scholarly journals Intragenic differential expression in archaea transcriptomes revealed by computational analysis of tiling microarrays

2017 ◽  
Author(s):  
Atlas Khan ◽  
Ricardo Z. N. Vêncio
Keyword(s):  
Differential Expression ◽  
Pyrococcus Furiosus ◽  
Sulfolobus Solfataricus ◽  
Halobacterium Salinarum ◽  
Self Organizing Map ◽  
Methanococcus Maripaludis ◽  
Tiling Microarrays ◽  
Whole Transcriptome Analysis ◽  
Low Dimensional ◽  
Whole Transcriptome

AbstractRecent advances, in high-throughput technologies allows whole transcriptome analysis, providing a complete and panoramic view of intragenic differential expression in eukaryotes. However, intragenic differential expression in prokaryotes still mystery and incompletely understood. In this study, we investigated and collected the evidence for intragenic differential expression in several archaeal transcriptomes such as, Halobacterium salinarum NRC-1, Pyrococcus furiosus, Methanococcus maripaludis, and Sulfolobus solfataricus, based on computational methods; specifically, by well-known self-organizing map (SOM) for cluster analysis, which transforms high dimensional data into low dimensional. We found 104 (3.86%) of genes in Halobacterium salinarum NRC-1, 59 (2.56%) of genes in Pyrococcus furiosus, 43 (2.41%) of genes Methanococcus maripaludis and 13 (0.42%) of genes in Sulfolobus solfataricus have two or more clusters, i.e., showed the intragenic differential expression at different conditions.

scholarly journals Whole transcriptome analysis of the fasting and fed Burmese python heart: insights into extreme physiological cardiac adaptation

2011 ◽  
Vol 43 (2) ◽  
pp. 69-76 ◽  
Author(s):  
Christopher E. Wall ◽  
Steven Cozza ◽  
Cecilia A. Riquelme ◽  
W. Richard McCombie ◽  
Joseph K. Heimiller ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Differential Expression ◽  
Molecular Mechanisms ◽  
Biological Processes ◽  
Rna Seq ◽  
Cardiac Adaptation ◽  
Python Molurus ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome ◽  
Novel Model

The infrequently feeding Burmese python ( Python molurus ) experiences significant and rapid postprandial cardiac hypertrophy followed by regression as digestion is completed. To begin to explore the molecular mechanisms of this response, we have sequenced and assembled the fasted and postfed Burmese python heart transcriptomes with Illumina technology using the chicken ( Gallus gallus ) genome as a reference. In addition, we have used RNA-seq analysis to identify differences in the expression of biological processes and signaling pathways between fasted, 1 day postfed (DPF), and 3 DPF hearts. Out of a combined transcriptome of ∼2,800 mRNAs, 464 genes were differentially expressed. Genes showing differential expression at 1 DPF compared with fasted were enriched for biological processes involved in metabolism and energetics, while genes showing differential expression at 3 DPF compared with fasted were enriched for processes involved in biogenesis, structural remodeling, and organization. Moreover, we present evidence for the activation of physiological and not pathological signaling pathways in this rapid, novel model of cardiac growth in pythons. Together, our data provide the first comprehensive gene expression profile for a reptile heart.

Gene expression analysis in modeling Parkinson’s disease

2020 ◽  
pp. 103-104
Author(s):  
М.М. Руденок ◽  
А.Х. Алиева ◽  
А.А. Колачева ◽  
М.В. Угрюмов ◽  
П.А. Сломинский ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Early Stage ◽  
Systemic Disease ◽  
Molecular Genetic ◽  
Presymptomatic Stage ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome ◽  
The Brain ◽  
Transcriptome Level

