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

Reference EPFL-CONF-177127View record in Web of Science Record created on 2012-05-15, modified on 2016-08-09

Analytical Carbon Probe Measurements On Iron-Meteorites

More and more marine areas are subjected to depleted-O2 concentration, mainly due to eutrophication induced by human activities. These phenomena affect benthic ecosystems, in particular continental shelves and coastal areas where the renewal of the bottom waters is low and/or the organic matter flux is high. Some species of benthic foraminifera are resistant to this hypoxic/anoxic events, surviving weeks to months without oxygen. One of the species known to survive to such extreme condition is the benthic one Ammonia tepida. However the metabolic process by which it succeed in it remains unknown. One hypothesis is that this species would be able to lower its metabolism under oxygen depleted conditions, until the return of better conditions. The aim of the present study is to understand the feeding behaviors of A. tepida under anoxia. For this purpose a laboratory experiment involving incubation with living A. tepida was carried out under controlled oxygen concentrations. The individuals were fed with a pulse of 13C-labeled diatoms (Navicula sp.) and then incubate in oxic or anoxic conditions during 28 days. Along the incubation time, observation of the cell ultrastructure with Transmission Electronic Microscope (TEM) and detection in the cell of the isotopic 13C signal using nanoSIMS, were made. The nanoSIMS (nanoscale Secondary-Ion Mass Spectrometry) is an analytical technique that allows to visualize the incorporation and transfer of isotopically labeled compounds in organisms; thus in our case to follow the ingestion of labeled-diatoms and further transfer of carbon in the cytoplasm of the foraminifera. According to the results acquired in this study, in both conditions the foraminifera directly integrate the diatoms in their cytoplasm during the first hours of the incubation. Then, in oxic conditions, these diatoms are quickly fully degraded, within 3 days, and the 13C-labeled compounds are transferred in the organelles of the cytoplasm. Whereas in anoxia, only a fraction of the diatoms are degraded and the transfer to the foraminifera cytoplasm is weak. These results are confirmed by the δ13C of the foraminifera, measured in bulk by mass spectrometry (GC-MS). In anoxia the δ13C is slightly increasing the first 24h, meaning that the 13C content of the cell increased, and then it remains stable until the end of the experiment. This leads us to assume that the foraminifera stop, or at least strongly lower their metabolic rate under anoxic condition.

Feeding behaviour of a benthic species (Ammonia tepida) under oxic and anoxic conditions; TEM-NanoSIMS correlation

Physiological functions of Ammonia tepida in different oxygenated conditions: evidence for dormancy under anoxia

Near-IR reflectance temperature sensitivity: Lunar soils, meteorites, and minerals

Reference EPFL-CONF-177134View record in Web of Science Record created on 2012-05-15, modified on 2016-08-09

Anders Meibom

Papers

Analytical Carbon Probe Measurements On Iron-Meteorites

Feeding behaviour of a benthic species (Ammonia tepida) under oxic and anoxic conditions; TEM-NanoSIMS correlation

Physiological functions of Ammonia tepida in different oxygenated conditions: evidence for dormancy under anoxia

Near-IR reflectance temperature sensitivity: Lunar soils, meteorites, and minerals

Os Isotopes, Deep-rooted Mantle Plumes and the Timing of Inner Core Formation