A simple, sensitive and selective quantum-dot-based western blot method for the simultaneous detection of multiple targets from cell lysates

Quantum dots (Qdots) are fluorescent nanoparticles that have great potential as detection agents in biological applications. Their optical properties, including photostability and narrow, symmetrical emission bands with large Stokes shifts, and the potential for multiplexing of many different colours, give them significant advantages over traditionally used fluorescent dyes. Here, we report the straightforward generation of stable, covalent quantum dot-protein A/G bioconjugates that will be able to bind to almost any IgG antibody, and therefore can be used in many applications. An additional advantage is that the requirement for a secondary antibody is removed, simplifying experimental design. To demonstrate their use, we show their application in multiplexed western blotting. The sensitivity of Qdot conjugates is found to be superior to fluorescent dyes, and comparable to, or potentially better than, enhanced chemiluminescence. We show a true biological validation using a four-colour multiplexed western blot against a complex cell lysate background, and have significantly improved previously reported non-specific binding of the Qdots to cellular proteins.

Development and validation of an HPLC method for the rapid and simultaneous determination of 6-mercaptopurine and four of its metabolites in plasma and red blood cells

An HPLC method has been developed and validated for the rapid determination of mercaptopurine and four of its metabolites; thioguanine, thiouric acid, thioxanthine and methylmercaptopurine in plasma and red blood cells. The method involves a simple treatment procedure based on deproteinisation by perchloric acid followed by acid hydrolysis and heating for 45min at 100 degrees C. The developed method was linear over the concentration range studied with a correlation coefficient >0.994 for all compounds in both plasma and erythrocytes. The lower limits of quantification were 13, 14, 3, 2, 95pmol/8 x 10(8) RBCs and 2, 5, 2, 3, 20ng/ml plasma for thioguanine, thiouric acid, mercaptopurine, thioxanthine and methylmercaptopurine, respectively. The method described is selective and sensitive enough to analyse the different metabolites in a single run under isocratic conditions. Furthermore, it has been shown to be applicable for monitoring these metabolites in paediatric patients due to the low volume requirement (200microl of plasma or erythrocytes) and has been successfully applied for investigating population pharmacokinetics, pharmacogenetics and non-adherence to therapy in these patients.

Validation of an Analytical Method for the Identification of SmartWater CSI Forensic Marking Technology

SmartWater is a chemical taggant used as a crime deterrent. The chemical taggant is a colorless liquid that fluoresces yellow under ultra-violet (UV) light and contains distinctive, identifiable and traceable elemental composition. For instance, upon a break and entry scenario, the burglar is sprayed with a solution that has an elemental signature custom-made to a specific location. The residues of this taggant persist on skin and other objects and can be easily recovered for further analysis. The product has been effectively used in Europe as a crime deterrent and has been recently introduced in South Florida. In 2014, Fourt Lauderdale Police Department reported the use of SmartWater products with a reduction in burglaries of 14% [1]. The International Forensic Research Institute (IFRI) at FIU validated the scientific foundation of the methods of recovery and analysis of these chemical tagging systems using LA-ICP-MS. Analytical figures of merit of the method such as precision, accuracy, limits of detection, linearity and selectivity are reported in this study. Moreover, blind samples were analyzed by LA-ICP-MS to compare the chemical signatures to the company’s database and evaluate error rates and the accuracy of the method. This study demonstrated that LA-ICP-MS could be used to effectively detect these traceable taggants to assist law enforcement agencies in the United States with cases involving transfer of these forensic coding systems.

A deformation model of flexible, high area-to-mass ratio debris under perturbations and validation method

