Lessons Learned: Transfer of the High-Definition Circulating Tumor Cell Assay Platform to Development as a Commercialized Clinical Assay Platform.

Planning and transfer of a new technology platform developed in an academic setting to a start-up company for medical diagnostic product development may appear daunting and costly in terms of complexity, time, and resources. In this review we outline the key steps taken and lessons learned when a technology platform developed in an academic setting was transferred to a start-up company for medical diagnostic product development in the interest of elucidating development toolkits for academic groups and small start-up companies starting on the path to commercialization and regulatory approval.

Moving towards a reliable HIV incidence test - current status, resources available, future directions and challenges ahead.

In 2011 the Incidence Assay Critical Path Working Group reviewed the current state of HIV incidence assays and helped to determine a critical path to the introduction of an HIV incidence assay. At that time the Consortium for Evaluation and Performance of HIV Incidence Assays (CEPHIA) was formed to spur progress and raise standards among assay developers, scientists and laboratories involved in HIV incidence measurement and to structure and conduct a direct independent comparative evaluation of the performance of 10 existing HIV incidence assays, to be considered singly and in combinations as recent infection test algorithms. In this paper we report on a new framework for HIV incidence assay evaluation that has emerged from this effort over the past 5 years, which includes a preliminary target product profile for an incidence assay, a consensus around key performance metrics along with analytical tools and deployment of a standardized approach for incidence assay evaluation. The specimen panels for this evaluation have been collected in large volumes, characterized using a novel approach for infection dating rules and assembled into panels designed to assess the impact of important sources of measurement error with incidence assays such as viral subtype, elite host control of viraemia and antiretroviral treatment. We present the specific rationale for several of these innovations, and discuss important resources for assay developers and researchers that have recently become available. Finally, we summarize the key remaining steps on the path to development and implementation of reliable assays for monitoring HIV incidence at a population level.

Inflammatory and cardiac biomarkers are differentially expressed in clinical stages of Chagas disease.

BACKGROUND: Chagas disease has a long clinically silent period following Trypanosoma cruzi infection and before development of overt clinical pathology; detectable biomarkers of infection and pathogenesis are urgently needed. We tested 22 biomarkers known to be associated with cardiomyopathy to evaluate if a biomarker signature could successfully classify T. cruzi seropositive subjects into clinical Chagas disease stage groups. METHODS: This cross-sectional retrospective case-control study enrolled T. cruzi seropositive blood donors (BD) who were further characterized as having chronic Chagas cardiomyopathy (CC-BD) or not (nonCC-BD) and seronegative (SN) control donors; we also included clinically diagnosed Chagas cardiomyopathy patients (CC-P). All subjects underwent a health history questionnaire, medical examination, electro- and echocardiograms (ECG and Echo) and phlebotomy. Biomarkers were measured on blinded samples by luminex bead array and Ortho VITROS. RESULTS: A clear biomarker pattern was observed only in more severe cardiac disease; this pattern included significantly elevated levels of inflammatory cytokines IFN-γ, IL-6, IL-10 and TNF-α and soluble cardiovascular disease biomarkers CK-MB, troponin, myoglobin, VCAM and NTproBNP while there were lower levels of MPO, PAI-1, and MCP-1. The markers determined to be the most predictive of disease by ROC curve analysis were NTproBNP and T. cruzi PCR status. CONCLUSIONS: Although many biomarkers demonstrated increased or decreased concentrations among the clinical forms of Chagas disease, NTproBNP and T. cruzi PCR were the only tests that would independently be of clinical value for disease staging, in concert with ECG, Echo and clinical assessments.

Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project.

Biologists are increasingly recognising that computational modelling is crucial for making sense of the vast quantities of complex experimental data that are now being collected. The systems biology field needs agreed-upon information standards if models are to be shared, evaluated and developed cooperatively. Over the last four years, our team has been developing the Systems Biology Markup Language (SBML) in collaboration with an international community of modellers and software developers. SBML has become a de facto standard format for representing formal, quantitative and qualitative models at the level of biochemical reactions and regulatory networks. In this article, we summarise the current and upcoming versions of SBML and our efforts at developing software infrastructure for supporting and broadening its use. We also provide a brief overview of the many SBML-compatible software tools available today.

Generation of an LFA-1 antagonist by the transfer of the ICAM-1 immunoregulatory epitope to a small molecule.

The protein-protein interaction between leukocyte functional antigen-1 (LFA-1) and intercellular adhesion molecule-1 (ICAM-1) is critical to lymphocyte and immune system function. Here, we report on the transfer of the contiguous, nonlinear epitope of ICAM-1, responsible for its association with LFA-1, to a small-molecule framework. These LFA-1 antagonists bound LFA-1, blocked binding of ICAM-1, and inhibited a mixed lymphocyte reaction (MLR) with potency significantly greater than that of cyclosporine A. Furthermore, in comparison to an antibody to LFA-1, they exhibited significant anti-inflammatory effects in vivo. These results demonstrate the utility of small-molecule mimics of nonlinear protein epitopes and the protein epitopes themselves as leads in the identification of novel pharmaceutical agents.

