; messenger RNA; minnows; proton pump; receptors; salinity; seasonal variation; sodium; sodium-potassium-exchanging ATPase; temperature; tides; United States;     Show all 21 Subjects
Abstract:
... Fathead minnows, Pimephales promelas, are found throughout the continental United States in waters in which salinity can change with tides and temperatures vary seasonally. They have been used extensively in studies of environmental toxicology and are commercially important. In a very recent study in our labs RNA Seq was used to assemble transcriptomes from the gills of fatheads acclimated to eith ...
DOI:
10.1016/j.cbpa.2018.10.018

7. Acute immune stress improves cell resistance to chemical poison damage in SP600125-induced polyploidy of fish cells in vitro

Author:
Mo, Yanxiu; Fan, Yunpeng; Fu, Wen; Xu, Wenting; Chen, Shujuan; Wen, Yuanhui; Liu, Shaojun; Peng, Liangyue; Xiao, Yamei
Source:
Fish & shellfish immunology 2019 v.84 pp. 656-663
ISSN:
1050-4648
Subject:
transcriptome,   etc   ; breeding; carp; cell adhesion; cell lines; cell-mediated immunity; diploidy; gene expression regulation; homeostasis; inflammation; integrins; interleukin-1beta; mitochondria; shellfish; signal transduction; tetraploidy; toxicity; unigenes;     Show all 18 Subjects
Abstract:
... Previous research has indicated that the small compound, SP600125, could induce polyploidy of fish cells, and has established a stable tetraploid cell line from diploid fish cells. In order to explore how fish cells maintain homeostasis under SP600125-stress in vitro, this study investigates impacts of SP600125-stress on intracellular pathways, as well as on regulation of the cellular homeostasis ...
DOI:
10.1016/j.fsi.2018.10.063

8. Adaptation mechanisms of Rhodococcus sp. CNS16 under different temperature gradients: Physiological and transcriptome

Author:
Wang, Chen; Chen, Yangwu; Zhou, Houzhen; Li, Xudong; Tan, Zhouliang
Source:
Chemosphere 2019
ISSN:
0045-6535
Subject:
transcriptome,   etc   ; adverse effects; ambient temperature; amino acid metabolism; aniline; bioremediation; carotenoids; catalase; cell structures; energy metabolism; enzyme activity; fatty acid composition; gene expression regulation; genes; oxidative stress; peptidoglycans; peroxidase; riboflavin; seasonal variation; superoxide dismutase; temperature profiles; thiols; transcriptomics; unsaturated fatty acids; vitamin metabolism;     Show all 25 Subjects
Abstract:
... Rhodococcus exhibits strong adaptability to environmental stressors and plays a crucial role in environmental bioremediation. However, seasonal changes in ambient temperature, especially rapid temperature drops exert an adverse effect on in situ bioremediation. In this paper, we studied the cell morphology and fatty acid composition of an aniline-degrading strain Rhodococcus sp. CNS16 at temperatu ...
DOI:
10.1016/j.chemosphere.2019.124571

9. Adapting INTACT to analyse cell-type-specific transcriptomes and nucleocytoplasmic mRNA dynamics in the Arabidopsis embryo

Author:
Palovaara, Joakim; Weijers, Dolf
Source:
Plant reproduction 2019 v.32 no.1 pp. 113-121
ISSN:
2194-7953
Subject:
transcriptome,   etc   ; Arabidopsis thaliana; embryo (plant); embryogenesis; genes; messenger RNA; microarray technology; seedlings; stem cells; transcription (genetics); transcriptomics; vascular plants; zygote;     Show all 13 Subjects
Abstract:
... In the early embryo of vascular plants, the different cell types and stem cells of the seedling are specified as the embryo develops from a zygote towards maturity. How the key steps in cell and tissue specification are instructed by genome-wide transcriptional activity is poorly understood. Progress in defining transcriptional regulation at the genome-wide level in plant embryos has been hampered ...
DOI:
10.1007/s00497-018-0347-0

10. Adaptive gene regulation in wild mammals exposed to high predator abundance

Author:
Armenta, Tiffany C.; Cole, Steve W.; Wayne, Robert K.; Blumstein, Daniel T.
Source:
Animal behaviour 2019 v.152 pp. 53-61
ISSN:
0003-3472
Subject:
transcriptome,   etc   ; DNA repair; Marmota; animal behavior; anxiety; factor analysis; fearfulness; gene expression; gene expression regulation; gene ontology; genes; genomics; glucocorticoids; heat shock proteins; homeostasis; humans; leukocytes; messenger RNA; metabolism; predators; prey species; protein transport; psychological stress; sequence analysis; stress response; sympathetic nervous system; transcription (genetics); transcription factors; wild animals;     Show all 29 Subjects
Abstract:
... Psychological stress induced by exposure to predators has complex effects on the behaviour and physiology of prey species. This includes potential influences on gene expression mediated via stress-responsive physiological pathways such as the sympathetic nervous system and hypothalamus–pituitary–adrenal (HPA) axis. Laboratory studies have documented diverse transcriptional effects of predator-indu ...
DOI:
10.1016/j.anbehav.2019.04.008

11. A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation

Author:
Bogard, Nicholas; Linder, Johannes; Rosenberg, Alexander B.; Seelig, Georg
Source:
Cell 2019 v.178 no.1 pp. 91-106.e23
ISSN:
0092-8674
Subject:
transcriptome,   etc   ; DNA; engineering; genetic variation; humans; models; nucleotide sequences; prediction;     Show all 8 Subjects
Abstract:
... Alternative polyadenylation (APA) is a major driver of transcriptome diversity in human cells. Here, we use deep learning to predict APA from DNA sequence alone. We trained our model (APARENT, APA REgression NeT) on isoform expression data from over 3 million APA reporters. APARENT’s predictions are highly accurate when tasked with inferring APA in synthetic and human 3′UTRs. Visualizing features ...
DOI:
10.1016/j.cell.2019.04.046

12. A developmentally regulated spliced variant of PTBP1 is upregulated in type 1 diabetic hearts

Author:
Belanger, KarryAnne; Nutter, Curtis A.; Li, Jin; Yu, Peng; Kuyumcu-Martinez, Muge N.
Source:
Biochemical and biophysical research communications 2019 v.509 no.2 pp. 384-389
ISSN:
0006-291X
Subject:
transcriptome,   etc   ; RNA; RNA-binding proteins; adults; alternative splicing; binding sites; data collection; diabetes; genes; heart; mice; neonates;     Show all 12 Subjects
Abstract:
... Alternative splicing (AS) is dysregulated in Type 1 diabetic (T1D) hearts but mechanisms responsible are unclear. Here, we provide evidence that the RNA binding protein (RBP) PTBP1 is modulated in adult T1D hearts contributing to AS changes. We show that a spliced variant of PTBP1 that is highly expressed in normal newborn mouse hearts is aberrantly expressed in adult T1D mouse hearts. Comparing k ...
DOI:
10.1016/j.bbrc.2018.12.150

