The Role of Combined Proteins in Coding Information for Histone Modification
DNA in eukaryotes is packaged onto nucleosomes, which consist of histone proteins. Covalent modification of histones plays a critical regulatory role in controlling transcription, replication, and repair. Different histone modifications are recognized by different protein modules, and these modules can be found in regulatory complexes with different, even antagonistic functions. Li et al. (Science Magazine, 316:5827, p. 1050, 2007) tackle this apparent contradiction through analysis of the chromodomain protein Eaf3, which preferentially binds to histone H3 dimethylated at lysine 36. Eaf3 is a subunit of both the Rpd3S deacetylase complex and the NuA4 acetyltransferase complex. The affinity of the Rpd3S complex for nucleosomes and its control of global acetylation levels at transcribed chromatin are determined by the combined activities of Eaf3 and another protein, Rco1, which is not found in NuA4.
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Video-article publication: a JoVE initiative
Journal of Visualized Experiments (JoVE) is an online research journal employing visualization to increase reproducibility and transparency in biological sciences. The first issue of this online journal has been published on December 1st 2006. With participation of scientists from leading research institutions, the Journal of Visualized Experiments (JoVE) was established as a new, open access tool in life science publication and communication.
While promoting efficiency and performance of life science research, JoVE opens a new frontier in scientific publication. Visualization of the temporal component, the change over time, integral to many life science experiments, can now be done. For the first time, JoVE allows you to publish your experiments in all its dimensions, overcoming the inherent limitations of traditional print journals, thus adding a whole new quality to the communication of your experimental work and research results. The website of JoVE is accessible via: www.jove.com .
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A Report on the Workshop "From Computational Biophysics to Systems Biology 2007” (CBSB07) 2 to 4 May, Forschungszentrum Jülich
The workshop is organized by the John von Neumann Institute for Computing (NIC) at the Forschungszentrum Jülich, Jülich, Germany. The goal of the workshop is to bring together expertise from physics, biology, and computer science to discuss current trends in computational biophysics and systems biology. In brief, the workshop concerns the following general areas:
- Protein folding (both structure prediction and mechanics)
- Interaction between proteins and other molecules
- Assembly of nano-structures, multi-protein, protein-DNA/RNA complexes
- Cellular systems at the molecular level
The full report can be viewed in pdf format here: LINK TO REPORT
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BIO 2007 International Convention in Boston: Convergence of IT and Biotechnology in Agbiotech
During the BIO 2007 International Convention in Boston, a panel of experts from the United States, New Zealand, and Australia described how technology and agriculture are converging to create solutions to strategic global needs for food, feed and fuel. The convergence of information technology (IT) and molecular biology dramatically increases agriculture’s potential to supply fuel and animal feed as well as more nutritious food.
-------------------------------------------------------Source: BusinessWire.com
REPORT: 6th Workshop on Data Mining in Bioinformatics (BIOKDD)
Data Mining is the process of automatic discovery of novel and understandable models and patterns from large amounts of data. Bioinformatics is the science of storing, analyzing, and utilizing information from biological data such as sequences, molecules, gene expressions, and pathways. Development of novel data mining methods will play a fundamental role in understanding these rapidly expanding sources of biological data. Data mining approaches seem ideally suited for bioinformatics, which is data-rich, but lacks a comprehensive theory of life's organization at the molecular level. The extensive databases of biological information create both challenges and opportunities for developing novel data mining methods. The 6th Workshop on Data Mining in Bioinformatics (BIOKDD) was held on August 20th, 2006, Philadelphia, PA, USA, in conjunction with the 12th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. The goal of the workshop was to encourage KDD researchers to take on the numerous challenges that Bioinformatics offers. The BIOKDD workshops have been held annually in conjunction with the ACM SIGKDD Conferences, since 2001. Additional information about BIOKDD can be obtained online .
Five revised and expanded papers were selected from the BIOKDD workshop, out of a total of 18 submissions, to appear in Algorithms for Molecular Biology (AMB). These papers underwent another round of external reviewing prior to being accepted for AMB. An overview of each paper is given below. In the paper titled Automatic Layout and Visualization of Biclusters, Gregory A. Grothaus, Adeel Mufti and T. M. Murali [2], present a novel method to display biclusters mined from gene expression data. The approach allows querying and visual exploration of the clusters/sub-matrices. The software is also available as open-source.
In ExMotif: Efficient Structured Motif Extraction, Yongqiang Zhang and Mohammed J. Zaki [3], describe a new algorithm called EXMOTIF to extract frequent motifs from DNA sequences. The method can mine structured motifs and profiles which have variable gaps between different elements. The demonstrate the efficiency of the method compared to state-of-the-art methods, and also demonstrate an application in mining composite transcription factor binding sites.
