scholarly journals Erratum: Corrigendum: Transcriptome analysis identifies genes involved in adventitious branches formation of Gracilaria lichenoides in vitro

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Wenlei Wang ◽  
Huanqin Li ◽  
Xiangzhi Lin ◽  
Shanjun Yang ◽  
Zhaokai Wang ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Gracilaria Lichenoides

scholarly journals Dual RNA-Seq transcriptome analysis of chicken macrophage-like cells (HD11) infected in vitro with Eimeria tenella

Parasitology ◽  
2021 ◽  
Vol 148 (6) ◽  
pp. 712-725
Author(s):  
Arnar K. S. Sandholt ◽  
Feifei Xu ◽  
Robert Söderlund ◽  
Anna Lundén ◽  
Karin Troell ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Eimeria Tenella ◽  
Rna Seq ◽  
Chicken Macrophage

Abstract

scholarly journals Elucidation of the core betalain biosynthesis pathway in Amaranthus tricolor

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yu-Cheng Chang ◽  
Yi-Ching Chiu ◽  
Nai-Wen Tsao ◽  
Yuan-Lin Chou ◽  
Choon-Meng Tan ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Natural Antioxidants ◽  
Biosynthesis Pathway ◽  
Comparative Transcriptome ◽  
Amaranthus Tricolor ◽  
Enzymatic Assays ◽  
Comparative Transcriptome Analysis ◽  
Elevated Expression ◽  
Green Coloration

AbstractAmaranthus tricolor L., a vegetable Amaranthus species, is an economically important crop containing large amounts of betalains. Betalains are natural antioxidants and can be classified into betacyanins and betaxanthins, with red and yellow colors, respectively. A. tricolor cultivars with varying betalain contents, leading to striking red to green coloration, have been commercially produced. However, the molecular differences underlying betalain biosynthesis in various cultivars of A. tricolor remain largely unknown. In this study, A. tricolor cultivars with different colors were chosen for comparative transcriptome analysis. The elevated expression of AmCYP76AD1 in a red-leaf cultivar of A. tricolor was proposed to play a key role in producing red betalain pigments. The functions of AmCYP76AD1, AmDODAα1, AmDODAα2, and AmcDOPA5GT were also characterized through the heterologous engineering of betalain pigments in Nicotiana benthamiana. Moreover, high and low L-DOPA 4,5-dioxygenase activities of AmDODAα1 and AmDODAα2, respectively, were confirmed through in vitro enzymatic assays. Thus, comparative transcriptome analysis combined with functional and enzymatic studies allowed the construction of a core betalain biosynthesis pathway of A. tricolor. These results not only provide novel insights into betalain biosynthesis and evolution in A. tricolor but also provide a basal framework for examining genes related to betalain biosynthesis among different species of Amaranthaceae.

scholarly journals Transcriptome analysis of gravitational effects on mouse skeletal muscles under microgravity and artificial 1 g onboard environment

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Risa Okada ◽  
Shin-ichiro Fujita ◽  
Riku Suzuki ◽  
Takuto Hayashi ◽  
Hirona Tsubouchi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Muscle Mass ◽  
Muscle Atrophy ◽  
Transcriptome Analysis ◽  
Fiber Type ◽  
Expression Profiles ◽  
Space Station ◽  
Gene Expression Profiles

AbstractSpaceflight causes a decrease in skeletal muscle mass and strength. We set two murine experimental groups in orbit for 35 days aboard the International Space Station, under artificial earth-gravity (artificial 1 g; AG) and microgravity (μg; MG), to investigate whether artificial 1 g exposure prevents muscle atrophy at the molecular level. Our main findings indicated that AG onboard environment prevented changes under microgravity in soleus muscle not only in muscle mass and fiber type composition but also in the alteration of gene expression profiles. In particular, transcriptome analysis suggested that AG condition could prevent the alterations of some atrophy-related genes. We further screened novel candidate genes to reveal the muscle atrophy mechanism from these gene expression profiles. We suggest the potential role of Cacng1 in the atrophy of myotubes using in vitro and in vivo gene transductions. This critical project may accelerate the elucidation of muscle atrophy mechanisms.

Analysis of the transcription factors and their regulatory roles during a step-by-step differentiation of induced pluripotent stem cells into hepatocyte-like cells

2019 ◽  
Vol 15 (6) ◽  
pp. 383-398 ◽  
Author(s):  
Yannick Tauran ◽  
Stéphane Poulain ◽  
Myriam Lereau-Bernier ◽  
Mathieu Danoy ◽  
Marie Shinohara ◽  
...  
Keyword(s):  
Stem Cells ◽  
Transcription Factors ◽  
Induced Pluripotent Stem Cells ◽  
Transcriptome Analysis ◽  
Pluripotent Stem Cells ◽  
Original Method ◽  
Induced Pluripotent

Human induced pluripotent stem cells have been investigated through a sequential in vitro step-by-step differentiation into hepatocyte-like cells using nanoCAGE, an original method for promoters, transcription factors, and transcriptome analysis.

scholarly journals De novo transcriptome analysis of the critically endangered alpine Himalayan herb Nardostachys jatamansi reveals the biosynthesis pathway genes of tissue-specific secondary metabolites

