Cardiac Stress Test Induced by Dobutamine and Monitored by Cardiac Catheterization in Mice

Dobutamine is a β-adrenergic agonist with an affinity higher for receptor expressed in the heart (β₁) than for receptors expressed in the arteries (β₂). When systemically administered, it increases cardiac demand. Thus, dobutamine unmasks abnormal rhythm or ischemic areas potentially at risk of infarction. Monitoring of heart function during a cardiac stress test can be performed by either ecocardiography or cardiac catheterization. The latter is an invasive but more accurate and informative technique that the former.Cardiac stress test induced by dobutamine and monitored by cardiac catheterization accomplished as described here allows, in a single experiment, the measurement of the following hemodynamic parameters: heart rate (HR), systolic pressure, diastolic pressure, end-diastolic pressure, maximal positive pressure development (dP/dtmax) and maximal negative pressure development (dP/dt_min), at baseline conditions and under increasing doses of dobutamine.As expected, in normal mice we observed a dobutamine dose-related increase in HR, dP/dt_max and dP/dt_min. Moreover, at the highest dose tested (12 ng/g/min) the cardiac decompensation of high fat diet-induced obese mice was unmasked.     

Engineering genetic circuits: advancements in genetic design automation tools and standards for synthetic biology

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New software for finding transition states by probing accessible,or ergodic,regions

An automated, iterative approach to finding the lowest energy, ionic diffusion paths through a periodic structure has been developed within our new code (written in FORTRAN 77 and named Bubble). The approach is quite general in that it can be applied to find, at a chosen temperature, the accessible (ergodic) regions of a hyper-surface, which is defined across a uniform grid [1 Schön, J.C., Putz, H. and Jansen, M. 1996. Studying the energy hypersurface of continuous system—The threshold algorithm. J. Phys.-Conden. Matt., 8: 143[Crossref] , [Google Scholar]]. We describe both our implementation within the Bubble code and its application to locating the approximate transition states for Mg interstitial diffusion in forsterite, which can then be refined using standard transition state searching [2 Banerjee, A., Adams, N., Simons, J. and Shepard, R. 1985. Search for stationary points on surfaces. J. Phys. Chem., 89: 52[Crossref], [Web of Science ®] , [Google Scholar]].     

新型数值分类软件X-Cluster的开发及应用

针对目前常用数值分类软件的不足,采用多种设计模式开发了新型数值分类软件X-C luster。该软件具有界面友好、操作方便、体积小、速度快、功能强大、应用范围广等特点,能够满足大多数情况下数值分类研究工作的需求,并在芽孢杆菌分类研究中得到了验证。     

生物信息学软件研究的可视化分析

以Web of Science数据库为数据来源,利用Cite Space和UCINET软件对发表在Nucleic Acids Research期刊上有关生物信息学软件研究的文献做了可视化分析,揭示了该领域的研究力量、作者团队与高被引作者、知识基础、期刊分布、研究热点与前沿,为生物信息学软件的研究和发展提供必要的参考依据。     

The Role of Density Regulation in Extinction Processes and Population Viability Analysis

We review the role of density dependence in the stochastic extinction of populations and the role density dependence has played in population viability analysis (PVA) case studies. In total, 32 approaches have been used to model density regulation in theoretical or applied extinction models, 29 of them are mathematical functions of density dependence, and one approach uses empirical relationships between density and survival, reproduction, or growth rates. In addition, quasi-extinction levels are sometimes applied as a substitute for density dependence at low population size. Density dependence further has been modelled via explicit individual spacing behaviour and/or dispersal. We briefly summarise the features of density dependence available in standard PVA software, provide summary statistics about the use of density dependence in PVA case studies, and discuss the effects of density dependence on extinction probability. The introduction of an upper limit for population size has the effect that the probability of ultimate extinction becomes 1. Mean time to extinction increases with carrying capacity if populations start at high density, but carrying capacity often does not have any effect if populations start at low numbers. In contrast, the Allee effect is usually strong when populations start at low densities but has only a limited influence on persistence when populations start at high numbers. Contrary to previous opinions, other forms of density dependence may lead to increased or decreased persistence, depending on the type and strength of density dependence, the degree of environmental variability, and the growth rate. Furthermore, effects may be reversed for different quasi-extinction levels, making the use of arbitrary quasi-extinction levels problematic. Few systematic comparisons of the effects on persistence between different models of density dependence are available. These effects can be strikingly different among models. Our understanding of the effects of density dependence on extinction of metapopulations is rudimentary, but even opposite effects of density dependence can occur when metapopulations and single populations are contrasted. We argue that spatially explicit models hold particular promise for analysing the effects of density dependence on population viability provided a good knowledge of the biology of the species under consideration exists. Since the results of PVAs may critically depend on the way density dependence is modelled, combined efforts to advance statistical methods, field sampling, and modelling are urgently needed to elucidate the relationships between density, vital rates, and extinction probability.     

WHEN SPEED TRULY MATTERS, OPENNESS IS THE ANSWER

In this paper I analyse the ethical implications of the two main competing methodologies in genomic research. I do not aim to provide another contribution from the mainstream legal and public policy perspective; rather I offer a novel approach in which I analyse and describe the patent-and-publish regime (the proprietary regime) led by biologist J. Craig Venter and the 'open-source' methodologies led by biotechnology Nobel laureate John Sulston. The 'open-source methodologies' arose in biotechnology as an alternative to the patent-and-publish regime in the wake of the explosion in computer technology. Indeed, the tremendous increase in computer technology has generated a corresponding increase in the pace of genomics research. I conclude this paper by arguing that while the patent-and-publish method is a transactional method based on the exchange of extrinsic goods (patents in exchange for research funds), the free and open-source methodology (FLOSS) ¹ is a transformational method based on a visionary ideal of science, which leads to prioritizing intrinsic goods in scientific research over extrinsic goods.     

SwissPIT: An workflow‐based platform for analyzing tandem‐MS spectra using the Grid

The identification and characterization of peptides from MS/MS data represents a critical aspect of proteomics. It has been the subject of extensive research in bioinformatics resulting in the generation of a fair number of identification software tools. Most often, only one program with a specific and unvarying set of parameters is selected for identifying proteins. Hence, a significant proportion of the experimental spectra do not match the peptide sequences in the screened database due to inappropriate parameters or scoring schemes. The Swiss protein identification toolbox (swissPIT) project provides the scientific community with an expandable multitool platform for automated in‐depth analysis of MS data also able to handle data from high‐throughput experiments. With swissPIT many problems have been solved: The missing standards for input and output formats (A), creation of analysis workflows (B), unified result visualization (C), and simplicity of the user interface (D). Currently, swissPIT supports four different programs implementing two different search strategies to identify MS/MS spectra. Conceived to handle the calculation‐intensive needs of each of the programs, swissPIT uses the distributed resources of a Swiss‐wide computer Grid (http://www.swing‐grid.ch).