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Transcriptomics

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https://www.readbyqxmd.com/read/28817735/association-of-gene-expression-with-biomass-content-and-composition-in-sugarcane
#1
Nam V Hoang, Agnelo Furtado, Angela J O'Keeffe, Frederik C Botha, Robert J Henry
About 64% of the total aboveground biomass in sugarcane production is from the culm, of which ~90% is present in fiber and sugars. Understanding the transcriptome in the sugarcane culm, and the transcripts that are associated with the accumulation of the sugar and fiber components would facilitate the modification of biomass composition for enhanced biofuel and biomaterial production. The Sugarcane Iso-Seq Transcriptome (SUGIT) database was used as a reference for RNA-Seq analysis of variation in gene expression between young and mature tissues, and between 10 genotypes with varying fiber content...
2017: PloS One
https://www.readbyqxmd.com/read/28817687/morphologic-phenotypic-and-transcriptomic-characterization-of-classically-and-alternatively-activated-canine-blood-derived-macrophages-in-vitro
#2
Franziska Heinrich, Annika Lehmbecker, Barbara B Raddatz, Kristel Kegler, Andrea Tipold, Veronika M Stein, Arno Kalkuhl, Ulrich Deschl, Wolfgang Baumgärtner, Reiner Ulrich, Ingo Spitzbarth
Macrophages are a heterogeneous cell population playing a pivotal role in tissue homeostasis and inflammation, and their phenotype strongly depends on the micromilieu. Despite its increasing importance as a translational animal model for human diseases, there is a considerable gap of knowledge with respect to macrophage polarization in dogs. The present study comprehensively investigated the morphologic, phenotypic, and transcriptomic characteristics of unstimulated (M0), M1- (GM-CSF, LPS, IFNγ-stimulated) and M2- (M-CSF, IL-4-stimulated)-polarized canine blood-derived macrophages in vitro...
2017: PloS One
https://www.readbyqxmd.com/read/28817680/human-alpha-defensin-5-is-a-candidate-biomarker-to-delineate-inflammatory-bowel-disease
#3
Amanda D Williams, Olga Y Korolkova, Amos M Sakwe, Timothy M Geiger, Samuel D James, Roberta L Muldoon, Alan J Herline, J Shawn Goodwin, Michael G Izban, Mary K Washington, Duane T Smoot, Billy R Ballard, Maria Gazouli, Amosy E M'Koma
Inability to distinguish Crohn's colitis from ulcerative colitis leads to the diagnosis of indeterminate colitis. This greatly effects medical and surgical care of the patient because treatments for the two diseases vary. Approximately 30 percent of inflammatory bowel disease patients cannot be accurately diagnosed, increasing their risk of inappropriate treatment. We sought to determine whether transcriptomic patterns could be used to develop diagnostic biomarker(s) to delineate inflammatory bowel disease more accurately...
2017: PloS One
https://www.readbyqxmd.com/read/28817638/the-transcriptional-profiling-of-human-in-vivo-generated-plasma-cells-identifies-selective-imbalances-in-monoclonal-gammopathies
#4
Luis M Valor, Beatriz Rodríguez-Bayona, Ana B Ramos-Amaya, José A Brieva, Antonio Campos-Caro
Plasma cells (PC) represent the heterogeneous final stage of the B cells (BC) differentiation process. To characterize the transition of BC into PC, transcriptomes from human naïve BC were compared to those of three functionally-different subsets of human in vivo-generated PC: i) tonsil PC, mainly consisting of early PC; ii) PC released to the blood after a potent booster-immunization (mostly cycling plasmablasts); and, iii) bone marrow CD138+ PC that represent highly mature PC and include the long-lived PC compartment...
2017: PloS One
https://www.readbyqxmd.com/read/28817092/biochemical-and-comparative-transcriptomic-analyses-identify-candidate-genes-related-to-variegation-formation-in-paeonia-rockii
#5
Qianqian Shi, Long Li, Xiaoxiao Zhang, Jianrang Luo, Xiang Li, Lijuan Zhai, Lixia He, Yanlong Zhang
Paeonia rockii is a wild tree peony species with large and dark purple variegations at the base of its petals. It is the genetic resource for various variegation patterns in tree peony cultivars, which is in contrast to the pure white petals of Paeonia ostii. However, the molecular mechanism underlying the formation of variegation in this plant is still unknown. Here, we conducted Illumina transcriptome sequencing for P. rockii, P. ostii (with pure white petals) and their F1 individuals (with purple-red variegation)...
