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https://www.readbyqxmd.com/read/28527344/harnessing-plant-metabolic-diversity
#1
REVIEW
Charlie Owen, Nicola J Patron, Ancheng Huang, Anne Osbourn
Advances in DNA sequencing and synthesis technologies in the twenty-first century are now making it possible to build large-scale pipelines for engineering plant natural product pathways into heterologous production species using synthetic biology approaches. The ability to decode the chemical potential of plants by sequencing their transcriptomes and/or genomes and to then use this information as an instruction manual to make drugs and other high-value chemicals is opening up new routes to harness the vast chemical diversity of the Plant Kingdom...
May 17, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28527333/transcriptome-wide-analysis-of-jasmonate-treated-by-2-cells-reveals-new-transcriptional-regulators-associated-with-alkaloid-formation-in-tobacco
#2
Yuping Yang, Pengcheng Yan, Che Yi, Wenzheng Li, Yuhui Chai, Lingling Fei, Ping Gao, Heping Zhao, Yingdian Wang, Michael P Timko, Bingwu Wang, Shengcheng Han
Jasmonates (JAs) are well-known regulators of stress, defence, and secondary metabolism in plants, with JA perception triggering extensive transcriptional reprogramming, including both activation and/or repression of entire metabolic pathways. We performed RNA sequencing based transcriptomic profiling of tobacco BY-2 cells before and after treatment with methyl jasmonate (MeJA) to identify novel transcriptional regulators associated with alkaloid formation. A total of 107,140 unigenes were obtained through de novo assembly, and at least 33,213 transcripts (31%) encode proteins, in which 3419 transcription factors (TFs) were identified, representing 72 gene families, as well as 840 transcriptional regulators (TRs) distributed among 19 gene families...
May 4, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28527118/transcriptome-analysis-of-spodoptera-frugiperda-9-sf9-cells-infected-with-baculovirus-acmnpv-or-acmnpv-bmk-it
#3
Lili Wei, Leixi Cao, Yanyan Miao, Shuju Wu, Shumei Xu, Ruisheng Wang, Jun Du, Aihua Liang, Yuejun Fu
OBJECTIVES: To analyze the transcriptome of Spodoptera frugiperda 9 (Sf9) cells infected with AcMNPV or AcMNPV-BmK IT. RESULTS: A comprehensive transcriptome profile for Sf9 cells infected with AcMNPV or AcMNPV-BmK IT is shown. 43127572, 46529744 and 47235310 RNA-Seq profiles permitted the quantification of expression levels for control (C), AcMNPV-BmK IT treatment (ABT) and AcMNPV treatment (AT) groups. There were 997 up-regulated or down-regulated candidate genes with significant different expression level in these treatment groups...
May 19, 2017: Biotechnology Letters
https://www.readbyqxmd.com/read/28526936/fingerprint-of-long-non-coding-rna-regulated-by-cyclic-mechanical-stretch-in-human-aortic-smooth-muscle-cells-implications-for-hypertension
#4
Laura-Eve Mantella, Krishna K Singh, Paul Sandhu, Crystal Kantores, Azza Ramadan, Nadiya Khyzha, Adrian Quan, Mohammed Al-Omran, Jason E Fish, Robert P Jankov, Subodh Verma
Emerging evidence suggests that long non-coding RNAs (lncRNAs) represent a cellular hub coordinating various cellular processes that are critical in health and disease. Mechanical stress triggers changes in vascular smooth muscle cells (VSMCs) that in turn contribute to pathophysiological changes within the vasculature. We sought to evaluate the role that lncRNAs play in mechanical stretch-induced alterations of human aortic smooth muscle cells (HASMCs). RNA (lncRNA and mRNA) samples isolated from HASMCs that had been subjected to 10 or 20% elongation (1 Hz) for 24 h were profiled with the Arraystar Human LncRNA Microarray V3...
May 19, 2017: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/28526785/effects-of-arginine-on-growth-virulence-gene-expression-and-stress-tolerance-by-streptococcus-mutans
#5
Brinta Chakraborty, Robert A Burne
Streptococcus mutans is a common constituent of oral biofilms and a primary etiologic agent of human dental caries. The bacteria associated with dental caries have a potent ability to produce organic acids from dietary carbohydrates and to grow and metabolize in acidic conditions. In contrast, many commensal bacteria produce ammonia through the arginine deiminase system (ADS), which moderates the pH of oral biofilms. Arginine metabolism by the ADS is a significant deterrent to the initiation and progression of dental caries...
