The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

The influence of diet on the distribution of nitrogen isotopes in animals was investigated by analyzing animals grown in the laboratory on diets of constant nitrogen isotopic composition. 
The isotopic composition of the nitrogen in an animal reflects the nitrogen isotopic composition of its diet. The δ^(15)N values of the whole bodies of animals are usually more positive than those of their diets. Different individuals of a species raised on the same diet can have significantly different δ^(15)N values. The variability of the relationship between the δ^(15)N values of animals and their diets is greater for different species raised on the same diet than for the same species raised on different diets. Different tissues of mice are also enriched in ^(15)N relative to the diet, with the difference between the δ^(15)N values of a tissue and the diet depending on both the kind of tissue and the diet involved. The δ^(15)N values of collagen and chitin, biochemical components that are often preserved in fossil animal remains, are also related to the δ^(15)N value of the diet. 
The dependence of the δ^(15)N values of whole animals and their tissues and biochemical components on the δ^(15)N value of diet indicates that the isotopic composition of animal nitrogen can be used to obtain information about an animal's diet if its potential food sources had different δ^(15)N values. The nitrogen isotopic method of dietary analysis probably can be used to estimate the relative use of legumes vs non-legumes or of aquatic vs terrestrial organisms as food sources for extant and fossil animals. However, the method probably will not be applicable in those modern ecosystems in which the use of chemical fertilizers has influenced the distribution of nitrogen isotopes in food sources. 
The isotopic method of dietary analysis was used to reconstruct changes in the diet of the human population that occupied the Tehuacan Valley of Mexico over a 7000 yr span. Variations in the δ^(15)C and δ^(15)N values of bone collagen suggest that C_4 and/or CAM plants (presumably mostly corn) and legumes (presumably mostly beans) were introduced into the diet much earlier than suggested by conventional archaeological analysis.

Influence of Diet On the Distribtion of Nitrogen Isotopes in Animals

The mutually beneficial interactions between plants and their animal pollinators and seed dispersers have been paramount in the generation of Earth's biodiversity. These mutualistic interactions often involve dozens or even hundreds of species that form complex networks of interdependences. Understanding how coevolution proceeds in these highly diversified mutualisms among free-living species presents a conceptual challenge. Recent work has led to the unambiguous conclusion that mutualistic networks are very heterogeneous (the bulk of the species have a few interactions, but a few species are much more connected than expected by chance), nested (specialists interact with subsets of the species with which generalists interact), and built on weak and asymmetric links among species. Both ecological variables (e.g., phenology, local abundance, and geographic range) and past evolutionary history may explain such network patterns. Network structure has important implications for the coexistence and stability of...

/pdf/plant-animal-mutualistic-networks-the-architecture-of-413odbi3jn.pdf

Plant-Animal Mutualistic Networks: The Architecture of Biodiversity

Toxicological effects of malachite green.

Stable isotope mixing models are increasingly used to quantify consumer diets, but may be misused and misinter- preted. We address major challenges to their effective application. Mixing models have increased rapidly in sophistication. Current models estimate probability distributions of source contributions, have user-friendly interfaces, and incorporate com- plexities such as variability in isotope signatures, discrimination factors, hierarchical variance structure, covariates, and con- centration dependence. For proper implementation of mixing models, we offer the following suggestions. First, mixing models can only be as good as the study and data. Studies should have clear questions, be informed by knowledge of the system, and have strong sampling designs to effectively characterize isotope variability of consumers and resources on proper spatio-temporal scales. Second, studies should use models appropriate for the question and recognize their assumptions and limitations. Decisions about source grouping or incorporation of concentration dependence can influence results. Third, studies should be careful about interpretation of model outputs. Mixing models generally estimate proportions of assimilated resources with substantial uncertainty distributions. Last, common sense, such as graphing data before analyzing, is essential to maximize usefulness of these tools. We hope these suggestions for effective implementation of stable isotope mixing models will aid continued development and application of this field.

/pdf/best-practices-for-use-of-stable-isotope-mixing-models-in-nh1ffqcerz.pdf

Best practices for use of stable isotope mixing models in food-web studies

Increasing water temperature and disease risks in aquatic systems: Climate change increases the risk of some, but not all, diseases

Parasite-induced change in host behaviour and susceptibility to predation in an eye fluke–fish interaction

Manipulation of fish host by eye flukes in relation to cataract formation and parasite infectivity

https://www.otago.ac.nz/parasitegroup/PDF%20papers/PoulinValtonen2002-IJP.pdf

The predictability of helminth community structure in space: a comparison of fish populations from adjacent lakes.

Diplostomid metacercariae were found at a high prevalence and in large numbers in the eyes of a wide variety of fish species from widely differing freshwater and brackish water environments in northern Finland. These parasites were found to infect the following: 21 of 25 fish species, some of which were marine, studied in the oligohaline, brackish waters of the Bothnian Bay, Baltic Sea; all nine fish species studied from a large, oligotrophic lake in NE Finland (Yli-Kitka); and all five studied fish species in a small, hypereutrophic lake (Kuivasjarvi). Diplostomids in the lens of the fishes of the Bothnian Bay, studied during two periods extending over seven years, suggest the presence of a stable and predictable system, despite the extremely narrow transmission window between the first (snail) and second (fish) intermediate hosts. Diplostomids in the lens of fishes from the Bothnian Bay and Lake Kuivasjarvi predominated (> 50% infection in 14 of 21 species) over those from the vitreous body of the eye in most cases, but were much lower ( 80% prevalences in five of nine fish species). This difference is considered to be dependent on differences in the piscivorous bird fauna. The fact that diplostomid metacercariae accumulated in the fish, together with the lack of any real seasonal variation, confirms the longevity of these larvae in their fish intermediate hosts. Thus metacercariae form a reservoir which is mainly responsible for the maintenance of diplostomid suprapopulations in these northern latitudes.

/pdf/aspects-of-the-biology-of-diplostomid-metacercarial-digenea-2bnrg0yymn.pdf

E. Tellervo Valtonen

Papers

Increasing water temperature and disease risks in aquatic systems: Climate change increases the risk of some, but not all, diseases

Parasite-induced change in host behaviour and susceptibility to predation in an eye fluke–fish interaction

Manipulation of fish host by eye flukes in relation to cataract formation and parasite infectivity

The predictability of helminth community structure in space: a comparison of fish populations from adjacent lakes.

Aspects of the biology of diplostomid metacercarial (Digenea) populations occurring in fishes in different localities of northern Finland