Label-free detection of DNA hybridization with a compact LSPR-based fiber-optic sensor.

A miniaturized, robust, localized surface plasmon resonance (LSPR)-coupled fiber-optic (FO) nanoprobe providing an integrated and portable solution for detection of DNA hybridization and measurement of DNA concentrations has been demonstrated. The FO nanoprobe was created by constructing arrays of metallic nanostructures on the end facets of optical fibers utilizing nanofabrication technologies, including electron beam lithography and lift-off processes. The LSPR-FO nanoprobe device offers real-time, label-free, and low-sample-volume quantification of single-strand DNA in water with high sensitivity and selectivity, achieving a limit of detection around 10 fM. These results demonstrate the feasibility of the LSPR-FO nanoprobe device as a compact and low-cost biosensor for detection of short-strand DNA.

Common molecular mechanism of the hepatic lesion and the cardiac parasympathetic regulation in chronic hepatitis C infection: a critical role for the muscarinic receptor type 3.

BACKGROUND: The pathophysiological overlapping between Sjorgen's Syndrome (SS) and HCV, presence of anti- muscarinic receptor type 3 (M3R) antibodies in SS, the role that M3R plays in the regulation of the heart rate, has led to the assumption that cardiovagal dysfunction in HCV patients is caused by anti-M3R antibodies elicited by HCV proteins or by their direct interaction with M3R. RESULTS: To identify HCV protein which possibly is crossreactive with M3R or which binds to this receptor, we performed the Informational Spectrum Method (ISM) analysis of the HCV proteome. This analysis revealed that NS5A protein represents the most probable interactor of M3R or that this viral protein could elicit antibodies which modulate function of this receptor. Further detailed structure/function analysis of NS5A and M3R performed by the ISM method extended with other Digital Signal processing (DSP) approaches revealed domains of these proteins which participate in their crossreactivity or in their direct interaction, representing promising diagnostic and therapeutic targets. CONCLUSIONS: Application of the ISM with other compatible bioinformatics methods offers new perspectives for identifying diagnostic and therapeutic targets for complicated forms of HCV and other viral infections. We show how the electron-ion interaction potential (EIIP) amino-acid scale used in the ISM combined with a robust, high performance hydrophobicity scale can provide new insights for understanding protein structure/function and protein-protein interactions.

Novel stem-loop probe DNA arrays: detection of specific acetotrophic 16S ribosomal RNA signatures.

In a recent study, we showed how novel stem-loop DNA probes on dendron-modified aldehyde substrates could be used to detect synthetic nucleic acid targets without amplification. In this article, we demonstrate the application of stem-loop DNA probes as arrays for the detection of specific families and genera of methane-producing bacteria from sludge samples harvested from an anaerobic digester using 16S ribosomal RNA (rRNA) signatures. Specific 16S rRNA could be detected in samples that had 0.2ng/µl total sludge RNA without any target amplification.

Dendron-modified surfaces provide an ideal environment for stem-loop DNA probes.

Specificity and sensitivity are important factors affecting DNA microarrays. Stem-loop DNA probes (SLPs) can be more specific in their recognition of target sequences than linear DNA probes, but unless they are carefully designed, surface interactions can disrupt the native stem-loop structure. In this study, we show how dendron-modified surfaces with well-defined, uniform spacing of aldehyde chemical functionalities offer an ideal substrate to immobilize SLPs and use them to detect nucleic acid targets. The mesospacing provided by the dendron-modified surfaces produces a solution-like environment that allows the SLPs to detect target nucleic acids at concentrations as low as 1pM in concentration.

Innovations in Worksite Diagnosis of Urinary Tract Infections and the Occupational Health Nurse.

Occupational health nurses play a key role in evaluating innovative technologies that can aid in providing safe and rapid care and reduce lost work time. A nurse-led employee health clinic participated in a validation study of a novel pathogen detection technique developed by GeneCapture, Inc. Their proposed portable urinary tract infection (UTI) in vitro diagnostic test was challenged with discarded, deidentified urine samples from patients presenting with typical UTI symptoms collected at two university clinics and two multiphysician practices. GeneCapture's panel for this study was designed to rapidly identify the genetic signature of seven organisms: gram-negative Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, and Pseudomonas aeruginosa; gram-positive Enterococcus faecalis and Staphylococcus aureus; and fungal Candida species. The results from 40 clinical samples were in 95% agreement (90% specificity, 100% sensitivity) with traditional urine culture results from routine analysis. This successful occupational health nursing collaboration and validation study shows promise for point-of-care diagnoses and earlier treatment for workers with UTIs.

FTIR/ATR study of protein adsorption and brushite transformation to hydroxyapatite.

Previous study has demonstrated that brushite (CaHPO4 x 2H2O), modified by partial potassium substitution for calcium, can transform quickly into hydroxyapatite (HA, Ca5(PO4)3OH) when exposed to aqueous salt solutions at room temperature. Analyses techniques used in those studies required sample retrieval from solution, which may alter the sample surface. In this work FTIR/ ATR was used in analysis, enabling in situ study of the transformation within the aqueous environment. To test the biocompatibility of this brushite, cellular response to the transformation needs to be understood. Cellular response was initiated by bovine serum albumin adsorption on the brushite surface. The response was studied by monitoring the conformation of the adsorbed protein, which is critical to cellular reaction. This required monitoring the brushite transformation and surface adsorbed protein conformation simultaneously which can be realized using FTIR/ATR. Based on band fitting and second derivative results from the spectra it was found that the conformation of the adsorbed BSA changes during the brushite transformation to HA. This study also demonstrated that the deposition of the brushite could be monitored in real time which offers the possibility for studying surface bonding during electrodeposition.

Microarray analysis of shear stressed endothelial cells.

The cDNA microarray is an extremely beneficial tool for study of differential gene expression in the cardiovascular system. This technique is used in many different applications including drug discovery, environmental science, and the effects of mechanical forces on vascular cell phenotype. The paper reviews work by others, and describes our study on effects of shear stress on vascular endothelial cells. These microarray studies verified earlier findings using Northern and polymerase chain reaction (PCR) analyses in this area; and also found previously unidentified differentially expressed genes, leading to new hypotheses regarding how cells and tissues respond to biochemical and mechanical stimuli.