scholarly journals Time-course expression QTL-atlas of the global transcriptional response of wheat to Fusarium graminearum

2017 ◽  
Vol 15 (11) ◽  
pp. 1453-1464 ◽  
Author(s):  
Mina Samad-Zamini ◽  
Wolfgang Schweiger ◽  
Thomas Nussbaumer ◽  
Klaus F.X. Mayer ◽  
Hermann Buerstmayr
Keyword(s):  
Fusarium Graminearum ◽  
Time Course ◽  
Transcriptional Response ◽  
Expression Qtl

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.

Production of deoxynivalenol and related compounds in liquid culture by Fusarium graminearum

1983 ◽  
Vol 29 (9) ◽  
pp. 1171-1178 ◽  
Author(s):  
J. D. Miller ◽  
A. Taylor ◽  
R. Greenhalgh
Keyword(s):  
Fusarium Graminearum ◽  
Fungal Biomass ◽  
Organic Nitrogen ◽  
Time Course ◽  
Liquid Culture ◽  
Culture Method ◽  
Medium Ph ◽  
Organic Nitrogen Source ◽  
Major Factors ◽  
Related Compounds

A liquid culture method for the production of deoxynivalenol and related compounds by Fusarium graminearum was developed. Major factors which stimulate the biosynthesis of these compounds include reduced oxygen levels, depletion of carbohydrate in the medium, pH, and possibly a low concentration of an organic nitrogen source. Isolates of F. graminearum were tested for the yields of four trichothecene mycotoxins and zearalenone in this system. The time course of acetyl deoxynivalenol, deoxynivalenol, and zearalenone in the fermentation was measured over a 21-day period against pH, glucose concentration, protein, fungal biomass, and ergosterol. A new ester of deoxynivalenol, 15-acetyl-deoxynivalenol, is reported from North American isolates of F. graminearum.

scholarly journals Longitudinal Transcriptional Response of Glycosylation-Related Genes, Regulators, and Targets in Cancer Cell Lines Treated With 11 Antitumor Agents

2017 ◽  
Vol 16 ◽  
pp. 117693511774725 ◽  
Author(s):  
Julia Krushkal ◽  
Yingdong Zhao ◽  
Curtis Hose ◽  
Anne Monks ◽  
James H Doroshow ◽  
...  
Keyword(s):  
Cell Lines ◽  
Cancer Cell ◽  
Drug Targeting ◽  
Time Course ◽  
Antitumor Agents ◽  
Transcriptional Response ◽  
Cancer Cell Lines ◽  
Expression Data ◽  
Cancer Pathways ◽  
Genes Encoding

Cellular glycosylation processes are vital to cell functioning. In malignant cells, they are profoundly altered. We used time-course gene expression data from the NCI-60 cancer cell lines treated with 11 antitumor agents to analyze expression changes of genes involved in glycosylation pathways, genes encoding glycosylation targets or regulators, and members of cancer pathways affected by glycosylation. We also identified glycosylation genes for which pretreatment expression levels or changes after treatment were correlated with drug sensitivity. Their products are involved in N-glycosylation and O-glycosylation, fucosylation, biosynthesis of poly- N-acetyllactosamine, removal of misfolded proteins, binding to hyaluronic acid and other glycans, and cell adhesion. Tumor cell sensitivity to multiple agents was correlated with transcriptional response of C1GALT1C1, FUCA1, SDC1, MUC1; members of the MGAT, GALNT, B4GALT, B3GNT, MAN, and EDEM families; and other genes. These genes may be considered as potential candidates for drug targeting in combination therapy to enhance treatment response.

scholarly journals The transcriptomic response of cells to a drug combination is more than the sum of the responses to the monotherapies

2019 ◽  
Author(s):  
Jennifer E. L. Diaz ◽  
Mehmet Eren Ahsen ◽  
Thomas Schaffter ◽  
Xintong Chen ◽  
Ronald B. Realubit ◽  
...  
Keyword(s):  
Time Course ◽  
Transcriptional Response ◽  
Unrelated Individual ◽  
Drug Combinations ◽  
Prediction Algorithm ◽  
Transcriptional Responses ◽  
Transcriptomic Response ◽  
Transcriptional Signature ◽  
Activation Of Transcription ◽  
Sequential Activation

