Design and analysis of accelerated degradation tests for the stability of biological standards II. A flexible computer program for data analysis

The accelerated degradation test is commonly used to predict the stability of a biological standard during long-term storage at low temperature. A flexible computer program is described which has been written to analyse degradation test results by the method of maximum likelihood. In addition to predicting the degradation rate at low temperature, the program furnishes estimates of statistical precision and it carried out a test of goodness of fit of the data to the assumed Arrhenius equation model.     

Design and analysis of accelerated degradation tests for the stability of biological standards III. Principles of design

The principles of designing an accelerated degradation test for a biological standard are considered, with special emphasis on ensuring accuracy and precision of the predicted low temperature degradation rate. A three-stage design is proposed which initially monitors samples at the highest of the elevated temperatures, but which switches attention progressively to the lower temperatures as degradation begins to be detected. The advantages of this design over one where testing is carried out after a predetermined period are that it is (i) more efficient, (ii) more reliable and (iii) better suited to test the assumptions which underly the analysis of the results. Consideration is also given to additional checks which can be made on the stability of biological standards and to methods of monitoring long-term stability after the standard has been set up.     

The thermal stability of yellow fever vaccines

The assessment of yellow fever vaccine thermostability both in lyophilized form and after reconstitution were analyzed. Two commercial yellow fever vaccines were assayed for their thermal stability. Vaccines were exposed to test temperatures in the range of 8 degrees C to 45 degrees C. Residual infectivity was measured by a plaque assay using Vero cells. The titre values were used in an accelerated degradation test that follows the Arrhenius equation and the minimum immunizing dose was assumed to be 10(3) particles forming unit (pfu)/dose. Some of the most relevant results include that (i) regular culture medium show the same degradation pattern of a reconstituted 17D-204 vaccine; (ii) reconstituted YF-17D-204 showed a predictable half life of more than six days if kept at 0 degrees C; (iii) there are differences in thermostability between different products that are probably due to both presence of stabilizers in the preparation and the modernization in the vaccine production; (iv) it is important to establish a proper correlation between the mouse infectivity test and the plaque assay since the last appears to be more simple, economical, and practical for small laboratories to assess the potency of the vaccine, and (v) the accelerated degradation test appears to be the best procedure to quantify the thermostability of biological products.     

New analysis of the phylogenetic change of collagen thermostability

Recent data concerning the thermostability and the primary structure of type IV collagens, some invertebrate collagens, and for the stability of synthetic collagen-like polypeptides, show that our earlier analysis of the phylogenetic change of thermostability has some shortcomings. The results of the analysis were corrected and it has been shown that the dependence of denaturation temperature Td on 4-hydroxyproline content is hyperbolic and the total Gly-Pro-Hyp sequence content is a main, but not exclusive, factor influencing the change of collagen thermostability. It appears possible that the same mechanism underlies the thermostability of fibril-forming collagens of all animal life, ranging from Antarctic ice fish to at least one annelid (Alvinella pompejana) living at very high temperatures at the bottom of the ocean near thermal vents.     

Additives to biological substances. V--The stability of lactose as a carrier for Biological Standards

The stability of freeze-dried lactose has been studied, by accelerated degradation, after being ampouled under the conditions employed for the preparation of International Standards and Reference Preparations and also under less stringent conditions which might facilitate degradation. The possible formation of the reactive product, 5-hydroxymethyl-furfural, has been monitored over a period of 10 years at temperatures up to 56 degrees C. No evidence has been obtained to suggest that the formation of this compound would present a hazard to the stability of standards prepared by the procedures customarily employed.     

聚乙二醇对PEG化重组人促红细胞生成素热稳定性和生物学活性的影响

为了研究聚乙二醇对PEG化rhEPO热稳定性和生物学活性的影响,用酶学方法切除rhEPO和PEGrhEPO分子中的N连接糖基,研究酶切产物在37℃时287nm和350nm吸光度随时间的变化;用MTT比色法,网织红细胞法和HCT法比较体内和体外生物学活性的改变。结果显示聚乙二醇修饰能显著减少无N连接糖基的rhEPO分子间的聚集,降低rhEPO体外生物学活性,但增高体内生物学活性;无N连接糖基的PEG化rhEPO具有与rhEPO相当的体内生物学活性。因此聚乙二醇能提高rhEPO热稳定性;聚乙二醇可替代糖基,维持rhEPO的体内生物学活性。用PEG修饰原核细胞表达的rhEPO是开发rhEPO制品的新思路。     

Enhancing effect of calcium and vanadium ions on thermal stability of bromoperoxidase from Corallina pilulifera

Bromoperoxidase from the macro-alga Corallina pilulifera is an enzyme that possesses vanadate in the catalytic center, and shows a significant thermostability and stability toward organic solvents. The structural analysis of the recombinant enzyme overexpressed in yeast revealed that it contains one calcium atom per subunit. This has been confirmed by inductively coupled plasma emission spectrometry experiments. The study of the effect of metal ions on the apo-enzyme stability has shown that the calcium ion significantly increased the enzyme stability. In addition, vanadate also increased the thermostability and strontium and magnesium ions had similar effects as calcium. The holo-enzyme shows high stability in a range of organic solvents. The effect of the different ions and solvents on the structure of the enzyme has been studied by circular dichroism experiments. The high stability of the enzyme in the presence of organic solvents is useful for its application as a biocatalyst.     

