Proteomic signatures: amino acid and oligopeptide compositions differentiate among phyla

Availability of complete genome sequences allows in-depth comparison of single-residue and oligopeptide compositions of the corresponding proteomes. We have used principal component analysis (PCA) to study the landscape of compositional motifs across more than 70 genera from all three superkingdoms. Unexpectedly, the first two principal components clearly differentiate archaea, eubacteria, and eukaryota from each other. In particular, we contrast compositional patterns typical of the three superkingdoms and characterize differences between species and phyla, as well as among patterns shared by all compositional proteomic signatures. These species-specific patterns may even extend to subsets of the entire proteome, such as proteins pertaining to individual yeast chromosomes. We identify factors that affect compositional signatures, such as living habitat, and detect strong eukaryotic preference for homopeptides and palindromic tripeptides. We further detect oligopeptides that are either universally over- or underabundant across the whole proteomic landscape, as well as oligopeptides whose over- or underabundance is phylum- or species-specific. Finally, we report that species composition signatures preserve evolutionary memory, providing a new method to compare phylogenetic relationships among species that avoids problems of sequence alignment and ortholog detection.     

Production of Colletotrichum truncatum for use as a mycoherbicide: effects of culture, drying and storage on recovery and efficacy

Colletotrichum truncatum (Schwein.) Andrus and Moore NRRL 13737 (= NRRL 18434) is a fungal plant pathogen which shows promise as a bioherbicide against the troublesome weed Sesbania exaltata (Raf.) Rydb. ex A. W. Hill. Previous studies showed similar amounts of spores were produced/ml of medium in liquid and solid-state fermentations. In this study, Colletotrichum truncatum spores were produced in liquid (LC), solid/vermiculite (SV), and solid/perlite-cornmeal-agar (SP). After drying at room temperature with flowing air, SV and SP retained the most viability. Each product was then stored at 4 degrees, 15 degrees, and 25 degrees C. All three products stored at 4 degrees C and SP stored at 15 degrees C retained highest viability. Efficacy based upon assays utilizing equal numbers of viable spores showed SV and SP spores incited more severe disease symptoms than LC spores.     

Exchange diffusion of dopamine induced in planar lipid bilayer membranes by the ionophore X537A

The ionophore X537A causes a large increase in the [(14)C]dopamine (a catecholamine) permeability of planar bilayer membranes. Dopamine transport increases linearly with the ionophore concentration. At relatively high concentrations in the presence of dopamine, the ionophore omdices a conductance which is nearly ideally selective for the dopamine cation. However, the total dopamine flux as determined in tracer experiments is not affected by an electric field and is over 10(5) times larger than predicted from the estimated dopamine conductance. Increasing the dopamine concentration on the side containing radioactive dopamine (the cis side) saturates the dopamine transport. This saturation is relieved by trans addition of nonradioactive dopamine, tyramine, H(+), or K(+). With unequal concentrations of dopamine cis and trans (49 and 12.5 mM), the unidirectional dopamine fluxes are equal. Increasing H(+) cis and trans decreases dopamine transport. It is concluded that at physiological pH, the X537A-induced transport of dopamine occurs via an electrically silent exchange diffusion of dopamine cation with another cation (e.g., dopamine(+), H(+), or K(+)). X537A induces a Ca(++)-independent release of catecholamines from sympathetic nerves by interfering with intracellular storage within storage vesicles (R.W. Holz. 1975. Biochim. Biophys. Acta. 375:138-152). It is suggested that X537A causes an exchange of intravesicular catecholamine with a cytoplasmic cation (perhaps K(+) or H(+)) across the storage vesicle membrane.     

A neutral molecule in a cation-binding site: specific binding of a PEG-SH to acetylcholinesterase from Torpedo californica

The crystal structure of acetylcholinesterase from Torpedo californica complexed with the uncharged inhibitor, PEG-SH-350 (containing mainly heptameric polyethylene glycol with a terminal thiol group) is determined at 2.3 A resolution. This is an untypical acetylcholinesterase inhibitor, since it lacks the cationic moiety typical of the substrate (acetylcholine). In the crystal structure, the elongated ligand extends along the whole of the deep and narrow active-site gorge, with the terminal thiol group bound near the bottom, close to the catalytic site. Unexpectedly, the cation-binding site (formed by the faces of aromatic side-chains) is occupied by CH(2) groups of the inhibitor, which are engaged in C-H...pi interactions that structurally mimic the cation-pi interactions made by the choline moiety of acetylcholine. In addition, the PEG-SH molecule makes numerous other weak but specific interactions of the C-H...O and C-H...pi types.     

Widespread body pain and mortality: prospective population based study

ObjectiveTo determine whether there is excess mortality in groups of people who report widespread body pain, and if so to establish the nature and extent of any excess.DesignProspective follow up study over eight years. Mortality rate ratios were adjusted for age group, sex, and study location.SettingNorth west England.Participants6569 people who took part in two pain surveys during 1991-2.Results1005 (15%) participants had widespread pain, 3176 (48%) had regional pain, and 2388 (36%) had no pain. During follow up mortality was higher in people with regional pain (mortality rate ratio 1.21, 95% confidence interval 1.01 to 1.44) and widespread pain (1.31, 1.05 to 1.65) than in those who reported no pain. The excess mortality among people with regional and widespread pain was almost entirely related to deaths from cancer (1.55 (1.09 to 2.19) for regional pain and 2.07 (1.37 to 3.13) for widespread pain). The excess cancer mortality remained after exclusion of people in whom cancer had been diagnosed before the original survey and after adjustment for potential confounding factors. There were also more deaths from causes other than disease (for example, accidents, suicide, violence) among people with widespread pain (5.21, 0.94 to 28.78).ConclusionThere is an intriguing association between the report of widespread pain and subsequent death from cancer in the medium and long term. This may have implications for the long term follow up of patients with “unexplained” widespread pain symptoms, such as those with fibromyalgia.

