AMID: autonomous modeler of intragenic duplication

Intragenic duplication is an evolutionary process where segments of a gene become duplicated. While there has been much research into whole-gene or domain duplication, there have been very few studies of non-tandem intragenic duplication. The identification of intragenically replicated sequences may provide insight into the evolution of proteins, helping to link sequence data with structure and function. This paper describes a tool for autonomously modelling intragenic duplication. AMID provides: identification of modularly repetitive genes; an algorithm for identifying repeated modules; and a scoring system for evaluating the modules' similarity. An evaluation of the algorithms and use cases are presented.     

Lytic enzyme activity in peat is increased by substrate amendment with chitin: Implications for the control of<Emphasis Type="Italic">Phytophthora fragariae</Emphasis> in<Emphasis Type="Italic">Fragaria vesca</Emphasis>

Chitin is reported to stimulate mycorrhizas and antagonistic, lytic-enzyme producing soil microorganisms. Here mycorrhizal and non-mycorrhizal strawberry (Fragaria vesca) plants were grown in peat growth-substrate and in peat amended with chitin (Suppressor™). Chitinase and cellulase activity was determined and the plants were challenged by inoculation withPhytophthora fragariae, the causal agent of redcore disease. Disease resistance was only found in the mycorrhizal strawberry-chitin amendment treatment and depended on the duration of the mycorrhiza’s growth in the amended substrate before potting on to a chitin-free growth substrate. The practical application of chitin substrate amendment in the exploitation of mycorrhizal biological control is discussed.     

Identification of cytoskeletal regulatory proteins required for efficient phagocytosis in Drosophila

Phagocytosis is a complex and apparently evolutionarily conserved process that plays a central role in the immune response to infection. By ultrastructural and functional criteria, Drosophila hemocyte (macrophage) phagocytosis resembles mammalian phagocytosis. Using a non-saturated forward genetic screen for larval hemocyte phagocytosis mutants, D-SCAR and profilin were identified as important regulators of phagocytosis in Drosophila. In both hemocytes ex vivo and the macrophage-like S2 cell line, lack of D-SCAR significantly decreased phagocytosis of Escherichia coli and Staphylococcus aureus. In contrast, profilin mutant hemocytes exhibited increased phagocytic activity. Analysis of double mutants suggests that D-SCAR and profilin interact during phagocytosis. Finally, RNA interference studies in S2 cells indicated that the D-SCAR homolog D-WASp also participates in phagocytosis. This study demonstrates that Drosophila provides a viable model system in which to dissect the complex interactions that regulate phagocytosis.     

The relationship between nucleoside triphosphate hydrolase (NTPase) isoform and Toxoplasma strain virulence in rat and human toxoplasmosis

Avirulent strains of Toxoplasma gondii possess only the nucleoside triphosphate hydrolase II (NTPaseII) isoform, whilst virulent strains possess both NTPaseI and NTPaseII. To determine if it is possible to identify the infective strain type (virulent or avirulent) in T. gondii infections by serological methods, we developed isoform-specific peptide ELISAs from the NTPaseI and NTPaseII antigens of T. gondii. When rats were immunized with either recombinant NTPaseI or NTPaseII, the ELISA could differentially identify antibody reactivity to each NTPase isoform. This ELISA was then used to test six groups of rats that were infected with either one of three virulent (RH, P or Ent) or three avirulent (Me49, C or TPR) strains of T. gondii. No differential antibody reactivity was detected by either whole recNTPase ELISA or peptide ELISA in the sera of rats, whether infected by virulent or avirulent strains of T. gondii. We also studied a panel of human sera from patients infected with known laboratory strains of T. gondii or naturally infected patients where the parasite was isolated and its virulence determined in mice. Differential reactivity to whole recNTPase isoforms was detected in some human sera, but this reactivity was not detected by the isoform-specific peptide ELISAs. Although the NTPase peptides do exhibit differential antibody reactivity, this is not correlated with the virulence status of the infecting strain.     

Disulfide by Design: a computational method for the rational design of disulfide bonds in proteins

SUMMARY: Disulfide by Design is a program for the design of novel disulfide bonds in proteins. Protein structure files in PDB format are analyzed to identify residue pairs that are likely to form a disulfide bond if the respective amino acids are mutated to cysteines. The output displays residue pairs having the appropriate geometric characteristics for disulfide formation and provides automated generation of modified PDB files including modeled disulfides. Validation demonstrates a high level of accuracy for the algorithm. AVAILABILITY: http://www.ehscenter.org/dbd/ Supplementary information: http://www.ehscenter.org/dbd/     

In Vitro CuIture of the Tropical Sponge <Emphasis Type="Italic">Axinella corrugata</Emphasis> (Demospongiae): Effect of Food Cell Concentration on Growth,Clearance Rate,and Biosynthesis of Stevensine

In vitro culture is one possible method for supplying sponge metabolites for pharmaceutical applications, but appropriate feeding regimens that maximize both growth and metabolite biosynthesis are largely unknown. According to the natural concentration (NC) of cells 1 to 50 µm in size that are available to wild Axinella corrugata, we fed explants a multispecific diet of bacteria, microalgae, and yeast at 4 different concentrations: 1NC, 3NC, 5NC, and 5+1NC (the last consisted of 5 NC of bacteria and 1 NC of microalgae and yeast). Explants fed a 3NC diet had the best culture response, growing on average from 8.5 g to 10.3 g in 8 weeks, and showing a 110% increase in concentration (milligrams per gram of dry weight) of the antitumor compound stevensine. Stevensine production in 3NC explants, representing the total milligrams of metabolite per explant, increased by 157% over the study. Explants fed at 1NC had relatively stable weights, indicating that the diet met metabolic costs only. Explants fed at the two highest concentrations lost weight after 4 weeks, possibly because long-term high cell concentration blocked their aquiferous system, reducing their ability to feed efficiently. Stevensine production in explants fed the 1NC, 5NC, or 5+1NC diets were similar, and varied little from the initial amount. A separate experiment showed that the clearance rate for A. corrugata is similar between the examined food types and cell concentrations over 5 hours, averaging 766 ml h^–1 g DW^–1.Overall, this study demonstrates that relatively small changes in food abundance can greatly affect both sponge growth and metabolite biosynthesis. The good growth and increased production of the target metabolite stevensine for A. corrugata explants fed a 3NC diet suggests that in vitro culture is a viable method of supplying some sponge metabolites.     