Modelling of the immunoassay element of an optical immunosensor.

Several factors affect the viability of biosensor design. A computer-based model is being developed to enable the sources and effect of noise and variability within the sensor to be analysed. The work now presented details the modelling of the biochemical aspect of the biosensor model-the immunoassay. The equilibrium equations that describe the chemical reactions that occur when a sample containing the analyte is added to the immunosensor are cast as a sum of squares function that can be minimized using an optimization procedure. The optimization returns the concentrations of each species at equilibrium and the procedure is incorporated within a Monte Carlo simulation, which allows the variations in the resulting concentrations to be determined. Three classes of optimization technique are considered, classical regression techniques and two intelligent optimization techniques: simulated annealing and genetic algorithms. Several methods of imposing constraints are implemented and the issue of local minima is discussed. Classical regression procedures were found to be superior to the intelligent optimizations examined.

Sustained release of 5-fluorouracil from polymeric nanoparticles.

The use of biodegradable nanoparticles loaded with 5-fluorouracil was investigated as a potential means to sustain the release of this drug. Nanoparticles prepared from four biodegradable polymers were loaded with 5-fluorouracil using three loading concentrations of drug and three different concentrations of added polymer. Washing particles using a centrifugation/re-suspension with ultrasound protocol was found to dislodge the majority of drug, resulting in an over-estimation of incorporation efficiency and low levels of strongly entrapped drug. Increasing the initial 5-fluorouracil concentration before polymer/monomer addition increased the drug loading in both washed and unwashed particles. Increasing the amount of polymer used to make nanoparticles did not increase loadings, but did produce increased amounts of unusable polymer waste. Drug release from nanoparticles was evaluated using a Franz cell diffusion apparatus, which showed an initial burst effect followed by a slower release phase over 24 h. Indeed, nanoparticles prepared from poly(lactide-co-glycolide) released 66% of their 5-fluorouracil payload over this period. It was concluded that 5-fluorouracil-loaded nanoparticles could be readily included into a hydrogel-based delivery system to provide sustained drug release for trans-epithelial drug-delivery applications.

Response surface methodology as a predictive tool for determining the effects of preparation conditions on the physicochemical properties of poly(isobutylcyanoacrylate) nanoparticles.

Preparation conditions of nanoparticles greatly influence their physicochemical characteristics. A factorial design was used to evaluate the influence of these conditions on the particle diameter, zeta potential, polydispersity, percentage recovery, and molecular weight of poly(isobutylcyanoacrylate) nanoparticles. The relationship between these responses and the effects of simultaneously varying three preparation factors (monomer concentration, surfactant concentration, pH of the polymerization medium) were modelled by response-surface methodology. Three levels were chosen for each factor, giving 27 trials. The responses obtained in the experimental design were found to be modelled by either a reduced quadratic or second-order model. Particle diameter was found to be a function of the pH, whereas zeta potential depended on pH and to a lesser extent of the monomer concentration. Polydispersity depended on the pH and an interaction term between pH and the surfactant concentration. The particle recovery was significantly influenced by all three factors, whereas the pH was the primary influence on the molecular weight. Thus, response surface methodology gave detailed information on the predicted physicochemical characteristics found on poly(isobutylcyanoacrylate) nanoparticles prepared using a wide range of experimental conditions.

Transfer of a protein binding epitope to a minimal designed peptide.

Results from protein mutagenesis and x-ray crystallographic studies of the multidomain protein Vascular Cell Adhesion Molecule (VCAM) were used to design cyclic octapeptides that retain the critical structural and binding elements of the epitope of VCAM in the interaction with the integrin alpha 4 beta 1 (VLA-4). Changes in the activities of peptide analogues correlated with the relative activities of protein mutants of VCAM, and predicted the properties of two new mutants that bound alpha 4 beta 1 with improved affinity vs wild type protein. The nmr structures of two peptides revealed a high degree of similarity to the structure of the VCAM binding epitope. These results demonstrate that a compact binding epitope identified via protein structure-function studies may be transferred to a synthetically accessible small peptide with the key structure-activity relationships intact.

The limitations of intimate samples in sexual offences.

This article reviews the problems of sampling and interpretation of scientific findings from samples taken by doctors during their examination of victims and suspects in sexual offences. The problems which may be encountered with vaginal, anal, oral and penile swabs are highlighted. These include contamination between samples and the consequences thereof. The responsibilities of the medical examiner, the investigating police officer and the scientist are stressed. Surveys of results stored in a database and case examples are used to illustrate the problems.

