The measured level of prion infectivity varies in a predictable way according to the aggregation state of the infectious agent

Transmissible spongiform encephalopathies are believed to be caused by an infectious form of the prion protein, designated PrP(Sc). The concentration of PrP(Sc) is often poorly correlated to the level of infectivity. Infectivity can be measured in two ways, namely endpoint titration and the incubation time assay, but patterns of infectivity vary depending on which method is used. These discrepancies can be explained by variation in the aggregation state of PrP(Sc). Both methods of measuring infectivity are modelled mathematically, and the theoretical results are in agreement with published data. It was found to be theoretically impossible to characterise prion infectivity by a multiple of a single quantity representing 'one prion', no matter how it is measured. Infectivity is instead characterised by both the number and sizes of the PrP(Sc) aggregates. Apparent discrepancies arise when these complexities are reduced to a single number.     

Standardization and validation of a new atomic absorption spectroscopy technique for determination and quantitation of Aluminium adjuvant in immunobiologicals

In the present study, Aluminium quantification in immunobiologicals has been described using atomic absorption spectroscopy (AAS) technique. The assay was found to be linear in 25-125 microg/ml Aluminium range. The procedure was found to be accurate for different vaccines with recoveries of external additions ranging between 93.26 and 103.41%. The mean Limit of Variation (L.V.) for both intra- and inter-assay precision was calculated to be 1.62 and 2.22%, respectively. Further the procedure was found to be robust in relation to digestion temperature, alteration in acid (HNO(3) and H(2)SO(4)) ratio used for sample digestion and storage of digested vaccine samples up to a period of 15 days. After validation, AAS method was compared for its equivalency with routinely used complexometric titration method. On simultaneously applying on seven different groups of both bacterial and viral vaccines, viz., DPT, DT, TT, Hepatitis-A and B, Antirabies vaccine (cell culture) and tetravalent DPT-Hib, a high degree of positive correlation (+0.85-0.998) among AAS and titration methods was observed. Further AAS method was found to have an edge over complexometric titration method that a group of vaccines, viz., ARV (cell culture, adsorbed) and Hepatitis-A, in which Aluminium estimation is not feasible by pharmacopoeial approved complexometric titration method (possibly due to some interference in the sample matrix), this newly described and validated AAS assay procedure delivered accurate and reproducible results.     

Inhibition study of adenosine deaminase by caffeine using spectroscopy and isothermal titration calorimetry

Kinetic and thermodynamic studies were made on the effect of caffeine on the activity of adenosine deaminase in 50 mM sodium phosphate buffer, pH 7.5, using UV spectrophotometry and isothermal titration calorimetry (ITC). An uncompetitive inhibition was observed for caffeine. A graphical fitting method was used for determination of binding constant and enthalpy of inhibitor binding by using isothermal titration microcalorimetry data. The dissociation-binding constant is equal to 350 microM by the microcalorimetry method, which agrees well with the value of 342 microM for the inhibition constant that was obtained from the spectroscopy method. Positive dependence of caffeine binding on temperature indicates a hydrophobic interaction.     

Protein precipitation In Vitro as a measure of chemical-induced cytotoxicity: an EDIT sub-programme

As a priority area of the Evaluation-Guided Development of In Vitro Toxicity and Toxicokinetic Tests (EDIT) programme, an in vitro protein precipitation (PP) assay was used on the 50 reference chemicals of the Multicentre Evaluation of In Vitro Cytotoxicity (MEIC) project, to confirm and extend the MEIC results. Dose-response curves were generated for only 30 of the chemicals, and the concentrations causing 10% (EC10) and 50% (EC50) protein precipitation versus the positive control were chosen as endpoints. The number of chemicals with a positive response increased to 46 when a new endpoint, the minimum effect concentration (MEC) that induces protein precipitation with respect to the negative control, was used. When the results were correlated with in vitro cytotoxicity in human cell lines, a similarly good correlation was found between the various endpoints of the PP assay at 5 hours and the 24-hour IC50 average cytotoxicity in human cell lines, even though the number of chemicals included in the correlation was larger for the MEC. Using the prediction error, the endpoint that gave the best correlation between the PP assay and human cell cytotoxicity was once more found to be the 5-hour MEC, and this was chosen for the PP assay. The sensitivity of the PP assay is lower than that of the in vitro cell-line cytotoxicity assay, possibly due to its shorter exposure period and because precipitation is the ultimate event in the sequence of a protein disturbance. It is expected that earlier denaturation steps would give better sensitivity. However, this simple, inexpensive and rapid assay could be useful in the early stages of testing chemicals.     

