Whole transcriptome amplification for gene expression profiling and development of molecular archives.

Expression profiling of clinically obtainable tumor specimens has been hindered by the need for microgram quantities of RNA. In vitro transcription (IVT)-based amplifications are most commonly used to amplify small quantities of RNA for microarray analysis. However, significant drawbacks exist with IVT-based amplification, and the need for alternative amplification methods remains.

Delineation, functional validation, and bioinformatic evaluation of gene expression in thyroid follicular carcinomas with the PAX8-PPARG translocation.

A subset of follicular thyroid carcinomas contains a balanced translocation, t(2;3)(q13;p25), that results in fusion of the paired box gene 8 (PAX8) and peroxisome proliferator-activated receptor gamma (PPARG) genes with concomitant expression of a PAX8-PPARgamma fusion protein, PPFP. PPFP is thought to contribute to neoplasia through a mechanism in which it acts as a dominant-negative inhibitor of wild-type PPARgamma. To better understand this type of follicular carcinoma, we generated global gene expression profiles using DNA microarrays of a cohort of follicular carcinomas along with other common thyroid tumors and used the data to derive a gene expression profile characteristic of PPFP-positive tumors.

Importance of carbohydrate in the interaction of Tamm-Horsfall protein with complement 1q and inhibition of classical complement activation.

Tamm-Horsfall protein (THP) binds strongly to complement 1q (C1q), a key component of the classical complement pathway. The goals of this study were to determine whether THP altered the activation of the classical complement pathway and whether the carbohydrate portion of THP was involved in this glycoprotein's binding to C1q and alteration of complement activation. The ability of THP to prevent complement activation in diluted serum or plasma incubated at 37 degrees C was assessed using both a haemolytic assay with antibody-sensitized sheep RBC and a C4d ELISA.

TMPRSS2:ETV4 gene fusions define a third molecular subtype of prostate cancer.

Although common in hematologic and mesenchymal malignancies, recurrent gene fusions have not been well characterized in epithelial carcinomas. Recently, using a novel bioinformatic approach, we identified recurrent gene fusions between TMPRSS2 and the ETS family members ERG or ETV1 in the majority of prostate cancers. Here, we interrogated the expression of all ETS family members in prostate cancer profiling studies and identified marked overexpression of ETV4 in 2 of 98 cases.

Longitudinal analysis of human immunodeficiency virus type 1 nef/long terminal repeat sequences in a cohort of long-term survivors infected from a single source.

We studied the evolution of human immunodeficiency virus type 1 (HIV-1) in a cohort of long-term survivors infected with an attenuated strain of HIV-1 acquired from a single source. Although the cohort members experienced differing clinical courses, we demonstrate similar evolution of HIV-1 nef/long-terminal repeat (LTR) sequences, characterized by progressive sequence deletions tending toward a minimal nef/LTR structure that retains only sequence elements required for viral replication. The in vivo pathogenicity of attenuated HIV-1 is therefore dictated by viral and/or host factors other than those that impose a unidirectional selection pressure on the nef/LTR region of the HIV-1 genome.

The impact of the covert manipulation of macronutrient intake on energy intake and the variability in daily food intake in nonobese men.

Objective: To investigate the effect of macronutrient composition on ad libitum food intake in nonobese men.

Design: Balanced, incomplete-block, crossover study where subjects received two of three treatments. Macronutrient composition was manipulated by providing 2.

Relationship between SPRY and B30.2 protein domains. Evolution of a component of immune defence?

SPRY and B30.2 are homologous domains which can be identified in 11 protein families encoded in the human genome. These include cell surface receptors of the immunoglobulin super-family (BTNs), negative regulators of the JAK/STAT pathway (SOCS-box SSB1-4) and proteins encoded by the numerous TRIM genes.

Multiple emulsion stability: pressure balance and interfacial film strength.

