Protein structure alignment by incremental combinatorial extension (CE) of the optimal path

A new algorithm is reported which builds an alignment between two protein structures. The algorithm involves a combinatorial extension (CE) of an alignment path defined by aligned fragment pairs (AFPs) rather than the more conventional techniques using dynamic programming and Monte Carlo optimization. AFPs, as the name suggests, are pairs of fragments, one from each protein, which confer structure similarity. AFPs are based on local geometry, rather than global features such as orientation of secondary structures and overall topology. Combinations of AFPs that represent possible continuous alignment paths are selectively extended or discarded thereby leading to a single optimal alignment. The algorithm is fast and accurate in finding an optimal structure alignment and hence suitable for database scanning and detailed analysis of large protein families. The method has been tested and compared with results from Dali and VAST using a representative sample of similar structures. Several new structural similarities not detected by these other methods are reported. Specific one-on-one alignments and searches against all structures as found in the Protein Data Bank (PDB) can be performed via the Web at http://cl.sdsc.edu/ce.html.      

The Use of a Mobile Sludge Dewatering Unit at Small Sewage-Treatment Plants in Japan

The construction of small sewage-treatment works in Japan is increasing. In most municipalities, economical and effective treatment/maintenance systems, which match the local conditions, are needed. As one of its support strategies, the Japan Sewage Works Agency has initiated and implemented 'co-operation' projects. In one of these projects, a mobile sludge dewatering unit has been shown to be the most economical method of treatment. The first unit, which was commissioned in March 1992, is being used in three municipalities, and this paper appraises its use.     

Herpes simplex virus

CNS infections caused by human herpesvirus 1 and human herpesvirus 2-herpes simplex virus type 1 and herpes simplex virus type 2--are reviewed. The major diseases associated with these viruses are meningitis and encephalitis. Two forms of encephalitis are known, neonatal encephalitis and encephalitis occurring after the neonatal period. Both diseases are associated with high mortality and morbidity and require prompt diagnosis and aggressive antiviral chemotherapy. Methods for the specific diagnosis of these infections are reviewed and the value of intrathecal antibody assay and nucleic acid amplification techniques are emphasised.     

Perspectives on the use of the baboon in embryology and teratology research

This paper summarizes the developmental stages of the baboon during the period of organ formation and provides comparative information for other primates, including the human. Special attention is directed to the early development of the nervous system, eye, ear and nose/palate. The similarity in development of these structures with humans indicates that the baboon is a suitable model for studies of normal and abnormal neurological development. Spontaneous prenatal loss rates in the baboon (2.4-11.2%) are slightly lower than those reported in rhesus and cynomologus monkeys. The baboon, in addition to the cynomologus monkey and macaque, has been used as a model in teratology research to assess the potential risk of thalidomide, sex steroids, Bendectin and rubella virus, as well as to study the pathogenesis of malformations associated with the corticosteroid triamcinolone acetonide. The rate of spontaneous malformations (<1%) in baboons, similar to that reported for other commonly used primates, supports their continued use as a teratological model. In this regard, a sample protocol is provided for the safety evaluation of biotechnology products using nonhuman primates, which are the most appropriate model for those compounds which are bioactive in species closely related to humans.