Characterization and determination of titratable groups of proteins by linearization of titration curves. II. Application to lysozyme

The potentiometric acid-base titration curve of fully protonated lysozyme at ionic strengths of 0.10 and 1.0 m has been performed. The stoichiometry and the pK_a values of each titratable group have been determined through the linearization of titration curves. Two types of carboxylic groups with pK_a values of 3.76 and 5.02, the imidazole group with pK_a 7.37 and the amine group with pK_a 9.63, have been identified at an ionic strength of 0.10 m at 25.0°C. The number of titratable groups found per mole of protein has been 5.12 and 5.60 for the two types of carboxylic groups, 1.13 for the imidazole group, and 3.19 for the amino groups. The endpoint of the titration of the protein obtained by this method accords quite well with the endpoint obtained by the use of Gran function applied to the excess of strong base.     

Improved two‐stage group sequential procedures for testing a secondary endpoint after the primary endpoint achieves significance

In two‐stage group sequential trials with a primary and a secondary endpoint, the overall type I error rate for the primary endpoint is often controlled by an α‐level boundary, such as an O'Brien‐Fleming or Pocock boundary. Following a hierarchical testing sequence, the secondary endpoint is tested only if the primary endpoint achieves statistical significance either at an interim analysis or at the final analysis. To control the type I error rate for the secondary endpoint, this is tested using a Bonferroni procedure or any α‐level group sequential method. In comparison with marginal testing, there is an overall power loss for the test of the secondary endpoint since a claim of a positive result depends on the significance of the primary endpoint in the hierarchical testing sequence. We propose two group sequential testing procedures with improved secondary power: the improved Bonferroni procedure and the improved Pocock procedure. The proposed procedures use the correlation between the interim and final statistics for the secondary endpoint while applying graphical approaches to transfer the significance level from the primary endpoint to the secondary endpoint. The procedures control the familywise error rate (FWER) strongly by construction and this is confirmed via simulation. We also compare the proposed procedures with other commonly used group sequential procedures in terms of control of the FWER and the power of rejecting the secondary hypothesis. An example is provided to illustrate the procedures.     

Monitoring the microbial contamination of beef carcass tissue with a rapid chromogenic Limulus amoebocyte lysate endpoint assay

A chromogenic Limulus amoebocyte lysate (LAL) endpoint assay was found to be an accurate and rapid means of gauging levels of beef carcass microbial contamination within 10 min. The assay demonstrated a high correlation with the total mesophilic bacterial and coliform surface populations from inoculated beef carcass surface tissues. This assay was tested on a set of actual beef carcass surface samples (n = 121) demonstrating the utility of the chromogenic LAL test as a means of monitoring carcass microbial contamination in a near real-time fashion. Classifying the chromogenic LAL results into four contamination groups was found to be a sound means of utilizing the resultant chromogenic LAL data for detecting carcasses with high levels of microbial contamination. For beef carcass testing, this assay can be used with no instrumentation other than the required 37 degrees C incubator and, as an option, a microplate reader.     

A radiochemical enzymatic endpoint assay for GTP and GDP

We present here a radiochemical enzymatic endpoint assay for the guanine nucleotides GTP and GDP that is suitable for use with cell extracts. The major coupling enzyme used is phosphoenolpyruvate carboxykinase purified from chicken liver. The ancillary coupling enzyme, aspartate aminotransferase, was used to generate a low steady-state concentration of oxalacetate. GTP was determined by the overall conversion of [U-14C]aspartate into [14C]phosphoenolpyruvate. This reaction was also scaled-up as a preparative method for [U-14C]phosphoenolpyruvate. This was used with the same coupling enzymes in reverse to measure GDP by the formation of [14C]aspartate. The assay method was applied to isolated rat hepatocytes. The total GTP and GDP concentrations found were within the range reported by others for rat liver. The advantages of this assay are its sensitivity, specificity, and applicability to large numbers of samples.     

In vitro cytotoxicity assays. Potential alternatives to the Draize ocular allergy test

A short-term cytotoxicity assay carried out in multiwell test plates and a supplementary colony forming assay are both useful for screening and range finding of toxic concentrations of test agents. The highest tolerated dose (HTD), a concentration at which only minimal morphological changes were observed, was designated as endpoint in the assay. Epithelial rabbit cornea cells, murine fibroblasts, Chinese hamster lung cells, human hepatoma cells and mouse macrophage cultures were used as targets. Several of the alcohols tested at HTD in the colony forming assay were found to inhibit colony formation. An ID50 of colony formation was used as a quantitative corroborating test. The ranking of 34 toxicants was found to be virtually the same with all cell types examined. This easily reproducible, rapid in vitro test is cost-effective and can be used for preliminary large scale screening of potential toxicants.Abbreviations HTD highest tolerated dose - EGF epidermal growth factor - FITC fluorescein conjugated anti-guinea pig IgG - DMEM Dulbecco's modified Eagle's medium - FBS fetal bovine serum Supported in part by Revlon, Inc.     

