The Role of Informatics in the Coordinated Management of Biological Resources Collections

The term 'biological resources' is applied to the living biological material collected, held and catalogued in culture collections: bacterial and fungal cultures; animal, human and plant cells; viruses; and isolated genetic material. A wealth of information on these materials has been accumulated in culture collections, and most of this information is accessible. Digitalisation of data has reached a high level; however, information is still dispersed. Individual and coordinated approaches have been initiated to improve accessibility of biological resource centres, their holdings and related information through the Internet. These approaches cover subjects such as standardisation of data handling and data accessibility, and standardisation and quality control of laboratory procedures. This article reviews some of the most important initiatives implemented so far, as well as the most recent achievements. It also discusses the possible improvements that could be achieved by adopting new communication standards and technologies, such as web services, in view of a deeper and more fruitful integration of biological resources information in the bioinformatics network environment.     

Report of the FELASA Working Group on evaluation of quality systems for animal units

This report compares and considers the merits of existing, internationally available quality management systems suitable for implementation in experimental animal facilities. These are: the Good Laboratory Practice Guidelines, ISO 9000:2000 (International Organization for Standardization) and AAALAC International (Association for Assessment and Accreditation of Laboratory Animal Care International). Good laboratory practice (GLP) is a legal requirement for institutions undertaking non-clinical health and environmental studies for the purpose of registering or licensing for use and which have to be 'GLP-compliant'. GLP guidelines are often only relevant for and obtainable by those institutions. ISO is primarily an external business standard, which provides a management tool to master and optimize a business activity; it aims to implement and enhance 'customer satisfaction'. AAALAC is primarily a peer-reviewed system of accreditation which evaluates the organization and procedures in programmes of animal care and use to ensure the appropriate use of animals, safeguard animal well-being (ensuring state-of-the-art housing, management, procedural techniques, etc.) as well as the management of health and safety of staff. Management needs to determine, on the basis of a facility's specific goals, whether benefits would arise from the introduction of a quality system and, if so, which system is most appropriate. The successful introduction of a quality system confers peer-recognition against an independent standard, thereby providing assurance of standards of animal care and use, improving the quality of animal studies, and contributing to the three Rs-reduction, refinement and replacement.     

GLP原则在体外毒理学评价实验室的应用

在动物福利运动的推动下,以减少、优化和替代动物试验为核心内容的体外试验系统已成为安全评价不可或缺的组成部分,在药品、化学品、化妆品毒理学评价中起到重要作用。体外试验系统不同于体内动物实验,体外毒理学实验室GLP原则的建立和运行应充分考虑体外试验系统的特殊性。目前我国专业的体外安全评价实验室的建设刚刚起步,还没有可供借鉴的成熟经验。本文从实验室组织、试验系统维护、人员职责、质量管理和运行几个方面,介绍了GLP原则在化妆品体外毒理学检验和评价实验室的应用。     

Quality of core collections for effective utilisation of genetic resources review, discussion and interpretation

Definition of clear criteria for evaluation of the quality of core collections is a prerequisite for selecting high-quality cores. However, a critical examination of the different methods used in literature, for evaluating the quality of core collections, shows that there are no clear guidelines on the choices of quality evaluation criteria and as a result, inappropriate analyses are sometimes made leading to false conclusions being drawn regarding the quality of core collections and the methods to select such core collections. The choice of criteria for evaluating core collections appears to be based mainly on the fact that those criteria have been used in earlier publications rather than on the actual objectives of the core collection. In this study, we provide insight into different criteria used for evaluating core collections. We also discussed different types of core collections and related each type of core collection to their respective evaluation criteria. Two new criteria based on genetic distance are introduced. The consequences of the different evaluation criteria are illustrated using simulated and experimental data. We strongly recommend the use of the distance-based criteria since they not only allow the simultaneous evaluation of all variables describing the accessions, but they also provide intuitive and interpretable criteria, as compared with the univariate criteria generally used for the evaluation of core collections. Our findings will provide genebank curators and researchers with possibilities to make informed choices when creating, comparing and using core collections.     

Prevention of mycoplasma contamination in leukemia-lymphoma cell lines.

