Automatic synchronization and distribution of biological databases and software over low-bandwidth networks among developing countries

Bioinformatics involves the collection, organization and analysis of large amounts of biological data, using networks of computers and databases. Developing countries in the Asia-Pacific region are just moving into this new field of information-based biotechnology. However, the computational infrastructure and network bandwidths available in these countries are still at a basic level compared to that in developed countries. In this study, we assessed the utility of a BitTorrent-based Peer-to-Peer (btP2P) file distribution model for automatic synchronization and distribution of large amounts of biological data among developing countries. The initial country-level nodes in the Asia-Pacific region comprised Thailand, Korea and Singapore. The results showed a significant improvement in download performance using btP2P--three times faster overall download performance than conventional File Transfer Protocol (FTP). This study demonstrated the reliability of btP2P in the dissemination of continuously growing multi-gigabyte biological databases across the three Asia-Pacific countries. The download performance for btP2P can be further improved by including more nodes from other countries into the network. This suggests that the btP2P technology is appropriate for automatic synchronization and distribution of biological databases and software over low-bandwidth networks among developing countries in the Asia-Pacific region. AVAILABILITY: http://everest.bic.nus.edu.sg/p2p/     

Functional and structural genomics using PEDANT

MOTIVATION: Enormous demand for fast and accurate analysis of biological sequences is fuelled by the pace of genome analysis efforts. There is also an acute need in reliable up-to-date genomic databases integrating both functional and structural information. Here we describe the current status of the PEDANT software system for high-throughput analysis of large biological sequence sets and the genome analysis server associated with it. RESULTS: The principal features of PEDANT are: (i) completely automatic processing of data using a wide range of bioinformatics methods, (ii) manual refinement of annotation, (iii) automatic and manual assignment of gene products to a number of functional and structural categories, (iv) extensive hyperlinked protein reports, and (v) advanced DNA and protein viewers. The system is easily extensible and allows to include custom methods, databases, and categories with minimal or no programming effort. PEDANT is actively used as a collaborative environment to support several on-going genome sequencing projects. The main purpose of the PEDANT genome database is to quickly disseminate well-organized information on completely sequenced and unfinished genomes. It currently includes 80 genomic sequences and in many cases serves as the only source of exhaustive information on a given genome. The database also acts as a vehicle for a number of research projects in bioinformatics. Using SQL queries, it is possible to correlate a large variety of pre-computed properties of gene products encoded in complete genomes with each other and compare them with data sets of special scientific interest. In particular, the availability of structural predictions for over 300 000 genomic proteins makes PEDANT the most extensive structural genomics resource available on the web.     

Ensembl 2002: accommodating comparative genomics

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of human, mouse and other genome sequences, available as either an interactive web site or as flat files. Ensembl also integrates manually annotated gene structures from external sources where available. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. These range from sequence analysis to data storage and visualisation and installations exist around the world in both companies and at academic sites. With both human and mouse genome sequences available and more vertebrate sequences to follow, many of the recent developments in Ensembl have focusing on developing automatic comparative genome analysis and visualisation.     

Time Delay and Long-Range Connection Induced Synchronization Transitions in Newman-Watts Small-World Neuronal Networks

The synchronization transitions in Newman-Watts small-world neuronal networks (SWNNs) induced by time delay and long-range connection (LRC) probability have been investigated by synchronization parameter and space-time plots. Four distinct parameter regions, that is, asynchronous region, transition region, synchronous region, and oscillatory region have been discovered at certain LRC probability as time delay is increased. Interestingly, desynchronization is observed in oscillatory region. More importantly, we consider the spatiotemporal patterns obtained in delayed Newman-Watts SWNNs are the competition results between long-range drivings (LRDs) and neighboring interactions. In addition, for moderate time delay, the synchronization of neuronal network can be enhanced remarkably by increasing LRC probability. Furthermore, lag synchronization has been found between weak synchronization and complete synchronization as LRC probability is a little less than 1.0. Finally, the two necessary conditions, moderate time delay and large numbers of LRCs, are exposed explicitly for synchronization in delayed Newman-Watts SWNNs.     

Synchronization between beating cilia.

A novel quantitative parameter is proposed to define and measure the degree of synchronization between two small ciliary areas. These areas can be close to or far from one another. The Pearson correlation factor is used to define the degree of synchronization by a single number. This approach is based on a computerized, dual photoelectric method which simulataneously measures the scattered light from two small areas on the ciliary epithelium or its tissue culture. The measurements were performed on tissue culture from frog's palate epithelium. It was found that: (a) the degree of synchronization decreases, as a function of distance; (b) the correlation is fairly high even at relatively large separations, when measured on the same patch; (c) on a given patch the synchronization factor is independent of the direction of the metachronal wave; (d) close disconnected ciliary cells exhibit fairly high correlation; (e) disconnected randomly choosen ciliary cells at relatively large separation distances exhibit relatively low correlation, smaller by a factor of 2 than the correlation factor at the same distances when measured along the metachronal wave; (f) the average frequencies' ratio and the metachronal wavelength can be used as first-order indicators of ciliary synchronization; (g) there is a spread of metachronal wavelengths even over a single well-organized patch.     