Estimation of binding parameters of enzyme-ligand complex from fluorometric data by a curve fitting procedure: seryl-tRNA synthetase-tRNA Ser complex

A curve fitting procedure for the determination of the association constant, number of binding sites, and theoretical titration end point of an enzyme-ligand interaction monitored by fluorescence quenching titration is described and compared with classical graphical evaluation processes.     

BayBoots: a model-free Bayesian tool to identify class markers from gene expression data

One of the goals of gene expression experiments is the identification of differentially expressed genes among populations that could be used as markers. For this purpose, we implemented a model-free Bayesian approach in a user-friendly and freely available web-based tool called BayBoots. In spite of a common misunderstanding that Bayesian and model-free approaches are incompatible, we merged them in the BayBoots implementation using the Kernel density estimator and Rubin 's Bayesian Bootstrap. We used the Bayes error rate (BER) instead of the usual P values as an alternative statistical index to rank a class marker's discriminative potential, since it can be visualized by a simple graphical representation and has an intuitive interpretation. Subsequently, Bayesian Bootstrap was used to assess BER 's credibility. We tested BayBoots on microarray data to look for markers for Trypanosoma cruzi strains isolated from cardiac and asymptomatic patients. We found that the three most frequently used methods in microarray analysis: t-test, non-parametric Wilcoxon test and correlation methods, yielded several markers that were discarded by a time-consuming visual check. On the other hand, the BayBoots graphical output and ranking was able to automatically identify markers for which classification performance was consistent. BayBoots is available at: http://www.vision.ime.usp.br/~rvencio/BayBoots.     

Accurate measurement of avidin and streptavidin in crude biofluids with a new, optimized biotin-fluorescein conjugate

A new biotin-fluorescein conjugate with an ethylene diamine spacer was found to be the first fluorescent biotin derivative which truly mimicked d-biotin in terms of high affinity, fast association, and non-cooperative binding to avidin and streptavidin tetramers. These exceptional properties were attributed to the small size/length of the new ligand since all larger/longer biotin derivatives are known for their mutual steric hindrance and anti-cooperative binding in 4:1 complexes with avidin and streptavidin tetramers. Specific binding of the new biotin-fluorescein conjugate towards avidin and streptavidin was accompanied by 84-88% quenching of ligand fluorescence. In the accompanying study this effect was used for rapid estimation of avidin and streptavidin in a new 'single tube assay'. In the present study the strong quenching effect was utilized to accurately monitor stoichiometric titration of biotin-binding sites in samples with >/=200 pM avidin or streptavidin. The concentration was calculated from the consumption of fluorescent ligand up to the distinct breakpoint in the fluorescence titration profile which was marked by the abrupt appearance of strongly fluorescent ligands which were in excess. Due to this protocol the assay was not perturbed by background fluorescence or coloration in the unknown samples. The new fluorescence titration assay is particularly suited for quick checks on short notice because getting started only means to thaw an aliquot of a standardized stock solution of fluorescent ligand. No calibration is required for the individual assay and the ligand stock solution needs to be restandardized once per week (or once per year) when stored at -25 degrees C (or at -70 degrees C, respectively).     

用蚀斑法进行麻疹疫苗的病毒滴定

按世界银行中国疫苗项目对麻疹疫苗检定的要求,建立了麻疹疫苗病毒滴定的蚀斑方法。以蚀斑法对Ｈｕ１９１株生产的冻干麻疹活疫苗样品进行了测定。结果发现,Ｈｕ１９１株生产的麻疹疫苗在琼脂和甲基纤维素覆盖下所形成的蚀斑大小及形状不同,但滴度无显著性差异;在室温和３７℃吸附的滴度无显著性差异,但细胞在３７℃生长较好;在本实验条件下,蚀斑滴定和ＣＣＩＤ５０测定的滴度呈正相关,蚀斑滴定相对较敏感;采用国产６孔聚苯乙稀培养板,Ｖｅｒｏ细胞单层,在３７℃吸附,用甲基纤维素覆盖,经结晶紫及甲醛固定染色后计数空斑,操作简便易行,结果特异敏感,重复性好,可用于麻疹疫苗病毒滴定     

