ABSTRACT: To adapt the lives of organisms to the day-night cycle, evolution has built a complex machinery, whose molecular components are able to anticipate and drive changes in organism behavior and metabolism. A mutual bidirectional interaction exists between circadian abnormalities and development of diseases. Microarrays were used to determine whether circadian regulation occurs at the transcriptional level in response to Salmonella Typhimurium infection. Cecal tissues from wild type mice and Clock mutant mice infected with S. Typhimurium or mock control at two circadian times (10am and 10pm) were used for RNA extraction and hybridization on Affymetrix microarrays.
Project description:To adapt the lives of organisms to the day-night cycle, evolution has built a complex machinery, whose molecular components are able to anticipate and drive changes in organism behavior and metabolism. A mutual bidirectional interaction exists between circadian abnormalities and development of diseases. Microarrays were used to determine whether circadian regulation occurs at the transcriptional level in response to Salmonella Typhimurium infection.
Project description:A majority of individuals infected with human immunodeficiency virus (HIV) have inadequate access to antiretroviral therapy and ultimately develop debilitating oral infections that often correlate with disease progression. Our study evaluates the potential of simian immunodeficiency virus (SIV) infected rhesus macaques to serve as a non-human primate model for oral manifestations of HIV disease. Microarrays were used to characterize changes in gene expression in the dorsal tongue epithelium that occur during chronic SIV infection. Epithelial cells were laser microdissected from dorsal tongue tissue sections from healthy uninfected macaques and macaques with chronic stage SIV infection and used for RNA extraction and hybridization on Affymetrix microarrays.
Project description:A majority of individuals infected with human immunodeficiency virus (HIV) have inadequate access to antiretroviral therapy and ultimately develop debilitating oral infections that often correlate with disease progression. Our study evaluates the potential of simian immunodeficiency virus (SIV) infected rhesus macaques to serve as a non-human primate model for oral manifestations of HIV disease. Microarrays were used to characterize changes in gene expression in the tongue mucosa that occur during chronic SIV infection. Dorsal tongue tissues from healthy uninfected macaques and macaques with chronic stage SIV infection were used for RNA extraction and hybridization on Affymetrix microarrays.
Project description:There are currently no biological tests that differentiate patients with bipolar disorder (BPD) from healthy controls. While there is evidence that peripheral gene expression differences between patients and controls can be utilized as biomarkers for psychiatric illness, it is unclear whether current use or residual effects of antipsychotic and mood stabilizer medication drives much of the differential transcription. We therefore tested whether expression changes in first-episode, never-medicated bipolar patients, can contribute to a biological classifier that is less influenced by medication and could potentially form a practicable biomarker assay for BPD. We employed microarray technology to measure global leukocyte gene expression in first-episode (n=3) and currently medicated BPD patients (n=26), and matched healthy controls (n=25). Following an initial feature selection of the microarray data, we developed a cross-validated 10-gene model that was able to correctly predict the diagnostic group of the training sample (26 medicated patients and 12 controls), with 89% sensitivity and 75% specificity (p<0.001). The 10-gene predictor was further explored via testing on an independent test cohort consisting of three pairs of monozygotic twins discordant for BPD, plus the original enrichment sample cohort (the three never-medicated BPD patients and 13 matched control subjects), and a sample of experimental replicates (n=34). 83% of the independent test sample was correctly predicted, with a sensitivity of 67% and specificity of 100% (although this result did not reach statistical significance). Additionally, 88% of sample diagnostic classes were classified correctly for both the enrichment (p=0.015) and the replicate samples (p<0.001). Peripheral blood leukocytes (PBLs) from whole blood were collected from 26 patients with bipolar disorder who had previously received medication, three patients with bipolar disorder who were experiencing their first hospitalization and had not previously received medication, and 25 matched control subjects, for RNA extraction and hybridization on Affymetrix microarrays. Immediately after blood collection, blood samples were split into two (when a sufficient volume had been collected); an "1" and replicate "2" sample (thus two separate RNA extractions, cDNA and cRNA syntheses and array hybridizations were performed).
