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)

Two of the greatest challenges facing the 21st century involve providing sustainable supplies of clean water and energy, two highly interrelated resources, at affordable costs. Membrane technology is expected to continue to dominate the water purifica- tion technologies owing to its energy efficiency. However, there is a need for improved membranes that have higher flux, are more selective, are less prone to various types of fouling, and are more resistant to the chemical environment, especially chlorine, of these processes. This article summarizes the nature of the global water problem and reviews the state of the art of membrane technology. Existing deficiencies of current membranes and the opportunities to resolve them with innovative polymer chemistry and physics are identified. Extensive background is provided to help the reader understand the fundamental issues involved. V C 2010 Wiley Periodi- cals, Inc. J Polym Sci Part B: Polym Phys 48: 1685-1718, 2010

Water Purification by Membranes: The Role of Polymer Science

http://comenius.susqu.edu/biol/312/recentadvancesincheesemicrobiology.pdf

Recent advances in cheese microbiology

ABSTRACT Pulsed-fieldgel electrophoresis (PFGE) is the most common genotypic method used in reference and clinical laboratories for typing methicillin-resistant Staphylococcus aureus (MRSA). Many different protocols have been developed in laboratories that have extensive experience with the technique and have established national databases. However, the comparabilities of the different European PFGE protocols for MRSA and of the various national MRSA clones themselves had not been addressed until now. This multinational European Union (EU) project has established for the first time a European database of representative epidemic MRSA (EMRSA) strains and has compared them by using a new “harmonized” PFGE protocol developed by a consensus approach that has demonstrated sufficient reproducibility to allow the successful comparison of pulsed-field gels between laboratories and the tracking of strains around the EU. In-house protocols from 10 laboratories in eight European countries were compared by each center with a “gold standard” or initial harmonized protocol in which many of the parameters had been standardized. The group found that it was not important to standardize some elements of the protocol, such as the type of agarose, DNA block preparation, and plug digestion. Other elements were shown to be critical, namely, a standard gel volume and concentration of agarose, the DNA concentration in the plug, the ionic strength and volume of running buffer used, the running temperature, the voltage, and the switching times of electrophoresis. A new harmonized protocol was agreed on, further modified in a pilot study in two laboratories, and finally tested by all others. Seven laboratories' gels were found to be of sufficiently good quality to allow comparison of the strains by using a computer software program, while two gels could not be analyzed because of inadequate destaining and DNA overloading. Good-quality gels and inclusion of an internal quality control strain are essential before attempting intercenter PFGE comparisons. A number of clonally related strains have been shown to be present in multiple countries throughout Europe. The well-known Iberian clone has been demonstrated in Belgium, Finland, France, Germany, and Spain (and from the wider HARMONY collection in Portugal, Slovenia, and Sweden). Strains from the United Kingdom (EMRSA-15 and -16) have been identified in several othercountries, and other clonally related strains have also been identified. This highlights the need for closer international collaboration to monitor the spread of current epidemic strains as well as the emergence of new ones.

Harmonization of pulsed-field gel electrophoresis protocols for epidemiological typing of strains of methicillin-resistant Staphylococcus aureus: a single approach developed by consensus in 10 European laboratories and its applicatio

Advances in the study of proteolysis during cheese ripening.

The European Union is thanked for partly financing this project under ECLAIR contract CT-91-0064.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0022029997002185

Eric Beuvier

Papers

Characterization of the lactic acid bacteria in artisanal dairy products

Possible implications of milk pasteurization on the manufacture and sensory quality of ripened cheese

Ripening and quality of Swiss-type cheese made from raw, pasteurized or microfiltered milk

Influence of Pasteurization and Fat Composition of Milk on the Volatile Compounds and Flavor Characteristics of a Semi-hard Cheese

Origin and diversity of mesophilic lactobacilli in Comté cheese, as revealed by PCR with repetitive and species-specific primers