May 19, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28526728/genetic-subtraction-profiling-identifies-candidate-mirnas-involved-in-rice-female-gametophyte-abortion
#6
Liyu Yang, Ya Wu, Wenliang Wang, Bigang Mao, Bingran Zhao, Jianbo Wang
Female gametophyte is an important participant in sexual reproduction of plants. The molecular mechanism of its development has received much attention in recent years. As important regulators of gene expression, miRNAs have been certified to play a significant role in many biological processes of plants including sexual reproduction. In this study, to investigate the potential regulatory effects of miRNAs on rice female gametophytes abortion, we used the high-throughput sequencing method to compare the miRNA transcriptome in ovules of a high frequency female-sterile line (fsv1) and a rice wild-type line (Gui 99) during ovule development...
May 19, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28526607/the-merozoite-specific-protein-tggra11b-identified-as-a-component-of-the-toxoplasma-gondii-parasitophorous-vacuole-in-a-tachyzoite-expression-model
#7
Chandra Ramakrishnan, Robert A Walker, Ramon M Eichenberger, Adrian B Hehl, Nicholas C Smith
The apicomplexan, Toxoplasma gondii, infects all warm-blooded animals as intermediate hosts but only felids as definitive hosts. Dense granule proteins are critical for the survival of Toxoplasma within host cells but, whilst these proteins have been studied intensively in tachyzoites, little is known about their expression in the coccidian stages in the cat intestine. Transcriptomic profiling indicates that two putative dense granule proteins, TgGRA11A and TgGRA11B, are expressed uniquely in merozoites. Immunofluorescent microscopy of Toxoplasma-infected cat intestine and tachyzoites engineered to express TgGRA11B, reveals that it is a dense granule protein that traffics into the parasitophorous vacuole and its membrane...
May 16, 2017: International Journal for Parasitology
https://www.readbyqxmd.com/read/28526573/transcriptomic-variation-of-locally-infected-skin-of-epinephelus-coioides-reveals-the-mucosal-immune-mechanism-against-cryptocaryon-irritans
#8
Yazhou Hu, Anxing Li, Yang Xu, Biao Jiang, Geling Lu, Xiaochun Luo
Fish skin is the largest immunologically active mucosal organ, providing first-line defense against external pathogens. However, the skin-associated immune mechanisms of fish are still unclear. Cryptocaryon irritans is an obligate ectoparasitic ciliated protozoan that infects almost all marine fish, and is believed to be an excellent pathogen model to study fish mucosal immunity. In this study, a de novo transcriptome assembly of Epinephelus coioides skin post C. irritans tail-infection was performed for the first time using the Illumina HiSeq™ 2500 system...
May 16, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28526029/cell-fixation-and-preservation-for-droplet-based-single-cell-transcriptomics
#9
Jonathan Alles, Nikos Karaiskos, Samantha D Praktiknjo, Stefanie Grosswendt, Philipp Wahle, Pierre-Louis Ruffault, Salah Ayoub, Luisa Schreyer, Anastasiya Boltengagen, Carmen Birchmeier, Robert Zinzen, Christine Kocks, Nikolaus Rajewsky
BACKGROUND: Recent developments in droplet-based microfluidics allow the transcriptional profiling of thousands of individual cells in a quantitative, highly parallel and cost-effective way. A critical, often limiting step is the preparation of cells in an unperturbed state, not altered by stress or ageing. Other challenges are rare cells that need to be collected over several days or samples prepared at different times or locations. METHODS: Here, we used chemical fixation to address these problems...
May 19, 2017: BMC Biology
https://www.readbyqxmd.com/read/28526017/the-effect-of-hypoxia-on-the-lipidome-of-recombinant-pichia-pastoris
#10
Núria Adelantado, Pablo Tarazona, Karlheinz Grillitsch, Xavier García-Ortega, Sergi Monforte, Francisco Valero, Ivo Feussner, Günther Daum, Pau Ferrer
BACKGROUND: Cultivation of recombinant Pichia pastoris (Komagataella sp.) under hypoxic conditions has a strong positive effect on specific productivity when the glycolytic GAP promoter is used for recombinant protein expression, mainly due to upregulation of glycolytic conditions. In addition, transcriptomic analyses of hypoxic P. pastoris pointed out important regulation of lipid metabolism and unfolded protein response (UPR). Notably, UPR that plays a role in the regulation of lipid metabolism, amino acid metabolism and protein secretion, was found to be upregulated under hypoxia...
May 19, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28525982/blood-meal-induced-regulation-of-the-chemosensory-gene-repertoire-in-the-southern-house-mosquito
#11
Tanvi Taparia, Rickard Ignell, Sharon Rose Hill
BACKGROUND: The southern house mosquito, Culex quinquefasciatus, is one of the most prevalent vectors of lymphatic filariasis and flavivirus-induced encephalitis. Its vectorial capacity is directly affected by its reproductive feeding behaviors, such as host seeking, blood feeding, resting, and egg laying. In mosquitoes, these gonotrophic behaviors are odor-mediated and regulated following blood feeding. Immediately after a blood meal, female mosquitoes show reduced olfactory responsiveness and flight activity, as they enter a resting state...