13. A differential k-mer analysis pipeline for comparing RNA-Seq transcriptome and meta-transcriptome datasets without a reference

Author:
Chan, Chon-Kit Kenneth; Rosic, Nedeljka; Lorenc, Michał T.; Visendi, Paul; Lin, Meng; Kaniewska, Paulina; Ferguson, Brett J.; Gresshoff, Peter M.; Batley, Jacqueline; Edwards, David
Source:
Functional & integrative genomics 2019 v.19 no.2 pp. 363-371
ISSN:
1438-793X
Subject:
transcriptome,   etc   ; corals; data collection; gene expression; gene expression regulation; genes; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; sequence analysis; soybeans;     Show all 10 Subjects
Abstract:
... Next-generation DNA sequencing technologies, such as RNA-Seq, currently dominate genome-wide gene expression studies. A standard approach to analyse this data requires mapping sequence reads to a reference and counting the number of reads which map to each gene. However, for many transcriptome studies, a suitable reference genome is unavailable, especially for meta-transcriptome studies which assa ...
DOI:
10.1007/s10142-018-0647-3

14. African Orphan Crops Consortium (AOCC): status of developing genomic resources for African orphan crops

Author:
Hendre, Prasad S.; Muthemba, Samuel; Kariba, Robert; Muchugi, Alice; Fu, Yuan; Chang, Yue; Song, Bo; Liu, Huan; Liu, Min; Liao, Xuezhu; Sahu, Sunil Kumar; Wang, Sibo; Li, Linzhou; Lu, Haorong; Peng, Shufeng; Cheng, Shifeng; Xu, Xun; Yang, Huanming; Wang, Jian; Liu, Xin; Simons, Anthony; Shapiro, Howard-Yana; Mumm, Rita H.; Van Deynze, Allen; Jamnadass, Ramni
Source:
Planta 2019 v.250 no.3 pp. 989-1003
ISSN:
0032-0935
Subject:
transcriptome,   etc   ; abiotic stress; antioxidants; biotic stress; cultivars; farmers; food crops; food security; foods; genome; genomics; growth retardation; high-throughput nucleotide sequencing; hunger; malnutrition; minerals; nucleotide sequences; plant breeding; stakeholders; trees; vitamins; California; Sub-Saharan Africa;     Show all 23 Subjects
Abstract:
... MAIN CONCLUSION: The African Orphan Crops Consortium (AOCC) successfully initiated the ambitious genome sequencing project of 101 African orphan crops/trees with 6 genomes sequenced, 6 near completion, and 20 currently in progress. Addressing stunting, malnutrition, and hidden hunger through nutritious, economic, and resilient agri-food system is one of the major agricultural challenges of this ce ...
DOI:
10.1007/s00425-019-03156-9

15. A full-length transcriptome of Sepia esculenta using a combination of single-molecule long-read (SMRT) and Illumina sequencing

Author:
Zhang, Jinyong; Liu, Changlin; He, Muchun; Xiang, Zilong; Yin, Yanan; Liu, Shufang; Zhuang, ZhiMeng
Source:
Marine genomics 2019 v.43 pp. 54-57
ISSN:
1874-7787
Subject:
transcriptome,   etc   ; Sepia; animal ovaries; brain; databases; developmental stages; genomics; messenger RNA; microsatellite repeats; muscles; overfishing; reproduction; sequence analysis; spawning;     Show all 14 Subjects
Abstract:
... As an economically important cephalopods species, wild-caught Sepia esculenta fishery has suffered a server decline due to over-fishing and ocean environmental damage. To restore this seriously declining fishery resource, we should understand the genetic foundation and molecular mechanism of spawning, reproduction and mortal of golden cuttlefish. In this study, we generated the full-length transcr ...
DOI:
10.1016/j.margen.2018.08.008

16. A Gain-of-Function Screen Reveals Redundant ERF Transcription Factors Providing Opportunities for Resistance Breeding Toward the Vascular Fungal Pathogen Verticillium longisporum

Author:
Fröschel, Christian; Iven, Tim; Walper, Elisabeth; Bachmann, Vanessa; Weiste, Christoph; Dröge-Laser, Wolfgang
Source:
Molecular plant-microbe interactions 2019 v.32 no.9 pp. 1095-1109
ISSN:
0894-0282
Subject:
transcriptome,   etc   ; Arabidopsis thaliana; Brassica napus; Verticillium longisporum; biosynthesis; breeding; crop losses; crops; engineering; ethylene; fungi; gain-of-function mutation; gene activation; genes; genetic engineering; glucosinolates; indoles; leaves; loss-of-function mutation; mutants; open reading frames; pathogens; roots; transcription factors;     Show all 24 Subjects
Abstract:
... Verticillium longisporum is a vascular fungal pathogen leading to severe crop loss, particular in oilseed rape. Transcription factors (TF) are highly suited for genetic engineering of pathogen-resistant crops, as they control sets of functionally associated genes. Applying the AtTORF-Ex (Arabidopsis thaliana transcription factor open reading frame expression) collection, a simple and robust screen ...
DOI:
10.1094/MPMI-02-19-0055-R

17. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

Author:
Gasperini, Molly; Hill, Andrew J.; McFaline-Figueroa, José L.; Martin, Beth; Kim, Seungsoo; Zhang, Melissa D.; Jackson, Dana; Leith, Anh; Schreiber, Jacob; Noble, William S.; Trapnell, Cole; Ahituv, Nadav; Shendure, Jay
Source:
Cell 2019 v.176 no.1-2 pp. 377-390.e19
ISSN:
0092-8674
Subject:
transcriptome,   etc   ; genome; genomics; human genetics; humans; linkage disequilibrium; quantitative trait loci; regulatory sequences; sequence analysis; transcription factors;     Show all 10 Subjects
Abstract:
... Over one million candidate regulatory elements have been identified across the human genome, but nearly all are unvalidated and their target genes uncertain. Approaches based on human genetics are limited in scope to common variants and in resolution by linkage disequilibrium. We present a multiplex, expression quantitative trait locus (eQTL)-inspired framework for mapping enhancer-gene pairs by i ...
DOI:
10.1016/j.cell.2018.11.029

