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.

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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.

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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)

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

Hunter disease, Mucopolysaccharidosis type II, is an X-linked recessive lysosomal storage disorder caused by a deficiency in iduronate sulfatase activity. We studied at molecular level a Neapolitan family with the disease. We report, in patient, the delta 139 mutation on the third exon of the gene, on female family members, the DNA analysis that allowed to assess or exclude their carrier status and on fetal DNA from a pregnancy of patient's mother, a prenatal diagnosis that resulted negative.

Molecular genetic characterization and prenatal diagnosis in a family with Hunter disease.

Studies on the deamination of L-amino acids in mammalian tissues.

1 Weinstock MA, Sober AJ. The risk of progression of lentigo maligna to lentigo maligna melanoma. Br J Dermatol 1987; 116:303–10. 2 McLeod M, Choudhary S, Giannakakis G, Nouri K. Surgical treatments for lentigo maligna: a review. Dermatol Surg 2011; 37:1–19. 3 Kopera D. Treatment of lentigo maligna with the carbon dioxide laser. Arch Dermatol 1995; 131:735–6. 4 Zalaudek I, Horn M, Richtig E et al. Local recurrence in melanoma in situ: influence of sex, age, site of involvement and therapeutic modalities. Br J Dermatol 2003; 148:703–8. 5 Lee H, Sowerby LJ, Temple CL et al. Carbon dioxide laser treatment for lentigo maligna: a retrospective review comparing 3 different treatment modalities. Arch Facial Plast Surg 2011; 13:398–403. 6 Ellis LZ, Cohen JL, High W, Stewart L. Melanoma in situ treated successfully using imiquimod after nonclearance with surgery: review of the literature. Dermatol Surg 2012; 38:937–46. 7 Hyde MA, Hadley ML, Tristani-Firouzi P et al. A randomized trial of the off-label use of imiquimod, 5%, cream with vs without tazarotene, 0.1%, gel for the treatment of lentigo maligna, followed by conservative stages excisions. Arch Dermatol 2012; 148:592–6. 8 Ly L, Kelly JW, O’Keefe R et al. Efficacy of imiquimod cream, 5%, for lentigo maligna after complete excision: a study of 43 patients. Arch Dermatol 2011; 147:1191–5. 9 Missall TA, Hurley MY, Fosko SW. Lentiginous melanoma in situ treatment with topical imiquimod: need for individualized regimens. Arch Dermatol 2010; 146:1309–10. 10 Drobits B, Holcmann M, Amberg N et al. Imiquimod clears tumors in mice independent of adaptive immunity by converting pDCs into tumor-killing effector cells. J Clin Invest 2012; 122:575–85.

Different TGM1 mutation spectra in Italian and Portuguese patients with autosomal recessive congenital ichthyosis: evidence of founder effects in Portugal.

Unraveling unusual X-chromosome patterns during fragile-X syndrome genetic testing.

Unraveling the structural and functional features of an aldolase A mutant involved in the hemolytic anemia and severe rhabdomyolysis reported in a child

Francesco Salvatore

Papers

Molecular genetic characterization and prenatal diagnosis in a family with Hunter disease.

Studies on the deamination of L-amino acids in mammalian tissues.

Different TGM1 mutation spectra in Italian and Portuguese patients with autosomal recessive congenital ichthyosis: evidence of founder effects in Portugal.

Unraveling unusual X-chromosome patterns during fragile-X syndrome genetic testing.

Unraveling the structural and functional features of an aldolase A mutant involved in the hemolytic anemia and severe rhabdomyolysis reported in a child