Impact of vitamin E supplement in standard laboratory animal diet on microvascular manifestation of ischemia/reperfusion injury

Aimed at improving animal fertility and health, diets for farm and laboratory animals have over the last few years been supplemented with increasing amounts of the antioxidant vitamin E. We now demonstrate by intravital microscopy that feeding hamsters with a vitamin E-supplemented “standard” rodent diet (60 ppm vitamin E) significantly reduces the microvascular manifestations of ischemia/reperfusion injury when compared to animals fed a nonsupplemented diet. Postischemic leukocyte adhesion to venular endothelium was reduced from 770 ± 204 cells/mm² at 24 h after reperfusion in control animals on the nonsupplemented diet to 403 ± 105 cells/mm² in animals on the “standard” rodent diet (means ± SD, N = 7 animals per group, p < 0.01). Animals on the nonsupplemented diet showed a dramatic loss of capillary perfusion density until 7 days after reperfusion (to 21 ± 13% of preischemic baseline values), whereas this loss was significantly attenuated (to 71 ± 12% of preischemic values, p < 0.01) in animals on the “standard” rodent diet. No difference in the extent of reperfusion injury was seen between animals on the “standard” rodent diet and animals on diets with substantially higher vitamin E supplements (300 ppm–30.000 ppm). Besides underscoring the benefit of vitamin E in reducing the extent of ischemia/reperfusion injury, this study raises the concern that vitamin E supplements in “standard” laboratory animal diets may have a far-reaching impact on biomedical research by jeopardizing established animal models of disease.     

Behavioural deprivation: A central problem in animal welfare

A key issue in animal welfare is whether keeping animals in conditions where they cannot or do not perform behaviour typical of more naturally-kept members of their species causes them to suffer. Various measures have been used to resolve this issue. The cost an animal is prepared to pay for the opportunity to perform different behaviour can be used as a measure of the importance of that behaviour to the animal. Manipulation of time-budgets is the most reliable method of measuring such costs and of relating “deprivation” to “suffering”.     

A database application for long‐term ecological field experiments

Problem: A series of long‐term field experiments is described, with particular reference to monitoring and quality control. This paper addresses problems in data‐management of particular importance for long‐term studies, including data manipulation, archiving, quality assessment, and flexible retrieval for analysis Method: The problems were addressed using a purpose‐built database system, using commercial software and running under Microsoft Windows. Conclusion: The database system brings many advantages compared to available software, including significantly improved quality checking and access. The query system allows for easy access to data sets thus improving the efficiency of analysis. Quality assessments of the initial dataset demonstrated that the database system can also provide general insight into types and magnitudes of error in data‐sets. Finally, the system can be generalised to include data from a number of different projects, thus simplifying data manipulation for meta‐analysis.     

Map Manager QTX, cross-platform software for genetic mapping

Map Manager QTX (QTX) is software for analysis of genetic mapping experiments in experimental plants and animals. It includes functions for mapping both Mendelian and quantitative trait loci. QTX is an enhanced version of Map Manager QT, rewritten with the aid of cross-platform libraries (XVT, Boulder Software Foundry, Inc.), which allow it to be compiled for multiple computer platforms. It currently is distributed for Microsoft Windows and Mac OS and is available at http://mapmgr.roswellpark.org/mmQTX.html. Received: 2 July 2001 / Accepted: 20 August 2001     

The development of a “microtitre” fluctuation test for the detection of indirect mutagens, and its use in the evaluation of mixed enzyme induction of the liver

The “Microtitre” Fluctuation test recently introduced for the detection of direct mutagens has been adapted for the detection of indirect mutagens through the incorporation of an “S9-mix” metabolic system. It compares favourably with Greens' original method for the detection of a range of chemical mutagens.

The technique has been employed in the evaluation of mixed enzyme induction using phenobarbitone and β-naphthoflavone (benzoflavone). as a safe substitute for Aroclor-1254. The post-mitochondrial preparations from rats induced with the combined inducers had a similar “metabolic competence” to those derived from Aroclor induced animals. Such a combination would therefore provide a useful alternative to Aroclor-1254 for routine screening.