AbstractOur ability to predict the effects of drug combinations is limited, in part by limited understanding of how the transcriptional response of two monotherapies results in that of their combination. We performed the first analysis of matched time course RNAseq profiling of cells treated with both single drugs and their combinations. The transcriptional signature of the synergistic combination we studied had unique gene expression not seen in either constituent monotherapy. This can be explained mechanistically by the sequential activation of transcription factors in time in the gene regulatory network. The nature of this transcriptional cascade suggests that drug synergy may ensue when the transcriptional responses elicited by two unrelated individual drugs are correlated. We used these results as the basis of a simple prediction algorithm attaining an AUROC of 0.84 in the prediction of synergistic drug combinations in an independent dataset.

scholarly journals Global mRNA and miRNA Analysis Reveal Key Processes in the Initial Response to Infection with WSSV in the Pacific Whiteleg Shrimp

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1140
Author(s):  
Rebecca S. Millard ◽  
Lisa K. Bickley ◽  
Kelly S. Bateman ◽  
Audrey Farbos ◽  
Diana Minardi ◽  
...  
Keyword(s):  
Time Course ◽  
Transcriptional Response ◽  
Penaeid Shrimp ◽  
Initial Response ◽  
Early Infection ◽  
White Spot ◽  
Limited Information ◽  
Major Barrier ◽  
White Spot Disease ◽  
Immune Priming

White Spot Disease (WSD) presents a major barrier to penaeid shrimp production. Mechanisms underlying White Spot Syndrome Virus (WSSV) susceptibility in penaeids are poorly understood due to limited information related to early infection. We investigated mRNA and miRNA transcription in Penaeus vannamei over 36 h following infection. Over this time course, 6192 transcripts and 27 miRNAs were differentially expressed—with limited differential expression from 3–12 h post injection (hpi) and a more significant transcriptional response associated with the onset of disease symptoms (24 hpi). During early infection, regulated processes included cytoskeletal remodelling and alterations in phagocytic activity that may assist WSSV entry and translocation, novel miRNA-induced metabolic shifts, and the downregulation of ATP-dependent proton transporter subunits that may impair cellular recycling. During later infection, uncoupling of the electron transport chain may drive cellular dysfunction and lead to high mortalities in infected penaeids. We propose that post-transcriptional silencing of the immune priming gene Dscam (downregulated following infections) by a novel shrimp miRNA (Pva-pmiR-78; upregulated) as a potential mechanism preventing future recognition of WSSV that may be suppressed in surviving shrimp. Our findings improve our understanding of WSD pathogenesis in P. vannamei and provide potential avenues for future development of prophylactics and treatments.

scholarly journals RNA-seq Analysis of Salt-Stressed Versus Non Salt-Stressed Transcriptomes of Chenopodium quinoa Landrace R49

Genes ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1042 ◽  
Author(s):  
Karina B. Ruiz ◽  
Jonathan Maldonado ◽  
Stefania Biondi ◽  
Herman Silva
Keyword(s):  
Time Course ◽  
Average Length ◽  
Chenopodium Quinoa ◽  
Transcriptional Response ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
Crop Species ◽  
Transcriptional Reprogramming ◽  
Transcriptomic Level ◽  
Shed Light

