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Transcriptomics

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https://www.readbyqxmd.com/read/28645186/igf-i-gene-therapy-in-aging-rats-modulates-hippocampal-genes-relevant-to-memory-function
#1
Joaquín Pardo, Martin C Abba, Ezequiel Lacunza, Olalekan M Ogundele, Isabel Paiva, Gustavo R Morel, Tiago F Outeiro, Rodolfo G Goya
In rats, learning and memory performance decline during normal aging, which makes this rodent species a suitable model to evaluate therapeutic strategies. In aging rats, insulin-like growth factor-I (IGF-I), is known to significantly improve spatial memory accuracy as compared to control counterparts. A constellation of gene expression changes underlie the hippocampal phenotype of aging but no studies on the effects of IGF-I on the hippocampal transcriptome of old rodents have been documented. Here, we assessed the effects of IGF-I gene therapy on spatial memory performance in old female rats and compared them with changes in the hippocampal transcriptome...
June 22, 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/28645179/system-wide-analysis-of-short-term-response-to-high-temperature-in-pinus-radiata
#2
Mónica Escandón, Luis Valledor, Jesús Pascual, Gloria Pinto, María Jesús Cañal, Mónica Meijón
Pinus radiata seedlings, the most widely planted pine species in the world, were exposed to temperatures within a range mimicking future scenarios based on current models of heat increase. The short-term heat response in P. radiata was studied in detail by exploring the metabolome, proteome and targeted transcriptome. The use of complementary mass spectrometry techniques, GC-MS and LC-Orbitrap-MS, together with novel bioinformatics tools allowed the reliable quantification of 2,075 metabolites and 901 protein groups...
June 22, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28645111/intersecting-transcriptomic-profiling-technologies-and-long-non-coding-rna-function-in-lung-adenocarcinoma-discovery-mechanisms-and-therapeutic-applications
#3
REVIEW
Jonathan Castillo, Theresa R Stueve, Crystal N Marconett
Previously thought of as junk transcripts and pseudogene remnants, long non-coding RNAs (lncRNAs) have come into their own over the last decade as an essential component of cellular activity, regulating a plethora of functions within multicellular organisms. lncRNAs are now known to participate in development, cellular homeostasis, immunological processes, and the development of disease. With the advent of next generation sequencing technology, hundreds of thousands of lncRNAs have been identified. However, movement beyond mere discovery to the understanding of molecular processes has been stymied by the complicated genomic structure, tissue-restricted expression, and diverse regulatory roles lncRNAs play...
June 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28644990/global-transcriptional-response-of-escherichia-coli-mg1655-cells-exposed-to-the-oxygenated-monoterpenes-citral-and-carvacrol
#4
Beatriz Chueca, Elisa Pérez-Sáez, Rafael Pagán, Diego García-Gonzalo
DNA microarrays were used to study the mechanism of bacterial inactivation by carvacrol and citral. After 10-min treatments of Escherichia coli MG1655 cells with 100 and 50ppm of carvacrol and citral, 76 and 156 genes demonstrated significant transcriptional differences (p≤0.05), respectively. Among the up-regulated genes after carvacrol treatment, we found gene coding for multidrug efflux pumps (acrA, mdtM), genes related to phage shock response (pspA, pspB, pspC, pspD, pspF and pspG), biosynthesis of arginine (argC, argG, artJ), and purine nucleotides (purC, purM)...
June 20, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28644989/transcriptome-analysis-shows-activation-of-the-arginine-deiminase-pathway-in-lactococcus-lactis-as-a-response-to-ethanol-stress
#5
Lorena Díez, Ana Solopova, Rocío Fernández-Pérez, Miriam González, Carmen Tenorio, Oscar P Kuipers, Fernanda Ruiz-Larrea
This paper describes the molecular response of Lactococcus lactis NZ9700 to ethanol. This strain is a well-known nisin producer and a lactic acid bacteria (LAB) model strain. Global transcriptome profiling using DNA microarrays demonstrated a bacterial adaptive response to the presence of 2% ethanol in the culture broth and differential expression of 67 genes. The highest up-regulation was detected for those genes involved in arginine degradation through the arginine deiminase (ADI) pathway (20-40 fold up-regulation)...