It was found that the level of “S9” present in the metabolic system greatly affected the quantitative mutagenic response. This varied considerably from chemical to chemical and underlined the need for such preliminary investigations in routine screening.     

On the Specificity of Allopurinol and Oxypurinol as Inhibitors of Xanthine Oxidase. A Pulse Radiolysis Determination of Rate Constants for Reaction of Allopurinol and Oxypurinol with Hydroxyl Radicals

Allopurinol has been employed as a “specific” inhihitor of xanthine oxidase in studies of hypoxic/ reoxygenation injury. Pulse radiolysis was used to establish rate constants for the reactions of allopurinol and its major metabolite oxypurinol with hydroxyl radicals: values were (1.45 ± 0.241 × 10⁹ M^-1 s^-1 for allopurinol and (4.95 ± 0.84) × 10⁹ M^-1 s^-1 for oxypurinol. These rate constants show that, in view of the amounts of allopurinol that have been used in animal studies. hydroxyl radical scavenging by this molecule could contribute to its biological actions. especially if animals are pre-treated with allopurinol. so allowing oxypurinol to form. The ability of allopurinol to protect tissues not containing xanthine oxidase against reoxygenation injury may be related to radical scavenging by allopurinol and oxypurinol.     

Databases and software for the analysis of mutations in the human p53 gene, human hprt gene and both the lacI and lacZ gene in transgenic rodents.

We have created databases and software applications for the analysis of DNA mutations at the human p53 gene, the human hprt gene and both the rodent transgenic lacI and lacZ loci. The databases themselves are stand-alone dBASE files and the software for analysis of the databases runs on IBM-compatible computers with Microsoft Windows. Each database has a separate software analysis program. The software created for these databases permit the filtering, ordering, report generation and display of information in the database. In addition, a significant number of routines have been developed for the analysis of single base substitutions. One method of obtaining the databases and software is via the World Wide Web. Open the following home page with a Web Browser: http://sunsite.unc.edu/dnam/mainpage. html . Alternatively, the databases and programs are available via public FTP from: anonymous@sunsite.unc.edu. There is no password required to enter the system. The databases and software are found beneath the subdirectory: pub/academic/biology/dna-mutations. Two other programs are available at the site, a program for comparison of mutational spectra and a program for entry of mutational data into a relational database.     

MAD: a suite of tools for microarray data management and processing

SUMMARY: Microarray data management and processing (MAD) is a set of Windows integrated software for microarray analysis. It consists of a relational database for data storage with many user-interfaces for data manipulation, several text file parsers and Microsoft Excel macros for automation of data processing, and a generator to produce text files that are ready for cluster analysis. AVAILABILITY: Executable is available free of charge on http://pompous.swmed.edu. The source code is also available upon request.     

DNA array analysis in a Microsoft Windows environment.

Microsoft Windows-based computers have evolved to the point that they provide sufficient computational and visualization power for robust analysis of DNA array data. In fact, smaller laboratories might prefer to carry out some or all of their analyses and visualization in a Windows environment, rather than alternative platforms such as UNIX. We have developed a series of manually executed macros written in Visual Basic for Microsoft Excel spreadsheets, that allows for rapid and comprehensive gene expression data analysis. The first macro assigns gene names to spots on the DNA array and normalizes individual hybridizations by expressing the signal intensity for each gene as a percentage of the sum of all gene intensities. The second macro streamlines statistical consideration of the confidence in individual gene measurements for sets of experimental replicates by calculating probability values with the Student's t test. The third macro introduces a threshold value, calculates expression ratios between experimental conditions, and calculates the standard deviation of the mean of the log ratio values. Selected columns of data are copied by a fourth macro to create a processed data set suitable for entry into a Microsoft Access database. An Access database structure is described that allows simple queries across multiple experiments and export of data into third-party data visualization software packages. These analysis tools can be used in their present form by others working with commercial E. coli membrane arrays, or they may be adapted for use with other systems. The Excel spreadsheets with embedded Visual Basic macros and detailed instructions for their use are available at http://www.ou.edu/microarray.     

