Comparative genomic hybridization analysis of 32 Nordic group I Clostridium botulinum type B strains isolated from various sources revealed two homogeneous clusters, clusters BI and BII. The type B strains differed from reference strain ATCC 3502 by 413 coding sequence (CDS) probes, sharing 88% of all the ATCC 3502 genes represented on the microarray. The two Nordic type B clusters differed from each other by their response to 145 CDS probes related mainly to transport and binding, adaptive mech ...[more]
Project description:The presence of Set2-mediated methylation of H3K36 (K36me) correlates with transcription frequency throughout the yeast genome. K36me targets the Rpd3S complex to deacetylate transcribed regions and suppress cryptic transcription initiation at certain genes. Here, using a genome-wide approach, we report that the Set2-Rpd3S pathway is generally required for controlling acetylation at coding regions. When using acetylation as a functional read-out for this pathway, we discovered that longer genes and, surprisingly, genes transcribed at lower frequency exhibit a stronger dependency. Moreover, a systematic screen using high resolution tiling microarrays allowed us to identify a group of genes that rely on Set2-Rpd3S to suppress spurious transcripts. Interestingly, most of these genes are within the group that depend the same pathway to maintain a hypo-acetylated state at coding regions. These data highlight the importance of using the functional readout of histone codes to define the roles of specific pathways.
Project description:The Goal of this study is to explore the transcriptional differences between angiogenic and non-angiogenic tumors generated in Dr. Folkman's Lab, Harvard Medical School.<br>Referneces:<br>Almog N, Henke V, Flores L, Hlatky L, Kung AL, Wright RD, Berger R, Hutchinson L, Naumov GN, Bender E, Akslen LA, Achilles EG, Folkman J.<br>Prolonged dormancy of human liposarcoma is associated with impaired tumor angiogenesis.<br>FASEB J. 2006 May;20(7):947-9.<br><br>Naumov GN, Bender E, Zurakowski D, Kang SY, Sampson D, Flynn E, Watnick RS, Straume O, Akslen LA, Folkman J, Almog N.<br>A model of human tumor dormancy: an angiogenic switch from the nonangiogenic phenotype.<br>J Natl Cancer Inst. 2006 Mar 1;98(5):316-25.<br>
Project description:Transcription profiling of fission yeast /yox1/ deletion and genome wide location analysis of Yox1p and Cdc10p transcription factors reveal a negative feedback interaction: /yox1 /is transcriptionally activated by MBF, and Yox1p in turn transcriptionally represses the MBF target genes (including /yox1 /itself).
Project description:Human dermal microvascular endothelial cells (HDMVECs) were irradiated with 2 Gy or non-irradiated. Two methods of RNA isolation were used to comparatively analyze the miRNA status after radiation treatment.
Project description:Abstract: Testicular cancers in young adult men derive from an inborn precursor lesion, called carcinoma in situ (CIS) of the testis. CIS cells are believed to arise from primordial germ cells or gonocytes that fail to differentiate into the male germ cell lineage, and show a remarkable resemblance to embryonic stem cells (ESC). With this study we aimed at further elucidating the origin of CIS using microarray analysis of genome-wide gene expression. CIS cells only constitute a small fraction of the tissue and therefore, to reduce contaminating RNA from other cell types, we developed a fast (160 sec) staining procedure specific for CIS and fetal germ cells. Highly enriched cell populations were obtained by laser microdissectioning. The expression profiles of CIS cells were compared to microdissected fetal gonocytes, oogonia and cultured ESC with and without genomic amplifications. The cell type most similar to CIS was the gonocytes indicating malignant transformation at this stage. The enriched cell populations allowed us to find unique expression patterns for the developmentally very related cell types. Analyses of the similarities and differences among the cell types may help us understand when and how the malignant transformation to CIS occurs.
Project description:The aim of the experiment was to identify novel genes with relevance to cellular cholesterol metabolism. HeLa cells were cultivated while sterol was depleted from the medium by applying 2-Hydroxypropyl-cyclodextrin. RNA for expression profiling was isolated 3h, 4.5h and 6h after depletion.
Project description:Anaemia negatively affects the prognosis of patients with head and neck squamous cell carcinoma (HNSCC). This study investigates whether anaemia is associated to genetic changes and whether these changes predict the clinical outcome.
Project description:To understand how metabolic and nutritional factors governing adaptation to the host niche contribute to the virulence of Aspergillus fumigatus we compared transcriptomes of developmentally matched A.fumigatus isolates following laboratory culture or initiation of infection in the neutropenic murine lung.
Project description:The aim of this experiment was to analyse the expression of two sets of genes identified as being putatively sporophyte-specific or gametophyte-specific by a suppressive subtraction hybridisation using cDNA from immature sporophytes and immature gametophytes of the Ectocarpus strain Esil32. The expression of these genes was analysed in the sporophyte and gametophyte generations of the life cycle (again using immature algae that had not yet produces zoidangia) and in the sporophyte generation of a mutant strain, immediate upright, that exhibits gametophyte-like characteristics during the sporophyte generation.