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

Antibacterial activity of zinc oxide nanoparticles (ZnO-NPs) has received significant interest worldwide particularly by the implementation of nanotechnology to synthesize particles in the nanometer region. Many microorganisms exist in the range from hundreds of nanometers to tens of micrometers. ZnO-NPs exhibit attractive antibacterial properties due to increased specific surface area as the reduced particle size leading to enhanced particle surface reactivity. ZnO is a bio-safe material that possesses photo-oxidizing and photocatalysis impacts on chemical and biological species. This review covered ZnO-NPs antibacterial activity including testing methods, impact of UV illumination, ZnO particle properties (size, concentration, morphology, and defects), particle surface modification, and minimum inhibitory concentration. Particular emphasize was given to bactericidal and bacteriostatic mechanisms with focus on generation of reactive oxygen species (ROS) including hydrogen peroxide (H2O2), OH− (hydroxyl radicals), and O2 −2 (peroxide). ROS has been a major factor for several mechanisms including cell wall damage due to ZnO-localized interaction, enhanced membrane permeability, internalization of NPs due to loss of proton motive force and uptake of toxic dissolved zinc ions. These have led to mitochondria weakness, intracellular outflow, and release in gene expression of oxidative stress which caused eventual cell growth inhibition and cell death. In some cases, enhanced antibacterial activity can be attributed to surface defects on ZnO abrasive surface texture. One functional application of the ZnO antibacterial bioactivity was discussed in food packaging industry where ZnO-NPs are used as an antibacterial agent toward foodborne diseases. Proper incorporation of ZnO-NPs into packaging materials can cause interaction with foodborne pathogens, thereby releasing NPs onto food surface where they come in contact with bad bacteria and cause the bacterial death and/or inhibition.

/pdf/review-on-zinc-oxide-nanoparticles-antibacterial-activity-2smaigi8sc.pdf

Review on Zinc Oxide Nanoparticles: Antibacterial Activity and Toxicity Mechanism.

The recent advances in nanotechnology and the corresponding increase in the use of nanomaterials in products in every sector of society have resulted in uncertainties regarding environmental impacts. The objectives of this review are to introduce the key aspects pertaining to nanomaterials in the environment and to discuss what is known concerning their fate, behavior, disposition, and toxicity, with a particular focus on those that make up manufactured nanomaterials. This review critiques existing nanomaterial research in freshwater, marine, and soil environments. It illustrates the paucity of existing research and demonstrates the need for additional research. Environmental scientists are encouraged to base this research on existing studies on colloidal behavior and toxicology. The need for standard reference and testing materials as well as methodology for suspension preparation and testing is also discussed.

Nanomaterials in the environment: Behavior, fate, bioavailability, and effects

The search for understanding the interactions of nanosized materials with living organisms is leading to the rapid development of key applications, including improved drug delivery by targeting nanoparticles, and resolution of the potential threat of nanotechnological devices to organisms and the environment. Unless they are specifically designed to avoid it, nanoparticles in contact with biological fluids are rapidly covered by a selected group of biomolecules to form a corona that interacts with biological systems. Here we review the basic concept of the nanoparticle corona and its structure and composition, and highlight how the properties of the corona may be linked to its biological impacts. We conclude with a critical assessment of the key problems that need to be resolved in the near future.

/pdf/biomolecular-coronas-provide-the-biological-identity-of-3m15njjzti.pdf

Biomolecular coronas provide the biological identity of nanosized materials

Modelling the attenuation of flowback chemicals for a soil-groundwater pathway from a hypothetical spill accident.

The size distribution of soluble copper complexing ligands ( 14,000 Dalton fraction As the majority of soluble iron was also associated with this fraction, it is likely that this complexing pool contains organic ligands adsorbed to the surface of inorganic colloids as well as large molecular weight ligands Destruction of dissolved organic matter by sample pre-treatment with UV light resulted in a complet

Size distribution of copper complexing ligands in tropical freshwaters

The use of plastic sheets as collectors of diagenetically-formed oxyhydroxides from riverine and estuarine sediments was evaluated. In a range of materials tested in the laboratory, Teflon and polycarbonate were found to be the most efficient collector materials. Laboratory optimisation experiments indicated that the deposition of oxyhydroxides on both materials occurred quickly (<2 weeks). In the field, oxyhydroxides were collected on Teflon sheets as depositional bands just below the sediment-water interface. These bands were much wider and more variable (1–5 cm) than those observed in laboratory experiments (typically 0.5 cm). This was attributed to the frequently changing redox conditions at the field sites caused by a combination of sediment movement and tidal processes. The deposits collected were predominantly iron with lesser amounts of manganese. At several sites strong correlations were observed between the concentrations of manganese and zinc deposited on the Teflon collector surfaces. In both ...

In situ collection of diagenetic and induced oxyhydroxide precipitates from riverine and estuarine sediments

Metals in the waters and sediments of Port Curtis, Queensland

The speciation of mercury in Lake Murray, Papua New Guinea and nine surrounding rivers was investigated. Total mercury concentrations in waters (0.52-9.5 ng L-1) and sediments (56-177 ng g-1 dry mass) were similar to those found in other remote lake environments. Total methylmercury (MeHg) concentrations in waters and sediments were also low. Of the 50 water samples analysed during three surveys, only six samples had total MeHg concentrations between 0.1 and 0.64 ng L-1 and 25 of the samples had total MeHg concentrations < 0.05 ng L-1. Methylmercury concentrations were very variable and could not be linked with parameters known to affect mercury methylation such as pH, dissolved organic carbon and sulfate concentrations. A statistically significant and unexplained correlation was observed between filterable MeHg and filterable silicon. Intermittent inputs of turbid water from the Strickland River inject particulates and filterable MeHg into the southern end of Lake Murray. This has resulted in the formation of a depositional footprint that contains higher concentrations of particulate mercury and other elements compared with the rest of the lake.

Simon C. Apte

Papers

Modelling the attenuation of flowback chemicals for a soil-groundwater pathway from a hypothetical spill accident.

Size distribution of copper complexing ligands in tropical freshwaters

In situ collection of diagenetic and induced oxyhydroxide precipitates from riverine and estuarine sediments

Metals in the waters and sediments of Port Curtis, Queensland

Mercury speciation in waters and sediments of Lake Murray, Papua New Guinea