A Laboratory Information Management System (LIMS) for a high throughput genetic platform aimed at candidate gene mutation screening

High throughput mutation screening in an automated environment generates large data sets that have to be organized and stored reliably. Complex multistep workflows require strict process management and careful data tracking. We have developed a Laboratory Information Management Systems (LIMS) tailored to high throughput candidate gene mutation scanning and resequencing that respects these requirements. Designed with a client/server architecture, our system is platform independent and based on open-source tools from the database to the web application development strategy. Flexible, expandable and secure, the LIMS, by communicating with most of the laboratory instruments and robots, tracks samples and laboratory information, capturing data at every step of our automated mutation screening workflow. An important feature of our LIMS is that it enables tracking of information through a laboratory workflow where the process at one step is contingent on results from a previous step. AVAILABILITY: Script for MySQL database table creation and source code of the whole JSP application are freely available on our website: http://www-gcs.iarc.fr/lims/. SUPPLEMENTARY INFORMATION: System server configuration, database structure and additional details on the LIMS and the mutation screening workflow are available on our website: http://www-gcs.iarc.fr/lims/     

MASTR-MS: a web-based collaborative laboratory information management system (LIMS) for metabolomics

Background

An increasing number of research laboratories and core analytical facilities around the world are developing high throughput metabolomic analytical and data processing pipelines that are capable of handling hundreds to thousands of individual samples per year, often over multiple projects, collaborations and sample types. At present, there are no Laboratory Information Management Systems (LIMS) that are specifically tailored for metabolomics laboratories that are capable of tracking samples and associated metadata from the beginning to the end of an experiment, including data processing and archiving, and which are also suitable for use in large institutional core facilities or multi-laboratory consortia as well as single laboratory environments.

Results

Here we present MASTR-MS, a downloadable and installable LIMS solution that can be deployed either within a single laboratory or used to link workflows across a multisite network. It comprises a Node Management System that can be used to link and manage projects across one or multiple collaborating laboratories; a User Management System which defines different user groups and privileges of users; a Quote Management System where client quotes are managed; a Project Management System in which metadata is stored and all aspects of project management, including experimental setup, sample tracking and instrument analysis, are defined, and a Data Management System that allows the automatic capture and storage of raw and processed data from the analytical instruments to the LIMS.

Conclusion

MASTR-MS is a comprehensive LIMS solution specifically designed for metabolomics. It captures the entire lifecycle of a sample starting from project and experiment design to sample analysis, data capture and storage. It acts as an electronic notebook, facilitating project management within a single laboratory or a multi-node collaborative environment. This software is being developed in close consultation with members of the metabolomics research community. It is freely available under the GNU GPL v3 licence and can be accessed from, https://muccg.github.io/mastr-ms/.

     

RGMIMS: a web-based Laboratory Information Management System for plant functional genomics research

A robust Laboratory Information Management System (LIMS) is required for the efficient handling of data generated from large-scale insertional mutagenesis projects. The Rice Gene Machine Information Management System (RGMIMS), a web-based modular LIMS, developed in a rice functional genomics laboratory at CSIRO, currently has four core modules: Seed Management, Transformation Management, Plant/Progeny Management, Phenotype Management, and an ad hoc querying module. RGMIMS manages, preserves and tracks large inventories of transgenic germplasm and enables efficient and accurate record keeping of the large quantities of experimental data. RGMIMS automates and seamlessly integrates multi-step experimental processes. A web user interface, incorporating barcoding utilities, enables rapid data capture and tracking of biological resources. Ontologies from Gramene and Plant Ontology consortium are used to describe mutant phenotypes. RGMIMS supports generic research processes in plant mutagenesis and could readily be adapted to general LIMS for high-throughput plant research.     

50 years of the Institute for Laboratory Animal Research (ILAR): 1953-2003

The history of the Institute for Laboratory Animal Research (ILAR) begins, as does all of laboratory animal science, with the ancient philosophers, anatomists, and physiologists whose work presaged the use of animals in biomedical research and the institutions that arose due to this use. Modern laboratory animal science and medicine began in the late 1940s and early 1950s as five Chicago-area institutions hired veterinarians to manage their animal facilities. Each of these men became instrumental in the founding of the organizations that collectively make up the laboratory animal science and medicine organizations. Nathan Brewer, one of the "Chicago five," was particularly influential in the founding of ILAR. His boss at the University of Chicago, Dr. Paul Weiss, a member of the National Academy of Sciences (NAS), asked him to help establish a committee with the stated purpose of preparing recommendations to the NAS to develop an office to obtain information on sources of supply for research animals. This office became ILAR, and Brewer was chairman of its first report on the diseases of laboratory animals. He was also a founding diplomat and first president of the American College of Laboratory Animal Medicine. This history recognizes the thoughtful and energetic contributions of scientists and veterinarians to ILAR. It provides a 50-year overview of the programs and reports of ILAR and highlights examples where these reports have been adopted by scientists and federal agencies and incorporated into national laws and policies governing the use of animals in research both in the United States and in other countries.     