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Nisha Dhiman ◽  
Anil Kumar ◽  
Dinesh Kumar ◽  
Amita Bhattacharya
Keyword(s):  
Secondary Metabolites ◽  
Transcriptome Analysis ◽  
Vegetative Growth ◽  
De Novo ◽  
Biosynthesis Pathway ◽  
De Novo Transcriptome ◽  
Tissue Specific ◽  
Nardostachys Jatamansi ◽  
Secondary Metabolite Biosynthesis

Abstract The study is the first report on de novo transcriptome analysis of Nardostachys jatamansi, a critically endangered medicinal plant of alpine Himalayas. Illumina GAIIx sequencing of plants collected during end of vegetative growth (August) yielded 48,411 unigenes. 74.45% of these were annotated using UNIPROT. GO enrichment analysis, KEGG pathways and PPI network indicated simultaneous utilization of leaf photosynthates for flowering, rhizome fortification, stress response and tissue-specific secondary metabolites biosynthesis. Among the secondary metabolite biosynthesis genes, terpenoids were predominant. UPLC-PDA analysis of in vitro plants revealed temperature-dependent, tissue-specific differential distribution of various phenolics. Thus, as compared to 25 °C, the phenolic contents of both leaves (gallic acid and rutin) and roots (p-coumaric acid and cinnamic acid) were higher at 15 °C. These phenolics accounted for the therapeutic properties reported in the plant. In qRT-PCR of in vitro plants, secondary metabolite biosynthesis pathway genes showed higher expression at 15 °C and 14 h/10 h photoperiod (conditions representing end of vegetative growth period). This provided cues for in vitro modulation of identified secondary metabolites. Such modulation of secondary metabolites in in vitro systems can eliminate the need for uprooting N. jatamansi from wild. Hence, the study is a step towards effective conservation of the plant.

RNA sequencing and transcriptome analysis of buffalo ( Bubalus bubalis ) blastocysts produced by somatic cell nuclear transfer and in vitro fertilization

2019 ◽  
Vol 86 (9) ◽  
pp. 1149-1167 ◽  
Author(s):  
Tanushri Jerath Sood ◽  
Swati Viviyan Lagah ◽  
Manishi Mukesh ◽  
Suresh Kumar Singla ◽  
Manmohan Singh Chauhan ◽  
...  
Keyword(s):  
In Vitro Fertilization ◽  
Somatic Cell ◽  
Rna Sequencing ◽  
Transcriptome Analysis ◽  
Somatic Cell Nuclear Transfer ◽  
Nuclear Transfer ◽  
Bubalus Bubalis ◽  
Vitro Fertilization

scholarly journals Prolyl Hydroxylase Domain Inhibitor Protects against Metabolic Disorders and Associated Kidney Disease in Obese Type 2 Diabetic Mice

2020 ◽  
Vol 31 (3) ◽  
pp. 560-577 ◽  
Author(s):  
Mai Sugahara ◽  
Shinji Tanaka ◽  
Tetsuhiro Tanaka ◽  
Hisako Saito ◽  
Yu Ishimoto ◽  
...  
Keyword(s):  
Kidney Disease ◽  
Transcriptome Analysis ◽  
Metabolic Disorders ◽  
Mesangial Cells ◽  
Endothelial Damage ◽  
Prolyl Hydroxylase ◽  
Macrophage Infiltration ◽  
Isolated Glomeruli ◽  
Prolyl Hydroxylase Domain

BackgroundProlyl hydroxylase domain (PHD) inhibitors, which stimulate erythropoietin production through the activation of hypoxia-inducible factor (HIF), are novel therapeutic agents used for treating renal anemia. Several PHD inhibitors, including enarodustat, are currently undergoing phase 2 or phase 3 clinical trials. Because HIF regulates a broad spectrum of genes, PHD inhibitors are expected to have other effects in addition to erythropoiesis, such as protection against metabolic disorders. However, whether such beneficial effects would extend to metabolic disorder–related kidney disease is largely unknown.MethodsWe administered enarodustat or vehicle without enarodustat in feed to diabetic black and tan brachyury (BTBR) ob/ob mice from 4 to 22 weeks of age. To elucidate molecular changes induced by enarodustat, we performed transcriptome analysis of isolated glomeruli and in vitro experiments using murine mesangial cells.ResultsCompared with BTBR ob/ob mice that received only vehicle, BTBR ob/ob mice treated with enarodustat displayed lower body weight, reduced blood glucose levels with improved insulin sensitivity, lower total cholesterol levels, higher adiponectin levels, and less adipose tissue, as well as a tendency for lower macrophage infiltration. Enarodustat-treated mice also exhibited reduced albuminuria and amelioration of glomerular epithelial and endothelial damage. Transcriptome analysis of isolated glomeruli revealed reduced expression of C-C motif chemokine ligand 2/monocyte chemoattractant protein-1 (CCL2/MCP-1) in enarodustat-treated mice compared with the vehicle-only group, accompanied by reduced glomerular macrophage infiltration. In vitro experiments demonstrated that both local HIF-1 activation and restoration of adiponectin by enarodustat contributed to CCL2/MCP-1 reduction in mesangial cells.ConclusionsThese results indicate that the PHD inhibitor enarodustat has potential renoprotective effects in addition to its potential to protect against metabolic disorders.

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