Analysis of distribution of ligands adsorbed on DNA fragments

The effect of finite fragment length on the distribution pattern of bound protein along the DNA fragment is considered. If the size of the binding site for a ligand on DNA is comparable with the length of the DNA fragment fluctuations in the amount of ligand bound to the fragment create some difficulties for evaluating the distribution pattern of ligand on DNA. A mathematical approach is developed which enables one to calculate the distribution pattern of ligand on DNA provided that the number of bound ligand on the DNA fragment is known. Expression are also obtained to treat the effects of fluctuations in the number of ligand molecules bound to the DNA fragment on the distribution pattern of ligand. A new procedure is proposed which may be useful for locating the preferable binding sites for ligand on DNA on the basis of footprinting experiments.     

Testing for ordered group effects in binary and continuous outcomes

A likelihood ratio test is proposed for the detection of an ordered group effect on bivariate responses where one response is binary and the other is continuous. The procedure is based on a conditional logistic model for the binary response given the continuous outcome. We also develop a likelihood ratio test for simultaneously determining the goodness of fit of the ordering assumption on both responses. Our approach is motivated by a particular toxicity study application involving laboratory animals that focused on the effect of a food color additive on the development of reticuloendothelial (RE) tumors. A brief discussion on extensions to the methodology introduced here is also given, along with a comparison of the approach with a marginal strategy where the presence of an ordered group effect is assessed independently for each of the two responses.     

Control of gluconeogenic growth by pps and pck in Escherichia coli.

It is well-known that Escherichia coli grows more slowly on gluconeogenic carbon sources than on glucose. This phenomenon has been attributed to either energy or monomer limitation. To investigate this problem further, we varied the expression levels of pck, encoding phosphoenolpyruvate carboxykinase (Pck), and pps, encoding phosphoenolpyruvate synthase (Pps). We found that the growth rates of E. coli in minimal medium supplemented with succinate and with pyruvate are limited by the levels of Pck and Pps, respectively. Optimal overexpression of pck or pps increases the unrestricted growth rates on succinate and on pyruvate, respectively, to the same level attained by the wild-type growth rate on glycerol. Since Pps is needed to supply precursors for biosyntheses, we conclude that E. coli growing on pyruvate is limited by monomer supply. However, because pck is required both for biosyntheses and catabolism for cells growing on succinate, it is possible that growth on succinate is limited by both monomer and energy supplies. The growth yield with respect to oxygen remains approximately constant, even though the overproduction of these enzymes enhances gluconeogenic growth. It appears that the constant yield for oxygen is characteristic of efficient growth on a particular substrate and that the yield is already optimal for wild-type strains. Further increases in either Pck or Pps above the optimal levels become growth inhibitory, and the growth yield for oxygen is reduced, indicating less efficient growth.     

基于HNP模型及相对熵的蛋白质设计方法在不同蛋白质体系中的应用

详细考察了基于HNP(H:hydtophobic,N:neutral,P:hydrophilic)模型及相对熵的蛋白质设计方法对于不同结构类型蛋白质的适用性,并与基于HP模型的结果进行了比较.通过对190个4种不同结构类型的蛋白质进行预测,结果表明,基于HNP模型及相对熵的设计方法对于不同结构类型的蛋白质具有普适性.进一步的研究发现,对于α螺旋、β折叠等规则的二级结构,该方法的预测成功率高于无规卷曲结构预测成功率.另外,还比较了对不同氨基酸的预测差异,结果显示亲水残基的预测成功率较高.此外,研究表明该方法对于蛋白质保守残基的预测成功率高于非保守残基.在以上分析的基础上,进一步讨论了导致这些差异的原因.这些研究为基于相对熵的蛋白质设计方法的实际应用和进一步的发展打下了良好基础.     

Modelling the effects of population aggregation on the efficiency of insect pest control

A methodology is developed to assess the effects of spatial distribution on the efficiency of insect pest control. This methodology is especially applicable to pest control methods whose efficiency of action depends either positively or negatively on pest density It is applied here to the sterile insect technique and pheromone trapping for male annihilation, which both depend negatively on density. This methodology relies on quantifying clumps of various size and then relating this to efficiency of control and predicting the total pest production given the information on clump sizes and efficiency of control for each clump size. It is found that control is about four times as difficult for a population that is highly clumped (k of the negative binomial distribution=0.25) as for a regularly dispersed population.     