The objective of this study was to investigate the significance of inner and outer phase pressure, as well as interfacial film strength on W/O/W multiple emulsion stability using microscopy and long-term stability tests. It was observed that immediately upon applying a coverslip to samples the multiple droplets deformed and there was coalescence of the inner aqueous droplets. Under certain conditions (such as lipophilic surfactant concentration and internal phase osmotic pressure) the destabilized multiple emulsions formed unique metastable structures that had a "dimpled" appearance.

Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression.

Molecular profiling of cancer at the transcript level has become routine. Large-scale analysis of proteomic alterations during cancer progression has been a more daunting task. Here, we employed high-throughput immunoblotting in order to interrogate tissue extracts derived from prostate cancer.

Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer.

Recurrent chromosomal rearrangements have not been well characterized in common carcinomas. We used a bioinformatics approach to discover candidate oncogenic chromosomal aberrations on the basis of outlier gene expression. Two ETS transcription factors, ERG and ETV1, were identified as outliers in prostate cancer.

Metastasis suppressor gene Raf kinase inhibitor protein (RKIP) is a novel prognostic marker in prostate cancer.

Background: Diminished expression of Raf kinase inhibitor protein (RKIP), an inhibitor of the Raf signaling cascade, promotes prostate cancer (PCa) metastasis in a murine model, suggesting that it is a metastasis suppressor gene. However, the prognostic significance of RKIP expression and its association with metastasis in PCa patients is unknown.

Methods: To investigate RKIP protein expression is a prognostic marker in PCa we performed immunohistochemical staining for RKIP expression in tissue microarrays consisting of 758 non-neoplastic prostate tissues, primary tumors and metastases from 134 PCa patients.

DNA-based therapeutics and DNA delivery systems: a comprehensive review.

The past several years have witnessed the evolution of gene medicine from an experimental technology into a viable strategy for developing therapeutics for a wide range of human disorders. Numerous prototype DNA-based biopharmaceuticals can now control disease progression by induction and/or inhibition of genes. These potent therapeutics include plasmids containing transgenes, oligonucleotides, aptamers, ribozymes, DNAzymes, and small interfering RNAs.

Telomere end-binding proteins control the formation of G-quadruplex DNA structures in vivo.

Telomere end-binding proteins (TEBPs) bind to the guanine-rich overhang (G-overhang) of telomeres. Although the DNA binding properties of TEBPs have been investigated in vitro, little is known about their functions in vivo. Here we use RNA interference to explore in vivo functions of two ciliate TEBPs, TEBPalpha and TEBPbeta.

Validation of a food frequency questionnaire by direct measurement of habitual ad libitum food intake.

Food frequency questionnaires are commonly used to assess habitual food intake. Although food frequency questionnaires are known to produce measurement error, the amount of error and effectiveness of correction methods are poorly understood. Twelve men from the Baltimore, MD/Washington, DC, area consumed an ad libitum diet for 16 weeks during the spring of 2001.

Probabilistic model of the human protein-protein interaction network.

A catalog of all human protein-protein interactions would provide scientists with a framework to study protein deregulation in complex diseases such as cancer. Here we demonstrate that a probabilistic analysis integrating model organism interactome data, protein domain data, genome-wide gene expression data and functional annotation data predicts nearly 40,000 protein-protein interactions in humans-a result comparable to those obtained with experimental and computational approaches in model organisms. We validated the accuracy of the predictive model on an independent test set of known interactions and also experimentally confirmed two predicted interactions relevant to human cancer, implicating uncharacterized proteins into definitive pathways.

Directed evolution and identification of control regions of ColE1 plasmid replication origins using only nucleotide deletions.

Genes can be mutated by altering DNA content (base changes) or DNA length (insertions or deletions). Most in vitro directed evolution processes utilize nucleotide content changes to produce DNA libraries. We tested whether gain of function mutations could be identified using a mutagenic process that produced only nucleotide deletions.

A novel aspochalasin with HIV-1 integrase inhibitory activity from Aspergillus flavipes.