遗传学实验显微图像采集与演示系统设计

利用 Microsoft® Visual Basic 6.0 设计开发了“遗传学实验显微图像采集与演示系统”,该系统主要包括图像采集和编辑、文本输入和编辑,实验指导和图像演示、图像检索和数据库管理、系统维护及帮助等功能,各部分都以窗口形式设计,既可采用视频图像采集卡实时捕获图像,又可通过扫描仪、数码相机、剪贴板或文件输入已有的图像,并经压缩技术处理后与文字说明、实验指导一同存入数据库,方便、快捷、灵活地实现了对图像的输入和编辑、查询和演示,无论是对教师的遗传学实验教学,还是对学生的遗传学实验的自学,都起到了良好的辅助作用。Abstract: A system for capturing and showing micrographs of genetics was designed with Microsoft® Visual Basic 6.0. The system includes many functions such as capturing and editing images, typing and editing text, teaching experiments, showing images, image retrieval, database management, system maintenance and help, all of them were developed with the form of windows. The system could collect images not only from image-grabber card in real-time but also from scanner, digital camera, clipboard and files. After utilizing the image compression technology, the images will be saved in database along with experiment instruction. With all the features referred above, the system can used as a wonderful assistant both for the teaching of genetics experiment and for the students’ learning by themselves.     

Utility and features of a customized PC Windows-based relational database for managing microbial strain data

In addition to storing microbes, culture collections in industry, government or universities manage a vast and continuously expanding library of information on strain history and properties. An efficient and cost-effective computer database system is required for entering, analyzing and searching these data. This report describes the utility and features of a comprehensive database which consists of a commercially available relational database system combined with customized screens for data entry, viewing and report generation. The application was developed using Microsoft Access and Visual Basic to operate in the Windows environment on a local area network. Received 18 June 1997/ Accepted in revised form 21 November 1997     

A low-temperature-sensitive intermediate state between S2 and S3 in photosynthetic water oxidation deduced by means of thermoluminescence measurements

The temperature dependence of S-state transitions in Photosystem II was measured by means of thermoluminescence using two different protocols for low-temperature flash excitation: protocol A, “last flash at low temperature”, and protocol B, “all flashes at low temperature”. Comparison of the temperature-dependence curves obtained by these two protocols revealed a marked difference particular for the three-flash experiments. The difference was attributed to the formation of a low-temperature sensitive precursor state between S₂ and S₃. The state is formed by two flash illumination given at −5 to −50°C, spontaneously transforms to normal S₃ on dark warming, and is not converted to S₀ by the 3rd flash. The precursor state was tentatively assigned to an S₃ in which H⁺ release is not completed.     

A software tool for standardised non-destructive biomass estimation in short rotation forestry

Following an evaluation of the various methods available for non-destructive biomass estimation in short rotation forestry, a standardised procedure was defined and incorporated into a computer programme (BioEst). Special efforts were made to ensure that the system can be used by people who are unfamiliar with computers and mathematics. BioEst provides an interface between a calliper and a spreadsheet programme which was written in Microsoft Excel macro language. Therefore, it is simple to modify the programme and create personal protocols. BioEst can be run on a portable PC with Microsoft Excel for Windows. The computer continuously recalculates an estimate of the amount of biomass per hectare, as well as some summary statistics, when fed data on shoot diameter obtained by making row-section-wise measurements with a standard digital calliper. BioEst is available without cost from the author.     

The Lower Row Monkey Cage: An Overlooked Variable in Biomedical Research

A survey of 96 primatological articles revealed that cage location of research monkeys is rarely mentioned, although the environment of upper and lower row-housed animals markedly differs in terms of light quality, light intensity, and living dimension. Not accounting for these uncontrolled variables may increase variability of data and, consequently, the number of experimental animals needed to obtain statistically acceptable results. This study concluded that single-tier housing would be an important refinement of research methodology. Such housing would (a) enable all animals of a room to use the “arboreal ”dimension of their enclosure and retreat to “safe ”vantage points above the human “predator, ”(b) offer all animals access to uniform light, and (c) provide more favorable conditions for professional animal care.     