A cost-effective and efficacious method of pinworm treatment for large colonies of mice

Rodent pinworm infestations are common in modern animal facilities, and treatments to eradicate these nematodes are often costly and labor-intensive. The authors describe a method they developed to treat rodents with ivermectin using the automatic watering system available at their facility. This delivery method proved an efficacious and cost-effective means of eradicating Aspiculuris tetraptera from a large colony of mice. The system might also be used to provide other orally administered agents to mice and other species.     

A Novel Gaussian Extrapolation Approach for 2D Gel Electrophoresis Saturated Protein Spots

Analysis of images obtained from two-dimensional gel electrophoresis (2D-GE) is a topic of utmost importance in bioinformatics research, since commercial and academic software available currently has proven to be neither completely effective nor fully automatic, often requiring manual revision and refinement of computer generated matches. In this work, we present an effective technique for the detection and the reconstruction of over-saturated protein spots. Firstly, the algorithm reveals overexposed areas, where spots may be truncated, and plateau regions caused by smeared and overlapping spots. Next, it reconstructs the correct distribution of pixel values in these overexposed areas and plateau regions, using a two-dimensional least-squares fitting based on a generalized Gaussian distribution. Pixel correction in saturated and smeared spots allows more accurate quantification, providing more reliable image analysis results. The method is validated for processing highly exposed 2D-GE images, comparing reconstructed spots with the corresponding non-saturated image, demonstrating that the algorithm enables correct spot quantification.     

When to go with the crowd: Modelling synchronization of all-or-nothing activity transitions in grouped animals

For groups of animals to keep together, the group members have to perform switches between staying in one place and moving to another place in synchrony. However, synchronization imposes a cost on individual animals, because they have to switch from one to the other behaviour at a communal time rather than at their ideal times. Here we model this situation analytically for groups in which the ideal times vary quasinormally and grouping benefit increases linearly with group size. Across the parameter space consisting of variation in the grouping benefit/cost ratio and variation in how costly it is to act too early and too late, the most common optimal solutions are full synchronization with the group staying together and zero synchronization with immediate dissolution of the group, if the group is too small for the given benefit/cost ratio. Partial synchronization, with animals at the tails of the distribution switching individually and the central core of the group in synchrony, occurs only at a narrow stripe of the space. Synchronization cost never causes splitting of the group into two as either zero, partial or full synchronization is always more advantageous. Stable solutions dictate lower degree of synchrony and lower net benefits than optimal solutions for a large range of the parameter values. If groups undergo repeated synchronization challenges, they stay together or quickly dissolve, unless the animals assort themselves into a smaller group with less variation in the ideal times. We conclude with arguing that synchronization cost is different from other types of grouping costs since it does not increase much with increasing group size. As a result, larger groups may be more stable than smaller groups. This results in the paradoxical prediction that when the grouping benefit/grouping cost ratio increases, the average group sizes might decrease, since smaller groups will be able to withstand synchronization challenges.     

植物激素相关核酸和蛋白质二级数据库的构建与应用

以NCBI维护的一级数据库为数据源建立植物激素相关核酸和蛋白质二级数据库。将该二级数据库设计为基因、蛋白质和文献三部分, 编写软件从上述数据源中采集数据, 并以XML作为中间格式保存, 通过解析提交到二级数据库中并集成部分生物信息学工具软件, 初步实现了数据检索、统计分析、基于Web的本地化BLAST同源序列检索、序列的自动拼接以及蛋白质结构和功能位点的分析等功能。该二级数据库的构建为植物激素作用分子机理研究提供了高针对性的植物激素数据源和生物信息学辅助工具。     

The PEDANT genome database

The PEDANT genome database (http://pedant.gsf.de) provides exhaustive automatic analysis of genomic sequences by a large variety of established bioinformatics tools through a comprehensive Web-based user interface. One hundred and seventy seven completely sequenced and unfinished genomes have been processed so far, including large eukaryotic genomes (mouse, human) published recently. In this contribution, we describe the current status of the PEDANT database and novel analytical features added to the PEDANT server in 2002. Those include: (i) integration with the BioRS data retrieval system which allows fast text queries, (ii) pre-computed sequence clusters in each complete genome, (iii) a comprehensive set of tools for genome comparison, including genome comparison tables and protein function prediction based on genomic context, and (iv) computation and visualization of protein-protein interaction (PPI) networks based on experimental data. The availability of functional and structural predictions for 650 000 genomic proteins in well organized form makes PEDANT a useful resource for both functional and structural genomics.     

Mi-DISCOVERER: A bioinformatics tool for the detection of mi-RNA in human genome

MicroRNAs (miRNAs) are 22 nucleotides non-coding RNAs that play pivotal regulatory roles in diverse organisms including the humans and are difficult to be identified due to lack of either sequence features or robust algorithms to efficiently identify. Therefore, we made a tool that is Mi-Discoverer for the detection of miRNAs in human genome. The tools used for the development of software are Microsoft Office Access 2003, the JDK version 1.6.0, BioJava version 1.0, and the NetBeans IDE version 6.0. All already made miRNAs softwares were web based; so the advantage of our project was to make a desktop facility to the user for sequence alignment search with already identified miRNAs of human genome present in the database. The user can also insert and update the newly discovered human miRNA in the database. Mi-Discoverer, a bioinformatics tool successfully identifies human miRNAs based on multiple sequence alignment searches. It's a non redundant database containing a large collection of publicly available human miRNAs.     

