Microcomputer simulation as an aid in analyzing data and teaching the principles of glomerular dynamics

This report describes a simple program, written in BASIC language, that closely emulates a previously published network thermodynamic model of glomerular dynamics. While the latter requires the SPICE 2 simulation program and a mainframe computer for its execution, the present program operates on any IBM-compatible microcomputer. It has equal utility as an aid in the interpretation of laboratory studies of glomerular dynamics and as a tool for teaching the intricacies of the control of glomerular function. The program is available in 'user friendly' format that obviates the need for any expertise in the use of computers.     

Microbial aerosol generation during laboratory accidents and subsequent risk assessment

AIM: To quantify microbial aerosols generated by a series of laboratory accidents and to use these data in risk assessment. METHODS AND RESULTS: A series of laboratory accident scenarios have been devised and the microbial aerosol generated by them has been measured using a range of microbial air samplers. The accident scenarios generating the highest aerosol concentrations were, dropping a fungal plate, dropping a large bottle, centrifuge rotor leaks and a blocked syringe filter. Many of these accidents generated low particle size aerosols, which would be inhaled into the lungs of any exposed laboratory staff. Spray factors (SFs) have been calculated using the results of these experiments as an indicator of the potential for accidents to generate microbial aerosols. Model risk assessments have been described using the SF data. CONCLUSIONS: Quantitative risk assessment of laboratory accidents can provide data that can aid the design of containment laboratories and the response to laboratory accidents. SIGNIFICANCE AND IMPACT OF THE STUDY: A methodology has been described and supporting data provided to allow microbiological safety officers to carry out quantitative risk assessment of laboratory accidents.     

Occupational medicine programs for animal research facilities

Occupational medicine is a key component of a comprehensive occupational health and safety program in support of laboratory animal research and production facilities. The mission of the department is to maximize employee health and productivity utilizing a population health management approach, which includes measurement and analysis of health benefits utilization. The department works in close cooperation with other institutional health and safety professionals to identify potential risks from exposure to physical, chemical, and biological hazards in the workplace. As soon as exposures are identified, the department is responsible for formulating and providing appropriate medical surveillance programs. Occupational medicine is also responsible for targeted delivery of preventive and wellness services; management of injury, disease, and disability; maintenance of medical information; and other clinic services required by the institution. Recommendations are provided for the organization and content of occupational medicine programs for animal research facilities.     

Part-time employees in the research facility

As the "eyes and ears" of the biomedical research team, laboratory animal technicians perform functions essential to maintaining the health of the laboratory animals, and advocate their welfare. The author describes a program that allows part-time employees to perform some of the laboratory animal technician responsibilities when facilities are understaffed and low on funds.     

The concurrent growth of plants and chemical purification of wastewater used as a hydroponic unit

In this study the seedling of a variety of plants were successfully grown hydroponically on raw wastewater obtained from one of the main sewer outfalls in Beirut. In the first phase, a series of experiments was run on a batch system in glass or plastic containers provided with aeration facilities. A continuous-flow system with recirculation was adopted in the second phase. Iron supplementation was applied in all cases to compensate for its deficiency in the raw wastewater used. The immediate and ultimate objectives of the project were threefold: (a) to demonstrate the feasibility of utilizing as a hydroponic medium untreated municipal wastewater having relatively high mean values for BOD and mineral content; (b) to achieve the growth of useful plants on such readily available hydroponic media, thereby saving on fertilizers and scarce water resources; and (c) reclamation of the wastewater through biological purification leading to the gradual depletion of the nutritive constituents. Experimental conditions are described, and the data presented leads to the conclusion that the system is practicable on a laboratory scale. It has great potential for trial on a pilot scale prior to field applications in developing countries suffering from water shortage and hard currency expended on imported fertilizers and wastewater purification facilities.     

模型动物斑马鱼及其特定病原净化

虽然斑马鱼等实验用鱼已经成为生命科学研究的一类重要模型动物,但对于在集约化人工养殖过程中实验鱼的疾病却研究很少。实验用斑马鱼严重的健康问题使其在研究中常出现大面积甚至毁灭性的死亡。常见的感染也可以危及很多实验室的鱼群。因此,培育健康的实验用鱼群,建立必要的质量控制标准已经势在必行。本文收集和分析了大量相关的资料,为我国实验用鱼疾病的控制以及标准化研究和培育SPF斑马鱼提供帮助。     

A program against bacterial bioterrorism: improved patient management and acquisition of new knowledge on infectious diseases

In 2002 it was decided to establish laboratory facilities in Denmark for diagnosing agents associated with bioterrorism in order to make an immediate appropriate response to the release of such agents possible. Molecular assays for detection of specific agents and molecular and proteomic techniques for identification of bacteria were introduced as part of the program. All assays and techniques were made accessible for use in diagnosing patients, even when an intentional release was not suspected. Medical expertise on different diseases was established at the department as an integrated part of the program. The analyses included PCR assays for specific bacteria, identification of isolated bacteria by DNA sequencing, detection and identification of bacteria in clinical sample material by universal bacterial PCR and DNA sequencing, and identification of bacteria by mass spectrometry. The established analyses formed a basis on which a series of further developments was built. In addition to reducing the time for obtaining diagnoses and improving the accuracy of diagnosis of individual infected patients, the analyses provided new knowledge on the frequency and distribution of some bacterial infections, including Q fever, tularemia, trench fever, brucellosis, and melioidosis. The implementation of an antibioterrorism program in a clinical diagnostic setting improved the diagnostic possibilities for patients in Denmark and provided new epidemiologic information. It also introduced a number of diagnostic assays for bacterial infections not associated with bioterrorism that are difficult to culture or identify.     

