TransACTS: from science to innovation

The ACTS (Advanced Chemical Technologies for Sustainability) Symposium is a Dutch national meeting that brought together representatives of academia, industry and the Dutch government for innovation-driven research on sustainable chemical technologies. It provides an excellent network opportunity where all ACTS research programmes presented their work, focussing on their specific sustainable technologies. The ACTS symposium was held from 12 to 13 of January 2011 at De Werelt, Lunteren, The Netherlands. For more information about TransACTS, please visit .     

Chemoinformatics: A view of the field and current trends in method development

The chemoinformatics field continues to evolve at the interface between computer science and chemistry. Chemical information and computational approaches in pharmaceutical research are major focal points of chemoinformatics. However, the boundaries of this discipline are rather fluid and the chemoinformatics spectrum is difficult to delineate. The field is in flux, which also provides opportunities for further developments. As a lead-in to the Chemoinformatics Symposium-in-Print, we present a brief view of this discipline (with a little anecdotal touch), highlight current trends in method development, and discuss a number of representative examples.     

A bridge between chemistry and biology

Chemical biology is an interdisciplinary field that is undergoing rapid expansion around the globe. Recently, the Japanese Society for Chemical Biology sponsored its inaugural scientific meeting to discuss research at the interface of chemistry and biology.     

Organisation of biotechnological information into knowledge

The success of biotechnological research, development and marketing depends to a large extent on the international transfer of information and on the ability to organise biotechnology information into knowledge. To increase the efficiency of information-based approaches, an information strategy has been developed and consists of the following stages: definition of the problem, its structure and sub-problems; acquisition of data by targeted processing of computer-supported bibliographic, numeric, textual and graphic databases; analysis of data and building of specialized in-house information systems; information processing for structuring data into systems, recognition of trends and patterns of knowledge, particularly by information synthesis using the concept of information density; design of research hypotheses; testing hypotheses in the laboratory and/or pilot plant; repeated evaluation and optimization of hypotheses by information methods and testing them by further laboratory work. The information approaches are illustrated by examples from the university-industry joint projects in biotechnology, biochemistry and agriculture.The author is with the International Center for Chemical Studies, Faculty of Science and Technology, University of Ljubljana FNT-Kü Vegova 4. P.O. Box 18/1, 61001 Ljubljana, Slovenia     

Plant-insect interactions.

Recent research shows partially overlapping signal transduction pathways controlling responses to wounding, insects, and pathogens. Chemical and behavioral assays show that plants release herbivore-specific volatiles, and that parasitic wasps can distinguish between these emission patterns. QTL mapping and candidate gene studies are beginning to identify polymorphic resistance genes, and ecological analyses provide information on the physiological and fitness costs of resistance. Such multidisciplinary approaches can elucidate the physiological causes and ecological consequences of plant-herbivore interactions.     

Exploration of the central dogma at the interface of chemistry and biology: 2010 Yale Chemical Biology Symposium

Ever since the term "central dogma" was coined in 1958, researchers have sought to control information flow from nucleic acids to proteins. Talks delivered by Drs. Anna Pyle and Hiroaki Suga at this year's Chemical Biology Symposium at Yale in May 2010 applauded recent advances in this area, at the interface between chemistry and biology.     

Chemical information transfer between plants:: back to the future

Chemical information conveyance between organisms has been well established for a wide range of organisms including protozoa, invertebrates, vertebrates and plant-parasitic plants. During the past 20 years, various studies have addressed whether chemical information conveyance also occurs between damaged and undamaged plants and many interesting pieces of evidence have been presented. To date, this research field has been restricted to the question whether and how plants (in general) are involved in plant-to-plant communication. However, apart from mechanistic questions, evolutionary questions should be addressed asking why plants do (or do not) exploit their neighbour's information and whether their strategy is affected by e.g. environmental conditions or previous experience. Recent progress in the field of chemical information conveyance between damaged and undamaged plants warrants an intensified study of this exciting topic in chemical ecology.     

A Collaborative Informatics Infrastructure for Multi-Scale Science

The Collaboratory for Multi-scale Chemical Science (CMCS) is developing a powerful informatics-based approach to synthesizing multi-scale information in support of systems-based research and is applying it within combustion science. An open source multi-scale informatics toolkit is being developed that addresses a number of issues core to the emerging concept of knowledge grids including provenance tracking and lightweight federation of data and application resources into cross-scale information flows. The CMCS portal is currently in use by a number of high-profile pilot groups and is playing a significant role in enabling their efforts to improve and extend community maintained chemical reference information. James D. Myers received his B.A. in Physics from Cornell University in 1985 and his Ph.D. in Chemistry from the University of California at Berkeley in 1993. He is currently the Associate Director for Collaborative Technologies at the National Center for Supercomputing Applications (NCSA) at the University of Illinois, Urbana Champaign. Dr. Myers is the lead investigator on the U.S. Department of Energy (DOE) sponsored Scientific Annotation Middleware project (http://www.scidac.org/SAM/) (scientific content management, semantic annotation, and records functionality) and is serving as the Chief Technical Officer for the DOE-sponsored Collaboratory for Multiscale Chemical Science (CMCS) project. His is also the lead architect for the Mid-America Earthquake Center's MAEViz hazard risk management collaboratory and co-lead of NCSA's Collaborative Large-scale Engineering Analysis Network for Environmental Research (CLEANER) related cybercollaboratory effort. Open source software developed by Dr. Myers and his colleagues including the electronic laboratory notebook (ELN) and the Collaborative Research Environment (CORE) real-time collaboration environment have been downloaded from the Pacific Northwest National Laboratory (PNNL) Collaboratory website (http://collaboratory.pnl.gov) by thousands of researchers and educators. Due to space limitations, individual bios for all 28 authors are not shown. The CMCS project is led by Dr. Larry Rahn (rahn@sandia.gov) at Sandia National Laboratories. The team includes combustion researchers and computer science researchers and developers at five DOE National Laboratories (Argonne, Lawrence Livermore, Los Alamos, Pacific Northwest, and Sandia National Laboratories), the National Institute of Standards and Technology, Massachusetts Institute of Technology, and the University of California, Berkeley. Current contact information and biographic information for team members is available at http://cmcs.org/team.php.     