What's in a name?--Medical samples and scientific evidence in sexual assaults.

A survey of findings in relation to body swabs, hairs, fingernails and protectives is presented. The need to sample precisely and without contamination is stressed, since interpretation of findings depends on this.

The detection of amylase on swabs from sexual assault cases.

Results are presented of amylase tests performed on more than 400 casework swabs using Phadebas tablets. Amylase levels indicative of saliva were obtained from 25% of the penile swabs tested, 32% of the vaginal swabs and 50% of the breast swabs. The longest time interval between the offence and sampling when such levels were detected was 16 hours for penile swabs, 55 hours for vaginal swabs and 30 hours for breast swabs.

Oral sex--further information from sexual assault cases.

A survey was carried out of sexual assault cases submitted to the Metropolitan Police Forensic Science Laboratory during 1988 and 1989. There were 104 cases with male victims, and 1403 with females. In the all-male offences, fellatio was reported in 34%; nearly two-thirds of the acts were by the offender, one-third by the victim. In the offences on females, oral-genital acts were alleged in 22%, 78% of which were fellatio, and 22% cunnilingus. The majority of offenders were white. The few Afro-Caribbeans studied rarely performed oral sex on males or very young females.

Nanosecond fluorescence microscopy. Emission kinetics of fura-2 in single cells.

A microscope based time-correlated single photon counting instrument has been constructed to measure fluorescence intensity and emission anisotropy decays from fluorophores in single cells on a nanosecond time scale. The sample is excited and the emission collected using epi-illumination optics with frequency-doubled pulses from the cavity-dumped output of a synchronously pumped dye laser serving as an excitation source. Collection of decays from a single cell is possible due to the presence of an iris in the emission path that can be reduced to less than the diameter of a single cell. Using the instrument the decay of 60 nM 1,6-diphenyl-1,3,5-hexatriene was measured, demonstrating that adequate data for lifetime analysis can be recorded from fewer 10(3) molecules of the fluorophore in an illuminated volume of 23 fl. In addition, the intensity and anisotropy decays of fura-2 in single adherent cells and in suspensions of fura-2 loaded cells in suspension, although the relative amplitudes and decay constants vary somewhat from cell to cell. The results indicate that a significant but variable fraction of fura-2 is bound to relatively immobile macromolecular components in these cells.

Sexual assault patterns.

The numbers and types of all sexual offences examined at the Metropolitan Police Forensic Science Laboratory during the years 1978-1986 are presented. The largest number of sexual assaults took place during the month of August; they were mainly intra-racial and between adults of 18 to 30 years of age. A detailed breakdown is given of the offences against females recorded on the Sexual Assault Index. All these assaults were carried out by adult males, mainly strangers. Nearly half the assaults took place indoors, where victims were more likely to be bound and blindfolded, compared with one-third outdoors and one-sixth in vehicles. About one-fifth of the crimes were carried out by two men or more, and in one-third of cases, weapons were carried. Oral intercourse occurred in one-sixth and anal intercourse in one-twelfth of the offences, both performed more by white males and those of Mediterranean origin.

Information from penile swabs in sexual assault cases.

A survey has been made to assess the evidential value of tests carried out on 660 casework penile swabs. Most were from suspects in sexual assaults and were examined to see if the donor had had recent anal, oral or vaginal intercourse. The swabs were tested for one or more of the following: blood, faeces, saliva, vaginal secretions, semen. Blood was seldom found, it was usually weak and insufficient for grouping. Faeces were only identified on a pair of swabs from a dead homosexual showing that proof of buggery by this means is rare. Amylase, suggestive of saliva and oral intercourse, was occasionally detected. Glycogen-rich epithelial cells were sometimes present indicating vaginal intercourse. Semen was frequently found but its presence may not result from a recent sexual act. An ABO group different from the donor was obtained from a fifth of the swabs typed. Grouping in other blood group systems was rarely attempted or successful. Penile swabs provided a means of detecting a victim's ABO blood group on a suspect when it would not have been possible to demonstrate the suspect's group on samples from the victim. They also had value in assaults involving more than one offender. The main limitation of penile swabs was the paucity of material on them and the sampling site affected the interpretation of the results.

The isolation of spermatozoa from sexual assault swabs using proteinase K.

The most common examination in sexual offences is the identification of spermatozoa in aqueous extracts from swabs. Using Proteinase K with sodium dodecyl sulphate, it is possible to digest all the cellular material apart from the spermatozoa, resulting in a quick and effective method of their isolation. Spermatozoa were detected in 18 extracts using this treatment when the normal method had failed to reveal all but one of them.