A relational database of protein structures designed for flexible enquiries about conformation

A relational database of protein structure has been developed to enable rapid and flexible enquiries about the occurrence of many aspects of protein architecture. The coordinates of 294 proteins from the Brookhaven Data Bank have been processed by standard computer programs to generate many additional terms that quantify aspects of protein structure. These terms include solvent accessibility, main-chain and side-chain dihedral angles, and secondary structure. In a relational database, the information is stored in tables with columns holding the different terms and rows holding the different entries for the terms. The different relational base tables store the information about the protein coordinate set, the different chains in the protein, the amino acid residues and ligands, the atomic coordinates, the salt bridges, the hydrogen bonds, the disulphide bridges and the close tertiary contacts. The database was established under ORACLE management system. Enquiries are constructed in ORACLE using SQL (structured query language) which is simple to use and alleviates the need for extensive computer programs. A single table can be searched for entries that meet various criteria, e.g. all protein solved to better than a given resolution. The power of the database occurs when several tables, or the entries in a single table, are cross-correlated. For example the dihedral angles of proline in the fourth position in an alpha-helix in high resolution structures can be rapidly obtained. The structural database provides a powerful tool to obtain empirical rules about protein conformation. This database of protein structures is part of a joint project between Birkbeck College and Leeds University to establish an integrated data resource of protein sequences and structures (ISIS) that encodes the complex patterns of residues and coordinates that define protein conformation. The entire data resource (ISIS) will provide a system to guide all areas of protein modelling including structure prediction, site-directed mutagenesis and de novo protein design. The availability of ISIS is described in the paper.     

Isotope ratios of cellulose from plants having different photosynthetic pathways

Hydrogen and carbon isotope ratios of cellulose nitrate and oxygen isotope ratios of cellulose from C₃, C₄, and Crassulacean acid metabolism (CAM) plants were determined for plants growing within a small area in Val Verde County, Texas. Plants having CAM had distinctly higher deuterium/hydrogen (D/H) ratios than plants having C₃ and C₄ metabolism. When hydrogen isotope ratios are plotted against carbon isotope ratios, each photosynthetic mode separates into a distinct cluster of points. C₄ plants had many D/H ratios similar to those of C₃ plants, so that hydrogen isotope ratios cannot be used to distinguish between these two photosynthetic modes. Portulaca mundula, which may have a modified photosynthetic mode between C₄ and CAM, had a hydrogen isotope ratio between those of the C₄ and CAM plants. When oxygen isotope ratios are plotted against carbon isotope ratios, no distinct clustering of the C₄ and CAM plants occurs. Thus, oxygen isotope ratios are not useful in distinguishing between these metabolic modes. A plot of hydrogen isotope ratios versus oxygen isotope ratios for this sample set shows considerable overlap between oxygen isotope ratios of the different photosynthetic modes without a concomitant overlap in the hydrogen isotope ratios of CAM and the other two photosynthetic modes. This observation is consistent with the hypothesis that higher D/H ratios in CAM plants relative to C₃ and C₄ plants are due to isotopic fractionations occurring during biochemical reactions.     

Tannins and nitrogen dynamics in mangrove leaves at different age and decay stages (Jiulong River Estuary,China)

Changes in the total phenolics, condensed tannins (CT), protein-precipitable phenolics content and protein precipitation capacity were determined on mangrove leaves representing a range of maturation and senescence in the Jiulong River Estuary, Fujian, China. The results showed that the total phenolics, extractable condensed tannins, total condensed tannins, protein-precipitable phenolics content and protein precipitation capacity in young leaves were higher than those in mature and senescent leaves. With leaf maturation and senescence, total pehnolics decreased. The rapid loss of phenolics observed following senescence and abscission can be ascribed to leaching and degradation. Protein-bound CT and fibre-bound CT tended to increase with leaf maturity, and decreased with senescence. Protein-bound CT and fibre-bound CT increased with leaf decomposition, with CT binding more strongly to protein than to fibre. The increases in nitrogen contents and ash free caloric values, and declines in total phenolics and total condensed tannins of mangrove leaf litter suggests that partially decomposed mangrove detritus is a palatable heterotrophic substrate, and thus may be an important source of matter and energy for the estuarine food web. Handling editor: K. Martens     

