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Transcriptome sequencing of two Baikal (Eulimnogammarus verrucosus and E. cyaneus) and one Holarctic (Gammarus lacustris) amphipod species exposed to 1.5 and 12 degree Celsius

ABSTRACT: This project aims to find the molecular changes driving the cold stress response of freshwater amphipods with different overwintering strategies

ORGANISM(S): Eulimnogammarus cyaneus Eulimnogammarus verrucosus Gammarus lacustris

PROVIDER: GSE157288 | GEO | 2020/09/09

REPOSITORIES: GEO

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Transcriptome sequencing of two Baikal (Eulimnogammarus verrucosus and E. cyaneus) and one Holarctic (Gammarus lacustris) amphipod species exposed to 1.5 and 12 degree Celsius

Project description:Transcriptome sequencing of two Baikal (Eulimnogammarus verrucosus and E. cyaneus) and one Holarctic (Gammarus lacustris) amphipod species exposed to 1.5 and 12 degree Celsius

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Zero-Degree Celsius Capillary Electrophoresis Electrospray Ionization for Hydrogen Exchange Mass Spectrometry.

Project description:Currently, fast liquid chromatographic separations at low temperatures are exclusively used for the separation of peptides generated in hydrogen deuterium exchange (HDX) workflows. However, it has been suggested that capillary electrophoresis may be a better option for use with HDX. We performed in solution HDX on peptides and bovine hemoglobin (Hb) followed by quenching, pepsin digestion, and cold capillary electrophoretic separation coupled with mass spectrometry (MS) detection for benchmarking a laboratory-built HDX-MS platform. We found that capillaries with a neutral coating to eliminate electroosmotic flow and adsorptive processes provided fast separations with upper limit peak capacities surpassing 170. In contrast, uncoated capillaries achieved 30% higher deuterium retention for an angiotensin II peptide standard owing to faster separations but with only half the peak capacity of coated capillaries. Data obtained using two different separation conditions on peptic digests of Hb showed strong agreement of the relative deuterium uptake between methods. Processed data for denatured versus native Hb after deuterium labeling for the longest timepoint in this study (50,000 s) also showed agreement with subunit interaction sites determined by crystallographic methods. All proteomic data are available under DOI: 10.6019/PXD034245.

| S-EPMC9850406 | biostudies-literature

Transcriptional profiling of E. coli K-12 and E. coli O157 (Sakai) following heat shock at 45 degree celsius

Project description:Escherichia coli O157 presents a number of specific problems in terms of food safety and public health. It has been found that E. coli O157 is more resistant to a number of the stresses encountered during food production such as heat, pH and osmotic shock. This greater resistance is thought to contribute to the low infectious dose of E. coli O157 (<100 organisms). Moreover, E. coli O157 is associated with debilitating conditions such as haemorrhagic colitis and haemoytic uraemic syndrome, particularly in children and the elderly. We have been studying the stress responses of E. coli O157:H7 (Sakai) and comparing with a commensal strain of E. coli K-12, MG1655. We found that E. coli O157 (Sakai) is more resistant to heat stress than MG1655. A microarray study of these strains subjected to sub-lethal heat-stress at 45M-BM-0C was carried out. In E. coli O157 (Sakai), 380 genes responded significantly to the treatment compared to 410 genes in MG1655. Overnight cultures of E. coli O157 (Sakai) and E. coli K-12 MG1655 were grown in Neidhardt's EZ Rich Defined Medium and diluted 1:100 in 50 ml fresh medium in 125 ml Ehrlenmeyer flasks. The cultures were shaken at 37M-BM-0C until the optical density (OD600) reached 0.4. Each culture was divided into 2 equal parts in identical flasks. One flask flask was transferred to a shaking water bath and incubated at 45M-BM-0C for 10 min; the other flask was incubated at 37M-BM-0C for 10 min. After incubation, the cultures were transferred to 50 mL centrifuge tubes and treated with RNAprotectM-bM-^DM-" to stabilise the mRNA. The experiment was performed 3 times on different days. Six custom-made microarray slides were used in this study; each slide was hybridised with labelled cDNA made from untreated and heated E. coli O157 (Sakai) or MG1655.

2018-03-20 | E-MTAB-5912 | biostudies-arrayexpress

Transcriptome sequencing of two Lake Baikal endemic (Eulimnogammarus verrucosus and E. cyaneus) and one Holarctic (Gammarus lacustris) transcriptome species from the Baikal region subjected to different stressors

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-05-23 | GSE129070 | GEO

Proteomes of the cold-adapted Baikal region amphipods exposed to heat shock

Project description:The proteomes of three amphipod species, a Holarctic species Gammarus lacustris and two Biakal species Eulimnogammarus verrucosus and Eulimnogammarus cyaneus, were received by LC-MS/MS with TMT-labeling. All animals were collected in August 2018. Before the exposition, animals were acclimated in 6C for 25 days. Three species of amphipods were exposed to heat stress (24.6 C for 24 h) and control temperature (6C for 24 h).

2024-02-15 | PXD031000 | Pride

Putative carotenoid-binding proteins from the hemolymph of endemic Lake Baikal amphipod Eulimnogammarus cyaneus and E. vittatus

Project description:Color is an important trait in nature, playing a role in selection and speciation. The most important colorants in crustaceans are carotenoids, which in complexes with carotenoid-binding proteins provide an astonishing variety of colors from red to violet. Over 350 species and subspecies of amphipods (Crustacea: Amphipoda) endemic to Lake Baikal exhibit an impressive variability of colors and coloration patterns. However, the mechanisms forming this diversity are underexplored. In this work, we analyze the coloration of two species of endemic Lake Baikal amphipods, Eulimnogammarus cyaneus and E. vittatus. These species are brightly colored and, even more importantly, characterized by intraspecific color variability. We showed that the color of either species strongly correlated with the abundance of two putative carotenoid-binding proteins (the relative abundance of these proteins was higher in blue or teal-colored animals than in the orange- or yellow-colored ones.). With LC-MS/MS, we were able to identifiy these proteins, which turned out to be similar to the pheromone/odorant-binding protein family.

2020-06-04 | PXD018516 | Pride

Project description:The project aims at describing the transcriptome composition and differential expression of genes in response to different stressors (elevated temperature, heavy metals (cadmium) and organic pollutants (phenanthrene)).

2019-05-24 | GSE122811 | GEO

2019-05-23 | GSE129069 | GEO

Expression estimation with microarrays for Drosophila melanogaster DGRP lines at 18 degree celsius

Project description:DGRP lines were raised at 18 degree celsius, adult mated whole fly expression was estimated using microarrays. The same design was previous used to measure expression at 25 degree celsius (E-MTAB-3216).

2020-09-07 | E-MTAB-8953 | biostudies-arrayexpress

The effect of acute and chronic temperature stress in Baikal omul (Coregonus migratorius Georgi)

Project description:In this work, we describe the transcriptional profiles of Baikal omul juveniles after acute and chronic temperature stress exposure. The juveniles were kept for 1.5 months at 9–12 °C, followed by exposure to acute stress (heating to 21 °C for 1 hour) and chronic stress (heating to 21 °C for 24 hours 3 times a week for a month) in the Experimental Freshwater Aquarium Complex for Baikal Hydrobionts at the Limnological Institute (LIN SB RAS). The information on the transcriptional profiles will contribute to further understanding of the mechanisms of adaptation of whitefish to the environment.

2024-12-03 | GSE283291 | GEO

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