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 small (40S) subunit of eukaryotic ribosomes is believed to bind initially at the capped 5'-end of messenger RNA and then migrate, stopping at the first AUG codon in a favorable context for initiating translation. The first-AUG rule is not absolute, but there are rules for breaking the rule. Some anomalous observations that seemed to contradict the scanning mechanism now appear to be artifacts. A few genuine anomalies remain unexplained.

/pdf/the-scanning-model-for-translation-an-update-52r2in8l71.pdf

The scanning model for translation: an update.

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Principles Of Fluorescence Spectroscopy

Hydrogel delivery systems can leverage therapeutically beneficial outcomes of drug delivery and have found clinical use. Hydrogels can provide spatial and temporal control over the release of various therapeutic agents, including small-molecule drugs, macromolecular drugs and cells. Owing to their tunable physical properties, controllable degradability and capability to protect labile drugs from degradation, hydrogels serve as a platform in which various physiochemical interactions with the encapsulated drugs control their release. In this Review, we cover multiscale mechanisms underlying the design of hydrogel drug delivery systems, focusing on physical and chemical properties of the hydrogel network and the hydrogel-drug interactions across the network, mesh, and molecular (or atomistic) scales. We discuss how different mechanisms interact and can be integrated to exert fine control in time and space over the drug presentation. We also collect experimental release data from the literature, review clinical translation to date of these systems, and present quantitative comparisons between different systems to provide guidelines for the rational design of hydrogel delivery systems.

/pdf/designing-hydrogels-for-controlled-drug-delivery-3k03j5j2j9.pdf

Designing hydrogels for controlled drug delivery.

Objective: Diagnostic criteria for coeliac disease (CD) from the European Society for Paediatric Gastroenterology, Hepatology, and Nutrition (ESPGHAN) were published in 1990. Since then, the autoantigen in CD, tissue transglutaminase, has been identified; the perception of CD has changed from that of a rather uncommon enteropathy to a common multiorgan disease strongly dependent on the haplotypes human leukocyte antigen (HLA)-DQ2 and HLA-DQ8; and CD-specific antibody tests have improved. Methods: A panel of 17 experts defined CD and developed new diagnostic criteria based on the Delphi process. Two groups of patients were defined with different diagnostic approaches to diagnose CD: children with symptoms suggestive of CD (group 1) and asymptomatic children at increased risk for CD (group 2). The 2004 National Institutes of Health/ Agency for Healthcare Research and Quality report and a systematic literature search on antibody tests for CD in paediatric patients covering the years 2004 to 2009 was the basis for the evidence-based recommendations on CD-specific antibody testing. Results: In group 1, the diagnosis of CD is based on symptoms, positive serology, and histology that is consistent with CD. If immunoglobulin A anti-tissue transglutaminase type 2 antibody titers are high (>10 times the upper limit of normal), then the option is to diagnose CD without duodenal biopsies by applying a strict protocol with further laboratory tests. In group 2, the diagnosis of CD is based on positive serology and histology. HLADQ2 and HLA-DQ8 testing is valuable because CD is unlikely if both haplotypes are negative. Conclusions: The aim of the new guidelines was to achieve a high diagnostic accuracy and to reduce the burden for patients and their families. The performance of these guidelines in clinical practice should be evaluated prospectively. (JPGN 2012;54: 136–160)

/pdf/european-society-for-pediatric-gastroenterology-hepatology-ixq9y86ymv.pdf

European Society for Pediatric Gastroenterology, Hepatology, and Nutrition Guidelines for the Diagnosis of Coeliac Disease

/pdf/determination-of-the-tracer-diffusion-coefficient-in-a-2uwyjtxksx.pdf

Determination of the tracer diffusion coefficient in a cation exchange membrane

A novel Mbo II polymorphism in exon 15 of the human adenomatous polyposis coli gene

In this study the interactions of Riboflavin (Vitamin B2) with a mercury surface are investigated. Firstly, by using Cyclic Voltammetry, it is demonstrated that Riboflavin can be efficiently accumulated, by adsorption from buffered solutions containing an excess of NaClO4, onto the mercury drop of a HMDE. Secondly, it is shown that the adsorbed Riboflavin can be reduced through an electrochemical reaction whose stoichiometry is extricated by confronting simulated with experimental CV voltammograms acquired in a range of pH between about four and nine. Finally, the cathodic current, sustained by the surface reduction of Riboflavin, is exploited for assaying Riboflavin via Differential Pulse Adsorption Cathodic Stripping Voltammetry (DP AdCSV) within the frame of the standard additions calibration procedure.
By applying the suggested DP AdCSV procedure with standard voltammetric equipment, typical DP settings and pre-electrolysis time of about 10 s, a linear response is maintained if Riboflavin concentration in the electrolysed solution does not exceed about 2 mg/l. On the other side, a limit of detection (expressed as the concentration of Riboflavin in the electrolysed solution) of 7 μg/l has been achieved with a pre-electrolysis time of 68 s.

Riboflavin (Vitamin B2) Assay by Adsorptive Cathodic Stripping Voltammetry (Adcsv) at the Hanging Mercury Drop Electrode (HMDE)

We screened for22cystic fibrosis (CF) mutations inDNA fromafirst cohortof 69CF patients fromsouthern Italy using a semiautomated allele specific oligonucleotide (ASO)dotblotprocedure based on two multiplex PCR amplifications. Sevenmutations (AF508, N1303K, G542X, 1717-1 G-÷A,W1282X,1148T, andR553X) identified 77-6%ofCF chromosomes. Detection reached 79-8%withthe2183AA- G mutationanalysed withtherestriction generating PCR method.Thus,we includedthe2183AA-G mutationinthe ASO protocol andsetuptheconditions to amplify thegeneregions thatinclude the eight mutations inasingle multiplex PCR reaction. Withthismethodwe tested the DNA ofthefirst cohortof69CF patients, a secondcohortof63CF patients, and 300carrier relatives; wealsoperformed 12 prenatal diagnoses. Theresults fromthe 132CF patients showeddifferences inthe distribution ofCF mutations betweenthe southandnorthofItaly. TheXV2c,KM19, andintron 8VNDR haplotypes suggested thepresence, inCFchromosomes bearing undetected mutations, ofalimited number ofunknownmutations typical ofsouthern Italy. Finally, forsixoftheeight mutations, wecomparedtheASO procedure withthe methodsbasedonrestriction enzymes; the results obtained withthetwoprocedures wereidentical forallthe57chromosomes compared. ( MedGenet1996;33:475-479)

Francesco Salvatore

Papers

Determination of the tracer diffusion coefficient in a cation exchange membrane

A novel Mbo II polymorphism in exon 15 of the human adenomatous polyposis coli gene

Riboflavin (Vitamin B2) Assay by Adsorptive Cathodic Stripping Voltammetry (Adcsv) at the Hanging Mercury Drop Electrode (HMDE)

Molecular epidemiology ofcystic fibrosis mutations andhaplotypes insouthern Italy evaluated withan improved semiautomated robotic procedure

An improved method for determining pyruvic acid levels in tissues. Estimation of the aspartic-ketoglutaric and alanine-ketoglutaric transaminases.