Multivariate approach for selecting sets of differentially expressed genes

An important problem addressed using cDNA microarray data is the detection of genes differentially expressed in two tissues of interest. Currently used approaches ignore the multidimensional structure of the data. However it is well known that correlation among covariates can enhance the ability to detect less pronounced differences. We use the Mahalanobis distance between vectors of gene expressions as a criterion for simultaneously comparing a set of genes and develop an algorithm for maximizing it. To overcome the problem of instability of covariance matrices we propose a new method of combining data from small-scale random search experiments. We show that by utilizing the correlation structure the multivariate method, in addition to the genes found by the one-dimensional criteria, finds genes whose differential expression is not detectable marginally.     

红壤丘陵区土地利用方式变更后土壤有机碳动态变化的模拟

采用双组分模型模拟土地利用方式变更后土壤有机碳储量的变化,并用一些调查和监测数据进行了初步验证．此双组分模型将土壤有机碳分为新形成有机碳和原有有机碳两个组分．每个组分有机碳的形成转化用一级动力学方程描述．本文用此模型对亚热带土壤开垦利用为马尾松林地、湿地松林地、柑桔园和牧草地４种方式１０年来土壤有机碳储量的变化过程进行了模拟,初步结果表明,模拟值与实测值拟合较好．可见,此方法适于用来模拟不同土壤类型下土地利用系统变更初期的土壤有机碳储量动态变化过程．     

Demography and modelling of clonal fragments in the pseudoannual plant shape Trientalis europaea L.

The clonal growth pattern and demography of clonal fragments (aggregation of ramets derived from a common parent ramet) in the pseudoannual plant Trientalis europaea were studied in field conditions from 1991 to 1993. During this period the population of clonal fragments declined, with a half-life of 7.4 years. Number and size of the clonal progeny and stolon length were positively related to the size of the mother ramet. Survival rates of ramets and tubers increased with size. The rate of clonal growth was low: after three years, about 70% of the clonal fragments had only one ramet. This suggests that the pseudoannual growth habit in T. europaea is more important as mechanism of perennation than of ramet multiplication.Field data were used in a simulation model of architecture and population dynamics of clonal fragments. About 10% of the clonal fragments survived to the end of the simulation (15 years) and the mean survival was 4.7 years. The model predicted a positive correlation between persistence of the clonal fragment and number of ramets produced. Sensitivity analysis showed that the production of a daughter ramet of at least the same size as the parent ramet was the most important pathway for the survival and the number of ramets of the clonal fragment, whereas the production of secondary ramets had a very small effect. This confirms the interpretation of the pseudoannual life-cycle as a mechanism of ramet replacement in this species. Sensitivity analysis also revealed that changes in survival probabilities of the smallest ramets had the largest impact on clonal fragment dynamics. This reflects the important role of the smallest size class of ramets as a source of new vegetative propagules, maintaining a hierarchy in the size structure of the population.     

医学院校生物技术专业发酵工程实验体系的构建

为建设有特色的生物技术专业和培养创新复合型人才,本研究结合医学院校特点,充分利用"医"和"药"的资源,合理安排实验项目,构建了科学的发酵工程实验教学体系。结果表明该实验教学体系教学效果良好。学生的操作能力显著提高。为强化发酵工程教学,探索产学研联合培养模式将成必然。     

留学生医学微生物学教学的体会与改革

通过分析留学生及医学微生物学的特点,从教师的选择、教材的选取、运用现代教育技术、改革考试方法和加强实验教学等环节改进留学生医学微生物学的教学;采用启发式教学、归纳对比法教学、典型病案教学法和以问题为基础教学法(PBL)来提高授课质量等,探索医学微生物学留学生教学,为医学微生物学留学生教学改革提供一定的依据。     

WPBL教学法在“微生物学检验”教学中应用的探索

为了探讨WPBL教学法在"微生物学检验"教学中的应用效果,对本院2008级检验医学专业66名学生进行分组教学,实验组采用WPBL教学法,对照组采用传统教学法。课后对2组学生进行理论测试,同时对实验组进行问卷调查。经统计,实验组的测试成绩明显优于对照组(P0.01),且2组学生测试成绩的及格率差异有统计学意义(P0.05);问卷调查显示90%以上的学生对WPBL教学法感兴趣,认为WPBL教学法能提高学习兴趣、自学能力和分析解决问题的能力。从结果看,WPBL教学法能够提高"微生物学检验"教学质量。     

