季铵型阳离子皂荚胶的合成

本文介绍了以皂荚胶粉,与阳离子试剂3-氯-2-羟丙基三甲基氯化铵(CHPTMA)为原料,制备季铵型阳离子皂荚胶,通过正交试验确定了生产一定取代度胶粉的最佳反应条件：反应温度65℃;反应时间6h;氢氧化钠与阳离子试剂摩尔比为0．8;乙醇质量分数90％。     

Optimization of fermentation conditions for the production of ethanol from sago starch using response surface methodology

The quantitative effects of temperature, pH and time of fermentation were investigated on simultaneous saccharification and fermentation (SSF) of ethanol from sago starch with glucoamylase (AMG) and Zymomonas mobilis ZM4 using a Box–Wilson central composite design protocol. The SSF process was studied using free enzyme and free cells and it was found that with sago starch, maximum ethanol concentration of 70.68 g/l was obtained using a starch concentration of 140 g/l, which represents an ethanol yield of 97.08%. The optimum conditions for the above yield were found to be a temperature of 36.74 °C, pH of 5.02 and time of fermentation of 17 h. Thus by using the central composite design, it is possible to determine the accurate values of the fermentation parameters where maximum production of ethanol occurs.     

Synthetic peptides mimicking the interleukin-6/gp130 interaction: a two-helix bundle system. Design and conformational studies.

The objective of our study was to mimic in a typical reductionist approach the molecular interactions observed at the interface between the gp130 receptor and interleukin-6 during formation of their complex. A peptide system obtained by reproducing some of the interleukin-6/gp130 molecular interactions into a two-helix bundle structure was investigated. The solution conformational features of this system were determined by CD and NMR techniques. The CD titration experiments demonstrated that the interaction between the designed peptides is specific and based on a well-defined stoichiometry. The NMR data confirmed some of the structural features of the binding mechanism as predicted by the rational design and indicated that under our conditions the recognition specificity and affinity can be explained by the formation of a two-helix bundle. Thus, the data reported herein represent a promising indication on how to develop new peptides able to interfere with formation of the interleukin-6/gp130 complex.     

A latent contingency table approach to dose finding for combinations of two agents

Summary .  Two-agent combination trials have recently attracted enormous attention in oncology research. There are several strong motivations for combining different agents in a treatment: to induce the synergistic treatment effect, to increase the dose intensity with nonoverlapping toxicities, and to target different tumor cell susceptibilities. To accommodate this growing trend in clinical trials, we propose a Bayesian adaptive design for dose finding based on latent 2 × 2 tables. In the search for the maximum tolerated dose combination, we continuously update the posterior estimates for the unknown parameters associated with marginal probabilities and the correlation parameter based on the data from successive patients. By reordering the dose toxicity probabilities in the two-dimensional space, we assign each coming cohort of patients to the most appropriate dose combination. We conduct extensive simulation studies to examine the operating characteristics of the proposed method under various practical scenarios. Finally, we illustrate our dose-finding procedure with a clinical trial of agent combinations at M. D. Anderson Cancer Center.     

A Frailty‐Model‐Based Approach to Estimating the Age‐Dependent Penetrance Function of Candidate Genes Using Population‐Based Case‐Control Study Designs: An Application to Data on the BRCA1 Gene

Summary The population‐based case–control study design is perhaps one of, if not the most, commonly used designs for investigating the genetic and environmental contributions to disease risk in epidemiological studies. Ages at onset and disease status of family members are routinely and systematically collected from the participants in this design. Considering age at onset in relatives as an outcome, this article is focused on using the family history information to obtain the hazard function, i.e., age‐dependent penetrance function, of candidate genes from case–control studies. A frailty‐model‐based approach is proposed to accommodate the shared risk among family members that is not accounted for by observed risk factors. This approach is further extended to accommodate missing genotypes in family members and a two‐phase case–control sampling design. Simulation results show that the proposed method performs well in realistic settings. Finally, a population‐based two‐phase case–control breast cancer study of the BRCA1 gene is used to illustrate the method.     

Field‐based comparison of ligand and coactivator binding sites of nuclear receptors

A structure‐based comparison of the ligand‐binding domains of 35 nuclear receptors from five different subfamilies is presented. Their ligand and coactivator binding sites are characterized using knowledge‐based contact preference fields for hydrophobic and hydrophilic interactions implemented in the MOE modeling environment. Additionally, for polar knowledge‐based field points the preference for negative or positive electrostatic interactions is estimated using the Poisson‐Boltzmann equation. These molecular‐interaction fields are used to cluster the nuclear receptor family based on similarities of their binding sites. By analyzing the similarities and differences of hydrophobic and polar fields in binding pockets of related receptors it is possible to identify conserved interactions in ligand and coactivator binding pockets, which support e.g. design of specific ligands during lead optimization or virtual screening as docking filter. Examples of remarkable similarities between ligand binding sites of members from phylogenetically different nuclear receptor families (RXR, RAR, HNF4, NR5) and differences between closely related subtypes (LXR, RAR, TR) are discussed in more detail. Significant similarities and differences of coactivator binding sites are shown for NR3Cs, LXRs and PPARs. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 884–894, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