August 17, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28816598/short-versus-long-double-stranded-rna-activation-of-a-post-transcriptional-gene-knockdown-pathway
#6
Nir Shpak, Rivka Manor, Lihie Katzir Abilevich, Ortal Mantal, Keshet Shavit, Eliahu D Aflalo, Debra Toiber, Amir Sagi
RNA interference (RNAi) utilizes a conserved cellular autoimmune defense mechanism involving the internalization of dsRNA into cells and the activation of a set of RNAi related genes. Using RNAi, complete sex reversal is achievable in males of the prawn Macrobrachium rosenbergii by knocking down the transcript level of an insulin-like androgenic gland hormone (Mr-IAG) through injections of dsRNA of the entire Mr-IAG ORF sequence (dsMr-IAG - 518 bp). Interestingly, in-vivo knockdown success and dsMr-IAG lengths seemed to correlate, with long dsRNA being the most effective and short dsRNA fragments showing no effect...
August 17, 2017: RNA Biology
https://www.readbyqxmd.com/read/28816060/the-broad-spectrum-antimicrobial-potential-of-mn-co-4-s2cnme-ch2co2h-a-water-soluble-co-releasing-molecule-corm-401-intracellular-accumulation-transcriptomic-and-statistical-analyses-and-membrane-polarization
#7
Lauren Katie Wareham, Samantha McLean, Ronald Begg, Namrata Rana, Salar Ali, John J Kendall, Guido Sanguinetti, Brian E Mann, Robert K Poole
AIMS: Carbon monoxide (CO)-releasing molecules (CORMs) are candidates for animal and antimicrobial therapeutics. We aimed to probe the antimicrobial potential of a novel manganese CORM. RESULTS: [Mn(CO)4S2CNMe(CH2CO2H)], CORM-401, inhibits growth of Escherichia coli and several antibiotic-resistant clinical pathogens. CORM-401 releases CO that binds oxidases in vivo but is an ineffective respiratory inhibitor. Extensive CORM accumulation (assayed as intracellular manganese) accompanies antimicrobial activity...
August 17, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/28815885/novel-landscape-of-hla-g-isoforms-expressed-in-clear-cell-renal-cell-carcinoma-patients
#8
Diana Tronik-Le Roux, Julie Renard, Jérôme Vérine, Victor Renault, Emmanuel Tubacher, Joel LeMaoult, Nathalie Rouas-Freiss, Jean-François Deleuze, François Desgrandschamps, Edgardo D Carosella
Immune-checkpoints are powerful inhibitory molecules that promote tumor survival. Their blockade is now recognized as providing effective therapeutic benefit against cancer. HLA-G, a recently identified immune checkpoint, has been detected in many types of primary tumors and metastases, in malignant effusions as well as on tumor-infiltrating cells, particularly in patients with clear cell renal cell carcinoma (ccRCC). Here, in order to define a possible anti-cancer therapy, we used a molecular approach based on an unbiased strategy that combines transcriptome determination and immunohistochemical labeling, to analyze in-depth, the HLA-G isoforms expressed in these tumors...
