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Anne-Cécile Boulay, Alice Gilbert, Vanessa Oliveira Moreira, Corinne Blugeon, Sandrine Perrin, Juliette Pouch, Stéphane Le Crom, Bertrand Ducos, Martine Cohen-Salmon
Astrocytes are the most abundant glial cells of the central nervous system and have recently been recognized as crucial in the regulation of brain immunity. In most neuropathological conditions, astrocytes are prone to a radical phenotypical change called reactivity, which plays a key role in astrocyte contribution to neuroinflammation. However, how astrocytes regulate brain immunity in healthy conditions is an understudied question. One of the astroglial molecule involved in these regulations might be Connexin 43 (Cx43), a gap junction protein highly enriched in astrocyte perivascular endfeet-terminated processes forming the glia limitans...
March 22, 2018: Brain Sciences
Tomoyasu Marui, Youta Torii, Shuji Iritani, Hirotaka Sekiguchi, Chikako Habuchi, Hiroshige Fujishiro, Kenichi Oshima, Kazuhiro Niizato, Shotaro Hayashida, Katsuhisa Masaki, Junichi Kira, Norio Ozaki
OBJECTIVE: Recent studies based on the neuroimaging analysis, genomic analysis and transcriptome analysis of the postmortem brain suggest that the pathogenesis of schizophrenia is related to myelin-oligodendrocyte abnormalities. However, no serious neuropathological investigation of this protein in the schizophrenic brain has yet been performed. In this study, to confirm the change in neuropathological findings due to the pathogenesis of this disease, we observed the expression of myelin-oligodendrocyte directly in the brain tissue of schizophrenia patients...
March 22, 2018: Acta Neuropsychiatrica
Yoshihiko Tsukamoto
The mouse retina has a layered structure that is composed of five classes of neurons supported by Müller glial and pigment epithelial cells. Recent studies have made progress in the classification of bipolar and ganglion cells, and also in the wiring of rod-driven signaling, color coding, and directional selectivity. Molecular biological techniques, such as genetic manipulation, transcriptomics, and fluorescence imaging, have contributed a lot to these advancements. The mouse retina has consistently been an important experimental system for both basic and clinical neurosciences...
2018: Methods in Molecular Biology
Shatakshee Chatterjee, Rohan Chaubal, Arindam Maitra, Nilesh Gardi, Amit Dutt, Sudeep Gupta, Rajendra A Badwe, Partha P Majumder, Priyanka Pandey
PURPOSE: We have reported a survival benefit of single injection of hydroxyprogesterone prior to surgery for primary tumour in patients with node-positive operable breast cancer. Hydroxyprogesterone was meant to recapitulate the luteal phase of menstrual cycle in these women. We wanted to understand the molecular basis of action of hydroxyprogesterone on primary breast tumours in a peri-operative setting. METHODS: We performed whole transcriptome sequencing (RNA-Seq) of primary breast tumour samples collected from patients before and after hydroxyprogesterone exposure and controls...
March 21, 2018: Breast Cancer Research and Treatment
Xinxin Tian, Hui Zhang, Yali Zhao, Khalid Mehmood, Xiaoxing Wu, Zhenyu Chang, Min Luo, Xueting Liu, Muhammad Ijaz, Muhammad Tariq Javed, Donghai Zhou
Chromium (Cr) is one of the most important environmental pollutants which are released into the environment due to their wide usage in numerous industries. The excess of Cr (VI) can induce hepatotoxicity, while the molecular mechanism that is involved in Cr (VI)-induced hepatotoxicity is unclear. We demonstrated the induction of chromium poisoning model in chickens to identify the differentially expressed genes (DEGs), and their functions were analyzed under different physiological and pathological conditions...
March 21, 2018: Environmental Science and Pollution Research International
Yuanli Luo, Daiwen Dong, Yu Su, Xuyi Wang, Yumei Peng, Jiang Peng, Changyong Zhou
Mustard clubroot, caused by Plasmodiophora brassicae, is a serious disease that affects Brassica juncea var. tumida Tsen, a mustard plant that is the raw material for a traditional fermented food manufactured in Chongqing, China. In our laboratory, we screened the antagonistic bacteria Zhihengliuella aestuarii against P. brassicae. To better understand the biocontrol mechanism, three transcriptome analyses of B. juncea var. tumida Tsen were conducted using Illumina HiSeq 4000, one from B. juncea only inoculated with P...