Environmental enrichment for laboratory rodents

Modernization of housing and husbandry techniques for rodents has minimized confounding variables. The result has been vastly improved health maintenance and reproducibility of research findings, advances that have decreased the numbers of animals needed to attain statistically significant results. Even though not all aspects of rodent manipulation have been strictly defined, as housing and handling procedures have become increasingly standardized, many animal care personnel have recognized the lack of complexity of the rodents' environment. Concern for this aspect of animal well-being has led many research facilities to provide "environmental enrichment" for rodents. Additionally, regulatory agencies in the United States and Europe have also been increasingly concerned about this issue relative to laboratory animal husbandry. However, little is known about the influence such husbandry modifications may have on biological parameters. In this article, laws and guidelines relating to rodent enrichment are reviewed, the natural behaviors of select rodent species are discussed, and an overview of widely used types of enrichment in laboratory rodent management is provided. The literature evaluating effects of rodent enrichment is reviewed both in terms of neurological development and as an experimental variable, and results of a study evaluating the effect of enrichment on immune and physiological parameters are reported. Survey data on current enrichment practices in a large multi-institutional organization are presented, and practical aspects requiring consideration when devising a rodent enrichment program are discussed.     

A general purpose non-linear curve fitting program for the British Broadcasting Corporation Microcomputer

Software for non–linear curve fitting has been writtenin BASIC to execute on the British Broadcasting CorporationMicrocomputer. The program uses the direct search algorithmPattern–search, a robust algorithm that has the additionaladvantage of needing specification of the Junction without inclusionof the partial derivatives. Although less efficient than gradientmethods, the program can be readily configured to solve low–dimensionaloptimization problems that are normally encountered in lifesciences. In writing the software, emphasis has been placedupon the ‘user interface’ and making the most efficientuse of the facilities provided by the minimal configurationof this system. Received on March 4, 1985; accepted on March 14, 1985     

BicAT: a biclustering analysis toolbox

SUMMARY: Besides classical clustering methods such as hierarchical clustering, in recent years biclustering has become a popular approach to analyze biological data sets, e.g. gene expression data. The Biclustering Analysis Toolbox (BicAT) is a software platform for clustering-based data analysis that integrates various biclustering and clustering techniques in terms of a common graphical user interface. Furthermore, BicAT provides different facilities for data preparation, inspection and postprocessing such as discretization, filtering of biclusters according to specific criteria or gene pair analysis for constructing gene interconnection graphs. The possibility to use different biclustering algorithms inside a single graphical tool allows the user to compare clustering results and choose the algorithm that best fits a specific biological scenario. The toolbox is described in the context of gene expression analysis, but is also applicable to other types of data, e.g. data from proteomics or synthetic lethal experiments. AVAILABILITY: The BicAT toolbox is freely available at http://www.tik.ee.ethz.ch/sop/bicat and runs on all operating systems. The Java source code of the program and a developer's guide is provided on the website as well. Therefore, users may modify the program and add further algorithms or extensions.     

Test facility for human exposure to AC and DC magnetic fields

For more than a decade, Midwest Research Institute (MRI) has investigated the effects of exposure to 60 Hz electric and magnetic fields (EMF) on human physiology, performance, and biochemistry. This accumulated experience, new research directions, and limited resources made it important to design more comprehensive and operationally cost-effective exposure facilities. Here we describe the new, integrated laboratory exposure test facilities recently constructed at MRI and present data on relevant characteristics of the exposure systems. Concentric coil systems were developed to generate uniform magnetic fields within the three new exposure rooms, with rapid cancellation of the field to ambient levels in the rest of the laboratory. Control systems are fully automated, computer-based, and independent. These provide the operational flexibility needed to present fields of different magnitudes, frequencies, and polarization. The local geomagnetic field can be modulated and/or canceled, and both AC and DC fields can be presented in various combinations. Capabilities for conducting double-blind experiments with true active-sham exposure conditions were implemented using bifilar windings and applying current flow in the opposite direction for each wire in a pair. The new facilities provide a comprehensive capability for laboratory-based human research on the potential effects of exposure to AC and DC magnetic fields.     