August 16, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28815541/long-noncoding-rnas-in-cancer-and-therapeutic-potential
#9
Arun Renganathan, Emanuela Felley-Bosco
Long noncoding RNAs (lncRNAs) are the major elements of the mammalian transcriptome that is emerging as a central player controlling diverse cellular mechanisms. Most of the well-studied lncRNAs so far are found to be crucial in regulating cellular processes such as cell cycle, growth, and apoptosis that ensure homeostasis. Owing to their location and distribution in the genome, lncRNAs influence the transcription of a wide range of proteins directly or indirectly by transcriptional and posttranscriptional alterations, which opens up the "LncRNA-cancer paradigm" in a context-dependent manner, i...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28815540/long-noncoding-rnas-in-mammalian-development-and-diseases
#10
Parna Saha, Shreekant Verma, Rashmi U Pathak, Rakesh K Mishra
Following analysis of sequenced genomes and transcriptome of many eukaryotes, it is evident that virtually all protein-coding genes have already been discovered. These advances have highlighted an intriguing paradox whereby the relative amount of protein-coding sequences remain constant but nonprotein-coding sequences increase consistently in parallel to increasing evolutionary complexity. It is established that differences between species map to nonprotein-coding regions of the genome that surprisingly is transcribed extensively...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28815535/history-discovery-and-classification-of-lncrnas
#11
Julien Jarroux, Antonin Morillon, Marina Pinskaya
The RNA World Hypothesis suggests that prebiotic life revolved around RNA instead of DNA and proteins. Although modern cells have changed significantly in 4 billion years, RNA has maintained its central role in cell biology. Since the discovery of DNA at the end of the nineteenth century, RNA has been extensively studied. Many discoveries such as housekeeping RNAs (rRNA, tRNA, etc.) supported the messenger RNA model that is the pillar of the central dogma of molecular biology, which was first devised in the late 1950s...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28815138/integrative-network-and-transcriptomics-based-approach-predicts-genotype-specific-drug-combinations-for-melanoma
#12
Kelly E Regan, Philip R O Payne, Fuhai Li
Computational methods for drug combination predictions are needed to identify effective therapies that improve durability and prevent drug resistance in an efficient manner. In this paper, we present SynGeNet, a computational method that integrates transcriptomics data characterizing disease and drug z-score profiles with network mining algorithms in order to predict synergistic drug combinations. We compare SynGeNet to other available transcriptomics-based tools to predict drug combinations validated across melanoma cell lines in three genotype groups: BRAF-mutant, NRAS-mutant and combined...
2017: AMIA Summits on Translational Science Proceedings
https://www.readbyqxmd.com/read/28814974/time-resolved-transcriptome-analysis-and-lipid-pathway-reconstruction-of-the-oleaginous-green-microalga-monoraphidium-neglectum-reveal-a-model-for-triacylglycerol-and-lipid-hyperaccumulation
#13
Daniel Jaeger, Anika Winkler, Jan H Mussgnug, Jörn Kalinowski, Alexander Goesmann, Olaf Kruse
BACKGROUND: Oleaginous microalgae are promising production hosts for the sustainable generation of lipid-based bioproducts and as bioenergy carriers such as biodiesel. Transcriptomics of the lipid accumulation phase, triggered efficiently by nitrogen starvation, is a valuable approach for the identification of gene targets for metabolic engineering. RESULTS: An explorative analysis of the detailed transcriptional response to different stages of nitrogen availability was performed in the oleaginous green alga Monoraphidium neglectum...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28814792/genetic-regulatory-effects-modified-by-immune-activation-contribute-to-autoimmune-disease-associations
#14
Sarah Kim-Hellmuth, Matthias Bechheim, Benno Pütz, Pejman Mohammadi, Yohann Nédélec, Nicholas Giangreco, Jessica Becker, Vera Kaiser, Nadine Fricker, Esther Beier, Peter Boor, Stephane E Castel, Markus M Nöthen, Luis B Barreiro, Joseph K Pickrell, Bertram Müller-Myhsok, Tuuli Lappalainen, Johannes Schumacher, Veit Hornung
The immune system plays a major role in human health and disease, and understanding genetic causes of interindividual variability of immune responses is vital. Here, we isolate monocytes from 134 genotyped individuals, stimulate these cells with three defined microbe-associated molecular patterns (LPS, MDP, and 5'-ppp-dsRNA), and profile the transcriptomes at three time points. Mapping expression quantitative trait loci (eQTL), we identify 417 response eQTLs (reQTLs) with varying effects between conditions...
August 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28814771/rna-sequencing-of-db-db-mice-liver-identifies-lncrna-h19-as-a-key-regulator-of-gluconeogenesis-and-hepatic-glucose-output
#15
Neha Goyal, Ambily Sivadas, K V Shamsudheen, Rijith Jayarajan, Ankit Verma, Sridhar Sivasubbu, Vinod Scaria, Malabika Datta
Liver plays a key role in maintaining glucose homeostasis and impaired hepatic glucose metabolism is associated with type 2 diabetes. In the present study, we used RNA sequencing to profile the transcriptome of the livers of diabetic db/db mice as compared to the normal db/+ mice and identified 218 differentially expressed genes. Amongst these, there were 3 lncRNAs that were significantly downregulated and H19 was the most altered lncRNA in the livers of db/db mice. H19 expression significantly correlated with the expression of genes of the glycolysis and gluconeogenesis pathways, which suggest that altered hepatic H19 levels can directly or indirectly modulate their expression...