A new type of space debris was recently discovered by Schildknecht in near -geosynchronous orbit (GEO). These objects were later identified as exhibiting properties associated with High Area-to-Mass ratio (HAMR) objects. According to their brightness magnitudes (light curve), high rotation rates and composition properties (albedo, amount of specular and diffuse reflection, colour, etc), it is thought that these objects are multilayer insulation (MLI). Observations have shown that this debris type is very sensitive to environmental disturbances, particularly solar radiation pressure, due to the fact that their shapes are easily deformed leading to changes in the Area-to-Mass ratio (AMR) over time. This thesis proposes a simple effective flexible model of the thin, deformable membrane with two different methods. Firstly, this debris is modelled with Finite Element Analysis (FEA) by using Bernoulli-Euler theory called “Bernoulli model”. The Bernoulli model is constructed with beam elements consisting 2 nodes and each node has six degrees of freedom (DoF). The mass of membrane is distributed in beam elements. Secondly, the debris based on multibody dynamics theory call “Multibody model” is modelled as a series of lump masses, connected through flexible joints, representing the flexibility of the membrane itself. The mass of the membrane, albeit low, is taken into account with lump masses in the joints. The dynamic equations for the masses, including the constraints defined by the connecting rigid rod, are derived using fundamental Newtonian mechanics. The physical properties of both flexible models required by the models (membrane density, reflectivity, composition, etc.), are assumed to be those of multilayer insulation. Both flexible membrane models are then propagated together with classical orbital and attitude equations of motion near GEO region to predict the orbital evolution under the perturbations of solar radiation pressure, Earth’s gravity field, luni-solar gravitational fields and self-shadowing effect. These results are then compared to two rigid body models (cannonball and flat rigid plate). In this investigation, when comparing with a rigid model, the evolutions of orbital elements of the flexible models indicate the difference of inclination and secular eccentricity evolutions, rapid irregular attitude motion and unstable cross-section area due to a deformation over time. Then, the Monte Carlo simulations by varying initial attitude dynamics and deformed angle are investigated and compared with rigid models over 100 days. As the results of the simulations, the different initial conditions provide unique orbital motions, which is significantly different in term of orbital motions of both rigid models. Furthermore, this thesis presents a methodology to determine the material dynamic properties of thin membranes and validates the deformation of the multibody model with real MLI materials. Experiments are performed in a high vacuum chamber (10-4 mbar) replicating space environment. A thin membrane is hinged at one end but free at the other. The free motion experiment, the first experiment, is a free vibration test to determine the damping coefficient and natural frequency of the thin membrane. In this test, the membrane is allowed to fall freely in the chamber with the motion tracked and captured through high velocity video frames. A Kalman filter technique is implemented in the tracking algorithm to reduce noise and increase the tracking accuracy of the oscillating motion. The forced motion experiment, the last test, is performed to determine the deformation characteristics of the object. A high power spotlight (500-2000W) is used to illuminate the MLI and the displacements are measured by means of a high resolution laser sensor. Finite Element Analysis (FEA) and multibody dynamics of the experimental setups are used for the validation of the flexible model by comparing with the experimental results of displacements and natural frequencies.

Biomarkers of Nitrosative Stress: Development and validation of a new analytical method for 3-Nitrotyrosine quantification

Background: The nitration of tyrosine residues in proteins is associated with nitrosative stress, resulting in the formation of 3-nitrotyrosine (3-NT). 3-NT levels in biological samples have been associated with numerous physiological and pathological conditions. For this reason, several attempts have been made in order to develop methods that accurately quantify 3-NT in biological samples. Regarding chromatographic methods, they seem to be very accurate, showing very good sensibility and specificity. However, accurate quantification of this molecule, which is present at very low concentrations both at physiological and pathological states, is always a complex task and a target of intense research. Objectives: We aimed to develop a simple, rapid, low-cost and sensitive 3-NT quantification method for use in medical laboratories as an additional tool for diagnosis and/or treatment monitoring of a wide range of pathologies. We also aimed to evaluate the performance of the HPLC-based method developed here in a wide range of biological matrices. Material and methods: All experiments were performed on a Hitachi LaChrom Elite® HPLC system and separation was carried out using a Lichrocart® 250-4 Lichrospher 100 RP-18 (5μm) column. The method was further validated according to ICH guidelines. The biological matrices tested were serum, whole blood, urine, B16 F-10 melanoma cell line, growth medium conditioned with the same cell line, bacterial and yeast suspensions. Results: From all the protocols tested, the best results were obtained using 0.5% CH3COOH:MeOH:H2O (15:15:70) as the mobile phase, with detection at wavelengths 215, 276 and 356 nm, at 25ºC, and using a flow rate of 1 mL/min. By using this protocol, it was possible to obtain a linear calibration curve (correlation coefficient = 1), limits of detection and quantification in the order of ng/mL, and a short analysis time (<15 minutes per sample). Additionally, the developed protocol allowed the successful detection and quantification of 3-NT in all biological matrices tested, with detection at 356 nm. Conclusion: The method described in this study, which was successfully developed and validated for 3-NT quantification, is simple, cheap and fast, rendering it suitable for analysis in a wide range of biological matrices.

