Project description:A number of macrophage and macrophage-like cells are responsible for immune response to challenges. Despite their shared role, these immune cells differ in the inflammatory response and impact on physiology and behavior. The purpose of this study was to profile mRNA levels (transcriptome) to better understand differences between immune cells under homeostasis using two mouse strains.
Project description:Ehrlichia chaffeensis is an obligatory intracellular organism, and causes human monocytic ehrlichiosis (HME), a tick-borne illness. Clinical signs of HME vary from asymptomatic infection to severe mobility that requires hospitalization or death. After whole genome sequencing of this bacterium, 425 open reading frames (38%) of 1115 in the genome were found as hypothetical gene with unknown function. A little is known about pathogenicity gene(s) and strain variation of this bacterium to date. Previously several E. chaffeensis strains were shown to be different based on comparison of limited gene sequences (p120, OMP-1[p28]s, and VLPT). To elucidate strain genetic variations and associated virulency, we carried out comparative genome hybridization (CGH) of E. chaffeensis Arkansas, Wakulla and Liberty strains, since these strains are most distinct in the previous studies. The tiling array containing approximately 300,000 probes of 29 nt spaced as dense as 8 bp on both strands of the genome of E. chaffeensis Arkansas was used. Keywords: Comparative genome hybridization
Project description:Xiphophorus interspecies hybrids represent a valuable model system to study heritable tumorigenesis, and the only model system that exhibits both spontaneous and inducible tumors. Types of tumorigenesis depend on the specific pedigree of the parental species, X. maculatus, utilized to produce interspecies hybrids. Although the ancestors of the two currently used X. maculatus parental lines, Jp163 A and Jp163 B, were originally siblings produced by the same mother, backcross interspecies hybrid progeny between X. hellerii and X. maculatus Jp163 A develop spontaneous melanoma initiating at the dorsal fin due to segregation of an oncogene and a regulator encoded by the X. maculatus genome, while the backcross hybrid progeny with X. hellerii or X. couchianus and Jp163 B exhibit melanoma on the flanks of their bodies, especially after treatment with ultraviolet light. Therefore, dissecting the genetic differences between these two closely related lines may lead to better understanding of functional molecular differences associated with tumorigenic mechanisms. For this purpose, comparative genomic analyses were undertaken to establish genetic variants between these two X. maculatus lines. Surprisingly, given the heritage of these two fish lines, we found genetic variants are clustered together in select chromosomal regions. Among these variants are non-synonymous mutations located in 381 genes. The non-random distribution of genetic variants between these two may highlight ancestral chromosomal recombination patterns that became fixed during subsequent inbreeding. Employing comparative transcriptomics, we also determined differences in the skin transcriptional landscape between the two lines. The genetic differences observed are associated with pathways highlighting fundamental cellular functions including inter-cellular and microenvironment-cellular interactions, and DNA repair. These results collectively lead to the conclusion that diverged functional genetic baselines are present between Jp163 A and B strains. Further, disruption of these fixed genetic baselines in the hybrids may give rise to spontaneous or inducible mechanisms of tumorigenesis.
Project description:rs11-10_urt1 - leaf transcriptome comparison between wt and urt1 (salk_087647) - Identification of mRNA targets of the terminal uridylyltransferase URT1 (AT2G45620) in Arabidopsis thaliana. - Identification of the RNA targets of the terminal uridylyl transferase URT1 (AT2G45620). Mature rosettte leaf transcriptomes were compared between WT and a urt1 knock-out mutant (SALK_087647).
Project description:Purpose: The present study provides the firstly large-scale characterization of miRNAs in Tetranychus cinnabarinus and the comparison between fenpropathrin resistant and susceptible strains gives a clue on study how miRNA involving in fenpropathrin resistance Methods: Using Illumina sequencing to identify the differentially expressed miRNAs between the fenpropathrin resistant and susceptible strains of Tetranychus cinnabarinus Results: 12 miRNAs that were expressed significantly differently were identified between thethe fenpropathrin resistant and susceptible strains of Tetranychus cinnabarinus
Project description:rs12-07_pnm1 - leaf transcriptome comparison between wt and pnm1dnls plants - Identification of nuclear genes regulated by PNM1 (At5g60960) in Arabidopsis thaliana. Mature rosettte leaf transcriptomes were compared between WT and PNM1DNLS mutants.