High quality visualization of biochemical pathways in BioPath

Biochemical reactions form large and complex networks. Comprehensible visual representations of these networks help biochemists understand the relationships between the chemical components. Typically pathway diagrams are manually produced drawings. Because of the steady progress of knowledge and the complex relationships in these networks, automatic visualizations are necessary. Bio-Path is a system for the exploration and automatic visualization of biochemical pathways. It has been developed to obtain an electronic version of the well-known Boehringer Biochemical Pathways poster and offers new possibilities to find information and to navigate through pathways. BioPath has a specific database containing reactions and a hierarchical clustering of reactions and reaction networks. One feature is the automatic generation of pathways from the database and their high quality visualization. This paper states the requirements for the visualization of biochemical pathways, presents a layout algorithm and shows how BioPath can be used to explore biochemical reaction networks.     

Unity and diversity in biochemistry.

A consideration of A Biochemical Phylogeny of the Protists, by M.A. Ragan and D.J. Chapman (Academic Press, 1978) and Biochemical Adaptation to Environmental Change, ed. by R.M.S. Smellie and J.F. Pennock (the Biochemical Society, 1976), within some thoughts on biochemical evolution.     

Internet assisted learning of biochemistry in Japan

The successful development of the internet assisted learning of biochemistry on both sides of university students and the Japanese Biochemical Society is described.     

Biochemical education in Romania: Report on a workshop held in Bucharest, 16–20 September 1991

The Workshop Team from IUBMB consisted of Professor W Rombauts (Leuven, Belgium), Professor F Vella (Saskatoon, Canada), and Dr E J Wood (Leeds, UK), with local arrangements being in the hands of Dr S A Hulea (Secretary of the Romanian Biochemical Society). The Workshop was held at the Institute of Biochemistry, Romanian Academy of Sciences (Head: Professor Dr Cecilia Motas) and there were participants from Bucharest, Constantin, Cluj-Napoca, Galati, Tasi and Sibiu. Support was kindly provided by the Romanian Biochemical Society, World Vision International, The Commission of Biochemistry, Romanian Academy of Sciences, Institute of Biochemistry, University of Medicine and Pharmacy “Carol Davilla”, University of Bucharest, and IUBMB     

Steroids,steroid receptors and disease

The 672nd Biochemical Society meeting was held at Sussex University, UK, from 19 to 21 December 2000. One session was dedicated to the study of steroids and their receptors, and related diseases.     

From beads on a string to the pearls of regulation: the structure and dynamics of chromatin

The assembly of eukaryotic chromatin, and the bearing of its structural organization on the regulation of gene expression, were the central topics of a recent conference organized jointly by the Biochemical Society and Wellcome Trust. A range of talks and poster presentations covered topical aspects of this research field and illuminated recent advances in our understanding of the structure and function of chromatin. The two-day meeting had stimulating presentations complemented with lively discourse and interactions of participants. In the present paper, we summarize the topics presented at the meeting, in particular highlighting subjects that are reviewed in more detail within this issue of Biochemical Society Transactions. The reports bring to life the truly fascinating molecular and structural biology of chromatin.     

DNA-damage signaling and apoptosis

A report on the 674th meeting of the Biochemical Society, Dublin, Ireland, 11-12 July 2001.     

Membranes and motors

The 55^th Harden Conference on the dynamics of membrane traffic convened on the 25^th August 2002 in the English Lake District. This meeting, which was organized by Bob Burgoyne and Viki Allan under the auspices of the Biochemical Society, comprised a highly enjoyable mixture of well-presented talks with uncommonly good weather. Presentations covered a broad range of topics relating to the dynamics of protein transport along both the exocytic and endocytic pathways of eukaryotic cells.     

Totally in vitro protein selection using mRNA-protein fusions and ribosome display.

Both chemists and biochemists have great interest in creating peptides and proteins with desired structure, recognition and catalytic properties. Recently, two techniques have been developed that afford functional selection of proteins entirely in vitro: mRNA-protein fusions, and ribosome display. Improvements in both methods have allowed peptide and protein libraries of unprecedented size (10(11)-10(13) different members) to be generated and screened for function.     

Archaea at St Andrews

A report of the Biochemical Society meeting 'The Molecular Biology of Archaea', St Andrews, UK, 19-21 August 2008.     

Evolving proteins at Darwin's bicentenary

A report of the Biochemical Society/Wellcome Trust meeting 'Protein Evolution - Sequences, Structures and Systems', Hinxton, UK, 26-27 January 2009.     

Making systems biology work in the 21st century

A report on the Biochemical Society meeting 'Systems biology: will it work?', Sheffield, UK, 5 January 2005.     

Nucleic acid–protein interactions: Wedding for love or circumstances?

