Suspension array technology: evolution of the flat-array paradigm.

Suspension arrays of microspheres analyzed using flow cytometry offer a new approach to multiplexed assays for large-scale screening applications. By optically encoding micron-sized polymer particles, suspension microarrays can be created to enable highly multiplexed analysis of complex samples. Each element in the array is comprised of a subpopulation of particles with distinct optical properties and each array element bears a different surface receptor. Nucleic acids, proteins, lipids or carbohydrates can serve as receptors to support the analysis of a wide range of biomolecular assemblies, and applications in genomic and proteomic research are being developed. Coupled with recent innovations for rapid serial analysis of samples, molecular analysis with microsphere arrays holds significant potential as a general analysis platform for both research and clinical applications.     

New tools for protein sequence analysis.

Analysis of protein sequence is an important tool in studies of both native and recombinant proteins. Novel techniques and instrumentation which facilitate determination of protein primary structure have recently been developed.     

基因表达数据聚类分析技术及其软件工具

随着DNA芯片技术的广泛应用,基因表达数据分析已成为生命科学的研究热点之一。概述基因表达聚类技术类型、算法分类与特点、结果可视化与注释;阐述一些流行的和新型的算法;介绍17个最新相关软件包和在线web服务工具;并说明软件工具的研究趋向。     

Analyzing gene regulation in ascidian embryos: new tools for new perspectives

Ascidians are marine protochordates at the evolutionary boundary between invertebrates and vertebrates. Ascidian larvae provide a simple system for unraveling gene regulation networks underlying the formation of the basic chordate body plan. After being used for over a century as a model for embryological studies, ascidians have become, in the past decade, an increasingly popular organism for studying gene regulation. Part of the renewed appeal of this system is the use of electroporation to introduce transgenic DNAs into developing embryos. This method is considerably more efficient than conventional microinjection assays and permits the simultaneous transformation of hundreds of embryos. Electroporation has allowed the identification and characterization of cis-regulatory DNAs that mediate gene expression in a variety of tissues, including the notochord, tail muscles, CNS, and endoderm. Electroporation has also provided a simple method for misexpressing patterning genes and producing dominant mutant phenotypes. Recent studies have used electroporation to create "knock-out" phenotypes by overexpressing dominant negative forms of particular proteins. Here we review the past and present uses of electroporation in ascidian development, and speculate on potential future uses.     

Genomics tools for QTL analysis and gene discovery

In recent years, several new genomics resources and tools have become available that will greatly assist quantitative trait locus (QTL) mapping and cloning of the corresponding genes. Genome sequences, tens of thousands of molecular markers, microarrays, and knock-out collections are being applied to QTL mapping, facilitating the use of natural accessions for gene discovery.     

Improved process analytical technology for protein a chromatography using predictive principal component analysis tools

Protein A chromatography is widely employed for the capture and purification of antibodies and Fc‐fusion proteins. Due to the high cost of protein A resins, there is a significant economic driving force for using these chromatographic materials for a large number of cycles. The maintenance of column performance over the resin lifetime is also a significant concern in large‐scale manufacturing. In this work, several statistical methods are employed to develop a novel principal component analysis (PCA)‐based tool for predicting protein A chromatographic column performance over time. A method is developed to carry out detection of column integrity failures before their occurrence without the need for a separate integrity test. In addition, analysis of various transitions in the chromatograms was also employed to develop PCA‐based models to predict both subtle and general trends in real‐time protein A column yield decay. The developed approach has significant potential for facilitating timely and improved decisions in large‐scale chromatographic operations in line with the process analytical technology (PAT) guidance from the Food and Drug Administration (FDA). Biotechnol. Bioeng. 2011; 108:59–68. © 2010 Wiley Periodicals, Inc.     

Protein Peeling 3D: new tools for analyzing protein structures

We present an improved version of our Protein Peeling web server dedicated to the analysis of protein structure architecture through the identification of protein units produced by an iterative splitting algorithm. New features include identification of structural domains, detection of unstructured terminal elements and evaluation of the stability of protein unit structures. AVAILABILITY: The website is free and open to all users with no login requirements at http://www.dsimb.inserm.fr/dsimb-tools/peeling3.     

