Comparison of the receptor FGFRL1 from sea urchins and humans illustrates evolution of a zinc binding motif in the intracellular domain

BACKGROUND: FGFRL1, the gene for the fifth member of the fibroblast growth factor receptor (FGFR) family, is found in all vertebrates from fish to man and in the cephalochordate amphioxus. Since it does not occur in more distantly related invertebrates such as insects and nematodes, we have speculated that FGFRL1 might have evolved just before branching of the vertebrate lineage from the other invertebrates (Beyeler and Trueb, 2006). RESULTS: We identified the gene for FGFRL1 also in the sea urchin Strongylocentrotus purpuratus and cloned its mRNA. The deduced amino acid sequence shares 62% sequence similarity with the human protein and shows conservation of all disulfides and N-linked carbohydrate attachment sites. Similar to the human protein, the S. purpuratus protein contains a histidine-rich motif at the C-terminus, but this motif is much shorter than the human counterpart. To analyze the function of the novel motif, recombinant fusion proteins were prepared in a bacterial expression system. The human fusion protein bound to nickel and zinc affinity columns, whereas the sea urchin protein barely interacted with such columns. Direct determination of metal ions by atomic absorption revealed 2.6 mole zinc/mole protein for human FGFRL1 and 1.7 mole zinc/mole protein for sea urchin FGFRL1. CONCLUSION: The FGFRL1 gene has evolved much earlier than previously assumed. A comparison of the intracellular domain between sea urchin and human FGFRL1 provides interesting insights into the shaping of a novel zinc binding domain.

Evidence for past variations in methane availability in a Siberian thermokarst lake based on δ13C of chitinous invertebrate remains

Understanding past methane dynamics in arctic wetlands and lakes is crucial for estimating future methane release. Methane fluxes from lake ecosystems have increasingly been studied, yet only few reconstructions of past methane emissions from lakes are available. In this study, we develop an approach to assess changes in methane availability in lakes based on δ13C of chitinous invertebrate remains and apply this to a sediment record from a Siberian thermokarst lake. Diffusive methane fluxes from the surface of ten newly sampled Siberian lakes and seven previously studied Swedish lakes were compared to taxon-specific δ13C values of invertebrate remains from lake surface sediments to investigate whether these invertebrates assimilated 13C-depleted carbon typical for methane. Remains of chironomid larvae of the tribe Orthocladiinae that, in the study lakes, mainly assimilate plant-derived carbon had higher δ13C than other invertebrate groups. δ13C of other invertebrates such as several chironomid groups (Chironomus, Chironomini, Tanytarsini, and Tanypodinae), cladocerans (Daphnia), and ostracods were generally lower. δ13C of Chironomini and Daphnia, and to a lesser extent Tanytarsini was variable in the lakes and lower at sites with higher diffusive methane fluxes. δ13C of Chironomini, Tanytarsini, and Daphnia were correlated significantly with diffusive methane flux in the combined Siberian and Swedish dataset (r = −0.72, p = 0.001, r = −0.53, p = 0.03, and r = −0.81, p < 0.001, respectively), suggesting that δ13C in these invertebrates was affected by methane availability. In a second step, we measured δ13C of invertebrate remains from a sediment record of Lake S1, a shallow thermokarst lake in northeast Siberia. In this record, covering the past ca 1000 years, δ13C of taxa most sensitive to methane availability (Chironomini, Tanytarsini, and Daphnia) was lowest in sediments deposited from ca AD 1250 to ca AD 1500, and after AD 1970, coinciding with warmer climate as indicated by an independent local temperature record. As a consequence the offset in δ13C between methane-sensitive taxa and bulk organic matter was higher in these sections than in other parts of the core. In contrast, δ13C of other invertebrate taxa did not show this trend. Our results suggest higher methane availability in the study lake during warmer periods and that thermokarst lakes can respond dynamically in their methane output to changing environmental conditions.

