Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma.

We characterized the mutational landscape of melanoma, the form of skin cancer with the highest mortality rate, by sequencing the exomes of 147 melanomas. Sun-exposed melanomas had markedly more ultraviolet (UV)-like C>T somatic mutations compared to sun-shielded acral, mucosal and uveal melanomas. Among the newly identified cancer genes was PPP6C, encoding a serine/threonine phosphatase, which harbored mutations that clustered in the active site in 12% of sun-exposed melanomas, exclusively in tumors with mutations in BRAF or NRAS.

[Preparation of molecularly imprinted polypyrrole/Fe3O4 composite material and its application in recognition of tryptophan enantiomers].

Ferrosoferric oxide (Fe(3)O(4)) magnetic material was first synthesized, and then the in-situ chemical polymerization of pyrrole was carried out on the surface of Fe(3)O(4) by using pyrole and L-tryptophan (L-Trp) as the functional monomer and templates, respectively. As a result, molecularly imprinted polypyrrole/Fe(3)O(4) composite material was obtained. This composite material was separated from the solution because of its magnetic property.

Upper respiratory tract microbial communities, acute otitis media pathogens, and antibiotic use in healthy and sick children.

The composition of the upper respiratory tract microbial community may influence the risk for colonization by the acute otitis media (AOM) pathogens Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis. We used culture-independent methods to describe upper respiratory tract microbial communities in healthy children and children with upper respiratory tract infection with and without concurrent AOM. Nasal swabs and data were collected in a cross-sectional study of 240 children between 6 months and 3 years of age.

Forward genetics uncovers Transmembrane protein 107 as a novel factor required for ciliogenesis and Sonic hedgehog signaling.

Cilia are dynamic organelles that are essential for a vast array of developmental patterning events, including left-right specification, skeletal formation, neural development, and organogenesis. Despite recent advances in understanding cilia form and function, many key ciliogenesis components have yet to be identified. By using a forward genetics approach, we isolated a novel mutant allele (schlei) of the mouse Transmembrane protein 107 (Tmem107) gene, which we show here is critical for cilia formation and embryonic patterning.

Length distribution of sequencing by synthesis: fixed flow cycle model.

Sequencing by synthesis is the underlying technology for many next- generation DNA sequencing platforms. We developed a new model, the fixed flow cycle model, to derive the distributions of sequence length for a given number of flow cycles under the general conditions where the nucleotide incorporation is probabilistic and may be incomplete, as in some single-molecule sequencing technologies. Unlike the previous model, the new model yields the probability distribution for the sequence length.

[Determination of cholesterol in drainage oil by solid phase extraction-gas chromatography-mass spectrometry].

An effective method was developed for the determination of cholesterol in drainage oil by solid phase extraction-gas chromatography-mass spectrometry (SPE-GC-MS). Firstly, the samples were purified by SPE on a column packed with silica. An extraction yield of 97% was obtained when a 20 mL of ethyl ether/n-hexane mixture (0.

AlleleSeq: analysis of allele-specific expression and binding in a network framework.

To study allele-specific expression (ASE) and binding (ASB), that is, differences between the maternally and paternally derived alleles, we have developed a computational pipeline (AlleleSeq). Our pipeline initially constructs a diploid personal genome sequence (and corresponding personalized gene annotation) using genomic sequence variants (SNPs, indels, and structural variants), and then identifies allele-specific events with significant differences in the number of mapped reads between maternal and paternal alleles. There are many technical challenges in the construction and alignment of reads to a personal diploid genome sequence that we address, for example, bias of reads mapping to the reference allele.

Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies.

Btrim is a fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines. It also can reliably identify barcodes and assign the reads to the original samples. Based on a modified Myers's bit-vector dynamic programming algorithm, Btrim can handle indels in adapters and barcodes.

Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project.

In the human genome, it has been estimated that considerably more sequence is under natural selection in non-coding regions [such as transcription-factor binding sites (TF-binding sites) and non-coding RNAs (ncRNAs)] compared to protein-coding ones. However, less attention has been paid to them. To study selective pressure on non-coding elements, we use next-generation sequencing data from the recently completed pilot phase of the 1000 Genomes Project, which, compared to traditional methods, allows for the characterization of a full spectrum of genomic variations, including single-nucleotide polymorphisms (SNPs), short insertions and deletions (indels) and structural variations (SVs).

Streptococcus pneumoniae clonal complex 199: genetic diversity and tissue-specific virulence.