18. A global survey of full-length transcriptome of Ginkgo biloba reveals transcript variants involved in flavonoid biosynthesis

Author:
Ye, Jiabao; Cheng, Shuiyuan; Zhou, Xian; Chen, Zexiong; Kim, Soo Un; Tan, Junping; Zheng, Jiarui; Xu, Feng; Zhang, Weiwei; Liao, Yongling; Zhu, Yongxing
Source:
Industrial crops and products 2019 v.139 pp. 111547
ISSN:
0926-6690
Subject:
transcriptome,   etc   ; Ginkgo biloba; Oriental traditional medicine; alternative splicing; bioactive compounds; biosynthesis; flavonoids; gene expression; gene regulatory networks; genetic engineering; medicinal plants; messenger RNA; structural genes; surveys; tissues; transcription factors;     Show all 16 Subjects
Abstract:
... Ginkgo biloba, which contains flavonoids as bioactive components, is widely used in traditional Chinese medicine. Increasing the flavonoid production of medicinal plants through genetic engineering generally focuses on the key genes involved in flavonoid biosynthesis. However, the molecular mechanisms underlying such biosynthesis are not yet well understood. To understand these mechanisms, a combi ...
DOI:
10.1016/j.indcrop.2019.111547

19. Alterations in transcriptome and antioxidant activity of naturally aged mice exposed to selenium-rich rice

Author:
Zeng, Rui; Liang, Yuanke; Farooq, Muhammad Umer; Zhang, Yujie; Ei, Hla Hla; Tang, Zhichen; Zheng, Tengda; Su, Yang; Ye, Xiaoying; Jia, Xiaomei; Zhu, Jianqing
Source:
Environmental science and pollution research international 2019 v.26 no.17 pp. 17834-17844
ISSN:
0944-1344
Subject:
transcriptome,   etc   ; antioxidant activity; antioxidants; apoptosis; blood serum; cardiovascular diseases; catalytic activity; diet; genes; glutathione peroxidase; heart; humans; immune system; liver; longevity; metabolism; methane; mice; rice; risk; selenium; sequence analysis; superoxide dismutase; tissues;     Show all 24 Subjects
Abstract:
... Selenium (Se) is a vital element which leads to strong antioxidation in animals and humans. However, the mechanism underlying natural cereal Se–induced biological changes is not well understood. This study intended to explore the gene differential expression in naturally aged mice exposed to selenium by RNA-Seq technique. A total spectrum of 53 differentially expressed genes was quantified in mice ...
DOI:
10.1007/s11356-019-05226-7

20. Alternative metabolic routes in channeling xylose to cordycepin production of Cordyceps militaris identified by comparative transcriptome analysis

Author:
Wongsa, Boontariga; Raethong, Nachon; Chumnanpuen, Pramote; Wong-ekkabut, Jirasak; Laoteng, Kobkul; Vongsangnak, Wanwipa
Source:
Genomics 2019
ISSN:
0888-7543
Subject:
transcriptome,   etc   ; Cordyceps militaris; adenosine monophosphate; biomass; biosynthesis; carbon; cordycepin; gene expression regulation; genes; glutamic acid; growth models; metabolites; pentoses; quantitative polymerase chain reaction; transcription (genetics); transcriptomics; xylose;     Show all 17 Subjects
Abstract:
... The responsive mechanism of C. militaris TBRC7358 on xylose utilization was investigated by comparative analysis of transcriptomes, growth kinetics and cordycepin productions. The result showed that the culture grown on xylose exhibited high production yield of cordycepin on dry biomass. Comparing xylose to other carbon sources, a set of significantly up-regulated genes in xylose were enriched in ...
DOI:
10.1016/j.ygeno.2019.04.015

21. Alternative polyadenylation coordinates embryonic development, sexual dimorphism and longitudinal growth in Xenopus tropicalis

Author:
Zhou, Xiang; Zhang, Yangzi; Michal, Jennifer J.; Qu, Lujiang; Zhang, Shuwen; Wildung, Mark R.; Du, Weiwei; Pouchnik, Derek J.; Zhao, Hui; Xia, Yin; Shi, Honghua; Ji, Guoli; Davis, Jon F.; Smith, Gary D.; Griswold, Michael D.; Harland, Richard M.; Jiang, Zhihua
Source:
Cellular and molecular life sciences 2019 v.76 no.11 pp. 2185-2198
ISSN:
1420-682X
Subject:
transcriptome,   etc   ; Xenopus tropicalis; embryogenesis; females; frogs; genes; information exchange; males; messenger RNA; sexual dimorphism; young adults;     Show all 11 Subjects
Abstract:
... RNA alternative polyadenylation contributes to the complexity of information transfer from genome to phenome, thus amplifying gene function. Here, we report the first X. tropicalis resource with 127,914 alternative polyadenylation (APA) sites derived from embryos and adults. Overall, APA networks play central roles in coordinating the maternal–zygotic transition (MZT) in embryos, sexual dimorphism ...
DOI:
10.1007/s00018-019-03036-1
CHORUS:
10.1007/s00018-019-03036-1

22. Alternative splicing coupled to nonsense-mediated mRNA decay contributes to the high-altitude adaptation of maca (Lepidium meyenii)

Author:
Shi, Yong; Su, Zechun; Yang, Hong; Wang, Wenzhi; Jin, Guihua; He, Guiqing; Siddique, Abu Nasar; Zhang, Liangsheng; Zhu, Andan; Xue, Runguang; Zhang, Chengjun
Source:
Gene 2019 v.694 pp. 7-18
ISSN:
0378-1119
Subject:
transcriptome,   etc   ; Lepidium meyenii; alpine plants; alternative splicing; altitude; cold; immunity; introns; messenger RNA; mitochondria; non-coding RNA; plant communities; proteins; sequence analysis; stress response; terrestrial ecosystems; transcription (genetics);     Show all 17 Subjects
Abstract:
... Alpine plants remain the least studied plant communities in terrestrial ecosystems. However, how they adapt to high-altitude environments is far from clear. Here, we used RNA-seq to investigate a typical alpine plant maca (Lepidium meyenii) to understand its high-altitude adaptation at transcriptional and post-transcriptional level. At transcriptional level, we found that maca root significantly u ...
DOI:
10.1016/j.gene.2018.12.082