The contamination of cell lines with mycoplasmas is certainly one of the major problems occurring in cultured cells. Analyzing more than 460 human leukemia-lymphoma (LL) cell lines, we found that 28% of the cultures were mycoplasma-positive. Mycoplasmas can produce extensive changes, growth arrest and cell death in the infected cultures. While mycoplasma-infected cell lines can be truly cleansed from the contaminants, all the efforts would be in vain when the cells return to a mycoplasma-infested environment or are handled with unsuitable culture practices. Hence, the main focus of mycoplasma control should be on preventing cell culture contamination. Mycoplasmas can be introduced through several routes including culture reagents and laboratory personnel. Cross-contamination from infected cell cultures within one laboratory continues to be the major source for the spread of mycoplasma. Specific technical protocols and cell culturing guidelines may be followed in order to minimize the risk of mycoplasma contamination of cell lines. This "good culture practice" is of utmost importance as faulty cell culture techniques appear to be also the main reason for the high incidence of cross-contaminated LL cell lines which according to our experience using DNA fingerprinting of some 500 LL cell lines is about 15%.     

Yeast culture collections of the world: meeting the needs of industrial researchers

The importance of selecting optimal yeast strains for research or industrial applications is often underestimated. For example, utilizing a strain background that already provides the desired stress tolerance or nutrient utilization profile can eliminate costly strain optimization. Yeast culture collections can provide not only the yeast strains but also data and curator expertise to help narrow the search for the optimal strain. While some collections are known for a broad range of cultures and services, other "boutique" collections can provide a broader selection of strains of certain categories, a surprising amount of characterization data, and assistance in selecting strains. This article provides information on dozens of yeast collections of the world, profiles of selected yeast culture collections, and the services that they provide: e.g., strain preservation for patent or safe deposit purposes, species identification service, training workshops, and consulting on yeast identification and physiology. Utilization of these services can save industrial researchers valuable time and resources.     

Safeguarding bacterial resources promotes biotechnological innovation

Environmental research delivers valuable bacterial resources for biotechnology. We believe that systematic long-term preservation of bacteria will promote future biotechnological innovations, by safeguarding the accessibility of bacteria already recognized to have interesting features and providing a “pool” of bacterial resources for novel applied research. To this end, we want to advocate the incorporation of preservation tests in environmental or applied microbiological research. This paper introduces non-specialists to different preservation methods for bacteria. Several parameters that influence long-term storage of bacterial resources are explained and practical tips and guidelines are formulated. Also, the vital role of public culture collections is highlighted and the state-of-the-art of preservation of non-pure cultures is described.     

Integrated data acquisition system for medical device testing and physiology research in compliance with good laboratory practices

In seeking approval from the US Food and Drug Administration (FDA) for clinical trial evaluation of an experimental medical device, a sponsor is required to submit experimental findings and support documentation to demonstrate device safety and efficacy that are in compliance with Good Laboratory Practices (GLP). The objective of this project was to develop an integrated data acquisition (DAQ) system and documentation strategy for monitoring and recording physiological data when testing medical devices in accordance with GLP guidelines mandated by the FDA. Data aquisition systems were developed as stand-alone instrumentation racks containing transducer amplifiers and signal processors, analog-to-digital converters for data storage, visual display and graphical user-interfaces, power conditioners, and test measurement devices. Engineering standard operating procedures (SOP) were developed to provide a written step-by-step process for calibrating, validating, and certifying each individual instrumentation unit and the integrated DAQ system. Engineering staff received GLP and SOP training and then completed the calibration, validation, and certification process for the individual instrumentation components and integrated DAQ system. Eight integrated DAQ systems have been successfully developed that were inspected by regulatory affairs consultants and determined to meet GLP guidelines. Two of these DAQ systems were used to support 40 of the pre-clinical animal studies evaluating the AbiCor artificial heart (ABIOMED, Danvers, MA). Based in part on these pre-clinical animal data, the AbioCor clinical trials began in July 2001. The process of developing integrated DAQ systems, SOP, and the validation and certification methods used to ensure GLP compliance are presented in this article.     

European guidelines for quality assurance in cervical cancer screening: recommendations for cytology laboratories.

