Thermal Analysis of a Disposable, Instrument-Free DNA Amplification Lab-on-a-Chip Platform.

Novel second-generation rapid diagnostics based on nucleic acid amplification tests (NAAT) offer performance metrics on par with clinical laboratories in detecting infectious diseases at the point of care. The diagnostic assay is typically performed within a Lab-on-a-Chip (LoC) component with integrated temperature regulation. However, constraints on device dimensions, cost and power supply inherent with the device format apply to temperature regulation as well.

Integrated self-regulating resistive heating for isothermal nucleic acid amplification tests (NAAT) in Lab-on-a-Chip (LoC) devices.

Isothermal nucleic acid amplification tests (NAAT) in a Lab-on-a-Chip (LoC) format promise to bring high-accuracy, non-instrumented rapid tests to the point of care. Reliable rapid tests for infectious diseases allow for early diagnosis and treatment, which in turn enables better containment of potential outbreaks and fewer complications. A critical component to LoC NAATs is the heating element, as all NAAT protocols require incubation at elevated temperatures.

Implementation of antimicrobial peptides for sample preparation prior to nucleic acid amplification in point-of-care settings.

Background: A variety of sample preparation techniques are used prior to nucleic acid amplification. However, their efficiency is not always sufficient and nucleic acid purification remains the preferred method for template preparation. Purification is difficult and costly to apply in point-of-care (POC) settings and there is a strong need for more robust, rapid, and efficient biological sample preparation techniques in molecular diagnostics.

The effect of main urine inhibitors on the activity of different DNA polymerases in loop-mediated isothermal amplification.

Background: The use of rapid amplification methods to detect pathogens in biological samples is mainly limited by the amount of pathogens present in the sample and the presence of inhibiting substances. Inhibitors can affect the amplification efficiency by either binding to the polymerase, interacting with the DNA, or interacting with the polymerase during primer extension. Amplification is performed using DNA polymerase enzymes and even small changes in their activity can influence the sensitivity and robustness of molecular assays Methods: The main purpose of this research was to examine which compounds present in urine inhibit polymerases with strand displacement activity.

Combination with antimicrobial peptide lyses improves loop-mediated isothermal amplification based method for Chlamydia trachomatis detection directly in urine sample.

Background: Chlamydia trachomatis is an obligate intracellular human pathogen and is the most common cause of sexually transmitted diseases affecting both men and women. The pathogen can cause prostatitis and epididymitis in men. In women, cervicitis, pelvic inflammatory disease, ectopic pregnancy and acute or chronic pelvic pain are frequent complications.

Peptide-ligand binding modeling of siRNA with cell-penetrating peptides.

The binding affinity of a series of cell-penetrating peptides (CPP) was modeled through docking and making use of the number of intermolecular hydrogen bonds, lipophilic contacts, and the number of sp3 molecular orbital hybridization carbons. The new ranking of the peptides is consistent with the experimentally determined efficiency in the downregulation of luciferase activity, which includes the peptides' ability to bind and deliver the siRNA into the cell. The predicted structures of the complexes of peptides to siRNA were stable throughout 10 ns long, explicit water molecular dynamics simulations.

Sensitive and rapid detection of Chlamydia trachomatis by recombinase polymerase amplification directly from urine samples.

Chlamydia trachomatis is the most common sexually transmitted human pathogen. Infection results in minimal to no symptoms in approximately two-thirds of women and therefore often goes undiagnosed. C.

Subchronic Oral and Inhalation Toxicities: a Challenging Attempt for Modeling and Prediction.

The article deals with a challenging attempt to model and predict "difficult" properties as long-term subchronic oral and inhalation toxicities (90 days) using nonlinear QSAR approach. This investigation is one of the first to tackle such multicomplex properties where we have employed nonlinear models based on artificial neural network for the prediction of NOAEL (no observable adverse effect level). Despite the complex nature of the NOAEL property based on in vivo rat experiments, the successful models can be used as alternative tools to non-animal tests for the initial assessment of these chronic toxicities.

A general treatment of solubility 4. Description and analysis of a PCA model for ostwald solubility coefficients.

Principal component analysis (PCA) of a large data matrix (153 solvents x 396 solutes) for Ostwald solubility coefficients (log L) resulted in a two-component model covering 98.6% of the variability. Analysis of the principal components exposed the structural characteristics of solutes and solvents that codify interactions which determine the behavior of a chemical in the surrounding media.

Prediction of Cell-Penetrating Peptides Using Artificial Neural Networks.

An investigation of cell-penetrating peptides (CPPs) by using combination of Artificial Neural Networks (ANN) and Principle Component Analysis (PCA) revealed that the penetration capability (penetrating/non-penetrating) of 101 examined peptides can be predicted with accuracy of 80%-100%. The inputs of the ANN are the main characteristics classifying the penetration. These molecular characteristics (descriptors) were calculated for each peptide and they provide bio-chemical insights for the criteria of penetration.

QSAR study of mosquito repellents using Codessa Pro.

Protection times provided by 31 synthetic repellents against Aedes aegypti mosquitoes were correlated with the chemical structures of these repellents using Codessa Pro software. Two statistically significant quantitative models with R2 values of ca. 0.

A general treatment of solubility. 3. Principal component analysis (PCA) of the solubilities of diverse solutes in diverse solvents.

A phenomenological study of solubility has been conducted using a combination of quantitative structure-property relationship (QSPR) and principal component analysis (PCA). A solubility database of 4540 experimental data points was used that utilized available experimental data into a matrix of 154 solvents times 397 solutes. Methodology in which QSPR and PCA are combined was developed to predict the missing values and to fill the data matrix.