Project description:This is a common-garden experiment comparing the transcriptional response to hypo-osmotic acclimation among multiple populations of the killifish Fundulus heteroclitus. Original data are in the archive: E-MTAB-524.additional.zip
Project description:This experiment profiled gene expression in livers of individual F. heteroclitus based on sex, mitochondrial genotype, and hypoxia. Each factor had two levels: normoxia and hypoxia for oxygen, North and South genotypes for mtDNA.
Project description:In this study we characterize the gill transcriptome changes that coincide with the arrival of contaminating oil in field-collected Gulf killifish Fundulus grandis. Gill transcription was contrasted before and after the arrival of oil, and between oil impacted and reference sites. Animals were sampled from field sites at four times. The oil impacted site is Grand Terre Island Louisiana (GT) and the two reference sites are Bay St. Louis Mississippi (BSL) and Bayou La Batre Alabama (BLB). The first timepoint (05/01/2010 to 05/09/2010) was before the arrival of contaminating oil, the second and third timepoints (06/28/2010 to 06/29/2010, and 08/30/2010 to 09/01/2010) were after the arrival of contaminating oil, and the fourth timepoint 08/28/2011) was over a year after the arrival of contaminating oil.
Project description:The goals of these studies are to explore the mechanisms that enable extreme physiological plasticity and that may account for evolutionary divergence of adaptive osmotic physiologies among taxa that occupy different osmotic niches. In a common-garden environment, we track physiological and genome expression responses to hypo-osmotic (freshwater) challenge during a time-course of acclimation, and contrast these responses within and between species. We seek to identify mechanisms that facilitate osmotic acclimation that are evolutionarily conserved between basal and derived physiologies, and identify mechanisms that are uniquely derived to enable the extreme osmotic plasticity exhibited by F. heteroclitus. Importantly, previous studies using a comparable experimental design have identified physiological changes and genome expression responses that are adaptive for populations of F. heteroclitus that live in fresh water. As such, this enables us to test whether mechanisms of adaptive micro-evolutionary divergence across osmotic gradients within F. heteroclitus are shared with the mechanisms that account for patterns of macro-evolutionary divergence between F. heteroclitus and F. majalis that we identify in this study. That is, are the targets of micro-evolutionary fine-tuning the same or different as the targets of macro-evolutionary divergence across osmotic boundaries? Population comparisons include between populations from Chesapeake Bay (CB), coastal Virginia (VA), and coastal Georgia (GA).
Project description:The goals of these studies are to explore the mechanisms that may account for evolutionary divergence of adaptive osmotic physiologies among taxa that occupy different osmotic niches. In a common-garden environment, we track genome expression responses to hyper-osmotic (brackish water) challenge during a time-course of acclimation, and contrast these responses between species. We seek to identify mechanisms that facilitate osmotic acclimation that are evolutionarily conserved between basal and derived physiologies, and also to identify mechanisms that are uniquely derived in alternate osmotic environments.
Project description:Microarray was performed on RNA extracted from mid-logarithmic phase in vitro grown non-M1 Streptococcus pyogenes isolates, with either intact or mutant covRS operons. These isolates were compared with corresponding M1 covRS intact and mutant forms to link the expression prolfiles of these non-M1 isolates with invasive pathogenesis. A dye-swapped cyclic design was used in this study in order that each strain could be compared across all samples in silico. For each strain treated, 2 biological replicates were each analysed in dye-swapped technical replicates, giving a total of n=4 peplicates for each strain.
Project description:Group A streptococci (GAS) may engage different sets of virulence strategies, depending on the site of infection and host context. We previously isolated 2 phenotypic variants of a globally disseminated M1T1 GAS clone: a virulent wild-type (WT) strain, characterized by a SpeB(+)/SpeA(-)/Sda1(low) phenotype, and a hypervirulent animal-passaged (AP) strain, better adapted to survive in vivo, with a SpeB(-)/SpeA(+)/Sda1(high) phenotype. This AP strain arises in vivo due to the selection of bacteria with mutations in covS, the sensor part of a key 2-component regulatory system, CovR/S. To determine whether covS mutations explain the hypervirulence of the AP strain, we deleted covS from WT bacteria (DeltaCovS) and were able to simulate the hypervirulence and gene expression phenotype of naturally selected AP bacteria. Correction of the covS mutation in AP bacteria reverted them back to the WT phenotype. Our data confirm that covS plays a direct role in regulating GAS virulence. A dye-swapped cyclic design was used in this study in order that each strain could be compared across all samples in silico. For each strain treated, 2 biological replicates were each analysed in dye-swapped technical replicates, giving a total of n=10 peplicates for each strain.
Project description:Gene expression analyses through cDNA microarray of fifteen gastrocnemius muscles from transgenic and wild-type SOD1G93A mouse model by the ages of 40 and 80 days old were performed. We used a customized cDNA array containing the cDNA platform comprised of 2352 spots, 326 of them orthologous to mouse, 1384 additional human cDNA sequences, 496 negative controls (DMSO) and 48 positive controls (the Q gene from λ-phage). Gene expression results for SOD1G93A and WT age matched mice pointed to eight up- (LOXL2, PIK4CA, FZD9, CUL1, CTNND1, SNF1LK, PRKX, DNER) and nine down-regulated genes (PIK3C2A, RIPK4, ID2, C1QDC1, EIF2AK2, RAC3, CDS1, INPPL1, TBL1X) at 40 days and also to one up- (PIK3CA) and five down-regulated genes (CD44, EEF2K, FZD2, CREBBP, PIKI3R1) at 80 days. Based on differentially expressed genes, analyses for gene priorization were performed and used to construct a network of protein-protein interaction. The network based on the genes of 40 and 80 days old mice was composed by 251 and 531 genes, respectively. GRB2 and SRC were identified as central genes of both networks. In conclusion, changes in gene expression of skeletal muscle from transgenic ALS mice in pre-symptomatic periods give further evidence of early neuromuscular abnormalities that precede motor neuron death. We performed gene expression analyses by customized cDNA array, using reference design, of fifteen gastrocnemius muscles from transgenic and wild-type SOD1G93A mouse model by the ages of 40 and 80 days old. These differentially expressed lists were submitted to analyses for gene priorization and used to construct a network of protein-protein interaction.