Candidatus Syngnamydia venezia, a novel member of the phylum Chlamydiae from the broad nosed pipefish, Syngnathus typhle

Chlamydia are obligate intracellular bacteria and important pathogens of humans and animals. Chlamydia-related bacteria are also major fish pathogens, infecting epithelial cells of the gills and skin to cause the disease epitheliocystis. Given the wide distribution, ancient origins and spectacular diversity of bony fishes, this group offers a rich resource for the identification and isolation of novel Chlamydia. The broad-nosed pipefish (Syngnathus typhle) is a widely distributed and genetically diverse temperate fish species, susceptible to epitheliocystis across much of its range. We describe here a new bacterial species, Candidatus Syngnamydia venezia; epitheliocystis agent of S. typhle and close relative to other chlamydial pathogens which are known to infect diverse hosts ranging from invertebrates to humans

Distinct carbon sources indicate strong differentiation between tropical forest and farmland bird communities

The conversion of forest into farmland has resulted in mosaic landscapes in many parts of the tropics. From a conservation perspective, it is important to know whether tropical farmlands can buffer species loss caused by deforestation and how different functional groups of birds respond to land-use intensification. To test the degree of differentiation between farmland and forest bird communities across feeding guilds, we analyzed stable C and N isotopes in blood and claws of 101 bird species comprising four feeding guilds along a tropical forest-farmland gradient in Kenya. We additionally assessed the importance of farmland insectivores for pest control in C4 crops by using allometric relationships, C stable isotope ratios and estimates of bird species abundance. Species composition differed strongly between forest and farmland bird communities. Across seasons, forest birds primarily relied on C3 carbon sources, whereas many farmland birds also assimilated C4 carbon. While C sources of frugivores and omnivores did not differ between forest and farmland communities, insectivores used more C4 carbon in the farmland than in the forest. Granivores assimilated more C4 carbon than all other guilds in the farmland. We estimated that insectivorous farmland birds consumed at least 1,000 kg pest invertebrates km−2 year−1. We conclude that tropical forest and farmland understory bird communities are strongly separated and that tropical farmlands cannot compensate forest loss for insectivorous forest understory birds. In tropical farmlands, insectivorous bird species provide a quantitatively important contribution to pest control.

Delaying mowing and leaving uncut refuges boosts orthopterans in extensively managed meadows: Evidence drawn from field-scale experimentation

Semi-natural grasslands are widely recognized for their high ecological value. They often count among the most species-rich habitats, especially in traditional cultural landscapes. Maintaining and/or restoring them is a top priority, but nevertheless represents a real conservation challenge, especially regarding their invertebrate assemblages. The main goal of this study was to experimentally investigate the influence of four different mowing regimes on orthopteran communities and populations: (1) control meadow (C-meadow): mowing regime according to the Swiss regulations for extensively managed meadows declared as ecological compensation areas, i.e. first cut not before 15 June; (2) first cut not before 15 July (delayed treatment, D-meadow); (3) first cut not before 15 June and second cut not earlier than 8 weeks from the first cut (8W-meadow); (4) refuges left uncut on 10–20% of the meadow area (R-meadow). Data were collected two years after the introduction of these mowing treatments. Orthopteran densities from spring to early summer were five times higher in D-meadows, compared to C-meadows. In R-meadows, densities were, on average, twice as high as in C-meadows, while mean species richness was 23% higher in R-meadows than in C-meadows. Provided that farmers were given the appropriate financial incentives, the D- and R-meadow regimes could be relatively easy to implement within agri-environment schemes. Such meadows could deliver substantial benefits for functional biodiversity, including sustenance to many secondary consumers dependent on field invertebrates as staple food.

Catch Rates, Composition and Fish Size from Reefs Managed with Periodically-Harvested Closures

Periodically-harvested closures are commonly employed within co-management frameworks to help manage small-scale, multi-species fisheries in the Indo-Pacific. Despite their widespread use, the benefits of periodic harvesting strategies for multi-species fisheries have, to date, been largely untested. We examine catch and effort data from four periodically-harvested reef areas and 55 continuously-fished reefs in Solomon Islands. We test the hypothesis that fishing in periodically-harvested closures would yield: (a) higher catch rates, (b) proportionally more short lived, fast growing, sedentary taxa, and (c) larger finfish and invertebrates, compared to catches from reefs continuously open to fishing. Our study showed that catch rates were significantly higher from periodically-harvested closures for gleaning of invertebrates, but not for line and spear fishing. The family level composition of catches did not vary significantly between open reefs and periodically-harvested closures. Fish captured from periodically-harvested closures were slightly larger, but Trochus niloticus were significantly smaller than those from continuously open reefs. In one case of intense and prolonged harvesting, gleaning catch rates significantly declined, suggesting invertebrate stocks were substantially depleted in the early stages of the open period. Our study suggests periodically-harvested closures can have some short term benefits via increasing harvesting efficiency. However, we did not find evidence that the strategy had substantially benefited multi-species fin-fisheries.

