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 solar chemical composition is an important ingredient in our understanding of the formation, structure, and evolution of both the Sun and our Solar System. Furthermore, it is an essential refer ...

The Chemical Composition of the Sun

Rising atmospheric carbon dioxide (CO2), primarily from human fossil fuel combustion, reduces ocean pH and causes wholesale shifts in seawater carbonate chemistry. The process of ocean acidification is well documented in field data, and the rate will accelerate over this century unless future CO2 emissions are curbed dramatically. Acidification alters seawater chemical speciation and biogeochemical cycles of many elements and compounds. One well-known effect is the lowering of calcium carbonate saturation states, which impacts shell-forming marine organisms from plankton to benthic molluscs, echinoderms, and corals. Many calcifying species exhibit reduced calcification and growth rates in laboratory experiments under high-CO2 conditions. Ocean acidification also causes an increase in carbon fixation rates in some photosynthetic organisms (both calcifying and noncalcifying). The potential for marine organisms to adapt to increasing CO2 and broader implications for ocean ecosystems are not well known; both are high priorities for future research. Although ocean pH has varied in the geological past, paleo-events may be only imperfect analogs to current conditions.

/pdf/ocean-acidification-the-other-co-2-problem-4h18mw2cpj.pdf

Ocean Acidification: The Other CO 2 Problem

Climate change 2014 - Synthesis Report

About Supramolecular Assemblies of π-Conjugated Systems

NanoSIMS and Electron Microscopy: A powerful combination in Life Science Research.

The determination of metallographic cooling rates of iron meteorites are presently based on measurements and modelling of disequilibrium profiles of Ni in taenite lamellae [1,2,3,4]. Key elements of such models are the FeNiP phase diagram (in case of IAB's also the FeNiC phase diagram [5]) and the diffusivities of Ni in both kamacite and taenite. Until 1995 the data have been interpreted in terms of a linear cooling history yielding a constant cooling rate in the Widmanstiitten pattern formation interval (-800-300°C). Rasmussen et al. (1995) [4] provide the first attempt to estimate a two-stage cooling history. Thus the obtained cooling rates only apply in a limited temperature. interval. We have initiated a search for alternatives to Ni as a cooling rate indicator that could yield cooling rates of iron meteorites in different temperature intervals. The idea is that elements with a strong partition between taenite and kamacite and a diffusivity significantly different from that of Ni will become immobilized at different temperatures. Disequilibrium profiles of these elements may therefore provide cooling rate information for other temperature intervals. We have applied p-PIXE analysis in the search for concentration profiles of Ge, Ga, and Cu in Toluca and Odessa (IAB), and Cape York (IIIAB).

Iron Meteorites: Profiles of Ge, Ga, and Cu using m-PIXE

Abstract Background The development of nanoscale secondary ion mass spectrometry (NanoSIMS) has revolutionized the study of biological tissues by enabling, e.g., the visualization and quantification of metabolic processes at subcellular length scales. However, the associated sample preparation methods all result in some degree of tissue morphology distortion and loss of soluble compounds. To overcome these limitations an entirely cryogenic sample preparation and imaging workflow is required. Results Here, we report the development of a CryoNanoSIMS instrument that can perform isotope imaging of both positive and negative secondary ions from flat block-face surfaces of vitrified biological tissues with a mass- and image resolution comparable to that of a conventional NanoSIMS. This capability is illustrated with nitrogen isotope as well as trace element mapping of freshwater hydrozoan Green Hydra tissue following uptake of 15 N-enriched ammonium. Conclusion With a cryo-workflow that includes vitrification by high pressure freezing, cryo-planing of the sample surface, and cryo-SEM imaging, the CryoNanoSIMS enables correlative ultrastructure and isotopic or elemental imaging of biological tissues in their most pristine post-mortem state. This opens new horizons in the study of fundamental processes at the tissue- and (sub)cellular level. Teaser CryoNanoSIMS: subcellular mapping of chemical and isotopic compositions of biological tissues in their most pristine post-mortem state. 

/pdf/correlated-cryo-sem-and-cryonanosims-imaging-of-biological-3t0miufp.pdf

Correlated cryo-SEM and CryoNanoSIMS imaging of biological tissue

Some sea slugs are able to steal functional chloroplasts (kleptoplasts) from their algal food sources, but the role and relevance of photosynthesis to the animal host remain controversial. While some researchers claim that kleptoplasts are slowly digestible ‘snacks’, others advocate that they enhance the overall fitness of sea slugs much more profoundly. Our analysis show light-dependent incorporation of 13C and 15N in the albumen gland and gonadal follicles of the sea slug Elysia timida, representing translocation of photosynthates to kleptoplast-free reproductive organs. Long-chain polyunsaturated fatty acids with reported roles in reproduction were produced in the sea slug cells using labelled precursors translocated from the kleptoplasts. Finally, we report reduced fecundity of E. timida by suppressing kleptoplast photosynthesis. The present study provides the first thorough experimental evidence that photosynthesis enhances the reproductive fitness of kleptoplast-bearing sea slugs, confirming the biological relevance of this remarkable association between a metazoan and an algal-derived organelle. Teaser Sea slugs incorporate functional chloroplasts from algae and use products of photosynthesis to maximize reproductive output.

/pdf/photosynthesis-from-stolen-chloroplasts-increases-sea-slug-1ke51lep0k.pdf

Photosynthesis from stolen chloroplasts increases sea slug reproductive fitness

Keywords: Allende Reference EPFL-CONF-177133View record in Web of Science Record created on 2012-05-15, modified on 2016-08-09

Forsteritic olivine material with refractory inclusions trapped by a type A/B calcium-aluminum-rich inclusion from the reduced CV chondrite Efremovka: Evidence for early accretion and alteration of refractory materials.

Anders Meibom

Papers

NanoSIMS and Electron Microscopy: A powerful combination in Life Science Research.

Iron Meteorites: Profiles of Ge, Ga, and Cu using m-PIXE

Correlated cryo-SEM and CryoNanoSIMS imaging of biological tissue

Photosynthesis from stolen chloroplasts increases sea slug reproductive fitness

Forsteritic olivine material with refractory inclusions trapped by a type A/B calcium-aluminum-rich inclusion from the reduced CV chondrite Efremovka: Evidence for early accretion and alteration of refractory materials.