Estimation of whole body muscle, adipose/fat mass, validation in health and during weight loss. Development of prediction equations using MRI as reference method

Background: Body composition is affected by diseases, and affects responses to medical treatments, dosage of medicines, etc., while an abnormal body composition contributes to the causation of many chronic diseases. While we have reliable biochemical tests for certain nutritional parameters of body composition, such as iron or iodine status, and we have harnessed nuclear physics to estimate the body’s content of trace elements, the very basic quantification of body fat content and muscle mass remains highly problematic. Both body fat and muscle mass are vitally important, as they have opposing influences on chronic disease, but they have seldom been estimated as part of population health surveillance. Instead, most national surveys have merely reported BMI and waist, or sometimes the waist/hip ratio; these indices are convenient but do not have any specific biological meaning. Anthropometry offers a practical and inexpensive method for muscle and fat estimation in clinical and epidemiological settings; however, its use is imperfect due to many limitations, such as a shortage of reference data, misuse of terminology, unclear assumptions, and the absence of properly validated anthropometric equations. To date, anthropometric methods are not sensitive enough to detect muscle and fat loss. Aims: The aim of this thesis is to estimate Adipose/fat and muscle mass in health disease and during weight loss through; 1. evaluating and critiquing the literature, to identify the best-published prediction equations for adipose/fat and muscle mass estimation; 2. to derive and validate adipose tissue and muscle mass prediction equations; and 3.to evaluate the prediction equations along with anthropometric indices and the best equations retrieved from the literature in health, metabolic illness and during weight loss. Methods: a Systematic review using Cochrane Review method was used for reviewing muscle mass estimation papers that used MRI as the reference method. Fat mass estimation papers were critically reviewed. Mixed ethnic, age and body mass data that underwent whole body magnetic resonance imaging to quantify adipose tissue and muscle mass (dependent variable) and anthropometry (independent variable) were used in the derivation/validation analysis. Multiple regression and Bland-Altman plot were applied to evaluate the prediction equations. To determine how well the equations identify metabolic illness, English and Scottish health surveys were studied. Statistical analysis using multiple regression and binary logistic regression were applied to assess model fit and associations. Also, populations were divided into quintiles and relative risk was analysed. Finally, the prediction equations were evaluated by applying them to a pilot study of 10 subjects who underwent whole-body MRI, anthropometric measurements and muscle strength before and after weight loss to determine how well the equations identify adipose/fat mass and muscle mass change. Results: The estimation of fat mass has serious problems. Despite advances in technology and science, prediction equations for the estimation of fat mass depend on limited historical reference data and remain dependent upon assumptions that have not yet been properly validated for different population groups. Muscle mass does not have the same conceptual problems; however, its measurement is still problematic and reference data are scarce. The derivation and validation analysis in this thesis was satisfactory, compared to prediction equations in the literature they were similar or even better. Applying the prediction equations in metabolic illness and during weight loss presented an understanding on how well the equations identify metabolic illness showing significant associations with diabetes, hypertension, HbA1c and blood pressure. And moderate to high correlations with MRI-measured adipose tissue and muscle mass before and after weight loss. Conclusion: Adipose tissue mass and to an extent muscle mass can now be estimated for many purposes as population or groups means. However, these equations must not be used for assessing fatness and categorising individuals. Further exploration in different populations and health surveys would be valuable.