Quinoa (Chenopodium quinoa Willd.), a model halophytic crop species, was used to shed light on salt tolerance mechanisms at the transcriptomic level. An RNA-sequencing analysis of genotype R49 at an early vegetative stage was performed by Illumina paired-ends method comparing high salinity and control conditions in a time-course pot experiment. Genome-wide transcriptional salt-induced changes and expression profiling of relevant salt-responsive genes in plants treated or not with 300 mM NaCl were analyzed after 1 h and 5 days. We obtained up to 49 million pairs of short reads with an average length of 101 bp, identifying a total of 2416 differentially expressed genes (DEGs) based on the treatment and time of sampling. In salt-treated vs. control plants, the total number of up-regulated and down-regulated genes was 945 and 1471, respectively. The number of DEGs was higher at 5 days than at 1 h after salt treatment, as reflected in the number of transcription factors, which increased with time. We report a strong transcriptional reprogramming of genes involved in biological processes like oxidation-reduction, response to stress and response to abscisic acid (ABA), and cell wall organization. Transcript analyses by real-time RT- qPCR supported the RNA-seq results and shed light on the contribution of roots and shoots to the overall transcriptional response. In addition, it revealed a time-dependent response in the expression of the analyzed DEGs, including a quick (within 1 h) response for some genes, suggesting a “stress-anticipatory preparedness” in this highly salt-tolerant genotype.

scholarly journals Global Transcriptional Response of Bacillus subtilis to Treatment with Subinhibitory Concentrations of Antibiotics That Inhibit Protein Synthesis

2005 ◽  
Vol 49 (5) ◽  
pp. 1915-1926 ◽  
Author(s):  
Janine T. Lin ◽  
Mariah Bindel Connelly ◽  
Chris Amolo ◽  
Suzie Otani ◽  
Debbie S. Yaver
Keyword(s):  
Protein Synthesis ◽  
Bacillus Subtilis ◽  
Time Course ◽  
Expression Patterns ◽  
Transcriptional Response ◽  
Global Gene Expression ◽  
Protein Synthesis Inhibitors ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Subinhibitory Concentrations

ABSTRACT Global gene expression patterns of Bacillus subtilis in response to subinhibitory concentrations of protein synthesis inhibitors (chloramphenicol, erythromycin, and gentamicin) were studied by DNA microarray analysis. B. subtilis cultures were treated with subinhibitory concentrations of protein synthesis inhibitors for 5, 15, 30, and 60 min, and transcriptional patterns were measured throughout the time course. Three major classes of genes were affected by the protein synthesis inhibitors: genes encoding transport/binding proteins, genes involved in protein synthesis, and genes involved in the metabolism of carbohydrates and related molecules. Similar expression patterns for a few classes of genes were observed due to treatment with chloramphenicol (0.4× MIC) or erythromycin (0.5× MIC), whereas expression patterns of gentamicin-treated cells were distinct. Expression of genes involved in metabolism of amino acids was altered by treatment with chloramphenicol and erythromycin but not by treatment with gentamicin. Heat shock genes were induced by gentamicin but repressed by chloramphenicol. Other genes induced by the protein synthesis inhibitors included the yheIH operon encoding ABC transporter-like proteins, with similarity to multidrug efflux proteins, and the ysbAB operon encoding homologs of LrgAB that function to inhibit cell wall cleavage (murein hydrolase activity) and convey penicillin tolerance in Staphylococcus aureus.

scholarly journals Early Expression of Yeast Genes Affected by Chemical Stress

2005 ◽  
Vol 25 (5) ◽  
pp. 1860-1868 ◽  
Author(s):  
A. Lucau-Danila ◽  
G. Lelandais ◽  
Z. Kozovska ◽  
V. Tanty ◽  
T. Delaveau ◽  
...  
Keyword(s):  
Time Course ◽  
Transcriptional Response ◽  
Chemical Stress ◽  
Early Expression ◽  
Antimitotic Drug ◽  
Transcription Activators ◽  
Yeast Genes ◽  
Expression Program ◽  
Genomic Response

ABSTRACT The variety of environmental stresses is probably the major challenge imposed on transcription activators and the transcriptional machinery. To precisely describe the very early genomic response developed by yeast to accommodate a chemical stress, we performed time course analyses of the modifications of the yeast gene expression program which immediately follows the addition of the antimitotic drug benomyl. Similar analyses were conducted with different isogenic yeast strains in which genes coding for relevant transcription factors were deleted and coupled with efficient bioinformatics tools. Yap1 and Pdr1, two well-known key mediators of stress tolerance, appeared to be responsible for the very rapid establishment of a transient transcriptional response encompassing 119 genes. Yap1, which plays a predominant role in this response, binds, in vivo, promoters of genes which are not automatically up-regulated. We proposed that Yap1 nuclear localization and DNA binding are necessary but not sufficient to elicit the specificity of the chemical stress response.

