Querying and computing with BioCyc databases

We describe multiple methods for accessing and querying the complex and integrated cellular data in the BioCyc family of databases: access through multiple file formats, access through Application Program Interfaces (APIs) for LISP, Perl and Java, and SQL access through the BioWarehouse relational database.     

Querying the Obvious: Lessons from a Degraded Stream

A detailed assessment of degradation issues is essential for the development of reasonable restoration strategies. The assessment may be a difficult task when fluxes of organic matter and energy are concerned, which are primarily mediated by microorganisms. In small streams, biofilms are hot spots of trophic interactions. Small weirs cause small‐scale changes of flow velocity, which affects the formation, structure, and function of biofilms. Weirs are superficially considered as disturbing cross barriers that should immediately be removed for the restoration of riparian systems. However, our empirical studies of weirs in the stream Ilm, Germany, and conceptual modeling approaches revealed a rather beneficial effect because weirs compensate the loss of natural retention structures in straightened rivers. Longer processing time of particulate organic matter in the weir reservoirs may have a positive effect on biofilm productivity and nutrient cycling in aquatic ecosystems. This is a striking example of thorough investigations that resulted in a complete and surprising reassessment of a degradation situation, and for a case in which uninformed gut feeling decisions about management plans would have had detrimental effects.     

QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks

Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for mapping interactions between DNA regions, e.g., ChIA-PET and HiC, can generate genome-wide maps of interactions between regulatory elements. These interaction datasets are important resources to infer distal gene targets of non-coding regulatory elements and to facilitate prioritization of critical loci for important cellular functions. With the increasing diversity and complexity of genomic information and public ontologies, making sense of these datasets demands integrative and easy-to-use software tools. Moreover, network representation of chromatin interaction maps enables effective data visualization, integration, and mining. Currently, there is no software that can take full advantage of network theory approaches for the analysis of chromatin interaction datasets. To fill this gap, we developed a web-based application, QuIN, which enables: 1) building and visualizing chromatin interaction networks, 2) annotating networks with user-provided private and publicly available functional genomics and interaction datasets, 3) querying network components based on gene name or chromosome location, and 4) utilizing network based measures to identify and prioritize critical regulatory targets and their direct and indirect interactions. AVAILABILITY: QuIN’s web server is available at http://quin.jax.org QuIN is developed in Java and JavaScript, utilizing an Apache Tomcat web server and MySQL database and the source code is available under the GPLV3 license available on GitHub: https://github.com/UcarLab/QuIN/.

This is a PLOS Computational Biology Software paper.

     

利用C++ Builder实现肿瘤遗传信息数据库的查询和利用

利用C＋＋ Builder,Microsoft SQL Server 2000数据库和ADO控件构建了肿瘤遗传信息的查询系统。先在数据库中建立肿瘤的生物信息表,通过C＋＋ Builder编写代码,添加ADO控件及其属性设置实现数据库的访问和信息查询。     

Querying the public databases for sequences using complex keywords contained in the feature lines

Background  

High throughput technologies often require the retrieval of large data sets of sequences. Retrieval of EMBL or GenBank entries using keywords is easy using tools such as ACNUC, Entrez or SRS, but has some limitations, in particular when querying with complex keywords.     

Morphological Approaches to Phylogeny

SYNOPSIS. Traditional views on the interrelationships of themajor animal groups are based on morphological characters, butmolecular data of various types have in the last decade givenindications of new and sometimes quite puzzling phylogenies.This should be an incentive not only to reevaluation of theavailable morphological characters but also to new studies tofill the voids in our knowledge. Modern morphology is not concernedonly with traditional studies of structure and ontogeny of organsystems, but also with newer methods, such as SEM, TEM, immunocytochemistry,and cell marking. This has given morphology new dimensions,but it also has shown that vast areas of the animal kingdomremain very poorly known even through traditional studies. Phylogenetictrees built on morphology (and molecular trees with morphologicalcharacters added) demonstrate morphological characters thatare in conflict with the phylogeny, and therefore should bereinvestigated; they also indicate areas where new researchcan contribute significantly to our understanding of the pathwaysof the evolution. Morphological phylogeny has the distinct advantagethat characters of ancestors can be inferred and the evolutionarychanges checked in terms of functional continuity and hypothesesof adaptation.     