May 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28525759/modeling-rett-syndrome-using-talen-edited-mecp2-mutant-cynomolgus-monkeys
#12
Yongchang Chen, Juehua Yu, Yuyu Niu, Dongdong Qin, Hailiang Liu, Gang Li, Yingzhou Hu, Jiaojian Wang, Yi Lu, Yu Kang, Yong Jiang, Kunhua Wu, Siguang Li, Jingkuan Wei, Jing He, Junbang Wang, Xiaojing Liu, Yuping Luo, Chenyang Si, Raoxian Bai, Kunshan Zhang, Jie Liu, Shaoyong Huang, Zhenzhen Chen, Shuang Wang, Xiaoying Chen, Xinhua Bao, Qingping Zhang, Fuxing Li, Rui Geng, Aibin Liang, Dinggang Shen, Tianzi Jiang, Xintian Hu, Yuanye Ma, Weizhi Ji, Yi Eve Sun
Gene-editing technologies have made it feasible to create nonhuman primate models for human genetic disorders. Here, we report detailed genotypes and phenotypes of TALEN-edited MECP2 mutant cynomolgus monkeys serving as a model for a neurodevelopmental disorder, Rett syndrome (RTT), which is caused by loss-of-function mutations in the human MECP2 gene. Male mutant monkeys were embryonic lethal, reiterating that RTT is a disease of females. Through a battery of behavioral analyses, including primate-unique eye-tracking tests, in combination with brain imaging via MRI, we found a series of physiological, behavioral, and structural abnormalities resembling clinical manifestations of RTT...
May 18, 2017: Cell
https://www.readbyqxmd.com/read/28525721/development-and-application-of-a-screening-method-of-absolute-qpcr-to-detect-the-abuse-of-sex-steroid-hormone-administration-in-male-bovine
#13
Laura Starvaggi Cuccuzza, Bartolomeo Biolatti, Sara Divari, Paola Pregel, Frine E Scaglione, Alessandra Sereno, Francesca T Cannizzo
A method for absolute quantification of regucalcin gene by quantitative PCR was developed to confirm that the decrease of regucalcin gene expression in the testis is a valid biomarker for detection of sex steroid hormone treatment in bovine husbandry. An external standard curve was developed with TaqMan technology. Based on in vivo experiments, specificity, sensitivity and criterion value of this potential biomarker were calculated by means of a ROC curve. Then, regucalcin gene expression was evaluated in beef and veal calves for human consumption...
May 19, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28525648/the-role-of-omics-in-the-application-of-adverse-outcome-pathways-for-chemical-risk-assessment
#14
Erica K Brockmeier, Geoff Hodges, Thomas H Hutchinson, Emma Butler, Markus Hecker, Knut Erik Tollefsen, Natalia Garcia-Reyero, Peter Kille, Dörthe Becker, Kevin Chipman, John Colbourne, Timothy W Collette, Andrew Cossins, Mark Cronin, Peter Graystock, Steve Gutsell, Dries Knapen, Ioanna Katsiadaki, Anke Lange, Stuart Marshall, Stewart F Owen, Edward J Perkins, Stewart Plaistow, Anthony Schroeder, Daisy Taylor, Mark Viant, Gerald Ankley, Francesco Falciani
In conjunction with the second International Environmental Omics Symposium (iEOS) conference, held at the University of Liverpool (UK) in September 2014, a workshop was held to bring together experts in toxicology and regulatory science from academia, government and industry. The purpose of the workshop was to review the specific roles that high-content omics datasets (e.g., transcriptomics, metabolomics, lipidomics, and proteomics) can hold within the adverse outcome pathway (AOP) framework for supporting ecological and human health risk assessments...
May 19, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28525595/gut-transcriptome-analysis-shows-different-food-utilization-efficiency-by-the-grasshopper-oedaleous-asiaticus-orthoptera-acrididae
#15
Xunbing Huang, Mark Richard McNeill, Jingchuan Ma, Xinghu Qin, Xiongbing Tu, Guangchun Cao, Guangjun Wang, Xiangqun Nong, Zehua Zhang
Oedaleus asiaticus B. Bienko is a persistent pest occurring in north Asian grasslands. We found that O. asiaticus feeding on Stipa krylovii Roshev. had higher approximate digestibility (AD), efficiency of conversion of ingested food (ECI), and efficiency of conversion of digested food (ECD), compared with cohorts feeding on Leymus chinensis (Trin.) Tzvel, Artemisia frigida Willd., or Cleistogenes squarrosa (Trin.) Keng. Although this indicated high food utilization efficiency for S. krylovii, the physiological processes and molecular mechanisms underlying these biological observations are not well understood...