直接免疫荧光法检测狂犬病毒滴度的可行性研究

实验研究中建立用于定量检测狂犬病毒滴度的直接免疫荧光法,并将检测结果与传统小鼠脑内滴定法进行了比较,对照两种试验方法的灵敏度、特异性和重复性。结果显示,两种检测方法特异性基本一致;相同样品经多次检测的病毒滴度相近,重复性好、灵敏度高。直接免疫荧光法具有特异、灵敏、快速、操作简单、无需使用动物等优点,可应用于狂犬病毒滴度的定量检测。     

Microbial Interaction Network Estimation via Bias-Corrected Graphical Lasso

With the increasing availability of microbiome 16S data, network estimation has become a useful approach to studying the interactions between microbial taxa. Network estimation on a set of variables is frequently explored using graphical models, in which the relationship between two variables is modeled via their conditional dependency given the other variables. Various methods for sparse inverse covariance estimation have been proposed to estimate graphical models in the high-dimensional setting, including graphical lasso. However, current methods do not address the compositional count nature of microbiome data, where abundances of microbial taxa are not directly measured, but are reflected by the observed counts in an error-prone manner. Adding to the challenge is that the sum of the counts within each sample, termed “sequencing depth,” is an experimental technicality that carries no biological information but can vary drastically across samples. To address these issues, we develop a new approach to network estimation, called BC-GLASSO (bias-corrected graphical lasso), which models the microbiome data using a logistic normal multinomial distribution with the sequencing depths explicitly incorporated, corrects the bias of the naive empirical covariance estimator arising from the heterogeneity in sequencing depths, and builds the inverse covariance estimator via graphical lasso. We demonstrate the advantage of BC-GLASSO over current approaches to microbial interaction network estimation under a variety of simulation scenarios. We also illustrate the efficacy of our method in an application to a human microbiome data set.

     

Application of theoretical considerations to the analysis of ELISA data

Solid-phase immunoassays such as the ELISA are in routine use in many areas of biological research. Data from these assays are analyzed in a variety of ways, frequently without taking into account the immunochemical principles of the assay. The Reference Standard Method is often used and is suitable and convenient for obtaining concentration (or activity) values from the antigen-specific ELISA or spRIA, sandwich assays, and inhibition assays. The standard curve required for this method may be obtained by simple linear regression analysis of logarithmic or logitlogarithmic transformed data obtained from titration of the reference standard. The shape of the logarithmic plot of the reference standard provides information on the performance of the assay. Examining data from multiple dilutions of the samples is essential to assure that each titrates with the same slope as does the reference standard; the analysis routine must permit this comparison to be made. ELISANALYSIS is a program for the IBM PC which was developed to perform such analyses. It is presented here as a model, with sufficient information provided for the development of similar analytical routines by interested users. This approach to ELISA data analysis is presented as an alternative to complicated empirical curve-fitting systems and simple endpoint methods, which can be immunochemically misleading or, in some cases, even invalid. The consistent use of the described routines would encourage greater uniformity in the means of data interpretation and thereby enhance our understanding of immunobiology.     

Frequentist model averaging for undirected Gaussian graphical models

Advances in information technologies have made network data increasingly frequent in a spectrum of big data applications, which is often explored by probabilistic graphical models. To precisely estimate the precision matrix, we propose an optimal model averaging estimator for Gaussian graphs. We prove that the proposed estimator is asymptotically optimal when candidate models are misspecified. The consistency and the asymptotic distribution of model averaging estimator, and the weight convergence are also studied when at least one correct model is included in the candidate set. Furthermore, numerical simulations and a real data analysis on yeast genetic data are conducted to illustrate that the proposed method is promising.     

Product Inhibition Study on Carbonic Anhydrase Using Spectroscopy and Calorimetry

Kinetic and thermodynamic studies have been made on the effect of the p -nitrophenol product on the activity of bovine carbonic anhydrase in 50 mM Tris buffer pH 7.5, at 300 K using UV spectrophotometry and isothermal titration calorimetry (ITC). A competitive inhibition was observed for p -nitrophenol as a product of the enzymatic reaction. A graphical fitting method was used for determination of the binding constant and enthalpy of inhibitor binding using ITC data. The dissociation binding constant was 0.10 mM by the microcalorimetric method, which is in good agreement with the value of 0.11 mM for the inhibition constant obtained from the spectrophotometric method.