Protein folding as a nonlinear nonequilibrium thermodynamic process

Biofurcational theory of protein folding is developed describing the process of formation of protein native structure as a sequence of non-equilibrium irreversible fluctuations, specific for a particular protein. The model gives explanation to all characteristic features of the folding process: stochastic mechanism, short time and precision of proteins self-assembling. A constructive role of entropy in the formation of a highly ordered structure out of disorder is discussed. A numerical method of a priori calculations of polypeptide structures basing on principles of bifractional folding model is presented.     

An Insight to Chiral Monolith for Enantioselective Nano and Micro HPLC: Preparation and Applications

This review gives an overview of chiral separation principles and their application in enantioselective nano/micro high performance liquid chromatography (n/μ‐HPLC) using chiral monolith. In particular, developments in silica and polymer chiral monolithic stationary phases are presented. The preparation and applications of chiral monoliths, the basic chiral separation principles and the mechanisms are discussed. Chirality 25:314–323, 2013. © 2013 Wiley Periodicals, Inc.     

Optimal systems: I. The vascular system

An approach to quantitative work on optimal systems is considered. Desired optimal principles are utilized in constructing a hypothetical system similar to the organ system considered. A comparison of this constructed system with the anatomical system then gives an indication of the importance of the optimal principles in the form or function of the organ system considered. These ideas are applied to the mammalian vascular system, and limiting values are obtained for some of its important component parts. The constructed system gives good agreement with anatomical data for vessel radii, lengths, and hydrodynamic resistance to flow.     

Electrophysiologic principles of radiofrequency lesion making.

Understanding of the electrophysiologic principles of radiofrequency lesion making is necessary to ensure reliable results in surgical procedures using this technique. A radiofrequency lesion is produced by tissue electrocoagulation. Its method of formation and factors affecting heat generation and loss are discussed. Guidelines for making radiofrequency lesions, based on electrophysiologic principles are outlined.     

A method for the preparation of high molecular weight yeast DNA

A method is described for the isolation of high molecular weight DNA in solution using the principles that have allowed electrophoresis of chromosome-sized DNA in pulse field gradient electrophoresis. Stationary phase yeast cells are converted to spheroplasts by the action of zymolyase in 1 M sorbitol. In the presence of EDTA and sodium lauroyl sarcosinate, proteins are digested with proteinase K. DNA is extracted with phenol and chloroform, and high molecular weight DNA is collected by ethanol precipitation. RNA is removed by RNase digestion of the redissolved pellet, and RNase is removed by chloroform extraction followed by a second ethanol precipitation. The method is rapid and gives a high yield of DNA that is readily digestible by restriction endonucleases.     

Application of ecological engineering principles in agriculture

To what extent modern industrialized agriculture violates the principles of ecological engineering and which changes agriculture needs to make to be consistent with these principles are discussed. The 12 ecological principles presented are used as the starting point for this discussion. For each principle it is discussed how the agriculture of today violates these principles and how relatively small changes could make the agriculture more according to ecological engineering concepts.     

Thresholds of toxic action of chemical compounds and their statistical assessment

The role of statistical methods in the estimation of the toxic effect thresholds upon the ecosystem of chemicals are discussed. The corresponding computational procedures and basic principles are characterized. A simplified statistical method of threshold calculation using the linear regression analysis is given.     

The problem of the stability of globular proteins

Summary The article gives a survey on protein stability. Starting out from approaches for stability measurement which are based on the determination of Gibbs energy change in protein unfolding by denaturants, protonation, heat, scanning calorimetry, and hydrogen exchange, their implications such as reversibility, completeness of unfolding and the two-state assumption are dealt with.A data compilation of Gibbs energy change in unfolding of different proteins is given. The data, which for the most part range between 25 and 60 kJ mol^–1, are discussed in terms of protein functioning, turnover, and structural properties. Phase diagrams are proposed in order to realize a more comprehensive thermodynamic treatment of proteins.Factors which contribute to protein stability are summarized. The paper includes the thermodynamic principles of protein stability as well as special studies on proteolytic fragments, amino acid replacements, cross links, prosthetic groups, and ions which contribute to protein stability.     