Human laminin a chain (LAMA) gene: Chromosomal mapping to locus 18p11.3

Laminin, an integral component of basement membranes, consists of three subunit polypeptides, A, B1, and B2 chains. We have recently isolated cDNAs corresponding to human laminin A chain. These cDNAs were utilized for chromosomal in situ hybridizations to establish the genomic location of the laminin A chain gene. Metaphase chromosomes of PHA-stimulated human peripheral blood leukocytes were examined by in situ hybridization with 3H-labeled cDNAs, and the chromosomes were identified by R-banding (fluorochrome-photolysis-Giemsa method). The results indicated that the human laminin A chain is at locus 18p11.3. Since human laminin B1 and B2 chain genes have been previously mapped to chromosomes 7 and 1, respectively, the results indicate that genes encoding human laminin chains reside in separate chromosomes.     

TreeSNPs: a laboratory information management system (LIMS) dedicated to SNP discovery in trees

TreeSNPs is a laboratory information management system with a user-friendly Web interface for the gathering and display of data generated through medium- to large-scale single nucleotide polymorphism (SNP) identification by resequencing, in the context of whole genome association, outlier detection, quantitative trait locus, and genetic mapping studies. Its multi-gene approach allows the tracking of all the steps from candidate gene classification and prioritization to SNP discovery. The system, source code, and documentation are available for download at . An online demo version can also be accessed from the above link.     

地方医科大学实验动物管理工作水平评价指标体系的构建

目的构建地方医科大学实验动物管理工作水平评价指标体系,为高校实验动物管理工作的评价提供参考。方法根据研究主题确定咨询专家人选37人,采用Delphi法进行问卷调查和统计分析。结果两轮咨询问卷回收率分别为70．27％和76．92％。权威系数为0．855;第二轮指标体系的协调系数为0．486。结论本次研究构成的地方医科大学实验动物管理工作水平评价指标体系是可靠的。     

Animal cooperation: keeping a clean(ing) reputation

Cleaner wrasses are a model for the study of animal cooperation. Prospective clients can observe whether the cleaner works faithfully, and cleaners being watched remove just parasites while those that are not, nip the client for a tastier snack.     

动物模型在细菌生物被膜研究中的应用与展望

细菌生物被膜的形成与其致病性、耐药性密切相关,在许多由细菌导致的慢性、亚慢性感染中发挥着重要作用。动物模型广泛应用于细菌生物被膜相关感染的研究中,为其致病机理和控制策略的探究提供了强有力的科学工具。因此,本文系统阐述了哺乳类(鼠、兔、猪等)和非哺乳类(黑腹果蝇、斑马鱼、秀丽隐杆线虫等)动物模型在细菌生物被膜相关研究中的应用,并对动物模型在细菌生物被膜研究中的应用前景进行了展望,以期为研究由生物被膜导致的相关感染而选择理想动物模型提供理论支撑,从而对生物被膜感染导致的潜在危害进行防控。     

Noise Exposure,Music, and Animals in the Laboratory: A Commentary Based on Laboratory Animal Refinement and Enrichment Forum (LAREF) Discussions

The effects of noise, in general, and music, in particular, on the behavior and welfare of animals in the laboratory deserve a great deal of empirical study. However, many laboratories must develop their current practices on the basis of sparse and conflicting data. With this commentary we seek to establish some of the factors that should be taken into account in deciding how to deal with sources of uncontrolled or deliberate sound and, specifically, in determining whether to play music in the laboratory. Views differ, however, the balance of evidence supports the use of quiet music during nonhuman animals' active periods, if this practice is introduced with an awareness of the risks to welfare and research.     

Environmental Enrichment for Laboratory Rodents: Animal Welfare and the Methods of Science

Because of the difficulty of' establishing objective measures of laboratory rodents' psychological well-being, developing environmental enrichment programs that are actually beneficial to rodents destined to participate in laboratory research is particularly challenging. Many studies of effects of environmental complexity, social housing, and increases in cage size suggest that professional judgments as to the impact of diverse types of environmental enrichment on rodent welfare are not a reliable basis for evaluating the outcomes of enrichment programs for laboratory rodents. Successful enrichment programs will vary from one rodent species to another, between sexes, as well as between age classes. There is a need for objective, measurable goals for proposed environmental enrichment programs for rodents, as well a s for empirical investigations of the beneficial and detrimental consequences of proposed environmental manipulations.     