The quality of a cervical cytology laboratory depends on adequate handling and staining of the samples, screening and interpretation of the slides and reporting of the results. These guidelines give an overview of procedures recommended in Europe to manage the balance between best patient care possible, laboratory quality assurance and cost effectiveness and will be published as a chapter 4 in the European Guidelines for Quality Assurance in Cervical Cancer Screening. The laboratory guidelines include protocols for personnel and organisation, material requirements, handling and analysing cervical samples, recording of results, quality management and communication. The section on quality management is comprehensive and includes protocols for all aspects of internal and external quality assurance. The guidelines are extensively referenced and as far as possible the recommendations are evidence-based.     

Examining the genetic variation of reference microbial cultures used within food and environmental laboratories using fluorescent amplified fragment length polymorphism analysis

Fluorescent amplified fragment length polymorphism (FAFLP) analysis was applied to genetically fingerprint 'working culture control strains' used by accredited food microbiology laboratories. A working culture control strain is defined as a subculture from a strain initially obtained from an authenticated source [such as the National Collection of Type Cultures (NCTC)] that is maintained for use with routine testing within the laboratory. Working culture control strains from eight food examination laboratories, representing four bacterial species, were analysed by FAFLP; these were Salmonella Nottingham, Staphylococcus aureus, Listeria monocytogenes and Bacillus cereus. The resultant FAFLP profiles of the eight working culture control strains for each of these species were compared against the appropriate freeze-dried ampoules obtained directly from NCTC. FAFLP results demonstrated that within 50% of working cultures analysed, several laboratories were routinely using working cultures that were genetically different from the original reference NCTC strains. This study highlights the need for laboratories to review the protocols used to process and maintain control strains and working cultures, with a potential view to utilize single-use quality control materials.     

Glycolipoprotein cytotoxin from Leptospira interrogans serovar copenhageni

Lipopolysaccharide (LPS), glycolipoprotein (GLP) and lipid extract were prepared from Leptospira interrogans serovar copenhageni. GLP, lipid extract or purified fatty acids from lipid extract produced cytotoxic effects seen as cell enzyme leakage followed by cytotoxic death when tested in mouse fibroblast L929 cells in tissue culture. All extracts also agglutinated mouse erythrocytes but purified LPS was not cytotoxic. Neither GLP nor LPS were pyrogenic but both gelled Limulus amoebocyte lysate. Specific anti-GLP IgG neutralized the cytotoxic and haemagglutinating effect of GLP; however, at higher concentrations it enhanced the cytotoxicity of GLP and mediated lysis of the erythrocytes. A high dose of leptospires (i.e. 10(10) organisms) killed weanling mice causing pathological changes similar to those seen in acute leptospirosis. Similar results were obtained with live, dead, pathogenic and saprophytic leptospires. The results suggest that toxicity is involved in leptospiral infection and that lipid components either of whole leptospires or of a leptospiral GLP may contribute to the pathogenesis of acute leptospirosis.     

In-Use Evaluation of a Commercially Available Set of Quality Control Cultures

Increasing awareness of the need for a uniform quality control program prompted an evaluation of a commercially available set (Bact-Chek) of eight organisms. A protocol was designed in which this set of control cultures was tested simultaneously in the clinical microbiology laboratory of a 400-bed hospital (the Berkshire Medical Center) and in the reference laboratories of the Bacteriology Section of the Center for Disease Control. The results indicate that the Bact-Chek organisms are essentially as advertised: they constitute a basic set of cultures for a quality control program in clinical microbiology. Ninety per cent of the media and reagents (excluding mycobacterial media and reagents) in the clinical laboratory were checked with this set of eight cultures. Additional cultures not in the set were used to check the remaining 10% of the media and reagents.     

Comparative evaluation of different preservation methods for cyanobacterial strains

Maintaining pure cultures using preservation methods is of high importance for biotechnological purposes. However, preservation does not necessarily guarantee the genetic stability of these cultures. Therefore, preservation methods are currently needed to assure viability as well as genetic, physiological, and morphological integrity across storage periods. In this study, preservation of five isolates from the microalgae and cyanobacteria collection of the Plant Biology Department, Federal University of Viçosa, Minas Gerais, Brazil was investigated via monthly analyses of cell viability, biomass recovery, and contaminant concentrations over a period of 120 days. Lyophilization was adequate for both heterocystous cyanobacteria and other strains that were able to differentiate hormogones or to synthesize thick layers of exopolysaccharides. Lyophilization was also able to maintain cultures with low levels of contaminants. Dimethyl sulfoxide was relatively efficient, though some of the strains were susceptible to its cytotoxic effects. Our results demonstrated that cryopreservation with glycerol was the most efficient method. The ability to routinely preserve cyanobacterial strains reduces costs associated with maintaining large culture collections and reduces the risks of losing particular strains or species through contamination and genetic drift. The results obtained in this study are therefore discussed in the context of the efficiency of the methods and the current need to develop suitable methods for maintenance of cyanobacterial collections.     