Taxon-specific δ13C analysis of chitinous invertebrate remains in sediments from Strandsjön, Sweden

Taxon-specific stable carbon isotope (δ13C) analysis of chitinous remains of invertebrates can provide valuable information about the carbon sources used by invertebrates living in specific habitats of lake ecosystems (for example, sediments, water column, or aquatic vegetation). This is complementary to δ13C of sedimentary organic matter (SOM), which provides an integrated signal of organic matter produced in a lake and its catchment, and of diagenetic processes within sediments. In a sediment record from Strandsjön (Sweden) covering the past circa 140 years, we analyzed SOM geochemistry (δ13C, C:Natomic, organic carbon content) and δ13C of chitinous invertebrate remains in order to examine whether taxon-specific δ13C records could be developed for different invertebrate groups and whether these analyses provide insights into past changes of organic carbon sources for lacustrine invertebrates available in benthic and planktonic compartments of the lake. Invertebrate taxa included benthic chironomids (Chironomus, Chironomini excluding Chironomus, Tanytarsini, and Tanypodinae), filter-feeders on suspended particulate organic matter (Daphnia, Plumatella and Cristatella mucedo), and Rhabdocoela. δ13C of chironomid remains indicated periodic availability of 13C-depleted carbon sources in the benthic environment of the lake as δ13C values of the different chironomid taxa fluctuated simultaneously between -34.7 and -30.5‰ (VPDB). Daphnia and Bryozoa showed parallel changes in their δ13C values which did not coincide with variations in δ13C of chironomids, though, and a 2-3‰ decrease since circa AD 1960. The decrease in δ13C of Daphnia and Bryozoa could indicate a decrease in phytoplankton δ13C as a result of lower lake productivity, which is in accordance with historical information about the lake that suggests a shift to less eutrophic conditions after AD 1960. In contrast, Rhabdocoela cocoons were characterized by relatively high δ13C values (-30.4 to -28.2‰) that did not show a strong temporal trend, which could be related to the predatory feeding mode and wide prey spectrum of this organism group. The taxon-specific δ13C analyses of invertebrate remains indicated that different carbon sources were available for the benthic chironomid larvae than for the filter-feeding Daphnia and bryozoans. Our results therefore demonstrate that taxon-specific analysis of δ13C of organic invertebrate remains can provide complementary information to measurements on bulk SOM and that δ13C of invertebrate remains may allow the reconstruction of past changes in carbon sources and their δ13C in different habitats of lake ecosystems.

Notch signaling in the brain: in good and bad times.

Notch signaling is an evolutionarily conserved pathway, which is fundamental for neuronal development and specification. In the last decade, increasing evidence has pointed out an important role of this pathway beyond embryonic development, indicating that Notch also displays a critical function in the mature brain of vertebrates and invertebrates. This pathway appears to be involved in neural progenitor regulation, neuronal connectivity, synaptic plasticity and learning/memory. In addition, Notch appears to be aberrantly regulated in neurodegenerative diseases, including Alzheimer's disease and ischemic injury. The molecular mechanisms by which Notch displays these functions in the mature brain are not fully understood, but are currently the subject of intense research. In this review, we will discuss old and novel Notch targets and molecular mediators that contribute to Notch function in the mature brain and will summarize recent findings that explore the two facets of Notch signaling in brain physiology and pathology.

Evolutionary conservation of the U7 small nuclear ribonucleoprotein in Drosophila melanogaster.