改革课程教学体系 加强实践和创新能力培养——水处理微生物学课程教学的改革探索

水处理微生物学是给水排水工程专业的一门重要的专业基础课。该课程的主要培养目标是学习和掌握微生物学基础知识和基本实验技能, 以及微生物在水处理领域的应用, 激发学生的学习兴趣, 培养学生独立思考和分析解决问题的能力, 发展学生的创新性思维和工程实践能力。根据自身的教学体会, 结合给水排水工程专业的学科特点和专业需要, 对水处理微生物学教学内容、教学方法和手段以及实验教学进行改革, 并取得良好效果。     

Proton transport in carbonic anhydrase: Insights from molecular simulation

This article reviews the insights gained from molecular simulations of human carbonic anhydrase II (HCA II) utilizing non-reactive and reactive force fields. The simulations with a reactive force field explore protein transfer and transport via Grotthuss shuttling, while the non-reactive simulations probe the larger conformational dynamics that underpin the various contributions to the rate-limiting proton transfer event. Specific attention is given to the orientational stability of the His64 group and the characteristics of the active site water cluster, in an effort to determine both of their impact on the maximal catalytic rate. The explicit proton transfer and transport events are described by the multistate empirical valence bond (MS-EVB) method, as are alternative pathways for the excess proton charge defect to enter/leave the active site. The simulation results are interpreted in light of experimental results on the wild-type enzyme and various site-specific mutations of HCA II in order to better elucidate the key factors that contribute to its exceptional efficiency.     

Economic consequences of reproductive performance in dairy cattle

The net economic value of reproductive efficiency in dairy cattle was estimated using a stochastic dynamic simulation model. The objective was to compare the economic consequences of reproductive performance scenarios (“average” and “poor”) of a cow having a good reproductive performance and to explore which reproductive factors have an important impact on economic efficiency. A “good” reproductive performance scenario was defined with 1 ovulation rate (POVU_i), 0.7 estrus detection rate (PEst), 0.7 conception rate (PCon), 0.03 incidence rate of postpartum disorders prolonging the ovarian cyclicity (CO), 0.2 incidence rate of postpartum disorders reducing conception (ME), 0.05 embryonic death rate (ED), and voluntary waiting period (VWP) of 9 wks pp (post partum). In the current situation of dairy cows in the Netherlands, an “average” reproductive scenario (0.95 POVU_i, 0.5 PEst, 0.5 Pcon, 0.07 CO, 0.27 ME, 0.07 ED and VWP of 12 wks pp) and a “poor” reproductive scenario (0.90 POVU_i, 0.3 PEst, 0.3 Pcon, 0.11 CO, 0.33 ME, 0.09 ED and VWP of 15 wks pp) were identified. A sensitivity analysis was performed by comparing changes of single effect of factors in a good and poor scenario with the average scenario. The mean net economic loss (NEL_i) compared with the good scenario was €34 and €231 per cow per year for the average and poor reproductive performance scenario, respectively. Increasing the calving interval resulted in greater economic loss. The important factors on the cost of reproductive efficiency were the involuntary culling cost and the return of milk production. Variation in PCon, PEst, ME, ED, and VWP had large impacts on economic benefits.     

A Mathematical Framework for Modeling Axon Guidance

In this paper, a simulation tool for modeling axon guidance is presented. A mathematical framework in which a wide range of models can been implemented has been developed together with efficient numerical algorithms. In our framework, models can be defined that consist of concentration fields of guidance molecules in combination with finite-dimensional state vectors. These vectors can characterize migrating growth cones, target neurons that release guidance molecules, or other cells that act as sources of membrane-bound or diffusible guidance molecules. The underlying mathematical framework is presented as well as the numerical methods to solve them. The potential applications of our simulation tool are illustrated with a number of examples, including a model of topographic mapping.