Aza-peptide epoxides: potent and selective inhibitors of Schistosoma mansoni and pig kidney legumains (asparaginyl endopeptidases)

Aza-peptide epoxides are a new class of irreversible cysteine protease inhibitors. Derivatives containing a P1 aza-asparagine residue are specific for Schistosoma mansoni and pig kidney legumains, which are clan CD cysteine proteases. The inhibitors have second-order rate constants of up to 10(4) M(-1) s(-1) with pig kidney legumain and IC50 values as low as 45 nM with S. mansoni legumain. The most potent epoxides contain an ester moiety with S,S stereochemistry attached to the epoxide. Interestingly, amide and amino acid derivatives of the epoxysuccinate moiety were not inhibitors of legumain, while disubstituted amide derivatives are quite potent. The inhibitors have little or no inhibitory activity with other proteases such as caspases, chymotrypsin, papain, cathepsin B, granzyme B, and various aspartyl proteases.     

Play and the evolution of fairness: a game theory model

Bekoff [J. Consci. Stud. 8 (2001) 81] argued that mammalian social play is a useful behavioral phenotype on which to concentrate in order to learn more about the evolution of fairness. Here, we build a game theoretical model designed to formalize some of the ideas laid out by Bekoff, and to examine whether ‘fair’ strategies can in fact be evolutionarily stable. The models we present examine fairness at two different developmental stages during an individual's ontogeny, and hence we create four strategies—fair at time 1/fair at time 2, not fair at time 1/not fair at time 2, fair at time 1/not fair at time 2, not fair at time 1/fair at time 2. Our results suggest that when considering species where fairness can be expressed during two different developmental stages, acting fairly should be more common than never acting fairly. In addition, when no one strategy was evolutionarily stable, we found that all four strategies we model can coexist at evolutionary equilibrium. Even in the absence of an overwhelming database from which to test our model, the general predictions we make have significant implications for the evolution of fairness.     

Amiloride is an ineffective conditioned stimulus in taste aversion learning in C57BL/6J and DBA/2J mice

The epithelial sodium channel (ENaC) blocker amiloride has been shown to increase the behaviorally measured NaCl detection threshold in mice. In this study, a conditioned taste aversion (CTA) paradigm was used to examine whether 100 microM amiloride has a perceptible taste that could contribute to this observed decrease in behavioral responsiveness. Eighty-four C57BL/6J (B6) and 64 DBA/2J (D2) mice were divided into eight groups (n=8-12 per group), in which half received an injection of 0.15 M LiCl (2 mEq/kg) and the other half an equivalent saline injection, in three conditioning trials. The four conditioned stimuli were 100 microM amiloride hydrochloride, water, 0.1 and 0.3 M NaCl. Neither strain demonstrated acquisition of a CTA to amiloride in a brief-access (BA) taste test (5 s trials in the gustometer). Although 0.3 M NaCl is inherently aversive, its pairing with LiCl led to significantly further decreases in licking during the BA test on salt trials in both strains. The D2 strain clearly avoided 0.1 M NaCl, whereas avoidance of this stimulus was more equivocal in B6 mice. The inefficacy of amiloride to serve as a conditioned stimulus in taste aversion learning involving three LiCl pairings suggests that the effects of this ENaC blocker on taste-related behavioral responses to NaCl are likely due to its pharmacological interference with sodium taste transduction.     

Oral amiloride treatment decreases taste sensitivity to sodium salts in C57BL/6J and DBA/2J mice

Sodium taste transduction is thought to occur via an amiloride-sensitive, sodium-selective pathway and an amiloride-insensitive, cation nonselective, anion-dependent pathway(s). It has been shown by others that amiloride, an epithelial sodium channel (ENaC) blocker, significantly reduces the chorda tympani nerve response to lingually applied NaCl in C57BL/6 (B6) mice but not in DBA/2 (D2) mice, suggesting that the latter strain might not possess functional ENaCs in taste receptor cells. We psychophysically measured and compared taste detection thresholds of NaCl and sodium gluconate (NaGlu) prepared with and without 100 microM amiloride in these two strains (eight/strain). Mice were trained and tested in a two-response operant signal detection procedure conducted in a gustometer. Surprisingly, no strain effect was found for the detection thresholds of both salts (approximately 0.05-0.06 M). Moreover, these thresholds were increased by almost an order of magnitude by amiloride adulteration of the solutions. This marked effect of amiloride on sodium detection thresholds suggests that ENaCs are necessary for normal sensitivity to sodium salts in both strains. In addition, because NaGlu is thought to stimulate primarily the amiloride-sensitive pathway, especially at low concentrations, the similarity of NaCl and NaGlu thresholds (r > 0.81 both strains) suggests that ENaCs are also sufficient to support the detection of sodium in weak solutions by B6 and D2 mice.