Streptococcus pneumoniae is an important cause of otitis media and invasive disease. Since introduction of the heptavalent pneumococcal conjugate vaccine, there has been an increase in replacement disease due to serotype 19A clonal complex (CC)199 isolates. The goals of this study were to 1) describe genetic diversity among nineteen CC199 isolates from carriage, middle ear, blood, and cerebrospinal fluid, 2) compare CC199 19A (n = 3) and 15B/C (n = 2) isolates in the chinchilla model for pneumococcal disease, and 3) identify accessory genes associated with tissue-specific disease among a larger collection of S.

A novel palygorskite-modified carbon paste amperometric sensor for catechol determination.

A palygorskite-modified carbon paste electrode (CPE) was constructed using graphite powder mixed with palygorskite particles. Compared with the unmodified CPE, the resulting palygorskite-modified CPE remarkably increases the peak currents of catechol, and greatly lowers the peak potential separation. Therefore, the palygorskite exhibits catalytic activity to catechol and significantly improves the determining sensitivity.

Microbial communities of the upper respiratory tract and otitis media in children.

Streptococcus pneumoniae asymptomatically colonizes the upper respiratory tract of children and is a frequent cause of otitis media. Patterns of microbial colonization likely influence S. pneumoniae colonization and otitis media susceptibility.

MU2A--reconciling the genome and transcriptome to determine the effects of base substitutions.

Next-generation sequencing technologies enable the identification of sequence variation in the genome and transcriptome. Differences between the reference genome and transcript libraries complicate the determination of the effect of genomic sequence variants on protein products; similarly, these differences complicate the mapping of sequence variants found in transcripts to their respective genomic position. We have developed MU2A, a publicly available web service for variant annotation that reconciles differences between the genome and transcriptome, enabling the rapid and accurate determination of the effects of genomic variants on protein products, and the mapping of variants detected in transcripts to genomic coordinates.

Construction and maintenance of randomized retroviral expression libraries for transmembrane protein engineering.

Genetic selection from libraries expressing proteins with randomized amino acid segments is a powerful approach to identify proteins with novel biological activities. Here, we assessed the utility of deep DNA sequencing to characterize the composition, diversity, size and stability of such randomized libraries. We used 454 pyrosequencing to sequence a retroviral library expressing small proteins with randomized transmembrane domains.

Determination of chromium(VI) in electronics materials using trioctylamine modified carbon paste electrode.

A trioctylamine (TOA) modified carbon paste electrode (TOA/CPE) was firstly utilized to determine Cr(VI) in electronics materials. The effects of preconcentration conditions, that is, TOA amount and accumulation time on Cr(VI) accumulation were examined and the optimum experiment conditions for the determination were identified. A sensitive reduction peak in the stripping voltammogram at -0.

The viability change of pigskin in vitro.

Background: It is widely recognised that take of grafts is strongly influenced by tissue viability. Although porcine skin is currently the most widely used xenograft, the viability change of pigskin in vitro has not been extensively studied. The purpose of this study was to assess the change of the viability of Bama miniature pigskin after harvest and cryopreservation, and to set up a guideline for pigskin preservation and storage that would allow the skin to retain the highest viability after treatment and still be used in the clinical applications.

Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants.

The goal of human genome re-sequencing is obtaining an accurate assembly of an individual's genome. Recently, there has been great excitement in the development of many technologies for this (e.g.

Statistical distributions of sequencing by synthesis with probabilistic nucleotide incorporation.

Sequencing by synthesis is used in many next-generation DNA sequencing technologies. Some of the technologies, especially those exploring the principle of single-molecule sequencing, allow incomplete nucleotide incorporation in each cycle. We derive statistical distributions for sequencing by synthesis by taking into account the possibility that nucleotide incorporation may not be complete in each flow cycle.

Calculating complexity of large randomized libraries.

Randomized libraries are increasingly popular in protein engineering and other biomedical research fields. Statistics of the libraries are useful to guide and evaluate randomized library construction. Previous works only give the mean of the number of unique sequences in the library, and they can only handle equal molar ratio of the four nucleotides at a small number of mutation sites.

Statistical distributions of pyrosequencing.

Pyrosequencing is emerging as one of the important next-generation sequencing technologies. We derive the statistical distributions of this technique in terms of nucleotide probabilities of the target sequences. We give exact distributions both for fixed number of flow cycles and for fixed sequence length.

Substrate discrimination among mitogen-activated protein kinases through distinct docking sequence motifs.

Mitogen-activated protein kinases (MAPKs) mediate cellular responses to a wide variety of extracellular stimuli. MAPK signal transduction cascades are tightly regulated, and individual MAPKs display exquisite specificity in recognition of their target substrates. All MAPK family members share a common phosphorylation site motif, raising questions as to how substrate specificity is achieved.