August 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28814645/zygotic-genome-activation-occurs-shortly-after-fertilization-in-maize
#16
Junyi Chen, Nicholas Strieder, Nadia G Krohn, Philippe Cyprys, Stefanie Sprunck, Julia C Engelmann, Thomas Dresselhaus
The formation of a zygote via the fusion of an egg and sperm cell and its subsequent asymmetric division (ACD) herald the start of the plant's life cycle. Zygotic genome activation (ZGA) is thought to occur gradually, with the initial steps of zygote and embryo development being primarily maternally controlled, and subsequent steps being governed by the zygotic genome. Here, using maize (Zea mays) as a model plant system, we determined the timing of zygote development and generated RNA-Seq transcriptome profiles of gametes, zygotes, and apical and basal daughter cells...
August 16, 2017: Plant Cell
https://www.readbyqxmd.com/read/28814335/comparative-transcriptome-analysis-of-second-and-third-generation-merozoites-of-eimeria-necatrix
#17
Shijie Su, Zhaofeng Hou, Dandan Liu, Chuanli Jia, Lele Wang, Jinjun Xu, Jianping Tao
BACKGROUND: Eimeria is a common genus of apicomplexan parasites that infect diverse vertebrates, most notably poultry, causing serious disease and economic losses. Eimeria species have complex life-cycles consisting of three developmental stages. However, the molecular basis of the Eimeria reproductive mode switch remains an enigma. METHODS: Total RNA extracted from second- (MZ-2) and third-generation merozoites (MZ-3) of Eimeria necatrix was subjected to transcriptome analysis using RNA sequencing (RNA-seq) followed by qRT-PCR validation...
August 16, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28814277/phenotypes-antioxidant-responses-and-gene-expression-changes-accompanying-a-sugar-only-diet-in-bactrocera-dorsalis-hendel-diptera-tephritidae
#18
Er-Hu Chen, Qiu-Li Hou, Dan-Dan Wei, Hong-Bo Jiang, Jin-Jun Wang
BACKGROUND: Diet composition (yeast:carbohydrate ratio) is an important determinant of growth, development, and reproduction. Recent studies have shown that decreased yeast intake elicits numerous transcriptomic changes and enhances somatic maintenance and lifespan, which in turn reduces reproduction in various insects. However, our understanding of the responses leading to a decrease in yeast ratio to 0% is limited. RESULTS: In the present study, we investigated the effects of a sugar-only diet (SD) on the gene expression patterns of the oriental fruit fly, Bactrocera dorsalis (Hendel), one of the most economically important pests in the family Tephritidae...
August 17, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28814270/transcriptional-analysis-of-abdominal-fat-in-chickens-divergently-selected-on-bodyweight-at-two-ages-reveals-novel-mechanisms-controlling-adiposity-validating-visceral-adipose-tissue-as-a-dynamic-endocrine-and-metabolic-organ
#19
C W Resnyk, W Carré, X Wang, T E Porter, J Simon, E Le Bihan-Duval, M J Duclos, S E Aggrey, L A Cogburn
BACKGROUND: Decades of intensive genetic selection in the domestic chicken (Gallus gallus domesticus) have enabled the remarkable rapid growth of today's broiler (meat-type) chickens. However, this enhanced growth rate was accompanied by several unfavorable traits (i.e., increased visceral fatness, leg weakness, and disorders of metabolism and reproduction). The present descriptive analysis of the abdominal fat transcriptome aimed to identify functional genes and biological pathways that likely contribute to an extreme difference in visceral fatness of divergently selected broiler chickens...
August 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28814268/the-genomic-architecture-of-mastitis-resistance-in-dairy-sheep
#20
G Banos, G Bramis, S J Bush, E L Clark, M E B McCulloch, J Smith, G Schulze, G Arsenos, D A Hume, A Psifidi
BACKGROUND: Mastitis is the most prevalent disease in dairy sheep with major economic, hygienic and welfare implications. The disease persists in all dairy sheep production systems despite the implementation of improved management practises. Selective breeding for enhanced mastitis resistance may provide the means to further control the disease. In the present study, we investigated the genetic architecture of four mastitis traits in dairy sheep. Individual animal records for clinical mastitis occurrence and three mastitis indicator traits (milk somatic cell count, total viable bacterial count in milk and the California mastitis test) were collected monthly throughout lactation for 609 ewes of the Greek Chios breed...
August 16, 2017: BMC Genomics
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