Most Undirected Random Graphs Are Amplifiers of Selection for Birth-Death Dynamics,but Suppressors of Selection for Death-Birth Dynamics

We analyze evolutionary dynamics on graphs, where the nodes represent individuals of a population. The links of a node describe which other individuals can be displaced by the offspring of the individual on that node. Amplifiers of selection are graphs for which the fixation probability is increased for advantageous mutants and decreased for disadvantageous mutants. A few examples of such amplifiers have been developed, but so far it is unclear how many such structures exist and how to construct them. Here, we show that almost any undirected random graph is an amplifier of selection for Birth-death updating, where an individual is selected to reproduce with probability proportional to its fitness and one of its neighbors is replaced by that offspring at random. If we instead focus on death-Birth updating, in which a random individual is removed and its neighbors compete for the empty spot, then the same ensemble of graphs consists of almost only suppressors of selection for which the fixation probability is decreased for advantageous mutants and increased for disadvantageous mutants. Thus, the impact of population structure on evolutionary dynamics is a subtle issue that will depend on seemingly minor details of the underlying evolutionary process.     

Synthetic biology: an emerging research field in China

Synthetic biology is considered as an emerging research field that will bring new opportunities to biotechnology. There is an expectation that synthetic biology will not only enhance knowledge in basic science, but will also have great potential for practical applications. Synthetic biology is still in an early developmental stage in China. We provide here a review of current Chinese research activities in synthetic biology and its different subfields, such as research on genetic circuits, minimal genomes, chemical synthetic biology, protocells and DNA synthesis, using literature reviews and personal communications with Chinese researchers. To meet the increasing demand for a sustainable development, research on genetic circuits to harness biomass is the most pursed research within Chinese researchers. The environmental concerns are driven force of research on the genetic circuits for bioremediation. The research on minimal genomes is carried on identifying the smallest number of genomes needed for engineering minimal cell factories and research on chemical synthetic biology is focused on artificial proteins and expanded genetic code. The research on protocells is more in combination with the research on molecular-scale motors. The research on DNA synthesis and its commercialisation are also reviewed. As for the perspective on potential future Chinese R&D activities, it will be discussed based on the research capacity and governmental policy.     

A simple experimental approach to the determination of carrier transport parameters for unlabeled substrate analogs.

A method is described by which affinities and transport rates for unlabeled substrate analogs are readily determined, and which is based on the effect of an unlabeled analog upon the rate of transport of a labeled substrate present at a low concentration on the trans side of the membrane. The procedure is widely applicable since it does not depend on assumptions about rrate-limiting steps and holds for both active and non-active systems. Here it is applied in an experimental study of the facilitated diffusion system for choline in erythrocytes, and it is shown that the transport parameters for a test substrate obtained by this method are the same as those found when the transport of the substrate is followed directly.     

Evolution of amino-acid sequences and codon usage on the Drosophila miranda neo-sex chromosomes

We have studied patterns of DNA sequence variation and evolution for 22 genes located on the neo-X and neo-Y chromosomes of Drosophila miranda. As found previously, nucleotide site diversity is greatly reduced on the neo-Y chromosome, with a severely distorted frequency spectrum. There is also an accelerated rate of amino-acid sequence evolution on the neo-Y chromosome. Comparisons of nonsynonymous and silent variation and divergence suggest that amino-acid sequences on the neo-X chromosome are subject to purifying selection, whereas this is much weaker on the neo-Y. The same applies to synonymous variants affecting codon usage. There is also an indication of a recent relaxation of selection on synonymous mutations for genes on other chromosomes. Genes that are weakly expressed on the neo-Y chromosome appear to have a faster rate of accumulation of both nonsynonymous and unpreferred synonymous mutations than genes with high levels of expression, although the rate of accumulation when both types of mutation are pooled is higher for the neo-Y chromosome than for the neo-X chromosome even for highly expressed genes.     

