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 hippocampal replay with subcortical inputs

During sleep, the hippocampus recapitulates neuronal patterns corresponding to behavioral trajectories during previous experiences. This hippocampal replay supports the formation of long-term memories. Yet, whether replay originates within the hippocampal circuitry or is initiated by extrahippocampal inputs is unknown. Here, I review recent findings regarding the organization of neuronal activity upstream to the hippocampus, in the head-direction (HD) and grid cell networks, and its relationship to replay. I argue that hippocampal activity at the onset of replay is under the influence of signals from primary spatial areas. In turn, hippocampal replay resets the HD network activity to select a new direction for the next replay event. This reciprocal interaction between the HD network and the hippocampus may be essential in grounding meaning to hippocampal activity, specifically by training decoders of hippocampal sequences. Neuronal dynamics in thalamo-hippocampal loops may thus be instrumental for memory processes during sleep.     

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.

     

Approaches for submicrosequencing

From a conventional SDS-acrylamide gel plate, protein (1 g), even after staining by dye, was extracted with 70% formic acid and purified by Biogel P-10 column chromatography in 70% formic acid. The recovery was 60–99% and the protein purified by this method was free from SDS, dyes, glycine, and buffer salts and ready to use for protein composition and sequence studies. The method can avoid the protease digestion of the protein that has often been observed in the electroelution method. For amino acid analysis, protein was hydrolyzed with a gas of a HCL/trifluoroacetic acid/H₂O mixture at 158°C for 22.5 and 45 min to avoid contamination (less than 1 pmole). The method provided sufficient hydrolysis even for hydrophobic protein. It is under process of automation. Carboxyl-terminal analysis was performed with carboxypeptidases A, B, and P in the presence of alcohols and detergents. The effects on the carboxypeptidases (and several proteases) are summarized. These additions increased the solubility of proteins and enhanced the digestion. For N-terminal sequencing, conventional Edman degradation was followed up to the ATZ-derivative and this ATZ-derivative was reacted with primary amines such as ¹²⁵I-histamine or 1-aminopyrene to produce a phenylthiocarbamyl-amino acid-amine derivative with a yield as high as 95%. The conventional procedure of Edman degradation was preserved, but instead of the acid conversion to PTH derivatives, the above coupling procedure was introduced in order to increase the sensitivity to the 1–100f mole range.This article was presented during the proceedings of the International Conference on Macromolecular Structure and Function, held at the National Defence Medical College, Tokorozawa, Japan, December 1985.     

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.     

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）的研究已成为人类后基因组时代的主要内容之一。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。文章系统地介绍了最新发展的几种SNP检测技术的原理和检测平台,详细阐述了等位基因特异性杂交、内切酶酶切技术、引物延伸法、寡核苷酸连接反应等SNP检测原理,以及平板读数仪、基因芯片、微球阵列技术和质谱仪等检测平台,并对SNP高通量检测技术的发展进行了展望。     

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.     

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.     

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.