23. Ammonia induces Treg/Th1 imbalance with triggered NF-κB pathway leading to chicken respiratory inflammation response

Author:
Shi, Qunxiang; Wang, Wei; Chen, Menghao; Zhang, Hongfu; Xu, Shiwen
Source:
The Science of the total environment 2019 v.659 pp. 354-362
ISSN:
0048-9697
Subject:
transcriptome,   etc   ; Western blotting; air pollutants; air pollution; ammonia; bioinformatics; chickens; cytochrome P-450; genes; heat shock proteins; humans; immune response; inflammation; models; particulates; quantitative polymerase chain reaction; respiratory system; reverse transcriptase polymerase chain reaction; risk; scanning electron microscopy; secretion; toxicity; tracheitis; transcription factor NF-kappa B;     Show all 24 Subjects
Abstract:
... Ammonia (NH3) is a severe air pollutant and a component of haze (PM2.5). The respiratory tract is the first route of exogenous ammonia's entry into the human and animal body. Many studies have suggested that exposure to NH3 is associated with a higher risk of respiratory tract tracheitis; however, the underlying mechanism remains unclear. In this study, chicken tracheas were used as a model to inv ...
DOI:
10.1016/j.scitotenv.2018.12.375

24. A moderately high level of dietary lipid inhibited the protein secretion function of liver in juvenile tiger puffer Takifugu rubripes

Author:
Xu, Houguo; Liao, Zhangbin; Zhang, Qinggong; Wei, Yuliang; Liang, Mengqing
Source:
Aquaculture 2019 v.498 pp. 17-27
ISSN:
0044-8486
Subject:
transcriptome,   etc   ; DNA replication; Takifugu rubripes; blood serum; dietary fat; endoplasmic reticulum; enzyme activity; experimental diets; fat intake; feed conversion; fish; gene ontology; genes; growth performance; high fat diet; histology; intestines; juveniles; lipids; liver; protein secretion; protein synthesis; proteins; tanks; transcription (genetics);     Show all 25 Subjects
Abstract:
... Tiger puffer have a unique lipid storage pattern. They store lipid predominantly in liver. To investigate the hepatic physiology of tiger puffer in response to a moderately high level of dietary lipid, a 74-day feeding trial was conducted, followed by a hepatic transcriptome assay. Two experimental diets which had an optimal (10.44%, Control) or moderately higher (14.64%, high-lipid diet, HL) diet ...
DOI:
10.1016/j.aquaculture.2018.08.033

25. A molecular survey of programmed cell death in rainbow trout: Structural and functional specifications of apoptotic key molecules

Author:
Verleih, Marieke; Borchel, Andreas; Rebl, Alexander; Brenmoehl, Julia; Kühn, Carsten; Goldammer, Tom
Source:
Comparative biochemistry and physiology 2019 v.230 pp. 57-69
ISSN:
1096-4959
Subject:
transcriptome,   etc   ; Oncorhynchus mykiss; adults; apoptosis; brain; caspase-3; cell lines; genes; homeostasis; humans; immune response; kidneys; messenger RNA; meta-analysis; protein content; regulatory proteins; staurosporine; surveys; temperature; tissues; trout;     Show all 21 Subjects
Abstract:
... Apoptosis is an integral part of homeostasis and supports multiple physiological processes such as development and immune defense, thereby directly targeting damaged or unwanted cells without affecting neighbor cells. In the present study, we characterized the apoptotic key factors caspase-3, −7, and − 8 as well as regulator protein TPT1 (translationally-controlled tumor protein 1) from rainbow tr ...
DOI:
10.1016/j.cbpb.2019.01.012

26. Analyses of genome‐scale variation reveal divergence of two Sinalliaria species (Brassicaceae) with continuous but limited gene flow

Author:
Wang, Tian‐Jing; Ru, Da‐Fu; Zhang, Dan; Hu, Quan‐Jun
Source:
Journal of systematics and evolution 2019 v.57 no.3 pp. 268-277
ISSN:
1674-4918
Subject:
transcriptome,   etc   ; Alliaria; climate change; divergent evolution; gene expression regulation; gene flow; gene frequency; genes; genetic variation; genomics; models; phytogeography; single nucleotide polymorphism; species diversity; China;     Show all 15 Subjects
Abstract:
... Numerous biogeographic studies have suggested that geographic isolations triggered by Quaternary climatic changes could have contributed greatly to the high species diversity of eastern Asia. However, little is known about how speciation proceeded during the evolutionary divergence of sister species in this region. In this study, we examined genomic divergence and investigated the speciation proce ...
DOI:
10.1111/jse.12461

27. Analysing the rice young panicle transcriptome reveals the gene regulatory network controlled by TRIANGULAR HULL1

Author:
Wang, Jun; Zhang, Qiang; Wang, Yi; Huang, Jing; Luo, Nengjie; Wei, Shengbo; Jin, Jian
Source:
Rice 2019 v.12 no.1 pp. 6
ISSN:
1939-8425
Subject:
transcriptome,   etc   ; filling period; gene expression regulation; gene regulatory networks; genes; heterozygosity; homozygosity; metabolism; mutation; panicles; plant hormones; rice; signal transduction; starch; sucrose; transgenic plants;     Show all 16 Subjects
Abstract:
... BACKGROUND: TRIANGULAR HULL1 (TH1), a member of the rice ALOG gene family, has been characterized as a rice lemma/palea-related gene. To understand the gene regulatory network that controlled by TH1, we analyzed the transcriptome from a TH1 knock out (KO) line, which was generated by CRISPR/Cas9. Our study may shed some light on the molecular mechanism of lemma/palea development. RESULTS: We obtai ...
DOI:
10.1186/s12284-019-0265-2

28. Analysis of ambient temperature-responsive transcriptome in shoot apical meristem of heat-tolerant and heat-sensitive broccoli inbred lines during floral head formation

Author:
Lin, Chung-Wen; Fu, Shih-Feng; Liu, Yu-Ju; Chen, Chi-Chien; Chang, Ching-Han; Yang, Yau-Wen; Huang, Hao-Jen
Source:
BMC plant biology 2019 v.19 no.1 pp. 3
ISSN:
1471-2229
Subject:
transcriptome,   etc   ; Brassica oleracea var. italica; DNA; apical meristems; biomarkers; broccoli; calcium signaling; genes; genotype; heat shock proteins; heat stress; heat tolerance; homeostasis; marker-assisted selection; microsatellite repeats; mitogen-activated protein kinase; models; reactive oxygen species; summer; temperature; thermosensitivity; transcriptomics; Taiwan;     Show all 23 Subjects
Abstract:
... BACKGROUND: Head formation of broccoli (Brassica oleracea var. italica) is greatly reduced under high temperature (22 °C and 27 °C). Broccoli inbred lines that are capable of producing heads at high temperatures in summer are varieties that are unique to Taiwan. However, knowledge of the early-activated pathways of broccoli head formation under high temperature is limited. RESULTS: We compared hea ...
DOI:
10.1186/s12870-018-1613-x