Letter: Recognition of structural domains in globular proteins

The polypeptide chain of many globular proteins is folded into two or more structural domains which are spatially separated from one another and are frequently based on different architectural principles. The conformation of such structural domains is, in general, conserved more faithfully (assuming divergent evolution) than the amino acid sequence. The preservation of structure may originate in the three-dimensional requirements for the conservation of essential functions. A method is discussed for the recognition and comparison of structural domains.     

On a method of estimating the genetic correlation between characters measured in different experimental units

Summary Yamada's method of estimating genetic co-variances between traits measured in different experimental units is discussed. It is shown that if the data are unbalanced, this method gives biased estimates of genetic covariances unless the traits have identical genetic and residual variances. An alternative unbiased procedure is suggested.     

In situ hybridization in human genome mapping

The methodological possibilities of non-radioactive in situ hybridization of nucleic acids and its application for an immediate localization of genes and chromosomes are discussed. The advantages of a non-isotope probe labeling versus a use of radioactive substances are emphasized. Various types of compounds used as a label are distinguished. The principles of use of the above labels and the ways to improve the method in terms of increasing its sensitivity are considered. Some results obtained while using non-radioactive labelled probes are reported. It is shown promising to use this method for molecular-genetic analysis of DNA polymorphism in human genome.     

A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes

The reconstruction of ancestral genome architectures and gene orders from homologies between extant species is a long-standing problem, considered by both cytogeneticists and bioinformaticians. A comparison of the two approaches was recently investigated and discussed in a series of papers, sometimes with diverging points of view regarding the performance of these two approaches. We describe a general methodological framework for reconstructing ancestral genome segments from conserved syntenies in extant genomes. We show that this problem, from a computational point of view, is naturally related to physical mapping of chromosomes and benefits from using combinatorial tools developed in this scope. We develop this framework into a new reconstruction method considering conserved gene clusters with similar gene content, mimicking principles used in most cytogenetic studies, although on a different kind of data. We implement and apply it to datasets of mammalian genomes. We perform intensive theoretical and experimental comparisons with other bioinformatics methods for ancestral genome segments reconstruction. We show that the method that we propose is stable and reliable: it gives convergent results using several kinds of data at different levels of resolution, and all predicted ancestral regions are well supported. The results come eventually very close to cytogenetics studies. It suggests that the comparison of methods for ancestral genome reconstruction should include the algorithmic aspects of the methods as well as the disciplinary differences in data aquisition.     

基因捕获技术及其最新进展

基因捕获技术是目前最具应用前景的基因克隆方法之一。利用该技术建立的随机插入突变的突变体文库,可用于寻找、鉴定和研究大量末知功能和已知功能的活化基因,它是继自然突变、物理突变和化学突变之后发展起来的新的分子生物学方法。基因捕获载体是带有报告基因和/或选择标记基因的不完整的基因表达载体;这些载体所带的基因只有在整合到宿主功能基因内部且与融合的宿主基因编码框一致时才能得以表达。经典的基因捕获载体有：增强子捕获载体、基因捕获载体和启动子捕获载体。增强子载体只有一个最小化的启动子控制下游报告基因的表达活性。只有当启动子上游存在一个增强子时才能启动其下游基因的转录：而单独依靠这个启动了则不能转录。狭义的基因捕获载体是指插入到结构基因内部从而捕获该基因的载体,分为内含子捕获载体和外显了捕获载体。前者插入内含子,因此需要在无启动子的报告基因前面添加一个splice acceptor（SA）位点：后者插入外显子,因此不需SA位点就能产生融合蛋白mRNA。启动子捕获载体由一个无启动子的报告基因和选择标记基因组成,只有在捕状载体捕入到内源基因的外显子中,且两阅读框一致的时候才会有报告基因和被捕获的内源基因上游编码区的融合蛋白的表达。利用某些遗传元件的遗传特性也可以构建非常有用的捕获载体。常用的有：逆转录病毒介导的捕抉载体和转座子介导的捕荻载体等等。该文较为全面地概括了转座子介导的捕获载体的用途和研究现状。比如：在拟南芥中应用Ac／Ds转座子元件,存果蝇中应用P-element和piggyBac转座元件,在斑马鱼中应用T012转座了元件,在脊椎动物研究中应用Tc1/meriner转座了超家族,以及存哺乳动物和小鼠ES细胞中应用piggyBac转座子元件。还列举了设计新颖的载体优化策略,比如：发展新的选择标记基因,利用内源核糖体识别／结合位点（IRES）,去掉起始密码子和加一小段接头（1inker）等方法。最后介绍了几种针特定实验目的而设计的捕获载体。附录部分还列出了关于基因捕获技术的网络资源。     

BIOASSAY SYSTEMS FOR THE PYRETHRINS: V. EXPERIMENTS WITH A RESISTANT STRAIN OF CALANDRA GRANARIA L.