ESTIMATING THE HERITABILITY OF FLUCTUATING ASYMMETRY IN FIELD DROSOPHILA

Some studies have found intermediate heritabilities for fluctuating asymmetry (FA) in traits, but almost all of these are flawed and/or based on laboratory experiments. We therefore tested if there was heritable variation for FA in bristle and wing traits in three field collections of Drosophila melanogaster by rearing F₁s from field flies under laboratory conditions. One of the collections was reared to the F₂ generation in the laboratory to compare heritability estimates from the laboratory with those from the field-laboratory comparison. Trait means indicated an increase in size under laboratory rearing. FAs increased in one collection, decreased in another collection, and showed no changes in the third collection under laboratory rearing. FAs from the collections tended to converge under laboratory conditions. Morphological traits were heritable under field conditions. However, FA was not significantly heritable for any of the individual traits or when FA was determined by combining traits. Comparisons of the two laboratory generations showed that FA heritability was low under laboratory conditions, in contrast to the morphological traits themselves. These findings suggest a very low heritability for FA in field and laboratory Drosophila. FA in bristle and wing traits may therefore be a poor indicator of genetic quality in Drosophila.     

High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates

Microbial diversity studies based on the cloning and sequencing of DNA from nature support the conclusion that only a fraction of the microbial diversity is currently represented in culture collections. Out of over 40 known prokaryotic phyla, only half have cultured representatives. In an effort to culture the uncultured phylotypes from oligotrophic marine ecosystems, we developed high-throughput culturing procedures that utilize the concept of extinction culturing to isolate cultures in small volumes of low-nutrient media. In these experiments, marine bacteria were isolated and cultivated at in situ substrate concentrations-typically 3 orders of magnitude less than common laboratory media. Microtiter plates and a newly developed procedure for making cell arrays were employed to raise the throughput rate and lower detection sensitivity, permitting cell enumeration from 200-microl aliquots of cultures with densities as low as 10(3) cells/ml. Approximately 2,500 extinction cultures from 11 separate samplings of marine bacterioplankton were screened over the course of 3 years. Up to 14% of the cells collected from coastal seawater were cultured by this method, which was 14- to 1,400-fold higher than the numbers obtained by traditional microbiological culturing techniques. Among the microorganisms cultured were four unique cell lineages that belong to previously uncultured or undescribed marine Proteobacteria clades known from environmental gene cloning studies. These cultures are related to the clades SAR11 (alpha subclass), OM43 (beta subclass), SAR92 (gamma subclass), and OM60/OM241 (gamma subclass). This method proved successful for the cultivation of previously uncultured marine bacterioplankton that have consistently been found in marine clone libraries.     

Quality assurance of computer systems what is needed to comply with ISO 9000, GMP,GLP, and GCP?

This paper will interpret the application of the different quality standards like Good Manufacturing Practice (GMP), Good Laboratory Practice (GLP), Good Clinical Practice (GCP) and ISO 9000-3 guidelines to computer systems. The ISO 9000-3 contains requirements for developing software, whereas the GxPs have more detailed requirements for use. ISO 9000-3 can be used profitably as a tool for the GxPs. The standards often have vague demands which need to be interpreted. The wordings of the standards are compared to current interpreted requirements. Tables for comparison of the wording of the standards are also included.     

Viability testing and characterization of germination of fungal spores by automatic image analysis

Fungal spores are used in the laboratory for culture maintenance and at laboratory and other scales as inocula for fermentations. The spore swelling and germination processes constitute a major part of the lag phase, and the subsequent culture morphology and productivity can be greatly influenced by the initial concentration and condition of the spores. An image analysis method has been developed for assessing the viability and the germination characteristics of fungal spores in submerged cultures. Structural variations during germination, i.e., swelling, germ tube formation, and germ tube elongation, are measured in terms of distributions of spore volumes and of germ tube lengths and volumes. These measurements are fully automatic and give a very rapid assessment of spore viability. This image analysis method might be used as a tool in culture maintenance and for determining the quality of inocula for fungal fermentations. (c) 1993 John Wiley & Sons, Inc.     

