Zebrafish for the study of the biological effects of nicotine.

Introduction: Zebrafish are emerging as a powerful animal model for studying the molecular and physiological effects of nicotine exposure. The zebrafish have many advantageous physical characteristics, including small size, high fecundity rates, and externally developing transparent embryos. When combined with a battery of molecular-genetic tools and behavioral assays, these attributes enable studies to be conducted that are not practical using traditional animal models.

Varenicline for smoking cessation: efficacy, safety, and treatment recommendations.

Smoking is the leading preventable cause of morbidity and mortality in the US, and decreasing smoking prevalence is a public health priority. Patients achieve the greatest success when quit attempts involve behavioral therapy combined with pharmacotherapy. Varenicline is the most recent addition to the pharmacotherapeutic armamentarium for the treatment of tobacco dependence.

Evaluation of oligonucleotide sequence capture arrays and comparison of next-generation sequencing platforms for use in molecular diagnostics.

Background: Next-generation DNA sequencing (NGS) techniques have the potential to revolutionize molecular diagnostics; however, a thorough evaluation of these technologies is necessary to ensure their performance meets or exceeds that of current clinical sequencing methods.

Methods: We evaluated the NimbleGen Sequence Capture 385K Human Custom Arrays for enrichment of 22 genes. We sequenced each sample on both the Roche 454 Genome Sequencer FLX (GS-FLX) and the Illumina Genome Analyzer II (GAII) to compare platform performance.

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.

Background: Massive parallel sequencing has the potential to replace microarrays as the method for transcriptome profiling. Currently there are two protocols: full-length RNA sequencing (RNA-SEQ) and 3'-tag digital gene expression (DGE). In this preliminary effort, we evaluated the 3' DGE approach using two reference RNA samples from the MicroArray Quality Control Consortium (MAQC).

Impact of sample acquisition and linear amplification on gene expression profiling of lung adenocarcinoma: laser capture micro-dissection cell-sampling versus bulk tissue-sampling.

Background: The methods used for sample selection and processing can have a strong influence on the expression values obtained through microarray profiling. Laser capture microdissection (LCM) provides higher specificity in the selection of target cells compared to traditional bulk tissue selection methods, but at an increased processing cost. The benefit gained from the higher tissue specificity realized through LCM sampling is evaluated in this study through a comparison of microarray expression profiles obtained from same-samples using bulk and LCM processing.

Meta-analysis of oncogenic protein kinase Ciota signaling in lung adenocarcinoma.

Purpose: Atypical protein kinase Ciota (PKCiota) is an oncogene in non-small cell lung cancer (NSCLC). Here, we identify four functional gene targets of PKCiota in lung adenocarcinoma (LAC), the most prominent form of NSCLC.

Experimental Design: Three independent public domain gene expression data sets were interrogated to identify genes coordinately expressed with PKCiota in primary LAC tumors.

Gene panel model predictive of outcome in men at high-risk of systemic progression and death from prostate cancer after radical retropubic prostatectomy.

Purpose: In men who are at high-risk of prostate cancer, progression and death from cancer after radical retropubic prostatectomy (RRP), limited prognostic information is provided by established prognostic features. The objective of this study was to develop a model predictive of outcome in this group of patients.

Methods: Candidate genes were identified from microarray expression data from 102 laser capture microdissected prostate tissue samples.

The zebrafish secretome.

The secretome is a functionally rich proteome subset, including cellular membrane and extracellular proteins processed through the secretory pathway. In this study, Danio rerio and Homo sapiens RefSeq proteins were analyzed with SignalP, TargetP, Phobius, and pTarget algorithms. About 16.

Challenges in translating plasma proteomics from bench to bedside: update from the NHLBI Clinical Proteomics Programs.

The emerging scientific field of proteomics encompasses the identification, characterization, and quantification of the protein content or proteome of whole cells, tissues, or body fluids. The potential for proteomic technologies to identify and quantify novel proteins in the plasma that can function as biomarkers of the presence or severity of clinical disease states holds great promise for clinical use. However, there are many challenges in translating plasma proteomics from bench to bedside, and relatively few plasma biomarkers have successfully transitioned from proteomic discovery to routine clinical use.

Identification of prognostic biomarkers for prostate cancer.

Purpose: This paper describes a process for the identification of genes that can report on the aggressiveness of prostate tumors and thereby add to the information provided by current pathologic analysis.

Materials And Methods: Expression profiling data from over 100 laser capture microdissection derived samples from nonneoplastic epithelium; Gleason patterns 3, 4, and 5 and node metastasis prostate cancer were used to identify genes at abnormally high levels in only some tumors. These variably overexpressed genes were stratified by their association with aggressive phenotypes and were subsequently filtered to exclude genes with redundant expression patterns.

Data mining for biomarker development: a review of tissue specificity analysis.

