Transcriptional profiling of TLR-4/7/8-stimulated guinea pig splenocytes and whole blood by bDNA assay.

Toll-like receptor (TLR) agonists are currently being examined as adjuvants for vaccines, with several lead candidates now in licensed products or in late-stage clinical development. Guinea pigs are widely used for preclinical testing of drugs and vaccines; however, evaluation of TLR agonists in this model is hindered by the limited availability of immunological tools and reagents. In this study, we validated the use of a branched-chain DNA (bDNA) assay known as the QuantiGene Plex 2.

Applying TLR synergy in immunotherapy: implications in cutaneous leishmaniasis.

Therapy of intracellular pathogens can be complicated by drug toxicity, drug resistance, and the need for prolonged treatment regimens. One approach that has shown promise is immunotherapy. Leishmaniasis, a vector-borne disease ranked among the six most important tropical infectious diseases by the World Health Organization, has been treated clinically with crude or defined vaccine preparations or cytokines, such as IFN-gamma and GM-CSF, in combination with chemotherapy.

LIP index for peptide classification using MS/MS and SEQUEST search via logistic regression.

This study addresses the issue of peptide identification resulting from tandem mass spectrometry proteomics analysis followed by database search. This work shows that the Logistic Identification of Peptides (LIP) Index achieves high sensitivity and specificity for peptide classification relative to a manually verified "gold" standard and also accurately estimates the probability of a correct peptide match. The LIP Index is a weighted average of SEQUEST output variables based on logistic regression models and is a transparent, easy to use, inclusive, extendable, and statistically sound approach to classify correct peptide identifications.

Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations.

The gamma-proteobacterium Shewanella oneidensis strain MR-1 is a metabolically versatile organism that can reduce a wide range of organic compounds, metal ions, and radionuclides. Similar to most other sequenced organisms, approximately 40% of the predicted ORFs in the S. oneidensis genome were annotated as uncharacterized "hypothetical" genes.

Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae.

The progress in genome sequencing has led to a rapid accumulation in GenBank submissions of uncharacterized 'hypothetical' genes. These genes, which have not been experimentally characterized and whose functions cannot be deduced from simple sequence comparisons alone, now comprise a significant fraction of the public databases. Expression analyses of Haemophilus influenzae cells using a combination of transcriptomic and proteomic approaches resulted in confident identification of 54 'hypothetical' genes that were expressed in cells under normal growth conditions.

Standard mixtures for proteome studies.

Mixtures of moderate complexity were formed from 23 peptides and 12 proteins digested with trypsin, all individually characterized. These mixtures were analyzed with replicates in full and windowed m/z ranges using online high-performance reverse phase liquid chromatography coupled via electrospray ionization to an ion trap mass spectrometer. The resulting spectra were searched using SEQUEST against databases of different sizes and contents and confidences of the observed identifications were evaluated by our earlier statistical model.

In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium.

The intermediary metabolism of Haemophilus influenzae strain Rd KW20 was studied by a combination of protein expression analysis using a recently developed direct proteomics approach, mutational analysis, and mathematical modeling. Special emphasis was placed on carbon utilization, sugar fermentation, TCA cycle, and electron transport of H. influenzae cells grown microaerobically and anaerobically in a rich medium.

Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20.

The proteome of Haemophilus influenzae strain Rd KW20 was analyzed by liquid chromatography (LC) coupled with ion trap tandem mass spectrometry (MS/MS). This approach does not require a gel electrophoresis step and provides a rapidly developed snapshot of the proteome. In order to gain insight into the central metabolism of H.

H. influenzae Consortium: integrative study of H. influenzae-human interactions.

Developments in high-throughput analysis tools coupled with integrative computational techniques have enabled biological studies to reach new levels. The ability to correlate large volumes of diverse data types into cohesive models of organism function has spawned a new systematic approach to biological investigation. The creation of a new consortium has been proposed to investigate a single organism utilizing these comprehensive approaches.