May 24, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28644920/genome-scale-metabolic-models-applied-to-human-health-and-disease
#6
REVIEW
Daniel J Cook, Jens Nielsen
Advances in genome sequencing, high throughput measurement of gene and protein expression levels, data accessibility, and computational power have allowed genome-scale metabolic models (GEMs) to become a useful tool for understanding metabolic alterations associated with many different diseases. Despite the proven utility of GEMs, researchers confront multiple challenges in the use of GEMs, their application to human health and disease, and their construction and simulation in an organ-specific and disease-specific manner...
June 23, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28644561/the-redox-sensitive-module-of-cyclophilin-20-3-2-cysteine-peroxiredoxin-and-cysteine-synthase-integrates-sulfur-metabolism-and-oxylipin-signaling-in-the-high-light-acclimation-response
#7
Sara M Müller, Shanshan Wang, Wilena Telman, Michael Liebthal, Helena Schnitzer, Andrea Viehhauser, Carsten Sticht, Carolina Delatorre, Markus Wirtz, Rüdiger Hell, Karl-Josef Dietz
The integration of redox- and reactive oxygen species-dependent signaling and metabolic activities are fundamental to plant acclimation to biotic and abiotic stresses. Previous data suggest the existence of a dynamically interacting module in the chloroplast stroma consisting of cyclophilin 20-3 (Cyp20-3), O-acetylserine(thiol)lyase B (OASTL-B), 2-cysteine peroxiredoxins A/B (2-CysPrx) and serine acetyltransferase 2;1 (SERAT2;1). The functionality of this COPS module is influenced by redox stimuli and oxophytodienoic acid (OPDA) which is the precursor for jasmonic acid...
June 23, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28644509/comparative-transcriptomic-analysis-of-two-important-life-stages-of-angiostrongylus-cantonensis-fifth-stage-larvae-and-female-adults
#8
Liang Yu, Binbin Cao, Ying Long, Meks Tukayo, Chonglv Feng, Wenzhen Fang, Damin Luo
The mechanisms involved in the fast growth of Angiostrongylus cantonensis from fifth-stage larvae (L5) to female adults and how L5 breaks through the blood-brain barrier in a permissive host remain unclear. In this work, we compared the transcriptomes of these two life stages to identify the main factors involved in the rapid growth and transition to adulthood. RNA samples from the two stages were sequenced and assembled de novo. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses of 1,346 differentially expressed genes between L5 and female adults was then undertaken...
April 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28644441/micrornas-143-and-145-induce-epithelial-to-mesenchymal-transition-and-modulate-the-expression-of-junction-proteins
#9
Lidia Avalle, Danny Incarnato, Aurora Savino, Marta Gai, Francesca Marino, Sara Pensa, Isaia Barbieri, Michael B Stadler, Paolo Provero, Salvatore Oliviero, Valeria Poli
Transforming growth factor (TGF)-β is one of the major inducers of epithelial to mesenchymal transition (EMT), a crucial program that has a critical role in promoting carcinoma's metastasis formation. MicroRNAs-143 and -145, which are both TGF-β direct transcriptional targets, are essential for the differentiation of vascular smooth muscle cells (VSMC) during embryogenesis, a TGF-β-dependent process reminiscent of EMT. Their role in adult tissues is however less well defined and even ambiguous, as their expression was correlated both positively and negatively with tumor progression...
June 23, 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/28643936/phenotypic-analysis-of-organoids-by-proteomics
#10
REVIEW
Alexis Gonneaud, Claude Asselin, François Boudreau, François-Michel Boisvert
The development of 3D cell cultures into self-organizing organ-like structures named organoids provides a model that better reflects in vivo organ physiology and their functional properties. Organoids have been established from several organs, such as the intestine, prostate, brain, liver, kidney and pancreas. With recent advances in high-throughput and -omics profiling technologies, it is now possible to study the mechanisms of cellular organisation at the systems level. It is therefore not surprising that these methods are now used to characterize organoids at the transcriptomic, proteomic, chromatin state and transcription factor DNA-binding levels...