The sixth Figeac meeting on nucleic acid–protein interactions was held in Figeac, France, from September 26th to October 1st, 2008. It was organized by the working group “nucleic acid–protein interactions and gene expression” from the French Society for Biochemistry and Molecular Biology. This report briefly summarizes the presentations by 40 speakers during the four plenary sessions, which were organised as follows: (1) nucleic acids: targets and tools, (2) RNA superstar, (3) nuclear structure and dynamics, and (4) new concepts – new approaches. A total of 22 plenary lectures, 18 oral communications and 40 posters were presented over the 5 days, providing a highly stimulating environment for scientific exchange between the ∼80 participants (biochemists, physicists, bio-informaticians and molecular and cellular biologists).     

Protein folding and misfolding inside and outside the cell.

The workshop was held at St Catherine's College, Oxford, from March 25-28, 1998, and attracted participants from 32 nations. Protein folding is one of the most important processes in biology since it adds functional flesh to the bare bones of genes, but it has traditionally been studied by people separated both intellectually and physically because they are training in different disciplines. The aim of the meeting was to bring together chemists and structural biologists studying how pure, denatured proteins refold spontaneously in the test tube, with biochemists and cell biologists who are concerned with how proteins fold inside living cells and medical scientists interested in the diseases that result when this process goes wrong. In this report we concentrate on general concepts and themes rather than on detailing every contribution.     

Inhibiting calpain,rescuing cells.

Drs. John Elce and Peter Davies, biochemists at Queen''s University, Kingston, Ont., are investigating the molecular structure of calpain, an enzyme that has been implicated in the cellular damage that occurs after such events as myocardial infarction and stroke. This damage is precipitated by an imbalance in the regulation of calpain that arises as an indirect result of ischemia. Elce and Davies hope that their research, which involves techniques such as recombinant DNA technology and x-ray crystallography, will lead to the development of a calpain inhibitor that will prevent such damage from occurring and enhance recovery.     

Histochemistry of myelin. IX. Neutral and acid proteinases in early Wallerian degeneration

Synopsis Acid and neutral proteinases, leucine aminopeptidase (l-leucyl--naphthylamidase) and acid phosphatase were studied in rat sciatic nerves undergoing Wallerian degeneration. Biochemical evidence indicated that increased activity of both proteases and acid phosphatase occurred by 12 hr after nerve section. Histochemical changes in these three enzymes were apparent after three days. Biochemical estimation of neutral leucine aminopeptidase (an enzyme predominantly located in myelin in the normal peripheral nerve) showed increased activity near the of the first week of degeneration. During the second week after nerve section all the enzymes studied became markedly more active. The parallel increase in activity of acid proteinase and acid phosphatase and the similarities in their histochemical distribution suggest that the acid proteinase is of lysosomal origin. Such changes in early Wallerian degeneration appear to precede macrophage invasion of the nerve and to arise mainly from the degenerating axon, the Schwann cell, or both. In spite of the delayed increase in leucine aminopeptidase it seems possible that some proteinase activity also arises from myelin.Research Associate supported by the British Multiple Sclerosis Society     

Polyamines and their role in human disease--an introduction

The naturally occurring polyamines are found in all living cells, where they fulfil a number of critical functions in relation to cell growth. The quest to identify these functions has been the subject of five independent colloquia hosted by the Biochemical Society and today still occupies several hundred scientists across Europe, the U.S.A. and Japan.     

Photosynthesis: 1900-1930.

During the second half of the 19th century Julius von Sachs established the main principles of the photosynthetic production of sugars. From then, a growing number of biochemists and physiologists attended to the process, that appeared like a "black box", in order to detect what came in and what went out of it. The English group of Frederick Blackman gave a remarkable contribution in individuating the close connection between temperature, light and CO2 concentration. Later, the great importance of light was stressed by Otto Warburg, who evaluated the radiant energy necessary to the process in terms of quantum theory. The biochemical mechanism of photosynthesis was interpreted by the main European schools on the basis of Adolf Baeyer's suggestion which posed formaldehyde as the core of the process. Formaldehyde's theory hold engaged the biochemists for about fifty years although some voices rose up against it. However, nobody could put forward more coherent theories until the 1940s, when Sam Ruben and Martin Kamen individuated the cyclic pattern of the process. Ultimately, the first thirty years of the 20th century must be seen as a preliminary stage studded with light and shade even if, in spite of controversial trends, several findings of remarkable interest became to disclose that "black box" as we know today chlorophyll photosynthesis.     

High performance capillary electrophoresis.

The application of recombinant-DNA methods for the production of therapeutic proteins has, over the past decade, driven the development of new technology for the analysis and characterization of biological molecules. High performance capillary electrophoresis (HPCE) has generated enormous interest among biochemists, analytical chemists and chromatographers, and is emerging as an extremely high-resolution separation technique, that may rival high performance liquid chromatography (HPLC) in its efficiency and breadth of application.