Project description:Metals, including copper (Cu) and nickel (Ni) are among the most common contaminants in soils in Europe. Although their effects are relatively well known regarding survival and reproduction of soil invertebrates, their modes of action in these organisms are still poorly studied. Enchytraeus albidus has been used in soil ecotoxicology for many years, and more recently has a gene library and an oligonucleotide microarray for this species which allowed gene expression studies. This has potentiated the means to study further in depth the mechanisms of response to stressors. The main aim of this study is to understand the mechanisms of response of E. albidus to Cu and Ni. For that we have 1) assessed and compared the transcriptomic profile of E. albidus in response to Cu and Ni and 2) compared the Cu, Ni, Cd and Zn transcriptomic profiles. For the microarray hybridizations, E. albidus were exposed to the reproduction effect concentrations EC50 and EC90 of Cu and Ni during 4 days. Results indicate that Cu and Ni have to some extent, similar mechanisms of toxicity and that have already been identified in other species, indicating cross-species conserved mechanisms. Based on hierarchical clustering, it was possible to observe a clear separation of Cd treatments from all other metals. This separation strongly correlates with the available information regarding the toxicokinetics of the tested metals, in which Ni shows properties similar to essential metals. Gene expression in E.albidus was measured 4 days after exposure to Copper, Nickel, Cadmium and Zinc at 2 concentrations of effect on reprocduction (EC50 and EC90). Three biological replicates per exposure condition and 6 biological replicates of control conditions were used.
Project description:Due to its antimicrobial activity, silver nanoparticles (Ag-NPs) are among the most used NPs worldwide, yet little information is available regarding their effects, particularly in soil dwelling organisms. Enchytraeids (Oligochaeta) are important members of the soil fauna which actively contribute to the acceleration of organic matter decomposition and nutrient recycling processes. Hence, for hazard and risk assessment it is important to provide toxicity data for these organisms and to understand more in regard to the mode of action of Ag-NPs within organism. To study this we conducted toxicity experiments using the OECD standard guideline, testing Ag-NPs and AgNO3, having assessed survival, reproduction and differential gene expression. Population toxicity responses were assessed showing higher toxicity for the AgNO3. In an attempt to understand the mode of action we performed transcription profiling using the microarray. Gene expression profile of Enchytraeus albidus was analysed after 2 days of exposure to 100 and 200 mg/kg of two silver forms (nanoparticles and salt_silver nitrate) in OECD soil. Three biological replicates per test treatment and control (clean OECD soil) were used.
Project description:We have compared the gene expression profiles of leukemic tissues in two different mouse models of AML, CALM-AF10 and NHD13, to clincally healthy transgenic and wildtype hematopoetic tissue to identify genes and pathways that can collaborate with these oncogenic fusion proteins to promote leukemic transformation. CA10 and NHD13 transgenic mice were sacrificed when clinical signs of leukemia manifested (mice were hunched, skinny, or had an abnormal complete blood count). For comparsion, we harvested age matched bone marrow, thymi, and spleen from wildtype and clinically healthy trangenic tissues. Transgenic animals were considered clinically healthy if no evident signs of leukemia were present.
Project description:We performed a microarray screening of adult rat retinas to identify genes that could show and up- or down-regulation due to exposure to light. This study was performed using ex-vivo retinas collected from adult Long Evans rats that were exposed to light (1000 Lux), or were left in dark as control. All experiments were performed at the same hour, so that the contribution from the circadian rhythm would not affect the observations. The hours to which the experiment was performed were at 7am (always in dark), 10am (under 1000 lux) and as control 10am (always kept in dark), 1pm (under 1000 Lux) and 1pm (Always in dark).
Project description:Cryptochromes were identified in plants and animals where they function as either photoreceptors or circadian clock components. In the filamentous fungus Neurospora, the biological function of cryptochrome has not yet been explored. Here, we demonstrate that Neurospora crassa cryptochrome (Nc cry) is a DASH-type of cryptochrome, capable of binding FAD and MTHF, whose transcript and protein levels are both strongly induced by blue light in a wc-1 dependent manner. Although the Nc cry transcript is circadian-regulated and antiphasic to frq, knockout strains of Nc cry appears to have a normal clock phenotype. Whole genome microarray and RT-QPCR analysis confirm that Nc cry is not involved in the signal transduction of either early or late light responses and seems to have no transcriptional regulatory activity under our laboratory conditions. Our study concludes that the only cryptochrome in Neurospora crassa is dispensable for the well-characterized blue light sensing cascade and is not part of the circadian clock system. Keywords: light response Two-color microarray. Alexa Fluor 555 was consistently used to label cDNA synthesized from reference RNA, which is a mixture containing equal amounts of RNA samples harvested from different circadian time points and light treatment durations. The same batch of pooled RNA was used as a reference for each array experiment. Alexa Fluor 647 was used exclusively to label cDNA representing sample RNA.