June 23, 2017: Proteomics
https://www.readbyqxmd.com/read/28643795/the-genomic-landscape-of-tuberous-sclerosis-complex
#11
Katie R Martin, Wanding Zhou, Megan J Bowman, Juliann Shih, Kit Sing Au, Kristin E Dittenhafer-Reed, Kellie A Sisson, Julie Koeman, Daniel J Weisenberger, Sandra L Cottingham, Steven T DeRoos, Orrin Devinsky, Mary E Winn, Andrew D Cherniack, Hui Shen, Hope Northrup, Darcy A Krueger, Jeffrey P MacKeigan
Tuberous sclerosis complex (TSC) is a rare genetic disease causing multisystem growth of benign tumours and other hamartomatous lesions, which leads to diverse and debilitating clinical symptoms. Patients are born with TSC1 or TSC2 mutations, and somatic inactivation of wild-type alleles drives MTOR activation; however, second hits to TSC1/TSC2 are not always observed. Here, we present the genomic landscape of TSC hamartomas. We determine that TSC lesions contain a low somatic mutational burden relative to carcinomas, a subset feature large-scale chromosomal aberrations, and highly conserved molecular signatures for each type exist...
June 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28643538/do-methodological-differences-account-for-the-current-controversy-on-tissue-factor-expression-in-platelets
#12
Marta Brambilla, Laura Rossetti, Chiara Zara, Paola Canzano, Peter L A Giesen, Elena Tremoli, Marina Camera
Tissue factor (TF), the key activator of the blood coagulation cascade and of thrombus formation, is also expressed by circulating human platelets. Despite the documented in-depth characterization of platelet TF carried out in the past 15 years, some authors still fail to identify TF in platelets, especially when assessment in platelet-rich plasma (PRP) or washed platelets is carried out. This study aims to extend the characterization of the subset of TF-positive platelets in PRP from healthy subjects and to verify how different centrifugation forces, used to prepare the PRP, could affect the analysis of TF-positive platelets...
June 23, 2017: Platelets
https://www.readbyqxmd.com/read/28643332/integrative-eqtl-analysis-of-tumor-and-host-omics-data-in-individuals-with-bladder-cancer
#13
Silvia Pineda, Kristel Van Steen, Núria Malats
Integrative analyses of several omics data are emerging. The data are usually generated from the same source material (i.e., tumor sample) representing one level of regulation. However, integrating different regulatory levels (i.e., blood) with those from tumor may also reveal important knowledge about the human genetic architecture. To model this multilevel structure, an integrative-expression quantitative trait loci (eQTL) analysis applying two-stage regression (2SR) was proposed. This approach first regressed tumor gene expression levels with tumor markers and the adjusted residuals from the previous model were then regressed with the germline genotypes measured in blood...
June 23, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28643089/time-lapse-observation-and-transcriptome-analysis-of-a-case-with-repeated-multiple-pronuclei-after-ivf-icsi
#14
J Dai, L Z Leng, C F Lu, F Gong, S P Zhang, W Zheng, G X Lu, G Lin
PURPOSE: The purpose of this study was to investigate the cause of repeated multipronucleus (MPN) formation in zygotes in a patient after both in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI). METHOD: This is a case study. A patient had unexplained primary infertility with recurring total MPN zygotes after IVF and ICSI cycles. Time-lapse monitoring of pronucleus formation was carried out. Embryos developed from MPN zygotes were analyzed by fluorescence in situ hybridization (FISH)...
June 22, 2017: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/28642865/spinal-muscular-atrophy-from-defective-chaperoning-of-snrnp-assembly-to-neuromuscular-dysfunction
#15
REVIEW
Maia Lanfranco, Neville Vassallo, Ruben J Cauchi
Spinal Muscular Atrophy (SMA) is a neuromuscular disorder that results from decreased levels of the survival motor neuron (SMN) protein. SMN is part of a multiprotein complex that also includes Gemins 2-8 and Unrip. The SMN-Gemins complex cooperates with the protein arginine methyltransferase 5 (PRMT5) complex, whose constituents include WD45, PRMT5 and pICln. Both complexes function as molecular chaperones, interacting with and assisting in the assembly of an Sm protein core onto small nuclear RNAs (snRNAs) to generate small nuclear ribonucleoproteins (snRNPs), which are the operating components of the spliceosome...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28642803/transcriptomic-profiles-of-aging-in-na%C3%A3-ve-and-memory-cd4-cells-from-mice
#16
Jackson Taylor, Lindsay Reynolds, Li Hou, Kurt Lohman, Wei Cui, Stephen Kritchevsky, Charles McCall, Yongmei Liu
BACKGROUND: CD4+ T cells can be broadly divided into naïve and memory subsets, each of which are differentially impaired by the aging process. It is unclear if and how these differences are reflected at the transcriptomic level. We performed microarray profiling on RNA derived from naïve (CD44(low)) and memory (CD44(high)) CD4+ T cells derived from young (2-3 month) and old (28 month) mice, in order to better understand the mechanisms of age-related functional alterations in both subsets...