29. Analysis of Chromosomal Numbers, Mitochondrial Genome, and Full-Length Transcriptome of Onychostoma brevibarba

Author:
Hu, Fangzhou; Fan, Jingjing; Wu, Chang; Zhu, Ming; Zhou, Yunfan; Wang, Shi; Zhang, Chun; Tao, Min; Zhao, Rurong; Tang, Chenchen; Luo, Kaikun; Qin, Qinbo; Ma, Ming; Chen, Bo; Wang, Jinpu; Zhou, Aiguo; Bai, Liangxiong; Liu, Shaojun
Source:
Marine biotechnology 2019 v.21 no.4 pp. 515-525
ISSN:
1436-2228
Subject:
transcriptome,   etc   ; Onychostoma; basins; chromosome number; chromosomes; data collection; diploidy; genomics; karyotyping; mitochondrial genome; rivers; tissues; unigenes; China; Yangtze River;     Show all 15 Subjects
Abstract:
... Onychostoma brevibarba is a new discovered species which is distributed in Xiang Jiang River of the middle Chang Jiang basin in Hunan Province, South China. In this study, the ploidy levels of O. brevibarba were confirmed by counting chromosomal numbers and analyzing karyotype. The complete mitochondrial genome of O. brevibarba was determined and analyzed. Besides, we firstly performed the full-le ...
DOI:
10.1007/s10126-019-09899-6

30. Analysis of codon usage patterns in “Lonicerae Flos” (Lonicera macranthoides Hand. -Mazz.) based on transcriptome data

Author:
Liu, Sisi; Qiao, Zhongquan; Wang, Xiaoming; Zeng, Huijie; Li, Yongxin; Cai, Neng; Chen, Yi
Source:
Gene 2019 v.705 pp. 127-132
ISSN:
0378-1119
Subject:
transcriptome,   etc   ; Lonicera; codons; correspondence analysis; evolution; gene expression; genetic engineering; mutation; prediction; transcriptomics; China;     Show all 11 Subjects
Abstract:
... Lonicera macranthoides Hand. -Mazz. is an important medicinal and economical plant in China, however, the codon usage bias (CUB) in L. macranthoides genes is still unknown. In this study, L. macranthoides transcriptome sequencing has been completed, and codon usage patterns in 36,090 reconstructed genes from the L. macranthoides transcriptome were examined. The mean GC content and GC3 value is 44. ...
DOI:
10.1016/j.gene.2019.04.065

31. Analysis of the Babesia microti proteome in infected red blood cells by a combination of nanotechnology and mass spectrometry

Author:
Magni, Ruben; Luchini, Alessandra; Liotta, Lance; Molestina, Robert E.
Source:
International journal for parasitology 2019 v.49 no.2 pp. 139-144
ISSN:
0020-7519
Subject:
transcriptome,   etc   ; Babesia microti; DNA; RNA; acute course; biosynthesis; carbohydrates; diagnostic techniques; energy metabolism; erythrocytes; genome; immune response; infectious diseases; lipids; mass spectrometry; nanotechnology; parasites; proteins; proteolysis; proteome; proteomics; surface antigens; translation (genetics);     Show all 23 Subjects
Abstract:
... Proteomics of Babesia microti has lagged behind other apicomplexans despite recent genome and transcriptome studies. Here, we used a combination of nanotechnology and mass spectrometry to provide a proteomic profile of B. microti acute infection. We identified ∼500 parasite proteins in blood with functions such as transport, carbohydrate and energy metabolism, proteolysis, DNA and RNA metabolism, ...
DOI:
10.1016/j.ijpara.2018.08.004

32. Analysis of the diversity and tissue specificity of sucrose synthase genes in the long read transcriptome of sugarcane

Author:
Thirugnanasambandam, Prathima P.; Mason, Patrick J.; Hoang, Nam V.; Furtado, Agnelo; Botha, Frederik C.; Henry, Robert J.
Source:
BMC plant biology 2019 v.19 no.1 pp. 160
ISSN:
1471-2229
Subject:
transcriptome,   etc   ; Saccharum officinarum; Saccharum spontaneum; corn; culms; gene expression regulation; genotype; internodes; introns; leaves; messenger RNA; polyploidy; roots; sucrose; sucrose synthase; sugarcane; tissues;     Show all 17 Subjects
Abstract:
... BACKGROUND: Sugarcane accumulates very high levels of sucrose in the culm. Elucidation of the molecular mechanisms that allows such high sucrose synthesis and accumulation (up to 650 mM) is made difficult by the complexity of the highly polyploid genome. Here we report the use of RNA Seq data to characterize the sucrose synthase (SuSy) genes expressed in the transcriptome of the mature sugarcane p ...
DOI:
10.1186/s12870-019-1733-y

33. Analysis of the expression of transcription factors and other genes associated with aleurone layer development in wheat endosperm

Author:
Nirmal, Ravi C.; Singh, Amit Kumar; Furtado, Agnelo; Henry, Robert J.
Source:
Journal of cereal science 2019 v.85 pp. 62-69
ISSN:
0733-5210
Subject:
transcriptome,   etc   ; aleurone layer; alleles; chromosomes; cultivars; endosperm; epistasis; flowering; gene expression; messenger RNA; seed development; sequence analysis; tissues; transcription factors; wheat;     Show all 15 Subjects
Abstract:
... Defective kernel1 (dek1), crinkly4 (cr4) and supernumerary aleurone layer 1 (sal1) have been suggested as key genes involved in aleurone differentiation in cereals. Transcription factors (TFs) may play a role in regulation of aleurone development by controlling the expression of genes involved in this process. In this study, expression patterns of TFs in developing aleurone and starchy endosperm t ...
DOI:
10.1016/j.jcs.2018.11.010

34. Analysis of the Gynaephora qinghaiensis pupae immune transcriptome in response to parasitization by Thektogaster sp

Author:
Wang, Hai‐Zhen; Zhong, Xin; Gu, Li; Li, Shao‐Song; Zhang, Gu‐Ren; Liu, Xin
Source:
Archives of insect biochemistry and physiology 2019 v.100 no.3 pp. e21553
ISSN:
0739-4462
Subject:
transcriptome,   etc   ; Gynaephora; biological control; databases; endoparasitoids; gene expression regulation; grasslands; hosts; immune response; parasitism; pupae; spawning; transcriptomics; unigenes; China;     Show all 15 Subjects
Abstract:
... As a pest on the Qinghai‐Tibet Plateau, Gynaephora qinghaiensis causes severe damage to grassland vegetation and its pupae are also natural hosts of Thektogaster sp. To successfully parasitize, endoparasitoids generally introduce or secrete multiple parasitic factors into the host body during the spawning stage to suppress the host immune response. To study the parasitic effects of Thektogaster sp ...
DOI:
10.1002/arch.21533