SOMAP: a novel interactive approach to multiple protein sequences alignment

A novel interactive method for generating multiple protein sequencealignments is described. The program has no internal limit tothe number or length of sequences it can handle and is designedfor use with DEC VAX processors running the VMS operating system.The approach used is essentially one of manual sequence manipulation,aided by built-in symbolic displays of identities and similarities,and strict and ‘fuzzy’ (ambiguous) pattern-matchingfacilities. Additional flexibility is provided by means of aninterface to a publicly available automatic alignment systemand to a comprehensive sequence analysis package. Received on August 28, 1990; accepted on November 20, 1990     

Use of a computer to group actinomycetes for studies on the ecology of soil microorganisms.

A computer program has been prepared for grouping soil actinomycetes into cluster groups based on the presence or absence of aerial mycelium, the color of soluble pigment, and the shade of color of surface and reverse mycelium. The program automatically condenses cultures with wide ranges of characteristics into a limited number of groups and provides a permanent record so that comparisons can be made among experiments performed over a span of time. The program permits the grouping of large numbers of cultures with minimal laboratory effort and has proven useful in defining some of the ecological factors that lead to changed actinomycete populations in soils.     

Redasoft Plasmid 1.1: software for easy, efficient cloning and map drawing

A computer program is described which creates circular and linear genetic maps with or without sequences, performs restriction analysis, and simulates basic molecular cloning operations. Redasoft Plasmid 1.1 is a user-friendly program for Windows 95/98/NT/2000, designed to generate high quality genetic maps for presentation and publication and to aid the molecular biologist in selecting restriction endonucleases for common molecular cloning experiments. The program incorporates an integrated web browser and can automatically generate complete, labeled maps from sequences on the Internet.     

DIODA: delineation and feature extraction of microscopical objects.

A computer program is described for delineation and measurement of microscopical objects, such as cells and chromosomes, which may have been scanned using absorbance, fluorescence or reflectance microscopy. The quality of the object delineation is optimized through the controur ratio, which is simply computed from the object contour. Geometrical features, like the perimeter and area are computed. A new definition is introduced for the background region, especially suited for the analysis of closely packed objects. This definition is based upon a comparison between total staining material content values resulting from a variety of methods and circumstances. The program is principally intended for use in the on-line real-time environment of a small laboratory computer, but may be used off-line as well. It has facilities for displaying the results and the process by which they are produced. A program module is described for displaying scan data on a bilevel display using an adaptation of the sigma-delta method.     

A 3-year experience of quality control and quality assurance in the multisite delivery of a lymphocyte-based cellular therapy for renal cell carcinoma

Autolymphocyte therapy (ALT) is outpatient-based adoptive immunotherapy using ex vivo-activated memory T-cells. To support the safe and reproducible delivery of ALT at three cell processing facilities (Boston, MA; Atlanta, GA; Orange, CA) we created a comprehensive quality assurance/quality control program compliant with recent FDA guidance relevant to activated lymphocytes and somatic cell therapies. Each facility performed extensive QC testing to ensure sterility, viability, and proper cell yield. Additonally, several QC tests were performed at Cellocr's centralized reference laboratory to monitor cell potency and identity of the ex vivo-processed lymphocytes. We report here the successful implementation of this QA/QC program for ALT which has resulted in the safe preparation and delivery of cell infusion products amounting to over 3600 treatments at seven clinical sites nationwide. We believe this program will serve as a model for other cellular therapies.     

A renewed look at laboratory rodent housing and management

Since its publication in 1996, the Guide for the Care and Use of Laboratory Animals (National Research Council, Washington DC, National Academy Press) has become a primary source of information for institutional animal care and use committees (IACUCs) and research facility managers. In the ensuing years, recommendations relating to laboratory animal care have evolved in response to new scientific information and use of new technology such as ventilated caging. In this article, recent publications are examined to determine the potential impact of new scientific evidence on current practices for the housing and care of laboratory rodents. The discussion points out recent advances in technology and new knowledge of the conditions for the housing of various laboratory rodents, including cage space, single versus group housing, ventilated caging systems, thermoregulation, bedding materials, and enrichment. This new information is provided to aid IACUCs and facility managers in making decisions regarding the housing and care of laboratory rodents.     

"SCINT," a Fortran IV program for the analysis of data for doubly labeled and variably quenched liquid scintillation samples

For some time now, we have been using double label techniques in our laboratory. In our work we generate large numbers of samples containing ¹⁴C and ³H and varying amounts of quenching agents. The analysis of this data led us to develop SCINT, a simple and versatile program written in FORTRAN IV for use on our Control Data 1700 computer facility. We feel that such a program may be of use to the many workers now involved with dual isotope procedures who also have access to similar computer facilities.     

A didactic computer simulation of the environmental impact of a pollution discharge

Algorithms for simulating the response of a benthic animal communityand several abiotic environmental variables to organic pollutionare described. An IBM PC compatible computer program incorporatingthese methods has been written. The program simulates the abundanceresponse of 23 species, the redox potential depth profile andseveral other sediment variables at any distance from a pointsource of pollution. The program has been designed as a teachingtool and examples of its use to study pollution biology andbiometrics are given. Received on April 3, 1990; accepted on September 6, 1990