High-throughput screening for enhanced protein stability

High thermostability of proteins is a prerequisite for their implementation in biocatalytic processes and in the evolution of new functions. Various protein engineering methods have been applied to the evolution of increased thermostability, including the use of combinatorial design where a diverse library of proteins is generated and screened for variants with increased stability. Current trends are toward the use of data-driven methods that reduce the library size by using available data to choose areas of the protein to target, without specifying the precise changes. For example, the half-lives of subtilisin and a Bacillus subtilis lipase were increased 1500-fold and 300-fold, respectively, using a crystal structure to guide mutagenesis choices. Sequence homology based methods have also produced libraries where 50% of the variants have improved thermostability. Moreover, advances in the high-throughput measurement of denaturation curves and the application of selection methods to thermostability evolution have enabled the screening of larger libraries. The combination of these methods will lead to the rapid improvement of protein stability for biotechnological purposes.     

High throughput metabolic stability screen for lead optimization in drug discovery

A high throughput approach for the determination of in vitro metabolic stability and metabolic profiles of drug candidates has been developed. This approach comprises the combination of a Biomek FX liquid handling system with 96-channel pipetting capability and a custom-designed 96-well format on-line incubator with efficient thermal conductivity. This combination facilitates automated reagent preparation, sample incubation, and sample purification for microsome stability studies. The overall process is both fast and accurate and meets the challenges of high throughput screening for drug discovery. A custom designed, user-friendly computer program has been incorporated for large-scale data processing and report generation. Several applications are discussed that implement this strategy for rapid selection of compounds in early drug discovery.     

The decomposition of the EPR spectra of multicomponent systems irradiated at 77 K into paramagnetic center signals of different natures]

Main principles of the way to decompose an EPR spectrum of a multicomponent system, irradiated at 77 K, into separate radiation-induced paramagnetic centre signals are given. The decomposition is possible due to the computer assistant spectra processing, and is based on different properties of different paramagnetic centres, namely, on different thermostability of the centres, on different rate of relaxation, and on different photosensitivity. Concrete examples of the EPR spectrum decomposition into different free radical signals are given for cases of murine liver and spleen irradiated at 77 K. Radiochemical yields of different free radicals, induced by gamma radiation at 77 K in whole biological tissues, were defined. The data on nature and properties of the paramagnetic centres induced by radiation in biological tissues are shortly reviewed.     

Resources, standards and tools for systems biology.

Modelling and simulation techniques are valuable tools for the understanding of complex biological systems. The design of a computer model necessarily has many diverse inputs, such as information on the model topology, reaction kinetics and experimental data, derived either from the literature, databases or direct experimental investigation. In this review, we describe different data resources, standards and modelling and simulation tools that are relevant to integrative systems biology.     

用于质量性状通径分析微机程序设计及其应用

基于质量性状通径分析模型,我们在IBM PC/XT微型计算机上,用BASIC语言设计了通径分析程序PATH。并用该程序分析了315个原因不明精神发育迟滞(MR)的核心家系。分析结果表明,轻度、中度和重度MR的遗传度分别为0.79、0.88和0.90。仅在轻度MR中发现有教养传递作用。该程序可用于教养和生物遗传分析。     

NEW: an interactive data management system for monitoring ambulatory patients

Biobehavioral monitoring is a method of gathering daily biological and behavioral measurements from ambulatory patients so that hospital-based care can be extended to the home. Such data can also serve many other purposes such as peer review and assesing the outcome of treatment. To assist in handling the increased information about patients, NEW, a system of three interactive APL Plus computer program packages, has been developed. The program packages, NEWDATA, EVALUATION, and WARNINGS, form an interactive data management system to provide: a rapid means of entering and verifying each patient's data from either a single day or a group of days; a flexible and simple means of retrieving and analyzing the data for an individual patient or for groups of patients; and a means of reviewing, detecting, and signaling trends in the data that deviate from present clinical criteria.     

A rigid network of long-range contacts increases thermostability in a mutant endoglucanase

Thermodynamic stability of a protein at elevated temperatures is a key factor for thermostable enzymes to catalyze their specific reactions. Yet our understanding of biological determinants of thermostability is far from complete. Many different atomistic factors have been suggested as possible means for such proteins to preserve their activity at high temperatures. Among these factors are specific local interatomic interactions or enrichment of specific amino acid types. The case of glycosyl hydrolase family endoglucanase of Trichoderma reesei defies current hypotheses for thermostability because a single mutation far from the active site (A35?V) converts this mesostable protein into a thermostable protein without significant change in the protein structure. This substantial change in enzymatic activity cannot be explained on the basis of local intramolecular interactions alone. Here we present a more global view of the induced thermostability and show that the A35?V mutation affects the underlying structural rigidity of the whole protein via a number of long-range, non-local interactions. Our analysis of this structure reveals a precisely tuned, rigid network of atomic interactions. This cooperative, allosteric effect promotes the transformation of this mesostable protein into a thermostable one.     

