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Temperature dependent RNA secondary structure in Trypanosoma brucei

ABSTRACT: Trypanosomes are a globally important group of parasites which together kill and debilitate millions of people world-wide. In trypanosomes, genes do not have individual promoters, rather ~10000 genes share ~200 promoters and all gene expression is thus regulated post-transcriptionally. While effector proteins which modulate the expression of many genes have been described, the mechanisms by which trypanosomes sense changes in their environment and manifest changes in gene expression remain elusive. This study demonstrates that trypanosomes sense changes in their environment through temperature sensitive RNA secondary structure. We show that the majority of observed mRNA abundance changes which distinguish insect adapted and bloodstream adapted life cycle stages can be explained through change in temperature alone.

INSTRUMENT(S): Illumina Genome Analyzer II

ORGANISM(S): Trypanosoma brucei

SUBMITTER: Steven Kelly

PROVIDER: E-MTAB-3335 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Temperature dependent RNA secondary structure in Trypanosoma brucei

Project description:Trypanosomes are a globally important group of parasites which together kill and debilitate millions of people world-wide. In trypanosomes, genes do not have individual promoters, rather ~10000 genes share ~200 promoters and all gene expression is thus regulated post-transcriptionally. While effector proteins which modulate the expression of many genes have been described, the mechanisms by which trypanosomes sense changes in their environment and manifest changes in gene expression remain elusive. This study demonstrates that trypanosomes sense changes in their environment through temperature sensitive RNA secondary structure. We show that the majority of observed mRNA abundance changes which distinguish insect adapted and bloodstream adapted life cycle stages can be explained through change in temperature alone.

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Arabidopsis early cold response phosphoproteomics

Project description:Cold stress is one of the major limiting factors for global crop production. For survival at low temperature, plants need to sense the temperature changes in the surrounding environment. How plants sense and respond to the earliest drop in temperature is still not clearly understood. The plasma membrane and its adjacent extracellular and cytoplasmic sites are the first checkpoints for sensing temperature changes and subsequent events such as signal generation and solute transport. To understand how plants respond to early cold exposure, we have used a mass spectrometry-based phosphoproteomic method to study temporal changes in protein phosphorylation events in Arabidopsis membranes during 5 to 60 min of cold exposure. Phosphoproteomic analysis was carried out by using the following process. Arabidopsis membrane fraction was extracted from leaves. Trypsin digestion and phosphopeptide enrichment by HAMMOC method were performed, then purified peptide sample was analyzed by TripleTOF5600 (AB-SCIEX).

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Transcriptional rearrangements associated with thermal stress and preadaptation in Baikal whitefish (Coregonus baicalensis)

Project description:In this work, we describe the transcriptional profiles of adapted and non-adapted one-month-old Baikal whitefish juveniles after heat shock exposure. Preadapted fish were exposed to a repeated thermal rise of 6 °C above control temperature every 3 days throughout embryonic development. One month after hatching, preadapted and non-adapted larvae were either maintained at control temperatures (12 °C) or exposed to an acute thermal stress (TS) of 12 °C above control temperature. The information on transcriptional profiles will contribute to further understanding of the mechanisms of adaptation of whitefish to the environment.

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Project description:Sense and Antisense Transcription Defines Mitochondrial RNA Boundaries in Trypanosomes

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A complementary role for ELF3 and TFL1 in the regulation of flowering time by ambient temperature, in Arabidopsis thaliana.

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2009-04-18 | E-GEOD-15689 | biostudies-arrayexpress

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Project description:Plants transcriptome react to environment temperature changes profoundly. In Arabidopsis seedlings, genes respond to temperature fluctuations to adopt the ever-changing ambient environment. We used microarrays to detail the global programme of gene expression underlying heat stress response progress in Arabidopsis.

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Project description:The aim of the experiment is to look at transcriptional changes in null mutants of APS kinase. There are four APS kinase isoforms in Arabidopsis, we are interested in the double mutant APK1/APK2, created by crossing two single salk lines. The transcriptomes of WT (Col-0) plants and the double knockout (ab) will be compared. The plants were grown under controlled environment conditions of 10h day, 14h night, 22 degrees centigrade, 60% humidity for five weeks. 10 whole rosettes were pooled for each replicate, there are three replicates for each genotype. Keywords: Expression profiling by array 6 samples were used in this experiment

2009-11-17 | E-GEOD-18980 | biostudies-arrayexpress

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