Approaches To New Vaccines

ABSTRACT:?

The explosive technological advances in the fields of immunology and molecular biology in the last 5 years had an enormous impact on the identification of candidate vaccines against diseases, which until a few years ago seemed uncontrollable. Increased knowledge of the immune system has helped to define the mechanisms that underlie successful immunization and is now being exploited to develop improved versions of existing vaccines and new vaccines against emerging pathogens, tumors, or autoimmune diseases. An understanding of the mechanisms of action of novel adjuvants and the development of new vector and delivery systems will have a major impact on vaccine strategies. The use of DNA encoding antigens from pathogenic viruses, bacteria, and parasites as vaccines is a new approach that is receiving considerable attention. This and other innovative approaches, including vaccine production in plants, are appraised in this review. The successful eradication of smallpox and the imminent eradication of poliomyelitis by worldwide immunization campaigns provide positive examples of how the vaccine-mediated approach can lead to disease elimination; with the advent of new vaccines and improved delivery systems, there is no scientific reason why these successes cannot be repeated.     

Approaches to library screening

Fuelled by the drive to complete the Human Genome Project, many laboratories have developed new methods of screening clone libraries. From PCR-based strategies to pooling schemes and increased automation, the tedious task of library screening has become less labour-intensive and more cost-efficient. Currently, two main screening methods dominate: hybridization and polymerase chain reaction (PCR). In the following article, we present a brief overview of hybridization and PCR-based screening of yeast and bacterial libraries. Multi-faceted approaches combining different techniques, as well as less frequently employed methods such as fingerprinting are also described.     

Drinking: Anthropological Approaches

Drinking: Anthropological Approaches . Igor de Garine and Valeria de Garine. New York: Berghahn Books, 2001. 248 pp.     

单核苷酸多态性检测方法的研究进展

单核苷酸多态性(single nucleotide polymorphism,SNP)作为第三代遗传标记已经广泛应用于基因作图、疾病相关性分析、群体遗传学及药物研究等领域.因此建立高度自动化和高通量的SNP检测分析技术十分重要.简要介绍了国内外几种主要SNP检测技术的原理和检测分析手段,并对SNP高通量检测技术的发展进行了展望.     

Approaches to antiviral drug development

At present, only a few drugs have been approved by the FDA for therapy of viral infections in humans. There is a great need for antiviral drugs with increased potency and decreased toxicity, as well as drugs to treat viral diseases for which no drug or vaccine is currently available. Two approaches for development of antiviral drugs are described--an empirical strategy and a rational strategy--with several examples of each. Although many compounds have potent antiviral activity in cell culture, only a small fraction of these will go on to become antiviral drugs for use in humans. At this time, only seven synthetic compounds and alpha interferon have been approved by the FDA for therapy of viral infections in humans. None of these approved drugs are without toxicities, however, and hence there is a great need for antiviral drugs with increased potency and decreased toxicity, as well as for drugs to treat viral diseases for which no drug or vaccine is currently available. Two approaches for the development of antiviral drugs--the empirical and the rational strategies--and their applications and future directions are discussed.     