Automatic document classification of biological literature

Background  

Document classification is a wide-spread problem with many applications, from organizing search engine snippets to spam filtering. We previously described Textpresso, a text-mining system for biological literature, which marks up full text according to a shallow ontology that includes terms of biological interest. This project investigates document classification in the context of biological literature, making use of the Textpresso markup of a corpus of Caenorhabditis elegans literature.     

Inter-species sequence conservation of single-spanning transmembrane regions

The extent of inter-species sequence identity in single-spanning transmembrane regions of integral membrane proteins was evaluated. The sequences of the 32 human transmembrane regions were compared with the respective rodent homologues. The identity between homologous transmembrane regions ranged from 32 to 100%, compared with a mean value of 14% identity between unrelated transmembrane sections. On average the identity between homologous transmembrane regions is slightly higher than for the rest of the chain. These values suggest that, in general, there are structural and/or functional constraints on the transmembrane regions beyond the simple requirement to act as a passive, nonpolar, connecting region across the cell membrane. Although there is limited experimental evidence available, the three transmembrane regions (CD2 antigen, MHC class I and ICAM-1) with particularly low values of inter-species identity (less than 50%) are probably not involved in an interaction with another transmembrane section in the same cell.     

ONYCHOMYCOSIS OF THE FEET—Treatment with Griseofulvin

Griseofulvin, a new orally administered antifungal antibiotic which has proved to be effective for the treatment of a wide variety of superficial fungus infections of man, was used in the treatment of 51 patients with infections of the toenails due to T. rubrum. Thirty-four of the patients were treated with griseofulvin alone and seven were treated with griseofulvin combined with surgical avulsion of all involved toenails. The remaining ten had bilateral infections, and avulsion was done on one foot but not the other before griseofulvin therapy was begun.Of 34 patients who were treated with griseofulvin alone, few had complete cure even after prolonged treatment. Some nails showed improvement for a time, then no further gain; some showed no improvement; some showed resistant wedges of infection which penetrated proximally toward the posterior nail fold.In the instances of surgical avulsion, clinically normal nails regrew during griseofulvin therapy. This simple procedure, with thorough removal of all underlying keratinous debris, apparently did away with foci of possible reinfection.The results of the study indicated that surgical avulsion of the toenails in combination with griseofulvin therapy is an effective and practical method of treating onychomycosis of the toenails due to T. rubrum.     

FOOD PLANT DERIVED DISEASE TOLERANCE AND RESISTANCE IN A NATURAL BUTTERFLY‐PLANT‐PARASITE INTERACTIONS

Organisms can protect themselves against parasite‐induced fitness costs through resistance or tolerance. Resistance includes mechanisms that prevent infection or limit parasite growth while tolerance alleviates the fitness costs from parasitism without limiting infection. Although tolerance and resistance affect host–parasite coevolution in fundamentally different ways, tolerance has often been ignored in animal–parasite systems. Where it has been studied, tolerance has been assumed to be a genetic mechanism, unaffected by the host environment. Here we studied the effects of host ecology on tolerance and resistance to infection by rearing monarch butterflies on 12 different species of milkweed food plants and infecting them with a naturally occurring protozoan parasite. Our results show that monarch butterflies experience different levels of tolerance to parasitism depending on the species of milkweed that they feed on, with some species providing over twofold greater tolerance than other milkweed species. Resistance was also affected by milkweed species, but there was no relationship between milkweed‐conferred resistance and tolerance. Chemical analysis suggests that infected monarchs obtain highest fitness when reared on milkweeds with an intermediate concentration, diversity, and polarity of toxic secondary plant chemicals known as cardenolides. Our results demonstrate that environmental factors—such as interacting species in ecological food webs—are important drivers of disease tolerance.