Some principles of testing for resistance in wild and laboratory stocks of insects are discussed, and experiments with Calandra granaria L. are described in which these insects are selected for pyrethrum resistance.
A new method is described of expressing relative tolerances when the relevant regression lines are not parallel, based on the 'generalized distance' of Mahalanobis. The method may equally be used for the comparison of two insecticides giving rise to lines of different slope. A limited increase in resistance occurred on selection. Non-random oscillatory sequences of slopes were observed when the resistant strain was assayed, and regression parameters computed. The nature of these oscillations is considered.     

Binding of ligands to a one-dimensional heterogeneous lattice. I. General model for the calculation of binding isotherms by a Monte Carlo approach

A Monte Carlo method is presented to calculate equilibria for the binding of ligands to one-dimensional heteropolymers. Equivalency with other methods suitable for particular cases was verified (i.e., matrix and combinatorial methods). The principal interest of this Monte Carlo method is in its facility for adaptation to any physically conceivable binding model and that it gives access to the parameters accounting for partial binding to each different type of site. General properties of binding isotherms with excluded-site effects and relations between partial binding ratios and partial free site ratios are discussed. An effective calculation is presented for illustration of the method.     

Feedback dynamics and cell function: Why systems biology is called Systems Biology

A new paradigm, like Systems Biology, should challenge the way research has been conducted previously. This Opinion article aims to present Systems Biology, not as the application of engineering principles to biology but as a merger of systems- and control theory with molecular- and cell biology. In our view, the central dogma of Systems Biology is that it is system dynamics that gives rise to the functioning and function of cells. The concepts of feedback regulation and control of pathways and the coordination of cell function are emphasized as an important area of Systems Biology research. The hurdles and risks for this area are discussed from the perspective of dynamic pathway modelling. Most of all, the aim of this article is to promote mathematical modelling and simulation as a part of molecular- and cell biology. Systems Biology is a success if it is widely accepted that there is nothing more practical than a good theory.     

表面质膜共振技术——一种检测蛋白质特异结合反应的方法

表面质膜共振 (SPR)技术是一种监测生物大分子之间特异结合反应的物理方法。该文综述了SPR技术的特点 ,操作方法 ,光学结构及监测原理 ,数据采集及分析方法 ,应用范围其存在的问题等。同时 ,展望了该技术在昆虫学研究中广阔的应用前景。     

Blasenfreie Begasung

Different methods of bubble-free oxygenation are discussed. Today, the surface oxygenation has lost its importance. Technically, membrane oxygenation methods are used in various fermentervolumes although the construction principles are quite complicated. The scale-up-potential is here very limited. On the other hand, the CHEMCELL-oxygenation is a simple method, safe in terms of sterility and applicable to all fermenter sizes common for cell culturing. A great benefit of this principle is that the amount of oxygenation is not dependent from the mixing parameters.     

Enhancement of biomolecule transport by electroporation: a review of theory and practical application to transformation of Corynebacterium glutamicum

Selective and reversible permeabilization of the cell wall permeability barrier is the focus for many biotechnological applications. In this article, the basic principles for reversible membrane permeabilization, based on biological, chemical, and physical methods are reviewed. Emphasis is given to electroporation (electropermeabilization) which tends to be the most popular method for membrane permeabilization and for introduction of foreign molecules into the cells. The applications of this method in industrial processes as well as the critical factors and parameters which affect the success of this approach are discussed. The different strategies developed throughout the years for increased transformation efficiencies of the industrially important amino acid-overproducing bacterium Corynebacterium glutamicum, are also summarized.     

The comet assay: a comprehensive review

The comet assay is a sensitive and rapid method for DNA strand break detection in individual cells. Its use has increased significantly in the past few years. This paper is a review of the studies published to date that have made use of the comet assay. The principles of strand break detection using both the alkaline and neutral versions of the technique are discussed, and a basic methodology with currently used variations is presented. Applications in different fields are reviewed and possible future directions of the technique are briefly explored.