Role of carnitine acetyltransferases in acetyl coenzyme A metabolism in Aspergillus nidulans

The flow of carbon metabolites between cellular compartments is an essential feature of fungal metabolism. During growth on ethanol, acetate, or fatty acids, acetyl units must enter the mitochondrion for metabolism via the tricarboxylic acid cycle, and acetyl coenzyme A (acetyl-CoA) in the cytoplasm is essential for the biosynthetic reactions and for protein acetylation. Acetyl-CoA is produced in the cytoplasm by acetyl-CoA synthetase during growth on acetate and ethanol while β-oxidation of fatty acids generates acetyl-CoA in peroxisomes. The acetyl-carnitine shuttle in which acetyl-CoA is reversibly converted to acetyl-carnitine by carnitine acetyltransferase (CAT) enzymes is important for intracellular transport of acetyl units. In the filamentous ascomycete Aspergillus nidulans, a cytoplasmic CAT, encoded by facC, is essential for growth on sources of cytoplasmic acetyl-CoA while a second CAT, encoded by the acuJ gene, is essential for growth on fatty acids as well as acetate. We have shown that AcuJ contains an N-terminal mitochondrial targeting sequence and a C-terminal peroxisomal targeting sequence (PTS) and is localized to both peroxisomes and mitochondria, independent of the carbon source. Mislocalization of AcuJ to the cytoplasm does not result in loss of growth on acetate but prevents growth on fatty acids. Therefore, while mitochondrial AcuJ is essential for the transfer of acetyl units to mitochondria, peroxisomal localization is required only for transfer from peroxisomes to mitochondria. Peroxisomal AcuJ was not required for the import of acetyl-CoA into peroxisomes for conversion to malate by malate synthase (MLS), and export of acetyl-CoA from peroxisomes to the cytoplasm was found to be independent of FacC when MLS was mislocalized to the cytoplasm.     

马铃薯AGPase大小亚基功能研究

马铃薯 1,6 二磷酸腺苷葡萄糖焦磷酸化酶 (AGPase)是淀粉合成的限速酶 ,该酶有大、小两个亚基形成异源四聚体。总结了迄今为止已克隆的马铃薯AGPase大、小亚基编码基因、小亚基和底物结合位点的识别、以及大亚基异构调控因子结合位点识别的研究结果 ,提出了大小亚基非自然重组是深入研究AGPase的途径 ,建立体内条件下高效可靠代谢调控研究手段是AGPase研究所必需的。     

Problems in nomenclature of craniofacial disorders

The diverse background of clinical geneticists may lead to problems of communication unless attention is paid to nomenclature. In this paper, consensus is sought on terms for normal and abnormal development, a system for labeling developmental defects of dentin is proposed, and terms for patterns of coexistent variations are defined. The major methods for naming coexistent variations are reviewed, with attention to the disadvantages of each. An informal study on recognition of patterns of variation based on the naming system used is also presented.     

Bayesian Nonparametric Nonproportional Hazards Survival Modeling

Summary .  We develop a dependent Dirichlet process model for survival analysis data. A major feature of the proposed approach is that there is no necessity for resulting survival curve estimates to satisfy the ubiquitous proportional hazards assumption. An illustration based on a cancer clinical trial is given, where survival probabilities for times early in the study are estimated to be lower for those on a high-dose treatment regimen than for those on the low dose treatment, while the reverse is true for later times, possibly due to the toxic effect of the high dose for those who are not as healthy at the beginning of the study.     

A Review of Methods for Non-Invasive Heart Rate Measurement on Wrist

When evaluating general health condition on a patient, heart rate is an essential indicator as it is directly representative of the cardiac system state. Continuous measurement methods of heart rate are required for ambulatory monitoring involved in preliminary diagnostic indicators of cardiac diseases or stroke. The growing number of recent developments in wearable devices is reflective of the increasing demand in wrist-worn activity trackers for fitness and health applications. Indeed, the wrist represents a convenient location in terms of form factor and acceptability for patients. While most commercially-available devices are based on optical methods for heart rate measurement, others methods were also developed, based on various physiological phenomena. This review is focused on heart rate measurement methods located on forearm and more specifically on the wrist. For each method, the physiological mechanism involved is described, and the associated transducers for bio-signal acquisition as well as practical developments and prototypes are presented. Methods are discussed on their advantages, limitations and their suitability for an ambulatory use. More specifically, the superposition of motion artefacts over the signal of interest is one of the largest drawbacks for these methods, when used out of laboratory conditions. As such, artefact reduction techniques proposed in the literature are also presented and discussed.     