May 19, 2017: Journal of Economic Entomology
https://www.readbyqxmd.com/read/28525563/omics-biomarkers-in-ophthalmology
#16
Susette Lauwen, Eiko K de Jong, Dirk J Lefeber, Anneke I den Hollander
"Omics" refers to high-throughput analyses of genes, proteins, or metabolites in a biological system, and is increasingly used for ophthalmic research. These system-based approaches can unravel disease-related processes and are valuable for biomarker discovery. Furthermore, potential therapeutic targets can be identified based on omics results, and targeted follow-up experiments can be designed to gain molecular understanding of the disease and to test new therapies. Here, we review the application of omics techniques in eye diseases, focusing on age-related macular degeneration (AMD), diabetic retinopathy (DR), retinal detachment (RD), myopia, glaucoma, Fuchs' corneal dystrophy (FCD), cataract, keratoconus, and dry eyes...
May 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28525556/transcriptome-of-the-gsh-depleted-lens-reveals-changes-in-detoxification-and-emt-signaling-genes-transport-systems-and-lipid-homeostasis
#17
Jeremy A Whitson, Xiang Zhang, Mario Medvedovic, Jenny Chen, Zongbo Wei, Vincent M Monnier, Xingjun Fan
Purpose: To understand the effects of glutathione (GSH)-deficiency on genetic processes that regulate lens homeostasis and prevent cataractogenesis. Methods: The transcriptome of lens epithelia and fiber cells was obtained from C57BL/6 LEGSKO (lens GSH-synthesis knockout) and buthionine sulfoximine (BSO)-treated LEGSKO mice and compared to C57BL/6 wild-type mice using RNA-Seq. Transcriptomic data were confirmed by qPCR and Western blot/ELISA on a subset of genes...
May 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28525384/secretome-analysis-of-breast-cancer-associated-adipose-tissue-to-identify-paracrine-regulators-of-breast-cancer-growth
#18
Lapeire Lore, Hendrix An, Lecoutere Evelyne, Van Bockstal Mieke, Vandesompele Jo, Maynard Dawn, Braems Geert, Van Den Broecke Rudy, Müller Cathérine, Bracke Marc, Cocquyt Véronique, Denys Hannelore, De Wever Olivier
Adipose tissue secretes a plethora of adipokines as evidenced by characterization of subcutaneous and visceral adipose tissue secretomes. However, adipose tissue composition and secretion pattern is depot and disease dependent, influencing the adipose tissue secretome. We investigated the secretome of cancer-associated adipose tissue (CAAT) explants from breast cancer patients and explored its role in breast cancer proliferation. CAAT proteins were identified by LC-MS/MS and human protein antibody arrays and stimulated proliferation of three breast cancer cell lines...
May 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28525372/overexpression-of-a-novel-candidate-oncogene-kif14-correlates-with-tumor-progression-and-poor-prognosis-in-prostate-cancer
#19
Yixiang Zhang, Yeqing Yuan, Pei Liang, Zhaoxia Zhang, Xiaojing Guo, Ligang Xia, Yingying Zhao, Xing-Sheng Shu, Shengkun Sun, Ying Ying, Yingduan Cheng
Prostate cancer (PCa) is the second leading cause of death from cancer in men. The mechanism underlying tumorigenesis and development of PCa is largely unknown. Here, we identified Kinesin family member 14 (KIF14) as a novel candidate oncogene in PCa. We found that KIF14 was overexpressed in multiple PCa cell lines and primary PCa tissues. Knockdown of KIF14 in DU145 and PC3 prostate cancer cells suppressed cell proliferation, induced cell cycle arrest and apoptosis. Transcriptome analysis by RNA-sequencing demonstrated that KIF4 suppression led to transcriptional changes of genes involved in p53 and TGF-beta signaling pathway...
May 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28524846/concerted-regulation-of-retinal-pigment-epithelium-basement-membrane-and-barrier-function-by-angiocrine-factors
#20
Ignacio Benedicto, Guillermo L Lehmann, Michael Ginsberg, Daniel J Nolan, Rohan Bareja, Olivier Elemento, Zelda Salfati, Nazia M Alam, Glen T Prusky, Pierre Llanos, Sina Y Rabbany, Arvydas Maminishkis, Sheldon S Miller, Shahin Rafii, Enrique Rodriguez-Boulan
The outer blood-retina barrier is established through the coordinated terminal maturation of the retinal pigment epithelium (RPE), fenestrated choroid endothelial cells (ECs) and Bruch's membrane, a highly organized basement membrane that lies between both cell types. Here we study the contribution of choroid ECs to this process by comparing their gene expression profile before (P5) and after (P30) the critical postnatal period when mice acquire mature visual function. Transcriptome analyses show that expression of extracellular matrix-related genes changes dramatically over this period...
May 19, 2017: Nature Communications
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