Knowledge-based simulation of DNA metabolism: prediction of enzyme action

We have developed a knowledge-based simulation of DNA metabolismthat accurately predicts the actions of enzymes on DNA undera large number of environmental conditions. Previous simulationsof enzyme systems rely predominantly on mathematical models.We use a frame-based representation to model enzymes, substratesand conditions. Interactions between these objects are expressedusing production rules and an underlying truth maintenance system.The system performs rapid inference and can explain its reasoning.A graphical interface provides access to all elements of thesimulation, including object representations and explanationgraphs. Predicting enzyme action is the first step in the developmentof a large knowledge base to envision the metabolic pathwaysof DNA replication and repair. Received on February 1, 1990; accepted on October 2, 1990     

Reactive oxygen species generation and human spermatozoa: The balance of benefit and risk

Although the generation of reactive oxygen species is an activity normally associated with phagocytic leucocytes, mammalian spermatozoa were, in fact, the first cell type in which this activity was described. In recent years it has become apparent that spermatozoa are not the only nonphagocytic cells to exhibit a capacity for reactive oxygen species production, because this activity has been detected in a wide variety of different cells including fibroblasts, mesangial cells, oocytes, Leyding cells endothelial cells, thryroid cells, adipocytes, tumour cell and platelets. Since the capacity to generate reactive oxygen species is apparently so widespread, the risk-benefit equation for these potentially pernicious molecules becomes a matter of intese interest. In the case of human spermatozoa, the risk of manufacturing reactive oxygen metabolites is considerable because these cells are particularly vulnerable to lipid peroxidation. Indeed, there is now good evidence to indicate that oxygen radicals are involved in the initiation of peroxidative damage to the sperm plasma membrane, seen in many cases of male infertility. This risk is off-set by recent data suggesting that superoxide anions and hydrogen peroxide also participate in the induction of key biological events such as hyperactiavated motility and the acrosome reaction. Thus, human spermatozoa appear to use reactive oxygen species for a physiological purpose and have the difficult task of ensuring the balanced generation of these potentially harmful, but biologically important, modulators of cellular function.     

The Lepocreadiidae (Digenea) of fishes from the north-east Atlantic: a review of the genusLepidapedon Stafford, 1904

The genusLepidapedon is subdivided into several species groups and subgroups of species based on the vitelline distribution and the length of the excretory vesicle. The species in each of the subgroups are listed and keys to the species in most subgroups are given. The following north-eastern Atlantic species are described or redescribed:Lepidapedon rachion fromMelanogrammus aeglefinus, Gadus morhua, Aspitrigla cuculus, Merlangius merlangus andPollachius pollachius; L. cambrensis fromEnchelyopus cimbrius; L. sommervillae n. sp. fromTrachyrincus scabrus, T. murrayi andCoryphaenoides guentheri; L. elongatum fromGadus morhua; L. gaevskayae fromCoryphaenoides (Nematonurus) armatus; L. discoveryi n. sp. fromCoryphaenoides (Nematonurus) armatus; L. arlenae n. sp. fromTrachyrincus scabrus andT. murrayi; L. mariannae n. sp. fromGaidropsarus argentatus; Lepidapedon spp. innom (Elongatum-group) fromCoryphaenoides guentheri andCoryphaenoides (Chalinura) leptolepis; L. desclersae n. sp. fromLepidion eques; L. beveridgei fromCoryphaenoides (Nematonurus) armatus andC. (Chalinura) mediterraneus; andL. zubchenkoi fromCoryphaenoides (Chalinura) leptolepis andC. (C.) profundicolus. The phylogeny, host-specificity and zoogeography of the genus are briefly discussed.     

Biochemical synthesis of chirally pure Rp oligonucleotide phosphorothioates

Oligonucleotide phosphorothioates have been synthesized using procaryotic DNA polymerase and oligonucleotide template/primer. The method facilitates the recovery of DNA polymerase and template/primer and is successful at the milligram scale. This revised version was published online in November 2006 with corrections to the Cover Date.     

Retinal Attachment Instability Is Diversified among Mammalian Melanopsins

Melanopsins play a key role in non-visual photoreception in mammals. Their close phylogenetic relationship to the photopigments in invertebrate visual cells suggests they have evolved to acquire molecular characteristics that are more suited for their non-visual functions. Here we set out to identify such characteristics by comparing the molecular properties of mammalian melanopsin to those of invertebrate melanopsin and visual pigment. Our data show that the Schiff base linking the chromophore retinal to the protein is more susceptive to spontaneous cleavage in mammalian melanopsins. We also find this stability is highly diversified between mammalian species, being particularly unstable for human melanopsin. Through mutagenesis analyses, we find that this diversified stability is mainly due to parallel amino acid substitutions in extracellular regions. We propose that the different stability of the retinal attachment in melanopsins may contribute to functional tuning of non-visual photoreception in mammals.     

Lytic transglycosylases: concinnity in concision of the bacterial cell wall

The lytic transglycosylases (LTs) are bacterial enzymes that catalyze the non-hydrolytic cleavage of the peptidoglycan structures of the bacterial cell wall. They are not catalysts of glycan synthesis as might be surmised from their name. Notwithstanding the seemingly mundane reaction catalyzed by the LTs, their lytic reactions serve bacteria for a series of astonishingly diverse purposes. These purposes include cell-wall synthesis, remodeling, and degradation; for the detection of cell-wall-acting antibiotics; for the expression of the mechanism of cell-wall-acting antibiotics; for the insertion of secretion systems and flagellar assemblies into the cell wall; as a virulence mechanism during infection by certain Gram-negative bacteria; and in the sporulation and germination of Gram-positive spores. Significant advances in the mechanistic understanding of each of these processes have coincided with the successive discovery of new LTs structures. In this review, we provide a systematic perspective on what is known on the structure–function correlations for the LTs, while simultaneously identifying numerous opportunities for the future study of these enigmatic enzymes.