A rigid network of long-range contacts increases thermostability in a mutant endoglucanase

Thermodynamic stability of a protein at elevated temperatures is a key factor for thermostable enzymes to catalyze their specific reactions. Yet our understanding of biological determinants of thermostability is far from complete. Many different atomistic factors have been suggested as possible means for such proteins to preserve their activity at high temperatures. Among these factors are specific local interatomic interactions or enrichment of specific amino acid types. The case of glycosyl hydrolase family endoglucanase of Trichoderma reesei defies current hypotheses for thermostability because a single mutation far from the active site (A35?V) converts this mesostable protein into a thermostable protein without significant change in the protein structure. This substantial change in enzymatic activity cannot be explained on the basis of local intramolecular interactions alone. Here we present a more global view of the induced thermostability and show that the A35?V mutation affects the underlying structural rigidity of the whole protein via a number of long-range, non-local interactions. Our analysis of this structure reveals a precisely tuned, rigid network of atomic interactions. This cooperative, allosteric effect promotes the transformation of this mesostable protein into a thermostable one.     

Differences in the thermostabilities of barley (1----3,1----4)-beta-glucanases are only partly determined by N-glycosylation.

Barley (1----3,1----4)-beta-glucan 4-glucanohydrolase (EC 3.2.1.73) isoenzyme EII carries 4% by weight carbohydrate and is more stable at elevated temperatures than isoenzyme EI, which has no associated carbohydrate. The relationship between carbohydrate content and thermostability has been investigated by treatment of the two isoenzymes with N-glycopeptidase F (EC 3.5.1.52). Removal of carbohydrate from isoenzyme EII results in a decrease in the enzyme's thermostability, but treatment of isoenzyme EI with the N-glycopeptidase F has no effect. In addition, removal of a single N-glycosylation site in isoenzyme EII (Asn190-Ala-Ser) by site-directed mutagenesis of the corresponding cDNA led to a reduction in thermostability, while the introduction of this site into isoenzyme EI enhanced stability. We conclude that N-glycosylation of Asn190 enhances the stability of isoenzyme EII at elevated temperatures, but that other factors related to their primary structures also contribute to the differences in thermostabilities of the barley (1----3,1----4)-beta-glucanases.     

Effects of a novel disulfide bond and engineered electrostatic interactions on the thermostability of azurin

Identification and evaluation of factors important for thermostability in proteins is a growing research field with many industrial applications. This study investigates the effects of introducing a novel disulfide bond and engineered electrostatic interactions with respect to the thermostability of holo azurin from Pseudomonas aeruginosa. Four mutants were selected on the basis of rational design and novel temperature-dependent atomic displacement factors from crystal data collected at elevated temperatures. The atomic displacement parameters describe the molecular movement at higher temperatures. The thermostability was evaluated by optical spectroscopy as well as by differential scanning calorimetry. Although azurin has a high inherent stability, the introduction of a novel disulfide bond connecting a flexible loop with small alpha-helix (D62C/K74C copper-containing mutant), increased the T(m) by 3.7 degrees C compared with the holo protein. Furthermore, three mutants were designed to introduce electrostatic interactions, K24R, D23E/K128R, and D23E/K128R/K24R. Mutant K24R stabilizes loops between two separate beta-strands and D23E/K128R was selected to stabilize the C-terminus of azurin. Furthermore, D23E/K128R/K24R was selected to reflect the combination of the electrostatic interactions in D23E/K128R and K24R. The mutants involving electrostatic interactions had a minor effect on the thermostability. The crystal structures of the copper-containing mutants D62C/K74C and K24R have been determined to 1.5 and 1.8 A resolution. In addition the crystal structure of the zinc-loaded mutant D62C/K74C has also been completed to 1.8 A resolution. These structures support the selected design and provide valuable information for evaluating effects of the modifications on the thermostability of holo azurin.     

A comparison of vials with ampoules for the storage of biological reference materials.

Lyophilization is a key strategy in the stabilization of biological materials. Protection of the lyophilized material from an oxidizing atmosphere is essential if stability is to be maintained under long term storage. Vials of lyophilized albumin closed by two methods and ampoules of albumin have been examined for moisture and oxygen ingress after storage both under conditions of stress for two months and under thermally accelerated conditions for one year. The results show that the gas and moisture contents of ampoules do not detectably change even under conditions of stress, in contrast to vials for which this study shows clearly detectable moisture ingress and suggests some oxygen ingress. This is consistent with the results of other studies. Thus, although vials may be satisfactory under constrained conditions of temperature and storage for limited periods of time, and are presently used satisfactorily for some working standards, it would be prudent to continue to use ampoules for storage of international reference materials which are intended for indefinite storage and for which stability is an essential requirement.     

A versatile digital computer program for non-linear regression analysis

1.

1. A general purpose digital computer program is described for application to biological experiments that require a non-linear regression analysis. The mathematical function, or model, to be fitted to a given set of experimental data is written as a section within the program. Given initial estimates for the parameters of the function, the program uses an iterative procedure to adjust the parameters until the sum of squares of residuals has converged to a minimum.