Levels of citation of nonhuman animal studies conducted at a Canadian research hospital

The publication of scientific articles that receive few or no citations raises questions of the appropriate use of resources as well as ethics. In the case of animal research, the ethics issue extends beyond human patients to nonhuman animals, as the research subjects them to pain and, typically, to death. This study is a citation analysis of animal research conducted at Toronto's Hospital for Sick Children (HSC). Of the 594 publications (1990 to 1995) on animal research by affiliates of HSC, 29% received fewer than 10 citations in a 10-year period. We compare the research history of 13 “best ”and 13 “worst ”HSC scientists. Worst researchers continue to do infrequently cited research. Recommendations indicate how institutions and researchers can become more effective and accountable.     

CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data

SUMMARY: This synopsis provides an overview of array-based comparative genomic hybridization data display, abstraction and analysis using CGHAnalyzer, a software suite, designed specifically for this purpose. CGHAnalyzer can be used to simultaneously load copy number data from multiple platforms, query and describe large, heterogeneous datasets and export results. Additionally, CGHAnalyzer employs a host of algorithms for microarray analysis that include hierarchical clustering and class differentiation. AVAILABILITY: CGHAnalyzer, the accompanying manual, documentation and sample data are available for download at http://acgh.afcri.upenn.edu. This is a Java-based application built in the framework of the TIGR MeV that can run on Microsoft Windows, Macintosh OSX and a variety of Unix-based platforms. It requires the installation of the free Java Runtime Environment 1.4.1 (or more recent) (http://www.java.sun.com).     

BioEditor-simplifying macromolecular structure annotation

SUMMARY: BioEditor is an application to enable scientists and educators to prepare and present structure annotations containing formatted text, graphics, sequence data, and interactive molecular views. It is intended to bridge the gap between printed journal articles and Internet presentation formats. BioEditor is relevant in the era of structural genomics, where annotation and publication could become the rate determining step in structure determination. AVAILABILITY: BioEditor is available at http://bioeditor.sdsc.edu. The Web site includes the latest version of the software for Microsoft Windows, including documentation, the opportunity to submit bug reports and suggestions, example documentaries prepared with BioEditor and a repository where users can submit documentaries for posting to the site.     

Actual and potential dark respiration rates and different electron transport pathways in freshwater aquatic plants

The rates of respiratory O₂ uptake have been studied in leaves, stems and whole shoots of several freshwater plants: 6 angiosperms, 2 bryophytes and one alga. For angiosperm leaves, rates varied widely with species (30–142 μmol O₂ (gDW)⁻¹ h⁻¹), were correlated with chlorophyll content and were higher than those of the stems (13–71 μmol O₂ (gDQ)⁻¹ h⁻¹). The rates for the shoots of bryophytes (53–66 μmol O₂ (gDW)⁻¹ h⁻¹) and for the alga Cladophora glomerata (L.) Kütz. (96 μmol O₂ (gDW)⁻¹ h⁻¹) were slightly higher than those of most angiosperm stems, but lower than those for most leaves.

These plants had a significant cyanide-resistant respiration, suggesting the existence of an alternative pathway to the “classic” cytochrome system. This pathway was found to be active in all the species studied, as judged by responses to a specific inhibitor, SHAM (salicylhydroxamic acid). Measurement of electron-transport system (ETS) activity showed that there is a large electron-transport capacity which is not normally used by respiration in vivo.     

GeneRecords: a relational database for GenBank flat file parsing and data manipulation in personal computers

Extracting the desired data from a database entry for later analysis is a constant need in the biological sequence analysis community; GeneRecords 1.0 is a solution for GenBank biological flat file parsing, as it implements a structured representation of each feature and feature qualifier in GenBank following import in a common database managing system usable in a personal computer (Macintosh and Windows environments). This collection of related databases enables the local management of GenBank records, allowing indexing, retrieval and analysis of both information and sequences on a personal computer. AVAILABILITY: The current release, including the FileMaker Pro runtime application (built for Windows and Macintosh environments), is freely available at http://apollo11.isto.unibo.it/software/