In the paper Refining Motifs by Improving Information Content Scores using Neighborhood Profile Search, Chandan K. Reddy, Yao-Chung Weng and Hsiao-Dong Chiang [4], show how one can refine the profile motifs discovered via Expectation Maximization and Gibbs Sampling based methods. They search the neighborhood regions of the initial alignments to obtain locally optimal solutions, which improve the information content of the discovered profiles.
In their paper, A Novel Functional Module Detection Algorithm for Protein-Protein Interaction Networks, Woochang Hwang, Young-Rae Cho, Aidong Zhang and Murali Ramanathan [5], describe the unexpected properties of the protein-protein interaction (PPI) networks and their use in a clustering method to detect biologically relevant functional modules. They propose a new method called STM (signal transduction model) to detect the PPI modules, and compare it with previous approaches to demonstrate its effectiveness in discovering large and arbitrary shaped clusters.
In A Spatio-temporal Mining Approach towards Summarizing and Analyzing Protein Folding Trajectories, Hui Yang, Srinivasan Parthasarathy and Duygu Ucar [6], describe a method to mine protein folding molecular dynamics simulations datasets. They describe a spatio-temporal association discovery approach to mine protein folding trajectories, to identify critical events and common pathways.
-------------------------------------------------------Source: Algorithms for Molecular Biology 2007, 2:4
RNA Mutagenesis: new opportunities for drug design?
Erfan Younesi, Life Science Informatics, B-IT Uni.Bonn, Germany
In a recent article in BMC Biotechnology (11 April 2007), a group of scientists has introduced a novel RNA-based random mutagenesis strategy that is rapid and simple to perform and generates large, highly diverse populations of proteins, each differing by only one or two amino acids from the parent protein. In general, availaibility of a rich library of protein variants is a crucial step for further screening of proteins with the preferred properties. This new method has been shown to not be as much biased as DNA mutagenesis for base substitutions. If combined with computational molecular modeling and drug design approaches, this might give a unique opportunity to construct a predicted model of protein in laboratory in a precise and efficient manner through this novel in vitro protein optimization technique.
-------------------------------------------------------Source: BMC Biotechnology 2007, 7:18
The more you know, the more you learn!
The ability to remember complex new information often depends on prior knowledge of the topic. This is because we have already formed a relevant mental schema as a framework. Tse et al. (p. 76; see the Perspective by Squire) used rats to study the effects of prior learning of schemas on the ability to acquire new episodic associations. These associations were acquired faster when the animals were first trained on a consistent set of associations than when they occurred in the context of a novel set of associations. The acquisition of novel associations was dependent on the hippocampus. However, within 48 hours the associations were independent of the hippocampus, which is substantially faster than typical memory consolidation. Thus, animals--like people--can bring activated mental schemas to bear during learning.
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Source: Science Volume 316, Number 5821, Issue of 06 April 2007
Bioinformatics research and education in Germany
Dietmar Schomburg1 and Martin Vingron2
1Universität zu Köln, Institut für Biochemie
Zülpicher Straße 47,
50674 Köln
E-mail: D.Schomburg@uni-koeln.de
2Max-Planck-Institut für Molekulare Genetik
Ihnestraße 73,
14195 Berlin
E-mail: vingron@molgen.mpg.de
Bioinformatics plays a key role in the progress of molecular biology and genome research. In fact, the ongoing transition of molecular and cellular biology into an industrial-style, large scale science with significant medical and thus economic impact would be inconceivable without bioinformatics. In many particular questions, existing techniques from mathematics and computer science have not been sufficient to support life science research. Bioinformatics, as a result, is not only bringing existing methods to bear on the new problems but also developing, or catalyzing the development of novel techniques in these formal sciences. With its increased importance, the fostering of bioinformatics has become a crucial part of German efforts to promote biotechnology and the life sciences in general. The difficulties, however, lie in the strongly interdisciplinary nature of the field as well as in getting computational methods accepted by laboratory biologists and medical researchers.
Since the funding scheme enacted by the German government in the early nineties a number of excellent, internationally recognized German groups have developed in the field and are still dominating the present national research situation. Although it is impossible to name all, some names should be mentioned here: Lengauer, formerly Bonn and now Saarbrücken, Schomburg, first Braunschweig, now Köln, Mewes, München, Suhai and Bork, Heidelberg, Vingron, Berlin - to name just a few. Essential and unique German contributions are the Mewes activities in genome data integration and annotation (in particular in the yeast and Arabidopsis sequencing projects), the enzyme and metabolic information system BRENDA run by the Schomburg group and the transcription factor database TRANSFAC run by the Wingender group in Braunschweig.