Networks in phylogenetic analysis: new tools for population biology

Phylogenetic analysis has changed greatly in the past decade, including the more widespread appreciation of the idea that evolutionary histories are not always tree-like, and may, thus, be best represented as reticulated networks rather than as strictly dichotomous trees. Reconstructing such histories in the absence of a bifurcating speciation process is even more difficult than the usual procedure, and a range of alternative strategies have been developed. There seem to be two basic uses for a network model of evolution: the display of real but unobservable evolutionary events (i.e. a hypothesis of the true phylogenetic history), and the display of character conflict within the data itself (i.e. a summary of the data). These two general approaches are briefly reviewed here, and the strengths and weaknesses of the different implementations are compared and contrasted. Each network methodology seems to have limitations in terms of how it responds to increasing complexity (e.g. conflict) in the data, and therefore each is likely to be more appropriate for one of the two uses than for the other. Several examples using parasitological data sets illustrate the uses of networks within the context of population biology.     

High-throughput and multiplexed protein array technology: protein-DNA and protein-protein interactions

Miniaturized protein arrays address protein interactions with various types of molecules in a high-throughput and multiplexed fashion. This review focuses on achievements in the analysis of protein-DNA and protein-protein interactions. The technological feasibility of protein arrays depends on the different factors that enable the arrayed proteins to recognize molecular partners and on the specificity of the interactions involved. Proteome-scale studies of molecular interactions require high-throughput approaches for both the production and purification of functionally active proteins. Various solutions have been proposed to avoid non-specific protein interactions on array supports and to monitor low-abundance molecules. The data accumulated indicate that this emerging technology is perfectly suited to resolve networks of protein interactions involved in complex physiological and pathological phenomena in different organisms and to develop sensitive tools for biomedical applications.     

Peptide aptamers: new tools to study protein interactions

The ability to specifically interfere with the function of proteins of pathological significance has been a goal for molecular medicine for many years. Peptide aptamers comprise a new class of molecules, with a peptide moiety of randomized sequence, which are selected for their ability to bind to a given target protein under intracellular conditions. They have the potential to inhibit the biochemical activities of a target protein, can delineate the interactions of the target protein in regulatory networks, and identify novel therapeutic targets. Peptide aptamers represent a new basis for drug design and protein therapy, with implications for basic and applied research, for a broad variety of different types of diseases.     

Discovery in toxicology: mediation by gene expression array technology

Toxicogenomics is a term that represents the merging of toxicology with novel genomics techniques. Data generated in the new-age era of toxicology is relatively complex, requires new bioinformatics tools for adequate interpretation, and allows for the rapid generation of testable hypotheses. Hazard identification and risk assessment processes will advance from the use of genomics techniques, which will lead to greater understanding of mechanism(s) of action of toxicants, development of novel biomarkers of exposure and effect, and better identification of sensitive subpopulations.     

ProteinHistorian: tools for the comparative analysis of eukaryote protein origin

The evolutionary history of a protein reflects the functional history of its ancestors. Recent phylogenetic studies identified distinct evolutionary signatures that characterize proteins involved in cancer, Mendelian disease, and different ontogenic stages. Despite the potential to yield insight into the cellular functions and interactions of proteins, such comparative phylogenetic analyses are rarely performed, because they require custom algorithms. We developed ProteinHistorian to make tools for performing analyses of protein origins widely available. Given a list of proteins of interest, ProteinHistorian estimates the phylogenetic age of each protein, quantifies enrichment for proteins of specific ages, and compares variation in protein age with other protein attributes. ProteinHistorian allows flexibility in the definition of protein age by including several algorithms for estimating ages from different databases of evolutionary relationships. We illustrate the use of ProteinHistorian with three example analyses. First, we demonstrate that proteins with high expression in human, compared to chimpanzee and rhesus macaque, are significantly younger than those with human-specific low expression. Next, we show that human proteins with annotated regulatory functions are significantly younger than proteins with catalytic functions. Finally, we compare protein length and age in many eukaryotic species and, as expected from previous studies, find a positive, though often weak, correlation between protein age and length. ProteinHistorian is available through a web server with an intuitive interface and as a set of command line tools; this allows biologists and bioinformaticians alike to integrate these approaches into their analysis pipelines. ProteinHistorian's modular, extensible design facilitates the integration of new datasets and algorithms. The ProteinHistorian web server, source code, and pre-computed ages for 32 eukaryotic genomes are freely available under the GNU public license at http://lighthouse.ucsf.edu/ProteinHistorian/.     

ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons

ProDom contains all protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases (http://www. toulouse.inra.fr/prodom.html ). ProDom-CG results from a similar domain analysis as applied to completed genomes (http://www.toulouse. inra.fr/prodomCG.html ). Recent improvements to the ProDom database and its server include: scaling up to include sequences from TrEMBL, addition of Pfam-A entries to the set of expert validated families, assignment of stable accession numbers, consistency indicators for domain families, domain arrangements of sub-families and links to Pfam-A.     

Power tools for gene expression and clonal analysis in Drosophila

The development of two-component expression systems in Drosophila melanogaster, one of the most powerful genetic models, has allowed the precise manipulation of gene function in specific cell populations. These expression systems, in combination with site-specific recombination approaches, have also led to the development of new methods for clonal lineage analysis. We present a hands-on user guide to the techniques and approaches that have greatly increased resolution of genetic analysis in the fly, with a special focus on their application for lineage analysis. Our intention is to provide guidance and suggestions regarding which genetic tools are most suitable for addressing different developmental questions.     

A new tool for G protein analysis.

G proteins play a pivotal role in cellular signaling by acting as molecular switches that undergo conformational changes upon binding GTP. The primary sequence constituting the binding cleft among the >160 G proteins in the human genome is highly conserved, consistent with the fact that these proteins share similar guanine nucleotide-binding characteristics. Recent work has demonstrated the feasibility of designing new analogs of GTP that can specifically activate G proteins whose nucleotide-binding sites have been remodeled through mutagenesis. This strategy has the potential to provide new insights into how G proteins act as molecular switches that engage their downstream target/effector proteins to generate specific signaling outputs.     

GAAS: gene array analyzer software for management,analysis and visualization of gene expression data

SUMMARY: GAAS, Gene Array Analyzer Software supports multi-user efficient management and suitable analyses of large amounts of gene expression data across replicated experiments. Its management framework handles input data generated by different technologies. A multi-user environment allows each user to store his/her own data visualization scheme, analysis parameters used, values and formats of the output data. The analysis engine performs: background and spot quality evaluation, data normalization, differential gene expression analyses in single and multiple replica experiments. Results of expression profiles can be interactively navigated through graphical interfaces and stored into output databases.     

Homologous recombination and RecA protein: towards a new generation of tools for genome manipulations

Homologous recombination (HR) is one of the central processes of DNA metabolism, combining roles in both cell housekeeping and the evolution of genomes. In eukaryotes, HR underlies meiosis and ensures genome stability. The complete sequencing of numerous bacterial genomes has shown that HR has a substantial role in the evolution of microorganisms, especially pathogens. HR systems from different species and their isolated components are finding an expanding field of applications in modern genetic engineering and bio- and nanotechnologies. Recently, much progress has been made in our understanding of HR mechanisms in eukaryotes and the practical applications of HR systems.     

A novel system for large-scale gene expression analysis: bacterial colonies array

In the present work, we report the use of bacterial colonies to optimize macroarray technique. The devised system is significantly cheaper than other methods available to detect large-scale differential gene expression. Recombinant Escherichia coli clones containing plasmid-encoded copies of 4,608 individual expressed sequence tag (ESTs) were robotically spotted onto nylon membranes that were incubated for 6 and 12 h to allow the bacteria to grow and, consequently, amplify the cloned ESTs. The membranes were then hybridized with a beta-lactamase gene specific probe from the recombinant plasmid and, subsequently, phosphorimaged to quantify the microbial cells. Variance analysis demonstrated that the spot hybridization signal intensity was similar for 3,954 ESTs (85.8%) after 6 h of bacterial growth. Membranes spotted with bacteria colonies grown for 12 h had 4,017 ESTs (87.2%) with comparable signal intensity but the signal to noise ratio was fivefold higher. Taken together, the results of this study indicate that it is possible to investigate large-scale gene expression using macroarrays based on bacterial colonies grown for 6 h onto membranes.