Molecular Approaches to Taenia asiatica

Taenia solium, T. saginata, and T. asiatica are taeniid tapeworms that cause taeniasis in humans and cysticercosis in intermediate host animals. Taeniases remain an important public health concerns in the world. Molecular diagnostic methods using PCR assays have been developed for rapid and accurate detection of human infecting taeniid tapeworms, including the use of sequence-specific DNA probes, PCR-RFLP, and multiplex PCR. More recently, DNA diagnosis using PCR based on histopathological specimens such as 10% formalin-fixed paraffin-embedded and stained sections mounted on slides has been applied to cestode infections. The mitochondrial gene sequence is believed to be a very useful molecular marker for not only studying evolutionary relationships among distantly related taxa, but also for investigating the phylo-biogeography of closely related species. The complete sequence of the human Taenia tapeworms mitochondrial genomes were determined, and its organization and structure were compared to other human-tropic Taenia tapeworms for which complete mitochondrial sequence data were available. The multiplex PCR assay with the Ta4978F, Ts5058F, Tso7421F, and Rev7915 primers will be useful for differential diagnosis, molecular characterization, and epidemiological surveys of human Taenia tapeworms.     

Approaches to chemical synthetic biology

Synthetic biology is first represented in terms of two complementary aspects, the bio-engineering one, based on the genetic manipulation of extant microbial forms in order to obtain forms of life which do not exist in nature; and the chemical synthetic biology, an approach mostly based on chemical manipulation for the laboratory synthesis of biological structures that do not exist in nature. The paper is mostly devoted to shortly review chemical synthetic biology projects currently carried out in our laboratory. In particular, we describe: the minimal cell project, then the "Never Born Proteins" and lastly the Never Born RNAs. We describe and critically analyze the main results, emphasizing the possible relevance of chemical synthetic biology for the progress in basic science and biotechnology.     

Audio-Visual Approaches to Science Teaching

From Instinct to Intelligence/How Animals Learn by Gloria Kirshner. Grosset &; Dunlap Publishers, 51 Madison Ave., New York, N.Y. 10010. 1970. 127 pp., $3.95. Reviewed by Robert C. Hayden.

A Pictorial History of Oceanographic Submersibles by James B. Sweeney, Crown Publishers, Inc., 419 Park Ave. South, New York, N.Y. 10016. 1970. 314 pp., Indexed, Bibliography. $9.95. Reviewed by Robert C. Hayden.

Where the Winds Sleep: Man's Future on the Moon—A Projected History by Neil P. Ruzic. Doubleday &; Co., Inc., Garden City, New York, 1970. 236 pp., Indexed. $5.95. Reviewed by Robert C. Hayden.

Hunters and Collectors by George H. T. Kimble. McGraw-Hill Book Co., 330 West 42nd St., New York, N.Y. 10036. 1970. 48 pp., Indexed. $4.95 trade edn., $4.72 lib. edn. Reviewed by Robert C. Hayden.

Life in Ponds by Jean Gorvett. American Heritage Press, New York. 1920. 31 pp. Reviewed by Robert C. Hayden.

Discovering What Goldfish Do by Seymour Simon. McGraw-Hill Book Co., 330 West 42nd St., New York, N.Y. 1970. 47 pp. $3.95 trade edn. $3.83 lib. edn. Reviewed by Robert C. Hayden.

Building and Flying Scale Model Aircraft 3rd Edition by Walter A. Musciano. Herman Publishing Service, Division of Cahners Pub. Co., Inc., 221 Columbus Ave., Boston, Mass. 02116. 1970. 245 pp. Glossary, $7.95. Reviewed by Robert C. Hayden.     

Approaches for Integrated Risk Assessment

Recognizing the need to enhance the effectiveness and efficiency of risk assessments globally, the World Health Organization's International Programme on Chemical Safety, the U.S. Environmental Protection Agency, the European Commission, and the Organization for Economic Cooperation and Development developed a collaborative partnership to foster integration of assessment approaches used to evaluate human health and ecological risks. The objectives of this effort included: improving understanding of the benefits of integration, identifying obstacles to the integration process, and engaging key agencies, organizations, and scientific societies to promote integration. A framework with supporting documentation was developed to describe an approach for integration. Four case studies were constructed to illustrate how integrated risk assessments might be conducted for chemical and nonchemical stressors. The concepts and approaches developed in the project were evaluated in an international workshop. The goal of this effort was international acceptance of guidance for integrated risk assessment.