Novel biomarker development requires a significant resource commitment to translate candidate markers into clinical assays. Consequently, it is imperative high quality candidates are selected early in a biomarker development program. High throughput gene expression data are routinely used to identify transcripts differentially expressed in diseased versus normal samples.

Quantitating tissue specificity of human genes to facilitate biomarker discovery.

We describe a method to identify candidate cancer biomarkers by analyzing numeric approximations of tissue specificity of human genes. These approximations were calculated by analyzing predicted tissue expression distributions of genes derived from mapping expressed sequence tags (ESTs) to the human genome sequence using a binary indexing algorithm. Tissue-specificity values facilitated high-throughput analysis of the human genes and enabled the identification of genes highly specific to different tissues.

Computational classification of classically secreted proteins.

The ability to identify classically secreted proteins is an important component of targeted therapeutic studies and the discovery of circulating biomarkers. Here, we review some of the most recent programs available for the in silico prediction of secretory proteins, the performance of which is benchmarked with an independent set of annotated human proteins. The description of these programs and the results of this benchmarking provide insights into the most recently developed prediction programs, which will enable investigators to make more informed decisions about which program best addresses their research needs.

LC-MS/MS quantification of Zn-alpha2 glycoprotein: a potential serum biomarker for prostate cancer.

Background: Zn-alpha2 glycoprotein (ZAG) is a relatively abundant glycoprotein that has potential as a biomarker for prostate cancer. We present a high-flow liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for measuring serum ZAG concentrations by proteolytic cleavage of the protein and quantification of a unique peptide.

Methods: We selected the ZAG tryptic peptide (147)EIPAWVPEDPAAQITK(162) as the intact protein for quantification and used a stable isotope-labeled synthetic peptide with this sequence as an internal standard.

Genome-wide reverse genetics framework to identify novel functions of the vertebrate secretome.

Background: Understanding the functional role(s) of the more than 20,000 proteins of the vertebrate genome is a major next step in the post-genome era. The approximately 4,000 co-translationally translocated (CTT) proteins - representing the vertebrate secretome - are important for such vertebrate-critical processes as organogenesis. However, the role(s) for most of these genes is currently unknown.

Evaluating eukaryotic secreted protein prediction.

Background: Improvements in protein sequence annotation and an increase in the number of annotated protein databases has fueled development of an increasing number of software tools to predict secreted proteins. Six software programs capable of high throughput and employing a wide range of prediction methods, SignalP 3.0, SignalP 2.

AMOD: a morpholino oligonucleotide selection tool.

AMOD is a web-based program that aids in the functional evaluation of nucleotide sequences through sequence characterization and antisense morpholino oligonucleotide (target site) selection. Submitted sequences are analyzed by translation initiation site prediction algorithms and sequence-to-sequence comparisons; results are used to characterize sequence features required for morpholino design. Within a defined subsequence, base composition and homodimerization values are computed for all putative morpholino oligonucleotides.

Identifying secretomes in people, pufferfish and pigs.

The proteins processed by the secretory pathway (secretome) are critical players in the development of multi-cellular eukaryotic organisms but have yet to be comprehensively studied at the genomic level. In this study, we use the Target P algorithm to predict human (13-20% of proteins found in individual datasets) and Fugu (14%) secretomes based on analysis of their nearly complete proteomes. We combine internal processing with prediction software to automate secreted protein identification and overcome one of the major challenges associated with EST data: identification of the minority of clones that encode N-terminally-complete proteins.

Lymphadenopathy and hepatosplenomegaly in the 1st year in children infected by HIV-1 in Zaire.

The children of 50 women positive for antibody to human immunodeficiency virus type 1 (HIV-1) and 42 children of antibody-negative mothers were examined for lymphadenopathy and hepatosplenomegaly at 3-month intervals during the 1st year of life. Lymphadenopathy was found to be significantly more frequent at 6 months (p less than 0.01), 9 months (p less than 0.

Severe anaemia in pregnancy: a problem of primigravidae in rural Zaire.

Haemoglobin levels were measured in 2950 pregnant women attending antenatal clinics in Kimpese, Bas Zaire. 72% were suffering from moderate anaemia (haemoglobin (Hb) 7-11 g/dl) and 3.7% from severe anaemia (Hb less than 7 g/dl) at their first visit, before receiving any haematinics or anti-malarial prophylaxis.

Viral involvement in Hodgkin's disease: detection of clonal type A Epstein-Barr virus genomes in tumour samples.

Thirty-five cases of Hodgkin's disease (HD) were analysed for the presence of Epstein-Barr virus (EBV) and human herpesvirus-6 (HHV-6) DNA. EBV genomes were detected in 11/35 cases while none of the cases was positive for HHV-6. Ten of the EBV-positive cases were subsequently analysed using a probe for the terminal region of the virus; the results suggested that the EBV-infected cells were clonally expanded.