The U7 snRNP involved in histone RNA 3' end processing is related to but biochemically distinct from spliceosomal snRNPs. In vertebrates, the Sm core structure assembling around the noncanonical Sm-binding sequence of U7 snRNA contains only five of the seven standard Sm proteins. The missing Sm D1 and D2 subunits are replaced by U7-specific Sm-like proteins Lsm10 and Lsm11, at least the latter of which is important for histone RNA processing. So far, it was unknown if this special U7 snRNP composition is conserved in invertebrates. Here we describe several putative invertebrate Lsm10 and Lsm11 orthologs that display low but clear sequence similarity to their vertebrate counterparts. Immunoprecipitation studies in Drosophila S2 cells indicate that the Drosophila Lsm10 and Lsm11 orthologs (dLsm10 and dLsm11) associate with each other and with Sm B, but not with Sm D1 and D2. Moreover, dLsm11 associates with the recently characterized Drosophila U7 snRNA and, indirectly, with histone H3 pre-mRNA. Furthermore, dLsm10 and dLsm11 can assemble into U7 snRNPs in mammalian cells. These experiments demonstrate a strong evolutionary conservation of the unique U7 snRNP composition, despite a high degree of primary sequence divergence of its constituents. Therefore, Drosophila appears to be a suitable system for further genetic studies of the cell biology of U7 snRNPs.

Divergent Macroparasite Infections in Parapatric Swiss Lake-Stream Pairs of Threespine Stickleback (Gasterosteus aculeatus)

Spatial heterogeneity in diversity and intensity of parasitism is a typical feature of most host-parasite interactions, but understanding of the evolutionary implications of such variation is limited. One possible outcome of infection heterogeneities is parasite-mediated divergent selection between host populations, ecotypes or species which may facilitate the process of ecological speciation. However, very few studies have described infections in population-pairs along the speciation continuum from low to moderate or high degree of genetic differentiation that would address the possibility of parasite-mediated divergent selection in the early stages of the speciation process. Here we provide an example of divergent parasitism in freshwater fish ecotypes by examining macroparasite infections in threespine stickleback (Gasterosteus aculeatus) of four Swiss lake systems each harbouring parapatric lake-stream ecotype pairs. We demonstrate significant differences in infections within and between the pairs that are driven particularly by the parasite taxa transmitted to fish from benthic invertebrates. The magnitude of the differences tended to correlate positively with the extent of neutral genetic differentiation between the parapatric lake and stream populations of stickleback, whereas no such correlation was found among allopatric populations from similar or contrasting habitats. This suggests that genetic differentiation is unrelated to the magnitude of parasite infection contrasts when gene flow is constrained by geographical barriers while in the absence of physical barriers, genetic differentiation and the magnitude of differences in infections tend to be positively correlated.

Isolation, N-glycosylations and Function of a Hyaluronidase-Like Enzyme from the Venom of the Spider Cupiennius salei.

STRUCTURE OF CUPIENNIUS SALEI VENOM HYALURONIDASE Hyaluronidases are important venom components acting as spreading factor of toxic compounds. In several studies this spreading effect was tested on vertebrate tissue. However, data about the spreading activity on invertebrates, the main prey organisms of spiders, are lacking. Here, a hyaluronidase-like enzyme was isolated from the venom of the spider Cupiennius salei. The amino acid sequence of the enzyme was determined by cDNA analysis of the venom gland transcriptome and confirmed by protein analysis. Two complex N-linked glycans akin to honey bee hyaluronidase glycosylations, were identified by tandem mass spectrometry. A C-terminal EGF-like domain was identified in spider hyaluronidase using InterPro. The spider hyaluronidase-like enzyme showed maximal activity at acidic pH, between 40-60°C, and 0.2 M KCl. Divalent ions did not enhance HA degradation activity, indicating that they are not recruited for catalysis. FUNCTION OF VENOM HYALURONIDASES Besides hyaluronan, the enzyme degrades chondroitin sulfate A, whereas heparan sulfate and dermatan sulfate are not affected. The end products of hyaluronan degradation are tetramers, whereas chondroitin sulfate A is mainly degraded to hexamers. Identification of terminal N-acetylglucosamine or N-acetylgalactosamine at the reducing end of the oligomers identified the enzyme as an endo-β-N-acetyl-D-hexosaminidase hydrolase. The spreading effect of the hyaluronidase-like enzyme on invertebrate tissue was studied by coinjection of the enzyme with the Cupiennius salei main neurotoxin CsTx-1 into Drosophila flies. The enzyme significantly enhances the neurotoxic activity of CsTx-1. Comparative substrate degradation tests with hyaluronan, chondroitin sulfate A, dermatan sulfate, and heparan sulfate with venoms from 39 spider species from 21 families identified some spider families (Atypidae, Eresidae, Araneidae and Nephilidae) without activity of hyaluronidase-like enzymes. This is interpreted as a loss of this enzyme and fits quite well the current phylogenetic idea on a more isolated position of these families and can perhaps be explained by specialized prey catching techniques.