What is already known on this topic

Widespread body pain, the cardinal symptom of fibromyalgia, is commonAn organic basis for symptoms is found in only a small proportion of peopleTreatment is difficult, and studies with short term follow up have shown that symptoms commonly persist

What this study adds

This was the first study with long term follow up of people with widespread pain in the communityThese people experience an increased mortality and the excess is principally related to deaths from cancer     

Population study of tender point counts and pain as evidence of fibromyalgia.

OBJECTIVE--To determine the relation between tender points, complaints of pain, and symptoms of depression, fatigue, and sleep quality in the general population. DESIGN--Two stage cross sectional study with an initial questionnaire about pain to classify those eligible for an examination of tender points. SETTING--Two general practices in north west England. SUBJECTS--Stratified random sample of adults from age-sex registers. Of the responders, 250 were selected for examination of tender points on the basis of their reported pain complaints; 177 subsequently participated. MAIN OUTCOME MEASURES--Tender point count (0 to 18) grouped into four categories with the highest (> or = 11) corresponding to the criteria of the American College of Rheumatology for fibromyalgia. Assessment of pain (chronic widespread, regional, none). Measures of depression, fatigue, and difficulty with sleeping. RESULTS--Women had a higher median tender point count (six) than did men (three). Counts were higher in those with pain than in those who had no pain and in those with widespread compared with regional pain. Most subjects with chronic widespread pain, however, had fewer than 11 tender points (27/45; 60%). Two people with counts of 11 or more were in the group reporting no pain. Mean symptom scores for depression, fatigue, and sleep problems increased as the tender point count rose (P value for trend < 0.001). These trends were independent of pain complaints. CONCLUSIONS--Tender points are a measure of general distress. They are related to pain complaints but are separately associated with fatigue and depression. Sleep problems are associated with tender points, although prospective studies are needed to determine whether they cause tenderness to develop. Fibromyalgia does not seem to be a distinct disease entity.     

Immunological cross-reactivity between electric-eel acetylcholinesterase and rat-tail-tendon collagen.

Immunological cross-reactivity between acetylcholinesterase from the electric organ of the electric eel and rat tail tendon collagen was examined both on the cellular and humoral levels. 1. Guinea pigs immunized with rat tail tendon collagen displayed a strong delayed-type skin reaction when tested with the elongated acetylcholinesterase preparation (i.e. 14-S + 18-S molecular forms). However, when the glubular 11-S enzyme was tested, almost no cross-reactivity was obtained. Similarly, guinea pigs immunized with 14-S + 18-S preparation exhibited skin sensitization to rat tail tendon collagen. 2. Using a radioimmunoassay, it was observed that 125I-labeled 14-S + 18-S acetylcholinesterase binds efficiently to rabbit antiserum elicited against rat tail tendon collagen, whereas 125I-labeled 11-S enzyme does not bind at all to this antiserum. Similar results were obtained by passive hemagglutination assay. The experiments suggest that 14-S + 18-S acetylcholinesterase, but not 11-S enzyme, which is devoid of the tail structure, has antigenic determinants in common with collagen from rat tail tendon.     

Compositional shifts in Costa Rican forests due to climate‐driven species migrations

Species are predicted to shift their distributions upslope or poleward in response to global warming. This prediction is supported by a growing number of studies documenting species migrations in temperate systems but remains poorly tested for tropical species, and especially for tropical plant species. We analyzed changes in tree species composition in a network of 10 annually censused 1‐ha plots spanning an altitudinal gradient of 70–2800 m elevation in Costa Rica. Specifically, we combined plot data with herbarium records (accessed through GBIF) to test if the plots' community temperature scores (CTS, average thermal mean of constituent species weighted by basal area) have increased over the past decade as is predicted by climate‐driven species migrations. In addition, we quantified the contributions of stem growth, recruitment, and mortality to the observed patterns. Supporting our a priori hypothesis of upward species migrations, we found that there have been consistent directional shifts in the composition of the plots, such that the relative abundance of lowland species, and hence CTS, increased in 90% of plots. The rate of the observed compositional shifts corresponds to a mean thermal migration rate (TMR) of 0.0065 °C yr^?1 (95% CI = 0.0005–0.0132 °C yr^?1). While the overall TMR is slower than predicted based on concurrent regional warming of 0.0167 °C yr^?1, migrations were on pace with warming in 4 of the 10 plots. The observed shifts in composition were driven primarily by mortality events (i.e., the disproportionate death of highland vs. lowland species), suggesting that individuals of many tropical tree species will not be able to tolerate future warming and thus their persistence in the face of climate change will depend on successful migrations. Unfortunately, in Costa Rica and elsewhere, land area inevitably decreases at higher elevations; hence, even species that are able to migrate successfully will face heightened risks of extinction.     

News from the Biological Stain Commission No. 5

In this fifth issue of News from the Biological Stain Commission (BSC), under the heading of Regulatory Affairs, the BSC's International Affairs Committee provides more information from the meeting of the International Standards Organization ISO/TC 212 Committee that took place on June 2–4, 2008 at Vancouver, Canada. In addition, we give an update on the current situation regarding the supplies of hematoxylin.