Comparison of the traditional pharmaceutical validation method versus an assisted pharmaceutical validation in hospitalized patients

Objective: To analyze pharmaceutical interventions that have been carried out with the support of an automated system for validation of treatments vs. the traditional method without computer support. Method: The automated program, ALTOMEDICAMENTOS® version 0, has 925 052 data with information regarding approximately 20 000 medicines, analyzing doses, administration routes, number of days with such a treatment, dosing in renal and liver failure, interactions control, similar drugs, and enteral medicines. During eight days, in four different hospitals (high complexity with over 1 000 beds, 400-bed intermediate, geriatric and monographic), the same patients and treatments were analyzed using both systems. Results: 3,490 patients were analyzed, with 42 155 different treatments. 238 interventions were performed using the traditional system (interventions 0.56% / possible interventions) vs. 580 (1.38%) with the automated one. Very significant pharmaceutical interventions were 0.14% vs. 0.46%; significant was 0.38% vs. 0.90%; non-significant was 0.05% vs. 0.01%, respectively. If both systems are simultaneously used, interventions are performed in 1.85% vs. 0.56% with just the traditional system. Using only the traditional model, 30.5% of the possible interventions are detected, whereas without manual review and only the automated one, 84% of the possible interventions are detected. Conclusions: The automated system increases pharmaceutical interventions between 2.43 to 3.64 times. According to the results of this study the traditional validation system needs to be revised relying on automated systems. The automated program works correctly in different hospitals.

VALIDATION OF A 'DISPLACEMENT TOMOGRAPHY' INVERSION METHOD FOR MODELING SHEET INTRUSIONS

The study of volcano deformation data can provide information on magma processes and help assess the potential for future eruptions. In employing inverse deformation modeling on these data, we attempt to characterize the geometry, location and volume/pressure change of a deformation source. Techniques currently used to model sheet intrusions (e.g., dikes and sills) often require significant a priori assumptions about source geometry and can require testing a large number of parameters. Moreover, surface deformations are a non-linear function of the source geometry and location. This requires the use of Monte Carlo inversion techniques which leads to long computation times. Recently, ‘displacement tomography’ models have been used to characterize magma reservoirs by inverting source deformation data for volume changes using a grid of point sources in the subsurface. The computations involved in these models are less intensive as no assumptions are made on the source geometry and location, and the relationship between the point sources and the surface deformation is linear. In this project, seeking a less computationally intensive technique for fracture sources, we tested if this displacement tomography method for reservoirs could be used for sheet intrusions. We began by simulating the opening of three synthetic dikes of known geometry and location using an established deformation model for fracture sources. We then sought to reproduce the displacements and volume changes undergone by the fractures using the sources employed in the tomography methodology. Results of this validation indicate the volumetric point sources are not appropriate for locating fracture sources, however they may provide useful qualitative information on volume changes occurring in the surrounding rock, and therefore indirectly indicate the source location.

Congenital thoracic vertebral malformations in brachycephalic “screw-tailed” dog breeds: Validation of a human classification scheme and a method of Cobb angle measurement in the assessment of vertebral column deformity

Congenital vertebral malformations are common in brachycephalic “screw-tailed” dog breeds such as French bulldogs, English bulldogs, Boston terriers, and Pugs. Those vertebral malformations disrupt the normal vertebral column anatomy and biomechanics, potentially leading to deformity of the vertebral column and subsequent neurological dysfunction. The initial aim of this work was to study and determine whether the congenital vertebral malformations identified in those breeds could be translated in a radiographic classification scheme used in humans to give an improved classification, with clear and well-defined terminology, with the expectation that this would facilitate future study and clinical management in the veterinary field. Therefore, two observers who were blinded to the neurologic status of the dogs classified each vertebral malformation based on the human classification scheme of McMaster and were able to translate them successfully into a new classification scheme for veterinary use. The following aim was to assess the nature and the impact of vertebral column deformity engendered by those congenital vertebral malformations in the target breeds. As no gold standard exists in veterinary medicine for the calculation of the degree of deformity, it was elected to adapt the human equivalent, termed the Cobb angle, as a potential standard reference tool for use in veterinary practice. For the validation of the Cobb angle measurement method, a computerised semi-automatic technique was used and assessed by multiple independent observers. They observed not only that Kyphosis was the most common vertebral column deformity but also that patients with such deformity were found to be more likely to suffer from neurological deficits, more especially if their Cobb angle was above 35 degrees.