“Enzyme Test Bench,” a high‐throughput enzyme characterization technique including the long‐term stability

A new high throughput technique for enzyme characterization with specific attention to the long term stability, called “Enzyme Test Bench,” is presented. The concept of the Enzyme Test Bench consists of short term enzyme tests in 96‐well microtiter plates under partly extreme conditions to predict the enzyme long term stability under moderate conditions. The technique is based on the mathematical modeling of temperature dependent enzyme activation and deactivation. Adapting the temperature profiles in sequential experiments by optimal non‐linear experimental design, the long term deactivation effects can be purposefully accelerated and detected within hours. During the experiment the enzyme activity is measured online to estimate the model parameters from the obtained data. Thus, the enzyme activity and long term stability can be calculated as a function of temperature. The engineered instrumentation provides for simultaneous automated assaying by fluorescent measurements, mixing and homogenous temperature control in the range of 10–85 ± 0.5°C. A universal fluorescent assay for online acquisition of ester hydrolysis reactions by pH‐shift is developed and established. The developed instrumentation and assay are applied to characterize two esterases. The results of the characterization, carried out in microtiter plates applying short term experiments of hours, are in good agreement with the results of long term experiments at different temperatures in 1 L stirred tank reactors of a week. Thus, the new technique allows for both: the enzyme screening with regard to the long term stability and the choice of the optimal process temperature regarding such process parameters as turn over number, space time yield or optimal process duration. The comparison of the temperature dependent behavior of both characterized enzymes clearly demonstrates that the frequently applied estimation of long term stability at moderate temperatures by simple activity measurements after exposing the enzymes to elevated temperatures may lead to suboptimal enzyme selection. Thus, temperature dependent enzyme characterization is essential in primary screening to predict its long term behavior. Biotechnol. Bioeng. 2009;103: 305–322. © 2008 Wiley Periodicals, Inc.     

THE RELATIONSHIP BETWEEN EVOLUTIONARY BIOLOGY AND RELIGION

Belief in creationism and intelligent design is widespread and gaining significance in a number of countries. This article examines the characteristics of science and of religions and the possible relationship between science and religion. I argue that creationism is sometimes best seen not as a misconception but as a worldview. In such instances, the most to which a science educator (whether in school, college or university) can normally aspire is to ensure that students with creationist beliefs understand the scientific position. In the short term, the scientific worldview is unlikely to supplant a creationist one for students who are firm creationists. We can help students to find their evolutionary biology courses interesting and intellectually challenging without their being threatening. Effective teaching in this area can help students not only learn about the theory of evolution but better appreciate the way science is done, the procedures by which scientific knowledge accumulates, the limitations of science, and the ways in which scientific knowledge differs from other forms of knowledge.     

Why Darwin rejected intelligent design

As a Cambridge University undergraduate Charles Darwin was fascinated and convinced by the argument for intelligent design, as set forth in William Paley’s 1802 classic, Natural Theology. Subsequently, during his five-year voyage on HMS Beagle (1831–1836), Darwin interpreted his biological findings through a creationist lens, including the thought-provoking evidence he encountered during his historic visit to the Galápagos Islands in September and October 1835. After his return to England in 1836 and his subsequent conversion to the idea of organic evolution in March 1837, Darwin searched for a theory that would explain both the fact of evolution and the widespread appearance of intelligent design. His insight into the process of natural selection, which occurred in September 1838, provided this alternative explanation. Darwin’s Origin of Species (1859) exemplifies his skillful deployment of the hypothetico-deductive method in testing and refuting the arguments for intelligent design that he had once so ardently admired.     

Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism

Elementary mode analysis is a useful metabolic pathway analysis tool to identify the structure of a metabolic network that links the cellular phenotype to the corresponding genotype. The analysis can decompose the intricate metabolic network comprised of highly interconnected reactions into uniquely organized pathways. These pathways consisting of a minimal set of enzymes that can support steady state operation of cellular metabolism represent independent cellular physiological states. Such pathway definition provides a rigorous basis to systematically characterize cellular phenotypes, metabolic network regulation, robustness, and fragility that facilitate understanding of cell physiology and implementation of metabolic engineering strategies. This mini-review aims to overview the development and application of elementary mode analysis as a metabolic pathway analysis tool in studying cell physiology and as a basis of metabolic engineering.