Project description:In this project we aimed to establish a proteome-based pipeline for a non-model Baikal endemic amphipod species Eulimnogammarus cyaneus (Dybowsky, 1874). We used next-generation transcriptome sequencing to create a database for protein identification and investigated the proteome of E. cyaneus with LC-MS with particular emphasis on sexual dimorphism and response to acute thermal stress. We were able to characterize ca. 1000 protein groups and found male- and female-specific proteins, as well as proteins specific for thermal stress conditions.
Project description:Coilin is a scaffold protein essential for the structural integrity of Cajal Bodies, which are non-membranous nuclear organelles that are thought to facilitate assembly and maturation of nuclear RNPs, including spliceosomal snRNPs. To investigate further coilin’s functions in plant cells, and to identify proteins that may functionally interact with coilin, we performed a genetic suppressor screen in Arabidopsis thaliana using a coilin (coi) mutant displaying altered splicing of a GFP pre-mRNA. The modified splicing pattern results in a ‘hyper-GFP’ phenotype in young coi seedlings relative to the intermediate level of GFP in wild-type seedlings. Additionally, in newly emerging leaves of older coi seedlings, the GFP gene frequently undergoes abrupt siRNA-associated posttranscriptional gene silencing that persists during growth. In the suppressor screen, we searched for mutations that subdue one or both of these GFP phenotypes and identified several understudied factors in plants: WRAP53, a putative Cajal body protein; SMU2, a predicted splicing-related factor; and ZC3HC1, an uncharacterized zinc finger protein. All three mutations return the hyper-GFP phenotype of the coi mutant to approximately the intermediate wild-type level. The zc3hc1 mutations in particular induce premature and more extensive posttranscriptional gene silencing similar to mutations in SOP1 and DCL4, which are known modifiers of posttranscriptional gene silencing. Candidate coilin-interacting proteins identified by immunoprecipitation-mass spectrometry include many splicing-related factors, nucleolar proteins, and mRNA export factors. Our results demonstrate the usefulness of the coi mutant to identify new modifiers of alternative splicing and posttranscriptional gene silencing, and suggest diverse roles for coilin in plant cells.
Project description:Analysis of leaves of wild-type and rice COI mutants treated with methyl jasmonate (MeJA). Results provide the role of rice COI on response to jasmonic acid.
Project description:Hemocytes are blood cell circulating in the hemolymph and playing important role in crustacean immunity. On the one side this cells functions as phagocytes and express immune compounds in the external milieu on the other side. To find out the protein composition of hemocytes, we obtained hemocytes proteome of Baikal endemic amphipod Eulimnogammarus verrucosus for the first time. For this, a proteomic analysis of the protein extract were performed using liquid chromatography/tandem mass spectrometry (LC-MS/MS). A total of 1152 unique proteins were discovered. Hemocyanin/phenoloxidase, actin and tubulin were detected in proteome in the greatest amount. Also we discovered proteins of the C-type lectin superfamily, which are probably involved in the molecular pattern recognition during immune response.
Project description:We assembled de novo transcriptomes for three Antarctic invertebrate species: the limpet Nacella concinna (foot muscle tissue), the amphipod Paracerodocus miersii (body wall tissue) and the urchin Sterechinus neumayeri (coelomic fluid). Individuals (n = 5 per treatment) were sampled following exposure to different rates of warming: 1°C per hour, 1°C per day, 1°C per 3 days, or after acclimation to 2°C for 3 months. For longer term experiments (1°C per day, 1°C per 3 days and acclimation), control animals were sampled at both the start and end of the experiment to identify possible seasonal effects. For the shorter term experiment (1°C per hour) only one set of controls was needed.
Project description:Mathematical model of the blood coagulation cascade including meizothrombin, protein C, thrombomodulin, factor VIIIa fragments, partially proteolyzed factor Va species and inactive factor Va fragments.
Project description:The southeastern Australian epibenthic amphipod Melita plumulosa was exposed to eight different contaminants for 48 hours. RNA from exposed animals (10 individuals, pooled) was hybridised against reference RNA from unexposed animals. Each treatment was replicated 5 times. Alternate arrays were dye swapped. Data are presented (exposed/unexposed).
Project description:The southeastern Australian epibenthic amphipod Melita plumulosa was exposed to copper via different routes of exposure for 48 hours. RNA from exposed animals (10 individuals, pooled) was hybridised against reference RNA from unexposed animals. Each treatment was replicated 5 times. Alternate arrays were dye swapped. Data are presented (exposed/ unexposed).
Project description:The transcriptome of the amphipod Echinogammarus marinus was sequenced after exposure to hypoxia following acclimation to different temperatures using 100BP paired-end Illumina HiSeq sequencing. Amphipods were acclimated to two temperatures, 10 or 20 °C, for one week before individuals were then acutely exposed to normoxic (80% air saturation) or hypoxic conditions (30% air saturation) at 10 °C (n = 5 per experimental treatment).