scholarly journals Mammalian K-ras2 Is a Corticosteroid-Induced Gene in Vivo

Endocrinology ◽  
2006 ◽  
Vol 147 (6) ◽  
pp. 2809-2816 ◽  
Author(s):  
Francine E. Brennan ◽  
Peter J. Fuller
Keyword(s):  
Mineralocorticoid Receptor ◽  
Time Course ◽  
Northern Blot Analysis ◽  
Transcriptional Response ◽  
Distal Colon ◽  
Distal Nephron ◽  
Rt Pcr ◽  
Ras Gene ◽  
Regulate Gene Expression

Abstract Aldosterone acts via the mineralocorticoid receptor to regulate gene expression. A number of aldosterone-induced genes have been characterized in the distal colon and/or the distal nephron. Using the Xenopus kidney-derived A6 cell line, the K-ras transcript of the K-ras gene was identified as aldosterone induced, with a role in epithelial sodium transport. This study sought to establish whether K-ras expression is also increased in mammalian epithelia in vivo in response to aldosterone. RNA was extracted from the kidney and distal colon of rats treated with aldosterone or dexamethasone. Northern blot analysis and real-time RT-PCR were performed using probes and primers specific for the K-rasA isoform and for total K-ras. The expression of both total K-ras and of the A isoform is induced in the distal colon by aldosterone and by dexamethasone. Given the relative abundances of the two isoforms, this would appear to indicate induction of both isoforms. The time course of the response is consistent with a primary transcriptional response. In contrast to the documented up-regulation in the amphibian kidney, we did not observe regulation by corticosteroids in the kidney. However, regulation in a subpopulation of cells cannot be excluded.

CopR of Sulfolobus solfataricus represents a novel class of archaeal-specific copper-responsive activators of transcription

Microbiology ◽  
2011 ◽  
Vol 157 (10) ◽  
pp. 2808-2817 ◽  
Author(s):  
Aramis Villafane ◽  
Yekaterina Voskoboynik ◽  
Ilona Ruhl ◽  
David Sannino ◽  
Yukari Maezato ◽  
...  
Keyword(s):  
Inductively Coupled Plasma ◽  
Time Course ◽  
Transcriptional Response ◽  
Optical Emission ◽  
Copper Tolerance ◽  
Emission Spectrometry ◽  
Copper Accumulation ◽  
Copper Binding ◽  
Wild Type ◽  
Copa Gene

In trace amounts, copper is essential for the function of key enzymes in prokaryotes and eukaryotes. Organisms have developed sophisticated mechanisms to control the cytosolic level of the metal, manage its toxicity and survive in copper-rich environments. Here we show that the Sulfolobus CopR represents a novel class of copper-responsive regulators, unique to the archaeal domain. Furthermore, by disruption of the ORF Sso2652 (copR) of the Sulfolobus solfataricus genome, we demonstrate that the gene encodes a transcriptional activator of the copper-transporting ATPase CopA gene and co-transcribed copT, encoding a putative copper-binding protein. Disruption resulted in a loss of copper tolerance in two copR-knockout mutants, while metals such as zinc, cadmium and chromium did not affect their growth. Copper sensitivity in the mutant was linked to insufficient levels of expression of CopA and CopT. The findings were further supported by time-course inductively coupled plasma optical emission spectrometry measurements, whereby continued accumulation of copper in the S. solfataricus mutant was observed. In contrast, copper accumulation in the wild-type stabilized after reaching approximately 6 pg (µg total protein)–1. Complementation of the disrupted mutant with a wild-type copy of the copR gene restored the wild-type phenotype with respect to the physiological and transcriptional response to copper. These observations, taken together, lead us to propose that CopR is an activator of copT and copA transcription, and the member of a novel class of copper-responsive regulators.

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