Несмотря на очевидный прогресс, достигнутый в изучении молекулярно-генетических факторов и механизмов патогенеза болезни Паркинсона (БП), в настоящее время стало ясно, что нарушения в структуре ДНК не описывают весь спектр патологических изменений, наблюдаемых при развитии заболевания. В настоящее время показано, что существенное влияние на патогенез БП могут оказывать изменения на уровне транскриптома. В работе были использованы мышиные модели досимптомной стадии БП, поздней досимптомной и ранней симптомной (РСС) стадиями БП. Для полнотранскриптомного анализа пулов РНК тканей черной субстанции и стриатума мозга мышей использовались микрочипы MouseRef-8 v2.0 Expression BeadChip Kit («Illumina», США). Полученные данные указывают на последовательное вовлечение транскриптома в патогенез БП, а также на то, что изменения на транскриптомном уровне процессов транспорта и митохондриального биогенеза могут играть важную роль в нейродегенерации при БП уже на самых ранних этапах. Parkinson’s disease (PD) is a complex systemic disease, mainly associated with the death of dopaminergic neurons. Despite the obvious progress made in the study of molecular genetic factors and mechanisms of PD pathogenesis, it has now become clear that violations in the DNA structure do not describe the entire spectrum of pathological changes observed during the development of the disease. It has now been shown that changes at the transcriptome level can have a significant effect on the pathogenesis of PD. The authors used models of the presymptomatic stage of PD with mice decapitation after 6 hours (6 h-PSS), presymptomatic stage with decapitation after 24 hours (24 h-PSS), advanced presymptomatic (Adv-PSS) and early symptomatic (ESS) stages of PD. For whole transcriptome analysis of RNA pools of the substantia nigra and mouse striatum, the MouseRef-8 v2.0 Expression BeadChip Kit microchips (Illumina, USA) were used. As a result of the analysis of whole transcriptome data, it was shown that, there are a greater number of statistically significant changes in the tissues of the brain and peripheral blood of mice with Adv-PSS and ESS models of PD compared to 6 h-PSS and 24 h-PSS models. In general, the obtained data indicate the sequential involvement of the transcriptome in the pathogenesis of PD, as well as the fact that changes at the transcriptome level of the processes of transport and mitochondrial biogenesis can play an important role in neurodegeneration in PD at an early stage.

scholarly journals Glyceraldehyde-3-Phosphate Ferredoxin Oxidoreductase from Methanococcus maripaludis

2007 ◽  
Vol 189 (20) ◽  
pp. 7281-7289 ◽  
Author(s):  
Myong-Ok Park ◽  
Taeko Mizutani ◽  
Patrik R. Jones
Keyword(s):  
Pyrococcus Furiosus ◽  
Substrate Inhibition ◽  
Physiological Role ◽  
Sodium Molybdate ◽  
Rare Metal ◽  
Growth Conditions ◽  
Defined Medium ◽  
Methanococcus Maripaludis ◽  
Ferredoxin Oxidoreductase ◽  
Gapdh Activity

ABSTRACT The genome sequence of the non-sugar-assimilating mesophile Methanococcus maripaludis contains three genes encoding enzymes: a nonphosphorylating NADP+-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPN), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and glyceraldehyde-3-phosphate ferredoxin oxidoreductase (GAPOR); all these enzymes are potentially capable of catalyzing glyceraldehyde-3-phosphate (G3P) metabolism. GAPOR, whose homologs have been found mainly in archaea, catalyzes the reduction of ferredoxin coupled with oxidation of G3P. GAPOR has previously been isolated and characterized only from a sugar-assimilating hyperthermophile, Pyrococcus furiosus (GAPORPf), and contains the rare metal tungsten as an irreplaceable cofactor. Active recombinant M. maripaludis GAPOR (GAPORMm) was purified from Escherichia coli grown in minimal medium containing 100 μM sodium molybdate. In contrast, GAPORMm obtained from cells grown in medium containing tungsten (W) and W and molybdenum (Mo) or in medium without added W and Mo did not display any activity. Activity and transcript analysis of putative G3P-metabolizing enzymes and corresponding genes were performed with M. maripaludis cultured under autotrophic conditions in chemically defined medium. The activity of GAPORMm was constitutive throughout the culture period and exceeded that of GAPDH at all time points. As GAPDH activity was detected in only the gluconeogenic direction and GAPN activity was completely absent, only GAPORMm catalyzes oxidation of G3P in M. maripaludis. Recombinant GAPORMm is posttranscriptionally regulated as it exhibits pronounced and irreversible substrate inhibition and is completely inhibited by 1 μM ATP. With support from flux balance analysis, it is concluded that the major physiological role of GAPORMm in M. maripaludis most likely involves only nonoptimal growth conditions.

scholarly journals Copper Availability Influences the Transcriptomic Response of Candida albicans to Fluconazole Stress

2021 ◽  
Vol 11 (4) ◽  
Author(s):  
Elizabeth W Hunsaker ◽  
Chen-Hsin Albert Yu ◽  
Katherine J Franz
Keyword(s):  
Candida Albicans ◽  
Time Course ◽  
Transcriptional Response ◽  
Metal Homeostasis ◽  
Metal Availability ◽  
Drug Induced ◽  
Transcriptomic Response ◽  
Opportunistic Fungal Pathogen ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome

Abstract The ability of pathogens to maintain homeostatic levels of essential biometals is known to be important for survival and virulence in a host, which itself regulates metal availability as part of its response to infection. Given this importance of metal homeostasis, we sought to address how the availability of copper in particular impacts the response of the opportunistic fungal pathogen Candida albicans to treatment with the antifungal drug fluconazole. The present study reports whole transcriptome analysis via time-course RNA-seq of C. albicans cells exposed to fluconazole with and without 10 µM supplemental CuSO4 added to the growth medium. The results show widespread impacts of small changes in Cu availability on the transcriptional response of C. albicans to fluconazole. Of the 2359 genes that were differentially expressed under conditions of cotreatment, 50% were found to be driven uniquely by exposure to both Cu and fluconazole. The breadth of metabolic processes that were affected by cotreatment illuminates a fundamental intersectionality between Cu metabolism and fungal response to drug stress. More generally, these results show that seemingly minor fluctuations in Cu availability are sufficient to shift cells’ transcriptional response to drug stress. Ultimately, the findings may inform the development of new strategies that capitalize on drug-induced vulnerabilities in metal homeostasis pathways.

scholarly journals Whole‐Transcriptome Analysis ofPlasmodium falciparumField Isolates: Identification of New Pathogenicity Factors

2007 ◽  
Vol 196 (11) ◽  
pp. 1603-1612 ◽  
Author(s):  
Anthony Siau ◽  
Fousseyni S. Touré ◽  
Odile Ouwe‐Missi‐Oukem‐Boyer ◽  
Liliane Cicéron ◽  
Nassira Mahmoudi ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Pathogenicity Factors ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome

PSS Business Case Map: Supporting Idea Generation in PSS Design

2012 ◽  
Author(s):  
Fumiya Akasaka ◽  
Kazuki Fujita ◽  
Yoshiki Shimomura
Keyword(s):  
Idea Generation ◽  
Business Case ◽  
Literature Survey ◽  
The Self ◽  
High Dimensional ◽  
Self Organizing Map ◽  
Two Dimensional ◽  
Service Type ◽  
Business Cases ◽  
Low Dimensional

This paper proposes the PSS Business Case Map as a tool to support designers’ idea generation in PSS design. The map visualizes the similarities among PSS business cases in a two-dimensional diagram. To make the map, PSS business cases are first collected by conducting, for example, a literature survey. The collected business cases are then classified from multiple aspects that characterize each case such as its product type, service type, target customer, and so on. Based on the results of this classification, the similarities among the cases are calculated and visualized by using the Self-Organizing Map (SOM) technique. A SOM is a type of artificial neural network that is trained using unsupervised learning to produce a low-dimensional (typically two-dimensional) view from high-dimensional data. The visualization result is offered to designers in a form of a two-dimensional map, which is called the PSS Business Case Map. By using the map, designers can figure out the position of their current business and can acquire ideas for the servitization of their business.

scholarly journals Human Bocavirus Infection of Permanent Cells Differentiated to Air-Liquid Interface Cultures Activates Transcription of Pathways Involved in Tumorigenesis

Cancers ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 410 ◽  
Author(s):  
Verena Schildgen ◽  
Monika Pieper ◽  
Soumaya Khalfaoui ◽  
Wolfgang Arnold ◽  
Oliver Schildgen
Keyword(s):  
Mrna Level ◽  
Tumor Development ◽  
Respiratory Pathogen ◽  
Human Bocavirus ◽  
Canonical Pathways ◽  
Infected Cells ◽  
Whole Transcriptome Analysis ◽  
Air Liquid Interface ◽  
Whole Transcriptome

The parvoviral human bocavirus (HBoV) is a respiratory pathogen, able to persist in infected cells. The viral DNA has been identified in colorectal and lung tumors and thus it was postulated that the virus could be associated with tumorigenesis. This assumption was supported by the fact that in HBoV-infected patients and in an in vitro cell culture system, pro-cancerogenic and -fibrotic cytokines were expressed. In this work, it is shown by a whole transcriptome analysis that, also at the mRNA level, several pathways leading to neoplasia and tumorigenesis are significantly upregulated. In total, a set of 54 transcripts are specifically regulated by HBoV, of which the majority affects canonical pathways that may lead to tumor development if they become deregulated. Moreover, pathways leading to necrosis, apoptosis and cell death are downregulated, supporting the hypothesis that HBoV might contribute to the development of some kinds of cancer.

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