A new progressive-iterative algorithm for multiple structure alignment

MOTIVATION: Multiple structure alignments are becoming important tools in many aspects of structural bioinformatics. The current explosion in the number of available protein structures demands multiple structural alignment algorithms with an adequate balance of accuracy and speed, for large scale applications in structural genomics, protein structure prediction and protein classification. RESULTS: A new multiple structural alignment program, MAMMOTH-mult, is described. It is demonstrated that the alignments obtained with the new method are an improvement over previous manual or automatic alignments available in several widely used databases at all structural levels. Detailed analysis of the structural alignments for a few representative cases indicates that MAMMOTH-mult delivers biologically meaningful trees and conservation at the sequence and structural levels of functional motifs in the alignments. An important improvement over previous methods is the reduction in computational cost. Typical alignments take only a median time of 5 CPU seconds in a single R12000 processor. MAMMOTH-mult is particularly useful for large scale applications. AVAILABILITY: http://ub.cbm.uam.es/mammoth/mult.     

The Ensembl genome database project

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is available as either an interactive web site or as flat files. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation. The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.     

Visuomotor synchronization: Analysis of the initiation and stable synchronization phases

The initiation phase of visuomotor synchronization and the phase of stable synchronization were studied in an experiment where eight adult subjects synchronized their motor responses with an isochronous sequence of visual stimuli. The period of the sequence varied in a wide range (from 500 to 2200 ms). Analysis of the statistical characteristics of synchronization errors (asynchronies) showed that the phase of stable visuomotor synchronization fit the model of current phase correction of a central timer; as in the case of audiomotor synchronization, the variability of the intervals of the central timer and the phase correction coefficient increased with increasing period of the stimulus sequence. The initiation phase of visuomotor synchronization was characterized by a considerable inter-and intraindividual variability of the form (exponential, linear, or step) and duration (from one to ten responses) of the transition from reacting to a sensory signal to synchronization. The shape and duration of the transitional region depend on the phase correction coefficient and the possibility of using an estimate of the sequence period stored in memory. The obtained data indicate that the initiation stage is not automatic throughout the studied range of periods of the visual stimulus sequence; in particular, working memory plays a substantial role in its organization.     

The intercellular synchronization of ca(2+) oscillations evaluates cx36-dependent coupling

Connexin36 (Cx36) plays an important role in insulin secretion by controlling the intercellular synchronization of Ca(2+) transients induced during stimulation. The lack of drugs acting on Cx36 channels is a major limitation in further unraveling the molecular mechanism underlying this effect. To screen for such drugs, we have developed an assay allowing for a semi-automatic, fluorimetric quantification of Ca(2+) transients in large populations of MIN6 cells. Here, we show that (1) compared to control cells, MIN6 cells with reduced Cx36 expression or function showed decreased synchrony of glucose-induced Ca(2+) oscillations; (2) glibenclamide, a sulphonylurea which promotes Cx36 junctions and coupling, increased the number of synchronous MIN6 cells, whereas quinine, an antimalarial drug which inhibits Cx36-dependent coupling, decreased this proportion; (3) several drugs were identified that altered the intercellular Ca(2+) synchronization, cell coupling and distribution of Cx36; (4) some of them also affected insulin content. The data indicate that the intercellular synchronization of Ca(2+) oscillations provides a reliable and non-invasive measurement of Cx36-dependent coupling, which is useful to identify novel drugs affecting the function of β-cells, neurons, and neuron-related cells that express Cx36.     

Construction of a fluorescent biosensor family

Bacterial periplasmic binding proteins (bPBPs) are specific for a wide variety of small molecule ligands. bPBPs undergo a large, ligand-mediated conformational change that can be linked to reporter functions to monitor ligand concentrations. This mechanism provides the basis of a general system for engineering families of reagentless biosensors that share a common physical signal transduction functionality and detect many different analytes. We demonstrate the facility of designing optical biosensors based on fluorophore conjugates using 8 environmentally sensitive fluorophores and 11 bPBPs specific for diverse ligands, including sugars, amino acids, anions, cations, and dipeptides. Construction of reagentless fluorescent biosensors relies on identification of sites that undergo a local conformational change in concert with the global, ligand-mediated hinge-bending motion. Construction of cysteine mutations at these locations then permits site-specific coupling of environmentally sensitive fluorophores that report ligand binding as changes in fluorescence intensity. For 10 of the bPBPs presented in this study, the three-dimensional receptor structure was used to predict the location of reporter sites. In one case, a bPBP sensor specific for glutamic and aspartic acid was designed starting from genome sequence information and illustrates the potential for discovering novel binding functions in the microbial genosphere using bioinformatics.