Project description:Thermococcus kodakarensis, which can grow in a wide range of temperatures, from 60M-BM-0C to 100M-BM-0C, optimally at 85M-BM-0C, has two transcription factor Bs, TFB1 and TFB2, both of which are basal transcription factor. TFB1 is unique to hyperthermophiles, but TFB2 is widely conserved in Euryarchaeota. To screen the genes dependent on each TFB in a temperature dependent manner, we investigated the transcriptional profilings of each TFB deletant strain grown at each temperature, 60M-KM-^ZC, 85M-KM-^ZC, and 93M-KM-^ZC, by comparing with the host strain, KU216. Data analyses showed that TFB1 apparently controls the expression of genes essential for motility and adhesion, such as flagellin genes, at 85M-KM-^ZC and 93M-KM-^ZC, but TFB2 regulates genes involved in basal metabolism including amino acid biosynthesis. Two-condition experiment, KU216 vs. DTF1 cells and KU216 vs. DTF2. Technical replicates: 2 DTF1 at 60M-KM-^ZC, 2 DTF1 at 85M-KM-^ZC, 2 DTF1 at 93M-KM-^ZC, 2 DTF2 at 60M-KM-^ZC, 2 DTF2 at 85M-KM-^ZC, 2 DTF2 at 93M-KM-^ZC, independently measured. One replicate per array.
Project description:Leishmania donovani WHO reference strain MHOM/IN/80/DD8 and Leptomonas seymouri isolates Ld 2001 and Ld39 were used for proteome analysis which were originally isolated from clinical cases of kala azar patients with different inherent antimonial sensitivities. Ld 2001 was Sb-S and Ld 39 was Sb-R. The genome sequencing of these isolates had confirmed co-infection with Leptomonas.
Project description:Candida lusitaniae is an emerging human opportunistic yeast, which can switch from yeast to pseudohyphae, and one of the rare Candida species capable of sexual reproduction. Its haploid genome and the genetic tools available make it a model of interest to study gene function. This study describes the consequences of DPP3 inactivation on cell morphology and mating, both altered in the dpp3Δ knock-out. Interestingly, reintroducing a wild-type copy of the DPP3 gene in the dpp3Δ mutant failed to restore the wild-type phenotypes. Proteomic analyses showed that about 150 proteins were statistically deregulated in the dpp3Δ mutant, and that most of them did not return to their wild-type level in the reconstituted DPP3 strain. The analysis of the segregation of the dpp3Δ mutation and the phenotypes in the progeny of a cross (between the dpp3Δ knock-out and a wild-type strain) showed that the phenotypes are not linked to dpp3Δ, but to a secondary mutation. Genome sequencing of the dpp3Δ mutant allowed us to identify this secondary mutation.
Project description:Cell transformation by the Src tyrosine kinase is characterized by extensive changes in gene expression. To describe these changes, investigators have relied extensively on the study of immortalized rodent cell lines or heterogeneous tumor samples that limit the identification of differentially expressed genes or may not represent the full spectrum of biological processes regulated during transformation. In this study, we took advantage of transformation-deficient and temperature sensitive mutants of the Rous sarcoma virus to characterize the patterns of gene expression in two types of primary cells, namely chicken embryo fibroblasts (CEF) and chicken neuro-retinal (CNR) cells. Keywords: viral transformation of primary cells, transformation, transformation deficient mutant, temperature sensitive mutant, v-Src Chicken embryo fibroblasts (CEF) were infected with the wild-type strain Schmidt-Ruppin A RSV or non-transforming strain NY315 RSV or the non-transforming control virus RCASBP(A) to assess genes involved in v-Src-dependent transformation of CEF. Chicken embryo fibroblasts (CEF) were infected with the temperature sensitve strain NY72-4 RSV and cultured either at non-permissive temperature (41.5M-KM-^ZC) or permissive temperature (37M-KM-^ZC) to assess genes involved in v-Src-dependent transformation of CEF. Chicken neuroretina cells (CNR) were infected with the temperature sensitve strain NY72-4 RSV and cultured either at non-permissive temperature (41.5M-KM-^ZC) or permissive temperature (37M-KM-^ZC) to assess genes involved in v-Src-dependent transformation of CNR and compared to CEF.