A comparison of five effects of ultraviolet light on the Arbacia egg

The demonstration of five different effects of ultraviolet radiation on the sea urchin's egg indicates that more than one basic photochemical process goes on there. Photorecovery is observed in only one of these. The need for caution in interpreting such effects is obvious. Evidence for a different mechanism for the timing of cleavage in eggs activated by ultraviolet radiation as compared to normally fertilized eggs is presented. The bearing of these studies on survival curves for microorganisms is discussed.     

Procedure for Drying Leptospiral Antibody on Sand and Sugar for Serological Studies in Leptospirosis

A simple technique is described for drying sera on washed, dry sand or ordinary sugar cubes for the sero-diagnosis of leptospirosis. The results are shown to be very similar to those obtained with fluid sera or sera dried on filter paper discs. Sera adsorbed on sand or absorbed in sugar eliminated some of the problems associated with sera dried on paper. This method is suitable for use in the field and is expected to be of value in epizootiological studies where contamination and chemical denaturation of fluid serum samples held without refrigeration is a problem.     

The use of pH indicators to identify suitable environments for freezing samples in aqueous and mixed aqueous/nonaqueous solutions

The colours of frozen solutions containing pH indicators are shown to provide a test for changes in pH in the solvent environment which occur on freezing. Yeast alcohol dehydrogenase loses activity on freezing in phosphate buffer (a buffer in which pH indicator colour changes shows a marked decrease in pH on freezing) but when frozen in bis-tris, Hepes, or N-glycylglycine buffers (all of which show little change in the colour of universal pH indicator and hence of pH on freezing) is stable on freezing. The effects of freezing in different buffer systems on the rate of decomposition of NADPH, and on the rate hydrolysis of 4-nitrophenyl acetate, are rationalised in terms of the pH shifts in these buffers which were determined using universal pH indicator. It is proposed that a major reason for the instability of samples on freezing is the pH changes which occur when some systems are frozen. From the results a general scheme for selecting the best environment for safely freezing samples is proposed which is based on the use of pH indicators.     

Kinetics of the immobilization of trypsin on activated silichrome

Trypsin is studied for kinetics of its immobilization on the surface of a porous spheric inorganic carrier with the grafted aldehyde groups in the surface layer. This process is found to be controlled by the enzyme diffusion. It is shown possible to use a body of mathematics known for kinetics of physical adsorption on the porous adsorbents to describe kinetics of protein chemosorption on the analogous carriers. A simple method is suggested for plotting a kinetic curve of the enzyme immobilization on the matrix with any sizes of particles from the experimentally obtained kinetic curve of its binding on the carrier with a definite diameter of particles.     

Enzyme reactor design under thermal inactivation

Temperature is a very relevant variable for any bioprocess. Temperature optimization of bioreactor operation is a key aspect for process economics. This is especially true for enzyme-catalyzed processes, because enzymes are complex, unstable catalysts whose technological potential relies on their operational stability. Enzyme reactor design is presented with a special emphasis on the effect of thermal inactivation. Enzyme thermal inactivation is a very complex process from a mechanistic point of view. However, for the purpose of enzyme reactor design, it has been oversimplified frequently, considering one-stage first-order kinetics of inactivation and data gathered under nonreactive conditions that poorly represent the actual conditions within the reactor. More complex mechanisms are frequent, especially in the case of immobilized enzymes, and most important is the effect of catalytic modulators (substrates and products) on enzyme stability under operation conditions. This review focuses primarily on reactor design and operation under modulated thermal inactivation. It also presents a scheme for bioreactor temperature optimization, based on validated temperature-explicit functions for all the kinetic and inactivation parameters involved. More conventional enzyme reactor design is presented merely as a background for the purpose of highlighting the need for a deeper insight into enzyme inactivation for proper bioreactor design.