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Lake Baikal is the oldest, by volume, the largest, and the deepest freshwater lake on Earth. It is characterized by an outstanding diversity of endemic faunas with more than 350 amphipod species and subspecies (Amphipoda, Crustacea, Arthropoda). They are the dominant benthic organisms in the lake, contributing substantially to the overall biomass. Eulimnogammarus verrucosus, E. cyaneus, and E. vittatus, in particular, serve as emerging models in ecotoxicological studies. It was, then, necessary to investigate whether these endemic littoral amphipods species form genetically separate populations across Baikal, to scrutinize if the results obtained --~for example, about stress responses~-- with samples from one single location (Bolshie Koty, where the biological station is located), could be extrapolated to the complete lake or not. The genetic diversity within those three endemic littoral amphipod species was determined based on fragments of Cytochrome C Oxidase I (COI) and 18S rDNA (only for E. verrucosus). Gammarus lacustris, a Holarctic species living in water bodies near Baikal, was examined for comparison. The intra-specific genetic diversities within E. verrucosus and E. vittatus (13% and 10%, respectively) were similar to the inter-species differences, indicating the occurrence of cryptic, morphologically highly similar species. This was confirmed with 18S rDNA for E. verrucosus. The haplotypes of E. cyaneus and G. lacustris specimens were, with intra-specific genetic distances of 3% and 2%, respectively, more homogeneous, indicating no --or only recent disruption of-- gene flow of E. cyaneus across Baikal, and recent colonization of water bodies around Baikal by G. lacustris. The data provide the first clear evidence for the formation of cryptic (sub)species within endemic littoral amphipod species of Lake Baikal and mark the inflows/outflow of large rivers as dispersal barriers. Lake Baikal has provided a stable environment for millions of years, in stark co

Polyaromatic hydrocarbons (PAH) are common pollutants of water ecosystems originating from incineration processes and contamination with mineral oil. Water solubility of PAHs is generally low; for toxicity tests with aquatic organisms, they are therefore usually dissolved in organic solvents. Here we examined the effects of a typical model PAH, phenanthrene, and a solvent, acetone, on amphipods as relevant aquatic invertebrate models. Two of these species, Eulimnogammarus verrucosus and Eulimnogammarus cyaneus, are common endemics of the oligotrophic and pristine Lake Baikal, while one, Gammarus lacustris, is widespread throughout the Holarctic and inhabits smaller and more eutrophic water bodies in the Baikal area. Neither solvent nor phenanthrene caused mortality at the applied concentrations, but both substances affected gene expression in all species. Differential gene expression was more profound in the species from Lake Baikal than in the Holarctic species. Moreover, in one of the Baikal species, E. cyaneus, we found that many known components of the cellular xenobiotic detoxification system reacted to the treatments. Finally, we detected a negative relationship between changes in transcript abundances in response to the solvent and phenanthrene. This mixture effect, weaker than the impact by a single mixture component, needs further exploration.

The unprecedented outbreak of Ebola in West Africa resulted in over 28,000 cases and 11,000 deaths, underlining the need for a better understanding of the biology of this highly pathogenic virus to develop specific counter strategies. Two filoviruses, the Ebola and Marburg viruses, result in a severe and often fatal infection in humans. However, bats are natural hosts and survive filovirus infections without obvious symptoms. The molecular basis of this striking difference in the response to filovirus infections is not well understood. We report a systematic overview of differentially expressed genes, activity motifs and pathways in human and bat cells infected with the Ebola and Marburg viruses, and we demonstrate that the replication of filoviruses is more rapid in human cells than in bat cells. We also found that the most strongly regulated genes upon filovirus infection are chemokine ligands and transcription factors. We observed a strong induction of the JAK/STAT pathway, of several genes encoding inhibitors of MAP kinases (DUSP genes) and of PPP1R15A, which is involved in ER stress-induced cell death. We used comparative transcriptomics to provide a data resource that can be used to identify cellular responses that might allow bats to survive filovirus infections.

The unprecedented outbreak of Ebola in West Africa resulted in over 28,000 cases and 11,000 deaths, underlining the need for a better understanding of the biology of this highly pathogenic virus to develop specific counter strategies. Two filoviruses, the Ebola and Marburg viruses, result in a severe and often fatal infection in humans. However, bats are natural hosts and survive filovirus infections without obvious symptoms. The molecular basis of this striking difference in the response to filovirus infections is not well understood. We report a systematic overview of differentially expressed genes, activity motifs and pathways in human and bat cells infected with the Ebola and Marburg viruses, and we demonstrate that the replication of filoviruses is more rapid in human cells than in bat cells. We also found that the most strongly regulated genes upon filovirus infection are chemokine ligands and transcription factors. We observed a strong induction of the JAK/STAT pathway, of several genes encoding inhibitors of MAP kinases (DUSP genes) and of PPP1R15A, which is involved in ER stress-induced cell death. We used comparative transcriptomics to provide a data resource that can be used to identify cellular responses that might allow bats to survive filovirus infections.

Eulimnogammarus verrucosus is an amphipod endemic to the unique ecosystem of Lake Baikal and serves as an emerging model in ecotoxicological studies. We report here on a survey sequencing of its genome as a first step to establish sequence resources for this species. From a single lane of paired-end sequencing data, we estimated the genome size as nearly 10 Gb and we obtained an overview of the repeat content. At least two-thirds of the genome are non-unique DNA, and a third of the genomic DNA is composed of just five families of repetitive elements, including low-complexity sequences. Attempts to use off-the-shelf assembly tools failed on the available low-coverage data both before and after removal of highly repetitive components. Using a seed-based approach we nevertheless assembled short contigs covering 33 pre-microRNAs and the homeodomain-containing exon of nine Hox genes. The absence of clear evidence for paralogs implies that a genome duplication did not contribute to the large genome size. We furthermore report the assembly of the mitochondrial genome using a new, guided “crystallization” procedure. The initial results presented here set the stage for a more complete sequencing and analysis of this large genome.