From estrogens via alkaloids to enzymes

This personal and professional autobiography covers the 57-year period from 1948 to 2005 and includes the studies at the Faculty of Chemical Technology of the Slovak Technical University and the Faculty of Pharmacy of Comenius University, both in Bratislava, as well as the activities at the Regional Pharmaceutical Research Institute and the Institute of Chemistry of the Slovak Academy of Sciences in Bratislava, the Institute of Organic Chemistry and Biochemistry in Prague, Karolinska Institutet in Stockholm and at other research and scientific working places in Slovakia and abroad. It highlights the research on natural substances and enzymes, especially the pectin methyl esterase.     

Chemical genomics: a systematic approach in biological research and drug discovery

The knowledge of complete sequences of different organisms is dramatically changing the landscape of biological research and pharmaceutical development. We are experiencing a transition from a trial-and-error approach in traditional biological research and natural product drug discovery to a systematic operation in genomics and target-specific drug design and selection. Small, cell-permeable and target-specific chemical ligands are particularly useful in systematic genomic approaches to study biological questions. On the other hand, genomic sequence information, comparative and structural genomics, when combined with the cutting edge technologies in synthetic chemistry and ligand screening/identification, provide a powerful way to produce target-specific and/or function-specific chemical ligands and drugs. Chemical genomics or chemogenomics is a new term that describes the development of target-specific chemical ligands and the use of such chemical ligands to globally study gene and protein functions. We anticipate that chemical genomics plays a critical role in the genomic age of biological research and drug discovery.     

PACSY, a relational database management system for protein structure and chemical shift analysis

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu.     

Advanced lipid technology

Abstract

Phospholipids and cholesterols are being spotlighted as raw materials for preparing liposomes, one of the key compounds for drug delivery systems (DDS), and as base compounds for converting water-soluble drugs to fat-soluble drugs. Other applications of phospholipids also are being explored. Nippon Fine Chemical, aware of the future of such lipids, has developed new processes for synthesizing and purifying phospholipids and is supplying them on an industrial scale. These products – used worldwide – are highly regarded as raw materials for preparing liposomes. In particular, Nippon Fine Chemical’s innovative research led to the development of “Presome®”, a base agent that facilitates the preparation of liposome solutions. To further this research, Nippon Fine Chemical has established an “Advanced Lipid Technology”.     

Physical energy-based ultrasound shifts M1 macrophage differentiation towards M2 state

Recently, we read with interest the article entitled “Unveiling the Morphogenetic Code: A New Path at the Intersection of Physical Energies and Chemical Signaling”. In this paper, the investigation into the systematic and comprehensive bio-effects of physical energies prompted us to reflect on our research. We believe that ultrasound, which possesses a special physical energy, also has a certain positive regulatory effect on macrophages, and we have already obtained some preliminary research results that support our hypothesis.     

Social functions of the sub-caudal scent gland secretion of the European badger Metes metes (Carnivora: Mustelidae)

This paper describes aspects of the biological function of the sub-caudal scent gland of the European badger. Chemical analyses of the secretion reveal that it contains information potentially useful in allowing individual identity and group membership. There is no evidence that the secretion contains information on the sex of its producer.     

Solution structure of human U1 snRNA. Derivation of a possible three-dimensional model.

The solution structure of human U1 snRNA was investigated by using base-specific chemical probes (dimethylsulfate, carbodiimide, diethylpyrocarbonate) and RNase V1. Chemical reagents were employed under various conditions of salt and temperature and allowed information at the Watson-Crick base-pairing positions to be obtained for 66% of the U1 snRNA bases. Double-stranded or stacked regions were examined with RNase V1. The dat gained from these experiments extend and support the previous 2D model for U1snRNA. However, to elucidate some aspects of the solution data that could not be accounted for by the secondary structure model, the information gathered from structure probing was used to provide the experimental basis required to construct and to test a tertiary structure model by computer graphics modeling. As a result, U1 snRNA is shown to adopt an asymmetrical X-shape that is formed by two helical domains, each one being generated by coaxial stacking of helices at the U1 snRNA cruciform. Chemical reactivities and model building show that a few nucleotides, previously proposed to be unpaired, can form A.G and U.U non Watson-Crick base-pairs, notably in stem-loop B. The structural model we propose for regions G12 to A124 integrates stereochemical constraints and is based both on solution structure data and sequence comparisons between U1 snRNAs.     

An unfolding story of helical transmembrane proteins

Reversible unfolding of helical transmembrane proteins could provide valuable information about the free energy of interaction between transmembrane helices. Thermal unfolding experiments suggest that this process for integral membrane proteins is irreversible. Chemical unfolding has been accomplished with organic acids, but the unfolding or refolding pathways involve irreversible steps. Sodium dodecyl sulfate (SDS) has been used as a perturbant to study reversible unfolding and refolding kinetics. However, the interpretation of these experiments is not straightforward. It is shown that the results could be explained by SDS binding without substantial unfolding. Furthermore, the SDS-perturbed state is unlikely to include all of the entropy terms involved in an unfolding process. Alternative directions for future research are suggested: fluorinated alcohols in homogeneous solvent systems, inverse micelles, and fragment association studies.