35. Analysis of the molecular basis of fruit cracking susceptibility in Litchi chinensis cv. Baitangying by transcriptome and quantitative proteome profiling

Author:
Wang, Jugang; Gao, Xiaomin; Ma, Zhiling; Chen, Jing; Liu, Yanan
Source:
Journal of plant physiology 2019 v.234-235 pp. 106-116
ISSN:
0176-1617
Subject:
transcriptome,   etc   ; Litchi chinensis; cultivars; fruit cracking; genes; orchards; oxidation; pericarp; photosynthesis; proteins; proteome; proteomics; transcriptomics; translation (genetics); unsaturated fatty acids;     Show all 15 Subjects
Abstract:
... Fruit cracking is a serious problem in Litchi chinensis cv. Baitangying orchards, but few advances have been made in understanding the molecular basis of cracking susceptibility in 'Baitangying'. In this work, we conducted transcriptome and quantitative proteome analyses of the pericarps of three kinds of litchi: noncracking 'Feizixiao' (cracking-resistant cultivar, F), noncracking 'Baitangying' ( ...
DOI:
10.1016/j.jplph.2019.01.014

36. Analysis of the role of geranylgeranyl diphosphate synthase 8 from Tripterygium wilfordii in diterpenoids biosynthesis

Author:
Su, Ping; Gao, Linhui; Tong, Yuru; Guan, Hongyu; Liu, Shuang; Zhang, Yifeng; Zhao, Yujun; Wang, Jiadian; Hu, Tianyuan; Tu, Lichan; Zhou, Jiawei; Ma, Baowei; Huang, Luqi; Gao, Wei
Source:
Plant science 2019 v.285 pp. 184-192
ISSN:
0168-9452
Subject:
transcriptome,   etc   ; Tripterygium wilfordii; biochemical pathways; biosynthesis; catalytic activity; chloroplasts; dimethylallyltranstransferase; diterpenoids; genes; geranylgeranyl diphosphate synthase; roots; terpene synthases;     Show all 12 Subjects
Abstract:
... Tripterygium wilfordii is known to contain various types of bioactive diterpenoids that exhibit many remarkable activities. Many studies have recently been targeted toward the elucidation of the diterpenoids biosynthetic pathways in attempts to obtain these compounds with a view to solving the dilemma of low yield in plants. However, the short-chain prenyltransferases (SC-PTSs) responsible for the ...
DOI:
10.1016/j.plantsci.2019.05.013

37. Analysis of transcripts and splice isoforms in Medicago sativa L. by single-molecule long-read sequencing

Author:
Chao, Yuehui; Yuan, Jianbo; Guo, Tao; Xu, Lixin; Mu, Zhiyuan; Han, Liebao
Source:
Plant molecular biology 2019 v.99 no.3 pp. 219-235
ISSN:
0167-4412
Subject:
transcriptome,   etc   ; Medicago sativa; alfalfa; alternative splicing; forage; high-throughput nucleotide sequencing; introns; leaves; messenger RNA; microsatellite repeats; non-coding RNA; open reading frames; transcription factors;     Show all 13 Subjects
Abstract:
... KEY MESSAGE: The full-length transcriptome of alfalfa was analyzed with PacBio single-molecule long-read sequencing technology. The transcriptome data provided full-length sequences and gene isoforms of transcripts in alfalfa, which will improve genome annotation and enhance our understanding of the gene structure of alfalfa. As an important forage, alfalfa (Medicago sativa L.) is world-wide plant ...
DOI:
10.1007/s11103-018-0813-y

38. Analysis of venom sac constituents from the solitary, aculeate wasp Cerceris rybyensis

Author:
Kote, Sachin; Faktor, Jakub; Dapic, Irena; Mayordomo, Marcos Yebenes; Kocikowski, Mikołaj; Kagansky, Alexander; Goodlett, David; Vojtesek, Borivoj; Hupp, Ted; Wilcockson, David; Piper, Ross
Source:
Toxicon 2019 v.169 pp. 1-4
ISSN:
0041-0101
Subject:
transcriptome,   etc   ; Cerceris; mass spectrometry; parasitic wasps; proteome; proteomics; venoms; wasps;     Show all 8 Subjects
Abstract:
... Solitary aculeate wasps are abundant and diverse hymenopteran insects that disable prey using venom. The venom may possess neuromodulation, immunomodulatory, metabolic-modulatory and antimicrobial functions. Venom analysis of transcriptomes and proteomes has been previously performed in social and parasitoid wasp species. We develop methodologies including mass spectrometry-based shotgun proteomic ...
DOI:
10.1016/j.toxicon.2019.07.012

39. Analysis on Microsatellite Loci of Daphnia similoides sinensis and Rapid Development of Primer Based on Transcriptome Sequencing

Author:
Wu, J. X.; Zhang, Y.-N.; Deng, D. D.; Xu, X. X.; Zhou, Z. Z.
Source:
Russian journal of genetics 2019 v.55 no.6 pp. 711-719
ISSN:
1022-7954
Subject:
transcriptome,   etc   ; Daphnia; alleles; capillary electrophoresis; evolution; genetic variation; loci; microsatellite repeats; oligodeoxyribonucleotides; polyacrylamide gel electrophoresis; transcriptomics;     Show all 11 Subjects
Abstract:
... In this study, we performed transcriptome sequencing of D. similoides sinensis and developing of simple sequence repeats (SSRs) markers to identify valuable markers for Daphnia molecular genetics. The total length of D. similoides sinensis transcriptome sequence was 40 093 546 bp, which contained 12 017 SSR markers and 21 344 microsatellite loci. 2164 SSR primer pairs were obtained through design ...
DOI:
10.1134/S1022795419060188

40. An Effector, BxSapB1, Induces Cell Death and Contributes to Virulence in the Pine Wood Nematode Bursaphelenchus xylophilus