Optimization and validation of an analytical method for determination of glyphosate and AMPA in apples using SPE-HPLC with post-column derivatization.

2008

Determination of paraquat and diquat: LC-MS method optimization and validation.

2016

Validation of a new method for human nerve decellularization: toward a new tool in peripheral nerve reconstructive surgery.

Defects of the peripheral nervous system are extremely frequent in trauma and surgeries and have high socioeconomic costs. In case of peripheral nerve injury, the first approach is primary neurorrhaphy, which is direct nerve repair with epineural microsutures of the two stumps. However, this is not feasible in case of stump retraction or in case of tissue loss (gap > 2 cm), where the main surgical options are autologous grafts, allogenic grafts, or nerve conduits. While the gold standard is the autograft, it has disadvantages related to its harvesting, with an inevitable donor site morbidity and functional deficit. Fresh nerve allografts have therefore become a viable alternative option, but they require immunosuppression, which is often contraindicated. Acellular Nerve Allografts (ANA) represent a valid alternative, they do not need immunosuppression and appear to be safe and effective based on recent studies. The purpose of this study is to propose and develop an innovative method of nerve decellularization (Rizzoli method), conforming to cleanroom requirements in order to perform the direct tissue manipulation step and the nerve decellularization process within five hours, so as to accelerate the detachment of myelin and cellular debris, without detrimental effects on nerve architecture. In this study, the safety and the efficacy of the new method are evaluated in vitro and in vivo by histological, immunohistochemical, and histomorphometric studies in rabbits and humans. The new method is rapid, safe, and cheaper if compared with available commercial ANAs. The present study shows that the method, previously optimized in vitro and in vivo on animal model presented by our group, can be applied on human nerve samples. This work represents the first step in providing a novel, safe, and inexpensive tool for use by European tissue banks to democratize the use of nerve tissue transplantation for nerve injury reconstruction.

A method to determine volatile contaminants in polyethylene terephthalate (PET) packages by HDC-GC-FID and its application to post-consumer materials

A simple and low cost method to determine volatile contaminants in post-consumer recycled PET flakes was developed and validated by Headspace Dynamic Concentration and Gas Chromatography-Flame Ionization Detection (HDC-GC-FID). The analytical parameters evaluated by using surrogates include: correlation coefficient, detection limit, quantification limit, accuracy, intra-assay precision, and inter-assay precision. In order to compare the efficiency of the proposed method to recognized automated techniques, post-consumer PET packaging samples collected in Brazil were used. GC-MS was used to confirm the identity of the substances identified in the PET packaging. Some of the identified contaminants were estimated in the post-consumer material at concentrations higher than 220 ng.g-1. The findings in this work corroborate data available in the scientific literature pointing out the suitability of the proposed analytical method.

Validation of the Deardorff model for estimating energy balance components for a sugarcane crop

The quantification of the available energy in the environment is important because it determines photosynthesis, evapotranspiration and, therefore, the final yield of crops. Instruments for measuring the energy balance are costly and indirect estimation alternatives are desirable. This study assessed the Deardorff's model performance during a cycle of a sugarcane crop in Piracicaba, State of São Paulo, Brazil, in comparison to the aerodynamic method. This mechanistic model simulates the energy fluxes (sensible, latent heat and net radiation) at three levels (atmosphere, canopy and soil) using only air temperature, relative humidity and wind speed measured at a reference level above the canopy, crop leaf area index, and some pre-calibrated parameters (canopy albedo, soil emissivity, atmospheric transmissivity and hydrological characteristics of the soil). The analysis was made for different time scales, insolation conditions and seasons (spring, summer and autumn). Analyzing all data of 15 minute intervals, the model presented good performance for net radiation simulation in different insolations and seasons. The latent heat flux in the atmosphere and the sensible heat flux in the atmosphere did not present differences in comparison to data from the aerodynamic method during the autumn. The sensible heat flux in the soil was poorly simulated by the model due to the poor performance of the soil water balance method. The Deardorff's model improved in general the flux simulations in comparison to the aerodynamic method when more insolation was available in the environment.