Laboratory evaluation of avermectin as a selective acaricide for use withMetaseiulus occidentalis (Nesbitt) (acarina: Phytoseiidae)

The suggestion that adding a light oil to avermectin B₁ would increase the toxicity of avermectin to spider mites and reduce its effect on predaceous mites was tested in laboratory trials withTetranychus urticae Koch andMetaseiulus occidentalis (Nesbitt) on almond and bean foliage. No differences were found in the toxicity of avermectin + oil vs. avermectin alone at the doses tested forT. urticae; all (0.025, 0.5, 1, and 5 ppm) were highly toxic. Mortality ofM. occidentalis females and larvae was not different on avermectin + oil vs. avermectin alone, but females produced more progeny on the avermectin + oil-treated foliage. At doses of 0.5 to 5 ppm, avermectin was sufficiently toxic to deplete predator populations in the field. Development of predator larvae on avermectin + oil and on avermectin alone was not different. Avermectin + oil on almond foliage aged outdoors was highly toxic after 96 h toT. urticae adults butM. occidentalis larvae survived well on residues by 96 h.M. occidentalis female survival and productivity were not different from the controls by 48 h. Hence a predator mite population might recover through larvae hatching onto residues. Avermectin + oil (3 ppm) residue on bean foliage held outdoors was still highly toxic toT. urticae after 33 days. In contrast,M. occidentalis females and larvae survived well on 48-to 96-hour-old residues. Neither predators nor spider mites placed on treated foliage (3 ppm) were able to reach untreated foliage in tests using bean plant seedlings with one leaf sprayed and one left unsprayed. Furthermore, whenM. occidentalis females were exposed to 3 ppm avermectin for 300 s or longer, mortality was significant and the fecundity of females that had been exposed for as few as 30 s was reduced significantly. Thus, while avermectin is significantly more toxic toT. urticae than toM. occidentalis, its value as a selective acaricide will depend upon learning to use it at rates that will allow the retention of sufficient prey so that surviving predators can persist. Based on these laboratory tests, such selective doses are likely to lie below 1 ppm and can best be determined in field trials.     

Animal models for photodynamic therapy (PDT)

Photodynamic therapy (PDT) employs non-toxic dyes called photosensitizers (PSs), which absorb visible light to give the excited singlet state, followed by the long-lived triplet state that can undergo photochemistry. In the presence of ambient oxygen, reactive oxygen species (ROS), such as singlet oxygen and hydroxyl radicals are formed that are able to kill cancer cells, inactivate microbial pathogens and destroy unwanted tissue. Although there are already several clinically approved PSs for various disease indications, many studies around the world are using animal models to investigate the further utility of PDT. The present review will cover the main groups of animal models that have been described in the literature. Cancer comprises the single biggest group of models including syngeneic mouse/rat tumours that can either be subcutaneous or orthotopic and allow the study of anti-tumour immune response; human tumours that need to be implanted in immunosuppressed hosts; carcinogen-induced tumours; and mice that have been genetically engineered to develop cancer (often by pathways similar to those in patients). Infections are the second biggest class of animal models and the anatomical sites include wounds, burns, oral cavity, ears, eyes, nose etc. Responsible pathogens can include Gram-positive and Gram-negative bacteria, fungi, viruses and parasites. A smaller and diverse group of miscellaneous animal models have been reported that allow PDT to be tested in ophthalmology, atherosclerosis, atrial fibrillation, dermatology and wound healing. Successful studies using animal models of PDT are blazing the trail for tomorrow''s clinical approvals.     

Live Varroa jacobsoni (Mesostigmata: Varroidae) fallen from honey bee (Hymenoptera: Apidae) colonies

The proportion of Varroa jacobsoni Oudemans that were alive and mobile when they fell from honey bees, Apis mellifera L., in hives was measured during a 20-wk period to determine the potential use of systems that prevent these mites from returning to the bees. Traps designed to discriminate between the live, fallen mites and those that are dead or immobile were used on hive bottom boards. A large fraction of the fallen mites was alive when acaricide was not in use and also when fluvalinate or coumaphos treatments were in the hives. The live proportion of mitefall increased during very hot weather. The proportion of mitefall that was alive was higher at the rear and sides of the hive compared with that falling from center frames near the hive entrance. More sclerotized than callow mites were alive when they fell. A screen-covered trap that covers the entire hive bottom board requires a sticky barrier to retain all live mites. This trap or another method that prevents fallen, viable mites from returning to the hive is recommended as a part of an integrated control program. It also may slow the development of acaricide resistance in V. jacobsoni and allow the substitution of less hazardous chemicals for the acaricides currently in use.     

Primer Design Assistant (PDA): A web-based primer design tool

Primer Design Assistant (PDA) is a web interface primer design service combined with thermodynamic theory to evaluate the fitness of primers. It runs in a Linux-Apache-MySQL-PHP structure on a PC equipped with dual CPU (Intel Pentium III 1.4 GHz) and 512 Mb of RAM. A succinct user interface of PDA is accomplished by built-in parameters setting. Advanced options on 5' GC content, 3' GC content, dimer check and hairpin check are available. The option of covered region constrains the PCR product to cover a user-defined segment. PDA accepts single sequence query or multiple ones in FASTA format. It produces optimal and homogenous primer pairs that meet the need in experimental design with large-scaled PCR amplifications. Considering the system loading, the size of a submitted sequence is limited to 10 kb and the total sequence number in a query is limited to 20. The authors may be contacted regarding other requirements for primer design. The web application can be found at http://dbb.nhri.org.tw/primer/.