Author:
Hu, Long-Jiao; Wu, Xiao-Qin; Li, Hai-Yang; Zhao, Qun; Wang, Yuan-Chao; Ye, Jian-Ren
Source:
Molecular plant-microbe interactions 2019 v.32 no.4 pp. 452-463
ISSN:
0894-0282
Subject:
transcriptome,   etc   ; Bursaphelenchus xylophilus; Nicotiana benthamiana; Pinus thunbergii; RNA interference; apoplast; cell death; coniferous forests; in situ hybridization; pathogenesis-related proteins; plant diseases and disorders; plant parasitic nematodes; protein-serine-threonine kinases; signal peptide; virulence; virulent strains; yeasts; China;     Show all 18 Subjects
Abstract:
... The pine wood nematode (PWN) Bursaphelenchus xylophilus has caused serious damage to pine forests in China. Effectors secreted by phytonematodes play a role in host infection. We identified and characterized an effector, BxSapB1, based on the B. xylophilus transcriptome at the early stages of infection and the transient expression of proteins in Nicotiana benthamiana. BxSapB1 triggered cell death ...
DOI:
10.1094/MPMI-10-18-0275-R

41. A Network Module for the Perseus Software for Computational Proteomics Facilitates Proteome Interaction Graph Analysis

Author:
Rudolph, Jan Daniel; Cox, Jürgen
Source:
Journal of proteome research 2019 v.18 no.5 pp. 2052-2064
ISSN:
1535-3907
Subject:
transcriptome,   etc   ; cell communication; computer software; phosphorylation; post-translational modification; proteins; proteome; proteomics; statistical analysis;     Show all 9 Subjects
Abstract:
... Proteomics data analysis strongly benefits from not studying single proteins in isolation but taking their multivariate interdependence into account. We introduce PerseusNet, the new Perseus network module for the biological analysis of proteomics data. Proteomics is commonly used to generate networks, e.g., with affinity purification experiments, but networks are also used to explore proteomics d ...
DOI:
10.1021/acs.jproteome.8b00927

42. An E3 ubiquitin ligase TRIM9 is involved in WSSV infection via interaction with β-TrCP

Author:
Sun, Mingzhe; Li, Shihao; Yu, Kuijie; Xiang, Jianhai; Li, Fuhua
Source:
Developmental and comparative immunology 2019 v.97 pp. 57-63
ISSN:
0145-305X
Subject:
transcriptome,   etc   ; Litopenaeus vannamei; RNA; White spot syndrome virus; amino acid sequences; antimicrobial peptides; apoptosis; autophagy; cell differentiation; gene expression; intestines; shrimp; signal transduction; tissues; transcription factor NF-kappa B; two hybrid system techniques; ubiquitin-protein ligase; viruses;     Show all 18 Subjects
Abstract:
... The TRIpartite Motif (TRIM) proteins are known to play key roles in cell differentiation, apoptosis, development, autophagy and innate immunity. In the present study, a TRIM9 homolog (named LvTRIM9) was identified from the transcriptome of the Pacific whiteleg shrimp Litopenaeus vannamei. The deduced amino acid sequence of LvTRIM9 possessed typical features of TRIMs, consisting of a RING domain, t ...
DOI:
10.1016/j.dci.2019.03.014

43. A new species of Echinoderes (Cyclorhagida: Echinoderidae) from the San Juan Islands, Washington State, USA, and insights into the kinorhynch transcriptome

Author:
Varney, Rebecca M.; Funch, Peter; Kocot, Kevin M.; Sørensen, Martin V.
Source:
Zoologischer Anzeiger 2019 v.282 pp. 52-63
ISSN:
0044-5231
Subject:
transcriptome,   etc   ; islands; new geographic records; new species; Washington (state);     Show all 5 Subjects
Abstract:
... A new kinorhynch species, Echinoderes kohni sp. nov., is described from the San Juan Archipelago, northwest Washington State, USA. The species’ spine/tube distribution combined with the presence of long, spiniform tergal extensions assign it to the Echinoderes spinifurca species group. It is distinguished from other species in the group by its enlarged fringe tips on the posterior sternal plate ma ...
DOI:
10.1016/j.jcz.2019.06.003

44. An important resource for understanding bio-adhesion mechanisms: Cement gland transcriptomes of two goose barnacles, Pollicipes pollicipes and Lepas anatifera (Cirripedia, Thoracica)

Author:
Machado, André M.; Sarropoulou, Elena; Castro, L. Filipe C.; Vasconcelos, Vitor; Cunha, Isabel
Source:
Marine genomics 2019 v.45 pp. 16-20
ISSN:
1874-7787
Subject:
transcriptome,   etc   ; Lepas anatifera; Pollicipes; Thoracica; adhesives; bioadhesion; biofouling; biotechnology; cement glands; estuaries; genes; high-throughput nucleotide sequencing;     Show all 12 Subjects
Abstract:
... Barnacles are sessile organisms globally distributed in marine and estuarine environments. The production of protein-based adhesives by cement glands is crucial for these organisms and plays a vital role in substrate attachment, thus inspiring biotechnological applications. Moreover, barnacles belong to bio-fouling communities, whose fixation onto man-made surfaces is of interest in terms of contr ...
DOI:
10.1016/j.margen.2018.11.001

45. An integrated analysis of mRNA and miRNA in skeletal muscle from myostatin-edited Meishan pigs

Author:
Xie, Shanshan; Li, Xiang; Qian, Lili; Cai, Chunbo; Xiao, Gaojun; Jiang, Shengwang; Li, Biao; Gao, Ting; Cui, Wentao
Source:
Genome 2019 v.62 no.5 pp. 305-315
ISSN:
1480-3321
Subject:
transcriptome,   etc   ; Meishan; gene expression regulation; genes; genetic engineering; growth and development; hypertrophy; loss-of-function mutation; messenger RNA; microRNA; muscles; myostatin; sequence analysis; signal transduction; skeletal muscle; swine; transcriptomics; transforming growth factor beta;     Show all 18 Subjects
Abstract:
... Myostatin (MSTN) is a key muscle factor that negatively regulates skeletal muscle growth and development. Our laboratory recently produced genetically engineered Meishan pigs containing a ZFN-edited MSTN loss-of-function mutation (MSTN⁻/⁻, MKO) that led to the hypertrophy of skeletal muscles. In this study, we performed transcriptome sequencing and miRNA sequencing in skeletal muscle samples from ...
DOI:
10.1139/gen-2018-0110