In spite of the strong research record - and similar to the situation worldwide - the universities were slow in teaching students in the field of bioinformatics. Academic and industrial research was hampered by a dramatic lack of bioinformatics researchers. This became especially obvious in the mid-nineties. In order to overcome this critical situation DFG, the basic science funding agency, enacted a five-year funding scheme for universities for bioinformatics teaching. Finally, to preserve the rather strong German position in bioinformatics research and to allow a quick "production" of trained bioinformaticians the German federal ministry of education and research (BMBF) started a funding scheme for six competence centers in bioinformatics.
Several of the centers funded by DFG and BMBF have meanwhile established strong educational programs in bioinformatics. With Bielefeld having had a lead role in teaching for many years, Tübingen, Munich, Saarbrücken, Berlin and several other universitites have now established curricula, too. Bioinformatics research, also strongly supported by the funding agencies, has different emphasis in the various centers. Munich, Berlin and Jena are strongholds of genome research. In Munich the group of Hans Werner Mewes has not only been in charge of data handling of large sequencing projects but has also developed the PEDANT analysis pipeline for genome data. Berlin is a center of genomic data production and its bioinformatics project "Berlin Center for Genome Based Bioinformatics" (BCB) aims at developing and implementing the bioinformatics for bridging the gap from genome research to medicine. The central theme of the Jena Centre of Bioinformatics (JCB) is molecular medicine, in particular molecular communication processes in normal and pathological states of cells. The association of University of Halle with the plant biology research laboratory in Gatersleben is, of course, focussing on the developlement of bioinformatics tools for plant genomics. CUBIC, the "Cologne University Bioinformatics Center", concentrates on molecular networks in organisms. In particular, using the parallel analysis of experimental genome, transcriptome, proteome, structure, function and metabolome data, new tools for the simulation of biochemical functions with the goal to simulate whole cells will be developed. The bioinformatics competence center "Intergenomics" in Braunschweig has the scientific goal to develop bioinformatic tools for modeling of the interactivity of genome-driven bacterial infection processes in mammals and plants. The presence of several large research labs, a strong university and a large bioinformatics company (LION Bioscience) makes Heidelberg an important center, too. There, as well as in Hamburg and Dresden, also private donors are skipping in to promote bioinformatics. Freiburg, another center of both life science research and computer science, is also currently building up bioinformatics. In Leipzig, the Interdisciplinary Center for Bioinformatics (IZBI) focuses on the study of evolution, gene regulation, signalling pathways and tissue organization.
Of the many branches of bioinformatics, German researchers have particularly pursued structural biology and computational chemistry, biomolecular sequence analysis, database development for genome research and more recently the computational support for functional genomics. With the availability of whole-genome sequence and functional data, also the integration of bioinformatics and theoretical biology with the goal of a new systems biology is entering the focus of research. Late in 2001 the Ministry of Research has announced that it will support initiatives in systems biology. At the same time, ongoing projects in genome research and its medical application (the "National Genome Research Network", NGFN) rely on and integrate bioinformatics. Service provision to molecular biology laboratories is currently being pursued by the Helmholtz Network Bioinformatics (HNB, funded by the Ministry of Research). This association of bioinformatics groups is developing a platform for integration of a wide range of services and tools in order to make them easily available, in particular to the German biological research community. Taken together, not only research and development in bioinformatics are growing in Germany, but also the acceptance of bioinformatics as a research tool has increased and is now widely recognized in the biomedical community.
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Source:http://www.bioinfo.de/isb/2002/02/0015/
Who said "Junk DNA"!
By Erfan Younesi,
Life Science Informatics,
B-IT Uni.Bonn, Germany
Presently, only the function of a few percent of the DNA is known, the rest has been believed to be useless garbage, commonly called "Junk DNA" by molecular biologists. Increasing evidence is now indicating that this DNA is not "junk" at all. Especially, it has been found to have various regulatory roles. This means that this so-called "non-coding DNA" influences the behavior of the genes, the "coding DNA", in important ways. However, the knowledge is still very incomplete about this DNA. And there is little knowledge about the relationship between non-coding DNA and the DNA of genes.
As far as I know, these non-coding parts of DNA have influenced evolution through giving the flexibility to human and other species to creat new proteins. For instance, Gil Ast and his colleagues at Tel Aviv University in Israel have figured out how the sequences, known as Alu elements, are incorporated into genes to create novel proteins.
Alu elements are short sequences of DNA that are peppered throughout the genome. They comprise approximately ten percent of the entire genome—ten times more than all the genes put together. Until recently, their function had remained a mystery.
Very recently, scientists at University of California (2004) have found that several great stretches of DNA were identical across three species: man, mous, and rat. They suggest that these non-coding elements play an important role in regulating the process of development and differentiation.
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