Quantification of biotic responses to rapid climatic changes around the Younger Dryas — a synthesis

To assess the presence or absence of lags in biotic responses to rapid climatic changes, we: (1) assume that the δ18O in biogenically precipitated carbonates record global or hemispheric climatic change at the beginning and at the end of the Younger Dryas without any lag at our two study sites of Gerzensee and Leysin, Switzerland; (2) derive a time scale by correlating the δ18O record from these two sites with the δ18O record of the GRIP ice core; (3) measure δ18O records in ostracods and molluscs to check the record in the bulk samples and to detect possible hydrological changes; (4) analyse at Gerzensee and Leysin as well as at two additional sites (that lack carbonates and hence a δ18O record) pollen, plant macrofossils, chironomids, beetles and other insects, and Cladocera; (5) estimate our sampling resolution using the GRIP time scale for the isotope stratigraphies and the biostratigraphies; and (6) summarise the major patterns of compositional change in the biostratigraphies by principal component analysis or correspondence analysis. We conclude that, at the major climatic shifts at the beginning and end of the Younger Dryas, hardly any biotic lags occur (within the sampling resolution of 8–30 years) and that upland vegetation responded as fast as aquatic invertebrates. We suggest that the minor climatic changes associated with the Gerzensee and Preboreal oscillations were weakly recorded in the biostratigraphies at the lowland site, but were more distinct at higher altitudes. Individualistic responses of plant and animal species to climatic change may reflect processes in individuals (e.g. productivity and phenology), in populations (e.g. population dynamics), in spatial distributions (e.g. migrations), and in ecosystems (e.g. trophic state). We suggest that biotic responses may be telescoped together into relatively short periods (50 to 150 years), perhaps disrupting functional interactions among species and thus destabilising ecosystems.

The Apis mellifera filamentous virus genome

A complete reference genome of the Apis mellifera Filamentous virus (AmFV) was determined using Illumina Hiseq sequencing. The AmFV genome is a double stranded DNA molecule of approximately 498,500 nucleotides with a GC content of 50.8%. It encompasses 247 non-overlapping open reading frames (ORFs), equally distributed on both strands, which cover 65% of the genome. While most of the ORFs lacked threshold sequence alignments to reference protein databases, twenty-eight were found to display significant homologies with proteins present in other large double stranded DNA viruses. Remarkably, 13 ORFs had strong similarity with typical baculovirus domains such as PIFs (per os infectivity factor genes: pif-1, pif-2, pif-3 and p74) and BRO (Baculovirus Repeated Open Reading Frame). The putative AmFV DNA polymerase is of type B, but is only distantly related to those of the baculoviruses. The ORFs encoding proteins involved in nucleotide metabolism had the highest percent identity to viral proteins in GenBank. Other notable features include the presence of several collagen-like, chitin-binding, kinesin and pacifastin domains. Due to the large size of the AmFV genome and the inconsistent affiliation with other large double stranded DNA virus families infecting invertebrates, AmFV may belong to a new virus family.

Changing ecology of Lake Victoria cichlids and their environment: evidence from C13 and N15 analyses

Eutrophication is an increasing global threat to freshwater ecosystems. East Africa’s Lake Victoria has suffered from severe eutrophication in the past decades which is partly responsible for the dramatic decline in haplochromine cichlid species diversity. However, some zooplanktivorous and detritivorous haplochromine species recovered and shifted their diet towards macro invertebrates and fish. We used four formalin preserved cichlid species caught over the past 35 years to investigate whether stable isotopes of these fish are reflecting the dietary changes, habitat differences and if these isotopes can be used as indicators of eutrophication. We found that d15N signatures mainly reflected dietary shifts to larger prey in all four haplochromine species. Shifts in d13C signatures likely represented habitat differences and dietary changes. In addition, a shift to remarkably heavy d13C signatures in 2011 was found for all four species which might infer increased primary production and thus eutrophication although more research is needed to confirm this hypothesis. The observed temporal changes confirm previous findings that preserved specimens can be used to trace historical changes in fish ecology and the aquatic environment. This highlights the need for continued sampling as this information could be of essence for reconstructing and predicting the effects of environmental changes.