A novel aspochalasin, aspochalasin L (1), was isolated from the fermentation broth of a soil-derived fungal culture identified as Aspergillus flavipes (Deuteromycota). Structure elucidation of 1 was accomplished by detailed spectroscopic data analyses and by comparison with related cytochalasins. Aspochalasin L demonstrated activity against HIV integrase with an IC50 of 71.

Integrative analysis of the cancer transcriptome.

DNA microarrays have been widely applied to the study of human cancer, delineating myriad molecular subtypes of cancer, many of which are associated with distinct biological underpinnings, disease progression and treatment response. These primary analyses have begun to decipher the molecular heterogeneity of cancer, but integrative analyses that evaluate cancer transcriptome data in the context of other data sources are often capable of extracting deeper biological insight from the data. Here we discuss several such integrative computational and analytical approaches, including meta-analysis, functional enrichment analysis, interactome analysis, transcriptional network analysis and integrative model system analysis.

Mining for regulatory programs in the cancer transcriptome.

DNA microarrays have been widely applied to cancer transcriptome analysis. The Oncomine database contains a large collection of such data, as well as hundreds of derived gene-expression signatures. We studied the regulatory mechanisms responsible for gene deregulation in these cancer signatures by searching for the coordinate regulation of genes with common transcription factor binding sites.

Biophysical characterization of anionic lipoplexes.

Transfection efficiency of liposomal gene delivery vectors depends on an optimal balance in the electro-chemical and structural properties of the transfection-capable complexes. We have recently reported a novel anionic lipoplex DNA delivery system composed of a ternary complex of endogenous occurring non-toxic anionic lipids, physiological Ca2+ cations, and plasmid DNA encoding a gene of interest with high transfection efficiency and low toxicity. In this work, we investigate the electro-chemical and structural properties anionic lipoplexes and compare them with those of Ca2+-DNA complexes.

Anionic liposomal delivery system for DNA transfection.

The present study investigates the use of novel anionic lipoplexes composed of physiological components for plasmid DNA delivery into mammalian cells in vitro. Liposomes were prepared from mixtures of endogenously occurring anionic and zwitterionic lipids, 1,2-dioleoyl-sn-glycero-3-[phospho-rac-(1-glycerol)] (sodium salt) (DOPG) and 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), respectively, at a molar ratio of 17:83 (DOPG:DOPE). Anionic lipoplexes were formed by complexation between anionic liposomes and plasmid DNA molecules encoding green fluorescence protein (GFP) using Ca2+ ions.

Preprandial ghrelin is not affected by macronutrient intake, energy intake or energy expenditure.

Background: Ghrelin, a peptide secreted by endocrine cells in the gastrointestinal tract, is a hormone purported to have a significant effect on food intake and energy balance in humans. The influence of factors related to energy balance on ghrelin, such as daily energy expenditure, energy intake, and macronutrient intake, have not been reported. Secondly, the effect of ghrelin on food intake has not been quantified under free-living conditions over a prolonged period of time.

Molecular breast imaging: a new technique using technetium Tc 99m scintimammography to detect small tumors of the breast.

Objective: To determine the sensitivity of molecular breast imaging (MBI) to detect small cancers of the breast.

Patients And Methods: A cadmium-zinc-telluride gamma camera with a field of view of 20 x 20 cm was used. The detector elements were 2.

A method for the in vitro reconstitution of a defined "30 nm" chromatin fibre containing stoichiometric amounts of the linker histone.

An understanding of the role of higher-order chromatin structure in the regulation of cellular processes such as transcription will require knowledge of the structure of the "30 nm" chromatin fibre and its folding and unfolding pathways. We report an in vitro chromatin reconstitution system, which uses arrays of 12 and 19 copies of a 200 bp repeat of the Widom 601 DNA sequence. Since this DNA sequence binds the histone octamer with much higher affinity than mixed sequence DNA, we have used competitor DNA in the reconstitutions to control the loading of both the histone octamer and linker histone onto the 601 DNA arrays.