Optimising the viability during storage of freeze-dried cell preparations of Campylobacter jejuni

Freeze-dried cultures of Campylobacter jejuni are used in the food and microbiological industry for reference materials and culture collections. However, C. jejuni is very susceptible to damage during freeze-drying and subsequent storage and it would be useful to have longer-lasting cultures. The survival of C. jejuni during freeze-drying and subsequent storage was investigated with the aim of optimising survival. C. jejuni was freeze-dried using cultures of different age (24-120 h), various lyoprotectants (10% phytone peptone, proteose peptone, peptonized milk, trehalose, soytone and sorbitol), various storage (air, nitrogen and vacuum) and re-hydration (media, temperature and time) conditions. One-day-old cultures had significantly greater survival after freeze-drying than older cultures. The addition of trehalose to inositol broth as a lyoprotectant resulted in almost 2 log(10) increase in survival after 2 months storage at 4 degrees C. Storage in a vacuum atmosphere and re-hydration in inositol broth at 37 degrees C increased recovery by 1-2 log(10) survival compared to re-hydration in maximal recovery diluent (MRD) after storage at 4 degrees C. Survival during storage was optimal when a one-day-old culture was freeze-dried in inositol broth plus 10% (w/v) trehalose, stored under vacuum at 4 degrees C and re-hydrated at the same incubation temperature (37 degrees C) in inositol broth for 30 min. The results demonstrate that the survival of freeze-dried cells of C. jejuni during storage can be significantly increased by optimising the culture age, the lyoprotectant, and the storage and re-hydration conditions. The logarithmic rate of loss of viability (K) followed very well an inverse dependence on the absolute temperature, i.e., the Arrhenius rate law. Extrapolation of the results to a more typical storage temperature (4 degrees C) predicted a very low K value of 1.5 x 10(-3). These results will be useful to the development of improved reference materials and samples held in culture collections.     

Murine lung injury caused by Leptospira interrogans glycolipoprotein,a specific Na/K-ATPase inhibitor

Background

Leptospiral glycolipoprotein (GLP) is a potent and specific Na/K-ATPase inhibitor. Severe pulmonary form of leptospirosis is characterized by edema, inflammation and intra-alveolar hemorrhage having a dismal prognosis. Resolution of edema and inflammation determines the outcome of lung injury. Na/K-ATPase activity is responsible for edema clearance. This enzyme works as a cell receptor that triggers activation of mitogen-activated protein kinase (MAPK) intracellular signaling pathway. Therefore, injection of GLP into lungs induces injury by triggering inflammation.

Methods

We injected GLP and ouabain, into mice lungs and compared their effects. Bronchoalveolar lavage fluid (BALF) was collected for cell and lipid body counting and measurement of protein and lipid mediators (PGE₂ and LTB₄). The levels of the IL-6, TNFα, IL-1B and MIP-1α were also quantified. Lung images illustrate the injury and whole-body plethysmography was performed to assay lung function. We used Toll-like receptor 4 (TLR4) knockout mice to evaluate leptospiral GLP-induced lung injury. Na/K-ATPase activity was determined in lung cells by nonradioactive rubidium incorporation. We analyzed MAPK p38 activation in lung and in epithelial and endothelial cells.

Results

Leptospiral GLP and ouabain induced lung edema, cell migration and activation, production of lipid mediators and cytokines and hemorrhage. They induced lung function alterations and inhibited rubidium incorporation. Using TLR4 knockout mice, we showed that the GLP action was not dependent on TLR4 activation. GLP activated of p38 and enhanced cytokine production in cell cultures which was reversed by a selective p38 inhibitor.

Conclusions

GLP and ouabain induced lung injury, as evidenced by increased lung inflammation and hemorrhage. To our knowledge, this is the first report showing GLP induces lung injury. GLP and ouabain are Na/K-ATPase targets, triggering intracellular signaling pathways. We showed p38 activation by GLP-induced lung injury, which was may be linked to Na/K-ATPase inhibition. Lung inflammation induced by GLP was not dependent on TLR4 activation.