2017: Immunity & Ageing: I & A
https://www.readbyqxmd.com/read/28642777/transcriptome-analysis-of-genes-associated-with-the-artemisinin-biosynthesis-by-jasmonic-acid-treatment-under-the-light-in-artemisia-annua
#17
Xiaolong Hao, Yijun Zhong, Xueqing Fu, Zongyou Lv, Qian Shen, Tingxiang Yan, Pu Shi, Yanan Ma, Minghui Chen, Xueying Lv, Zhangkuanyu Wu, Jingya Zhao, Xiaofen Sun, Ling Li, Kexuan Tang
Artemisinin is a sesquiterpene lactone endoperoxide extracted from a traditional Chinese medicinal plant Artemisia annua. Artemisinin-based combination therapies (ACTs) are recommended as the best treatment of malaria by the World Health Organization (WHO). Both the phytohormone jasmonic acid (JA) and light promote artemisinin biosynthesis in A. annua. Interestingly, we found that the increase of artemisinin biosynthesis by JA was dependent on light. However, the relationship between the two signal pathways mediated by JA and light remains unclear...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28642771/transcriptomic-analysis-of-avocado-hass-persea-americana-mill-in-the-interaction-system-fruit-chitosan-colletotrichum
#18
Luis-Ángel Xoca-Orozco, Esther Angélica Cuellar-Torres, Sandra González-Morales, Porfirio Gutiérrez-Martínez, Ulises López-García, Luis Herrera-Estrella, Julio Vega-Arreguín, Alejandra Chacón-López
Avocado (Persea americana) is one of the most important crops in Mexico as it is the main producer, consumer, and exporter of avocado fruit in the world. However, successful avocado commercialization is often reduced by large postharvest losses due to Colletotrichum sp., the causal agent of anthracnose. Chitosan is known to have a direct antifungal effect and acts also as an elicitor capable of stimulating a defense response in plants. However, there is little information regarding the genes that are either activated or repressed in fruits treated with chitosan...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28642770/interplay-between-carotenoids-abscisic-acid-and-jasmonate-guides-the-compatible-rice-meloidogyne-graminicola-interaction
#19
Tina Kyndt, Kamrun Nahar, Ashley Haeck, Ruben Verbeek, Kristof Demeestere, Godelieve Gheysen
In this study, we have characterized the role of carotenoids and chlorophyll in the compatible interaction between the sedentary root knot nematode (RKN) Meloidogyne graminicola and the monocot model plant rice (Oryza sativa). Previous transcriptome data showed a differential expression of carotenoid and chlorophyll biosynthesis genes in nematode-induced giant cells and gall tissue. Metabolite measurement showed that galls indeed accumulate chlorophyll a, b and carotenoids, as well as the hormone abscisic acid (ABA)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28642763/rootstock-sub-optimal-temperature-tolerance-determines-transcriptomic-responses-after-long-term-root-cooling-in-rootstocks-and-scions-of-grafted-tomato-plants
#20
Georgia Ntatsi, Dimitrios Savvas, Vassilis Papasotiropoulos, Anastasios Katsileros, Rita M Zrenner, Dirk K Hincha, Ellen Zuther, Dietmar Schwarz
Grafting of elite cultivars onto tolerant rootstocks is an advanced strategy to increase tomato tolerance to sub-optimal temperature. However, a detailed understanding of adaptive mechanisms to sub-optimal temperature in rootstocks and scions of grafting combinations on a physiological and molecular level is lacking. Here, the commercial cultivar Kommeet was grafted either onto 'Moneymaker' (sensitive) or onto the line accession LA 1777 of Solanum habrochaites (tolerant). Grafted plants were grown in NFT-system at either optimal (25°C) or sub-optimal (15°C) temperatures in the root environment with optimal air temperature (25°C) for 22 days...
2017: Frontiers in Plant Science
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