46. An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses

Author:
dos Santos, Tiago Benedito; Soares, João D. M.; Lima, Joni E.; Silva, Juliana C.; Ivamoto, Suzana T.; Baba, Viviane Y.; Souza, Silvia G. H.; Lorenzetti, Alan P. R.; Paschoal, Alexandre R.; Meda, Anderson R.; Nishiyama Júnior, Milton Y.; de Oliveira, Úrsula C.; Mokochinski, João B.; Guyot, Romain; Junqueira-de-Azevedo, Inácio L. M.; Figueira, Antônio V. O.; Mazzafera, Paulo; Júnior, Osvaldo R.; Vieira, Luiz G. E.; Pereira, Luiz F. P.; Domingues, Douglas S.
Source:
Functional & integrative genomics 2019 v.19 no.1 pp. 151-169
ISSN:
1438-793X
Subject:
transcriptome,   etc   ; Coffea arabica; acclimation; ammonium; asparagine; crops; genes; glutamic acid; messenger RNA; microRNA; nitrates; nitrogen; nutrient deficiencies; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; roots; sequence analysis; starvation; transcription (genetics);     Show all 19 Subjects
Abstract:
... Coffea arabica L. is an important agricultural commodity, accounting for 60% of traded coffee worldwide. Nitrogen (N) is a macronutrient that is usually limiting to plant yield; however, molecular mechanisms of plant acclimation to N limitation remain largely unknown in tropical woody crops. In this study, we investigated the transcriptome of coffee roots under N starvation, analyzing poly-A+ libr ...
DOI:
10.1007/s10142-018-0634-8

47. An odorant receptor mediates the attractiveness of cis‐jasmone to Campoletis chlorideae, the endoparasitoid of Helicoverpa armigera

Author:
Sun, Y.‐L.; Dong, J.‐F.; Ning, C.; Ding, P.‐P.; Huang, L.‐Q.; Sun, J.‐G.; Wang, C.‐Z.
Source:
Insect molecular biology 2019 v.28 no.1 pp. 23-34
ISSN:
0962-1075
Subject:
transcriptome,   etc   ; Campoletis chlorideae; Helicoverpa armigera; adults; antennae; bioassays; endoparasitoids; females; hosts; jasmone; larvae; males; messenger RNA; odor compounds; odorant receptors; oocytes; parasitic wasps; parasitism; reverse transcriptase polymerase chain reaction; smell; tobacco;     Show all 21 Subjects
Abstract:
... Parasitic wasps rely on olfaction to locate their hosts in complex chemical environments. Odorant receptors (ORs) function together with well‐conserved odorant coreceptors (ORcos) to determine the sensitivity and specificity of olfactory reception. Campoletis chlorideae (Hymenoptera: Ichneunmonidae) is a solitary larval endoparasitoid of the cotton bollworm, Helicoverpa armigera, and some other no ...
DOI:
10.1111/imb.12523

48. Anopheles aquasalis transcriptome reveals autophagic responses to Plasmodium vivax midgut invasion

Author:
Santana, Rosa Amélia Gonçalves; Oliveira, Maurício Costa; Cabral, Iria; Junior, Rubens Celso Andrade Silva; de Sousa, Débora Raysa Teixeira; Ferreira, Lucas; Lacerda, Marcus Vinícius Guimarães; Monteiro, Wuelton Marcelo; Abrantes, Patrícia; Guerra, Maria das Graças Vale Barbosa; Silveira, Henrique
Source:
Parasites & vectors 2019 v.12 no.1 pp. 261
ISSN:
1756-3305
Subject:
transcriptome,   etc   ; Anopheles aquasalis; Plasmodium vivax; antimalarials; autophagy; cDNA libraries; complementary DNA; control methods; epithelium; gametocytes; gene expression regulation; genes; malaria; messenger RNA; midgut; parasites; quality control; spermidine; transcription (genetics); transcriptomics;     Show all 20 Subjects
Abstract:
... BACKGROUND: Elimination of malaria depends on mastering transmission and understanding the biological basis of Plasmodium infection in the vector. The first mosquito organ to interact with the parasite is the midgut and its transcriptomic characterization during infection can reveal effective antiplasmodial responses able to limit the survival of the parasite. The vector response to Plasmodium viv ...
DOI:
10.1186/s13071-019-3506-8

49. A novel glutathione S-transferase gene from sweetpotato, IbGSTF4, is involved in anthocyanin sequestration

Author:
Kou, Meng; Liu, Ya-ju; Li, Zong-yun; Zhang, Yun-gang; Tang, Wei; Yan, Hui; Wang, Xin; Chen, Xiao-guang; Su, Zai-xing; Arisha, Mohamed Hamed; Li, Qiang; Ma, Dai-fu
Source:
Plant physiology and biochemistry 2019 v.135 pp. 395-403
ISSN:
0981-9428
Subject:
transcriptome,   etc   ; Arabidopsis thaliana; Cyclamen; Petunia hybrida; anthocyanins; endoplasmic reticulum; genes; glutathione transferase; luciferase; models; mutants; ornamental plants; phylogeny; sweet potatoes; tissues; transportation; vacuoles;     Show all 17 Subjects
Abstract:
... Anthocyanins are synthesized by multi-enzyme complexes localized at the cytoplasmic surface of the endoplasmic reticulum (synthesis site), and transported to the destination site, the vacuole. Three mechanisms for the vacuolar accumulation of anthocyanin in plant species have been proposed. Previous studies have indicated that glutathione S-transferase (GST) genes from model and ornamental plants ...
DOI:
10.1016/j.plaphy.2018.12.028

50. A novel Kunitz protein with proposed dual function from Eudiplozoon nipponicum (Monogenea) impairs haemostasis and action of complement in vitro

Author:
Jedličková, Lucie; Dvořák, Jan; Hrachovinová, Ingrid; Ulrychová, Lenka; Kašný, Martin; Mikeš, Libor
Source:
International journal for parasitology 2019 v.49 no.5 pp. 337-346
ISSN:
0020-7519
Subject:
transcriptome,   etc   ; Cyprinus carpio; Kunitz-type proteinase inhibitor; Monogenea; Pseudonaja; anticoagulants; blood; coagulation; complement; digestion; fibrinolysis; fish; hemostasis; immunohistochemistry; in situ hybridization; kinins; messenger RNA; parasites; parasitism; plasma kallikrein; plasmin; snake venoms;     Show all 22 Subjects
Abstract:
... Serine peptidases are involved in many physiological processes including digestion, haemostasis and complement cascade. Parasites regulate activities of host serine peptidases to their own benefit, employing various inhibitors, many of which belong to the Kunitz-type protein family. In this study, we confirmed the presence of potential anticoagulants in protein extracts of the haematophagous monog ...
DOI:
10.1016/j.ijpara.2018.11.010