March 22, 2018: Functional & Integrative Genomics
Suying Bao, Lilong Jia, Xueya Zhou, Zhi-Gang Zhang, Hazel Wai Lan Wu, Zhe Yu, Gordon Ng, Yanhui Fan, Dana S M Wong, Shishu Huang, Kelvin Kai Wang To, Kwok-Yung Yuen, Man Lung Yeung, You-Qiang Song
Host genetic factors play an important role in diverse host outcomes after influenza A (H7N9) infection. Studying differential responses of inbred mouse lines with distinct genetic backgrounds to influenza virus infection could substantially increase our understanding of the contributory roles of host genetic factors to disease severity. Here, we utilized an integrated approach of mRNA-seq and miRNA-seq to investigate the transcriptome expression and regulation of host genes in C57BL/6J and DBA/2J mouse strains during influenza virus infection...
March 21, 2018: Functional & Integrative Genomics
Johana Madroñero, Silas P Rodrigues, Tathiana F S Antunes, Paolla M V Abreu, José A Ventura, A Alberto R Fernandes, Patricia Machado Bueno Fernandes
Global gene expression analysis indicates host stress responses, mainly those mediated by SA, associated to the tolerance to sticky disease symptoms at pre-flowering stage in Carica papaya. Carica papaya plants develop the papaya sticky disease (PSD) as a result of the combined infection of papaya meleira virus (PMeV) and papaya meleira virus 2 (PMeV2), or PMeV complex. PSD symptoms appear only after C. papaya flowers. To understand the mechanisms involved in this phenomenon, the global gene expression patterns of PMeV complex-infected C...
March 21, 2018: Plant Cell Reports
Norman Goodacre, Aisha Aljanahi, Subhiksha Nandakumar, Mike Mikailov, Arifa S Khan
Detection of distantly related viruses by high-throughput sequencing (HTS) is bioinformatically challenging because of the lack of a public database containing all viral sequences, without abundant nonviral sequences, which can extend runtime and obscure viral hits. Our reference viral database (RVDB) includes all viral, virus-related, and virus-like nucleotide sequences (excluding bacterial viruses), regardless of length, and with overall reduced cellular sequences. Semantic selection criteria (SEM-I) were used to select viral sequences from GenBank, resulting in a first-generation viral database (VDB)...
March 2018: MSphere
Abigail L Lind, Fang Yun Lim, Alexandra A Soukup, Nancy P Keller, Antonis Rokas
Biosynthesis of many ecologically important secondary metabolites (SMs) in filamentous fungi is controlled by several global transcriptional regulators, like the chromatin modifier LaeA, and tied to both development and vegetative growth. In Aspergillus molds, asexual development is regulated by the BrlA > AbaA > WetA transcriptional cascade. To elucidate BrlA pathway involvement in SM regulation, we examined the transcriptional and metabolic profiles of Δ brlA , Δ abaA , and Δ wetA mutant and wild-type strains of the human pathogen Aspergillus fumigatus ...
March 2018: MSphere
Lorrayne Serra, Dennis Z Chang, Marissa Macchietto, Katherine Williams, Rabi Murad, Dihong Lu, Adler R Dillman, Ali Mortazavi
Most nematodes are small worms that lack enough RNA for regular RNA-seq protocols without pooling hundred to thousand of individuals. We have adapted the Smart-seq2 protocol in order to sequence the transcriptome of an individual worm. While developed for individual Steinernema carpocapsae and Caenorhabditis elegans larvae as well as embryos , the protocol should be adaptable for other nematode species and small invertebrates. In addition, we describe how to analyze the RNA-seq results using the Galaxy online environment...
February 20, 2018: Bio-protocol
Qi Zhao, Rui Li, Yang Zhang, Kejia Huang, Wenguo Wang, Jian Li
The bulbs of Fritillaria cirrhosa is wildly used in traditional Chinese medicine to treat lung-related disease, which has recently been found to have antitussive, anti-inflammatory, antihypertensive and anti-tumor activity. Steroidal alkaloids are the major effective ingredients of F. cirrhosa . In the current study, we demonstrated an efficient strategy for F. cirrhosa bulb regeneration in vitro by cytokinin/auxin induction. Our data showed that the regenerated bulbs accumulated higher alkaloid content that the wild ones...
April 2018: 3 Biotech
Sumetha Kannan, Gillian Halter, Tanya Renner, Elizabeth R Waters
Plants have evolved a variety of mechanisms to respond and adapt to abiotic stress. High temperature stress induces the heat shock response. During the heat shock response a large number of genes are up-regulated, many of which code for chaperone proteins that prevent irreversible protein aggregation and cell death. However, it is clear that heat shock is not the only mechanism involved in the plant heat stress response. Alternative splicing (AS) is also important during heat stress since this post-transcriptional regulatory mechanism can produce significant transcriptome and proteome variation...
March 2018: AoB Plants
Jasmine M Bracher, Maarten D Verhoeven, H Wouter Wisselink, Barbara Crimi, Jeroen G Nijland, Arnold J M Driessen, Paul Klaassen, Antonius J A van Maris, Jean-Marc G Daran, Jack T Pronk
Background: l-Arabinose occurs at economically relevant levels in lignocellulosic hydrolysates. Its low-affinity uptake via the Saccharomyces cerevisiae Gal2 galactose transporter is inhibited by d-glucose. Especially at low concentrations of l-arabinose, uptake is an important rate-controlling step in the complete conversion of these feedstocks by engineered pentose-metabolizing S. cerevisiae strains. Results: Chemostat-based transcriptome analysis yielded 16 putative sugar transporter genes in the filamentous fungus Penicillium chrysogenum whose transcript levels were at least threefold higher in l-arabinose-limited cultures than in d-glucose-limited and ethanol-limited cultures...
2018: Biotechnology for Biofuels
Jian Weng, Peixun Zhang, Xiaofeng Yin, Baoguo Jiang
Peripheral nerve injury (PNI) usually leads to progressive muscle atrophy and poor functional recovery. Previous studies have demonstrated that non-coding ribonucleic acid (ncRNA) is a key regulator of muscle atrophy and beneficial for the treatment of PNI. We aimed to analyze the whole transcriptome involved in denervated muscle atrophy after PNI. Animal models of sciatic nerve injury were assessed at 0 (control group), 1, 2, 4, and 8 weeks after injury. The expression patterns in the whole transcriptome in the gastrocnemius muscle were profiled using RNA sequencing at each time point and compared to that obtained in the control group...
2018: Frontiers in Molecular Neuroscience
Aparajita Banerjee, Björn Hamberger
Catalyzing stereo- and regio-specific oxidation of inert hydrocarbon backbones, and a range of more exotic reactions inherently difficult in formal chemical synthesis, cytochromes P450 (P450s) offer outstanding potential for biotechnological engineering. Plants and their dazzling diversity of specialized metabolites have emerged as rich repository for functional P450s with the advances of deep transcriptomics and genome wide discovery. P450s are of outstanding interest for understanding chemical diversification throughout evolution, for gaining mechanistic insights through the study of their structure-function relationship, and for exploitation in Synthetic Biology...
2018: Phytochemistry Reviews: Proceedings of the Phytochemical Society of Europe
Davar Abedini, Sajad Rashidi Monfared, Alireza Abbasi
Noscapine is an antitumor alkaloid produced in opium poppy (Papaver somniferum) and some members of the Papaveraceae family. It has been primarily used for its antitussive effects; more recently, its anticancer properties were shown. Herein, we detected an SSR embedded in the promoter region of the CYP82Y1 gene, which was found to be the first committed-step enzyme in the noscapine biosynthesis pathway, using the MISA program. Some collected ecotypes of P. somniferum were investigated for understanding of SSRs role in the regulation of gene expression and metabolite content...
March 21, 2018: Scientific Reports
Xiaomin Deng, Jianxiao Wang, Yan Li, Shaohua Wu, Shuguang Yang, Jinquan Chao, Yueyi Chen, Shixin Zhang, Minjing Shi, Weimin Tian
Two contrasting cold response rubber tree clones, the cold-resistant '93-114' and cold-sensitive 'Reken501', were subject to a global transcriptome response assessing via high-throughput RNA-seq technique and comprehensive bioinformatics analysis using the referenced rubber tree genome with the purpose of exploring the potential molecular cues underlying the tolerance of rubber trees to cold stress. As a result, a total of 1919 genes had significantly higher expression, while 2929 genes had significantly lower expression in '93-114' than in 'Reken501' without cold stress...
March 21, 2018: Scientific Reports
Hongyang Quan, Qianqian Fan, Chuang Li, Yan-Ying Wang, Lin Wang
The unfolded protein response (UPR) is activated, when the folding capacity is compromised in the endoplasmic reticulum (ER). To date, most studies focused on the coding genes and microRNAs in UPR. Other non-coding RNAs affected by UPR and their roles in UPR have not been systematically studied. Long noncoding RNAs (lncRNAs) are increasingly recognized as powerful epigenetic regulators. In this study, we transcriptomically profiled the lncRNAs and mRNAs from mouse embryonic fibroblasts under ER stress, and identified many differentially expressed lncRNAs and mRNAs...
March 21, 2018: Scientific Reports
Kayla M Valdes, Ganesh S Sundar, Ashton T Belew, Emrul Islam, Najib M El-Sayed, Yoann Le Breton, Kevin S McIver
Many bacterial pathogens coordinately regulate genes encoding important metabolic pathways during disease progression, including the phosphoenolpyruvate (PEP)-phosphotransferase system (PTS) for uptake of carbohydrates. The Gram-positive Group A Streptococcus (GAS) is a pathogen that infects multiple tissues in the human host. The virulence regulator Mga in GAS can be phosphorylated by the PTS, affecting Mga activity based on carbohydrate availability. Here, we explored the effects of glucose availability on the Mga regulon...
March 21, 2018: Scientific Reports
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