Proteome reference map for the plant growth‐promoting bacterium Pseudomonas putida UW4

A proteome reference map containing 326 2‐D gel spots representing 275 different proteins was constructed for the plant growth‐promoting bacterium Pseudomonas putida UW4. Protein identifications were obtained using Q‐TOF MS/MS spectra matching to homologous proteins from other Pseudomonas strains and confirmed by PMF analysis. This data set is accessible at http://world‐2dpage.expasy.org/repository/ and will aid in further characterization of Pseudomonas strains and interactions of plant growth‐promoting bacterium with the plant rhizosphere environment.     

New hypotheses about the structure–function of proprotein convertase subtilisin/kexin type 9: Analysis of the epidermal growth factor‐like repeat A docking site using WaterMap

LDL cholesterol (LDL‐C) is cleared from plasma via cellular uptake and internalization processes that are largely mediated by the low‐density lipoprotein cholesterol receptor (LDL‐R). LDL‐R is targeted for lysosomal degradation by association with proprotein convertase subtilisin‐kexin type 9 (PCSK9). Gain of function mutations in PCSK9 can result in excessive loss of receptors and dyslipidemia. On the other hand, receptor‐sparing phenomena, including loss‐of‐function mutations or inhibition of PCSK9, can lead to enhanced clearance of plasma lipids. We hypothesize that desolvation and resolvation processes, in many cases, constitute rate‐determining steps for protein–ligand association and dissociation, respectively. To test this hypothesis, we analyzed and compared the predicted desolvation properties of wild‐type versus gain‐of‐function mutant Asp374Tyr PCSK9 using WaterMap, a new in silico method for predicting the preferred locations and thermodynamic properties of water solvating proteins (“hydration sites”). We compared these results with binding kinetics data for PCSK9, full‐length LDL‐R ectodomain, and isolated EGF‐A repeat. We propose that the fast k_on and entropically driven thermodynamics observed for PCSK9‐EGF‐A binding stem from the functional replacement of water occupying stable PCSK9 hydration sites (i.e., exchange of PCSK9 H‐bonds from water to polar EGF‐A groups). We further propose that the relatively fast k_off observed for EGF‐A unbinding stems from the limited displacement of solvent occupying unstable hydration sites. Conversely, the slower k_off observed for EGF‐A and LDL‐R unbinding from Asp374Tyr PCSK9 stems from the destabilizing effects of this mutation on PCSK9 hydration sites, with a concomitant increase in the persistence of the bound complex. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Molecular phylogeny in endemic weevils: revision of the genera of Macaronesian Cryptorhynchinae (Coleoptera: Curculionidae)

A molecular phylogeny and lineage age estimates are presented for the Macaronesian representatives of the weevil subfamily Cryptorhynchinae, using two mitochondrial genes (cytochrome c oxidase subunit 1 and 16S). The Bayesian reconstruction is supplemented by observations on morphology, ecology, and reproductive biology. The present study often corroborates the groups previously outlined in higher‐level informal taxonomies. These and further groups are now assigned new taxonomic status. The following genera and subgenera are described (formerly Acalles): Aeoniacalles gen. nov. , Canariacalles gen. nov. , Ficusacalles gen. nov. , Madeiracalles gen. nov. , Silvacalles gen. nov. (with Tolpiacalles subgen. nov. , Tagasastacalles subgen. nov. ), Sonchiacalles gen. nov. , Echiumacalles gen. nov. (monotypic), Lauriacalles gen. nov. (monotypic), and Pseudodichromacalles gen. nov. (monotypic; formerly Dichromacalles). For the western Palaearctic genus Acalles Schoenherr, 1825 the first subgenus Origoacalles subgen. nov. is described and for the genus Onyxacalles Stüben, 1999 the first subgenus Araneacalles subgen. nov. ; Paratorneuma Roudier 1956 resyn. Except for one species of Acalles (Origoacalles), all of these new higher taxa are endemic to the Macaronesian Islands. All new taxa are presented, together with their host plants and further data, in a synoptic tabular overview. Based on the results of our phylogenetic analysis, we advocate the hypothesis that the evolution of the species in the new genera (of which most group into a ‘Macaronesian clade’) began in the comparatively arid succulent bush zone and that the shady and humid laurel forest of the thermo‐Canarian and thermo‐Madeiran zone was entered much later. Our reconstruction implies that the Canarian and Madeiran archipelagos were colonized by Cryptorhynchinae at least seven times from the continent but saw only one considerable adaptive radiation. It also becomes apparent that it is the ancestor species of the genus Canariacalles– and not Pseudodichromacalles– that features a close connection to the south‐western European and north‐western African species of Dichromacalles s.s. Finally, a key is presented for all genera and subgenera of the Macaronesian Cryptorhynchinae. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 160 , 40–87.     

Pollination strategies in Cretan Arum lilies

Flowers of the genus Arum are known to attract dung‐breeding flies and beetles through olfactory deceit. In addition to this strategy, the genus has evolved several other pollination mechanisms. The present study aimed to characterize the pollination strategies of the Cretan Arum species by investigating the flowering phenology, thermogeny, inflorescence odours, and the pollinating fauna. The results obtained show that Arum cyrenaicum and Arum concinnatum emit a strong dung smell and exhibit the distinctive features associated with this pollination syndrome. Both species are highly thermogenic, have a similar odour profile and attract small‐bodied Diptera. Although sharing the same habitat, these two plant species are never found growing sympatrically as a result of the early blooming period of A. cyrenaicum. By contrast, Arum creticum and Arum idaeum have evolved a more traditional and mutually beneficial pollination mechanism. The stinking smell has been replaced by a more flower‐like odour that attracts bees (Lasioglossum sp.) and, occasionally, bugs (Dionconotus cruentatus). Although attracting the same pollinator, the main compound present in the odour of A. creticum is different from that of A. idaeum. Principal component analysis (PCA), based on physiologically active components of the flower odours determined by testing on the antenna of the Lasioglossum bee, revealed two different clusters, indicating that pollinators can potentially discriminate between the odours of the two species. A further PCA on the main floral odour volatiles as identified by gas chroatography‐mass spectroscopy from all the Arum species under investigation displayed odour‐based similarities and differences among the species. The PCA‐gas chomotography‐electroantennographic detection active peaks analysis showed that the two species, A. creticum and A. idaeum, form two groups and are clearly separated from A. cyrenaicum and A. concinnatum, which, conversely, cluster together. The evolutionary forces and selective pressures leading to diversification of pollination mechanisms in the Cretan Arum spp. are discussed. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 991–1001.     

The need for validation of large administrative databases: Veterans Health Administration ICD-9CM coding of exudative age-related macular degeneration and ranibizumab usage

We performed a validation study by chart review of data for exudative age-related macular degeneration (eAMD) and, because of the Veterans Administration (VA) therapy policy, ranibizumab usage in the largest electronic medical record system in the USA. We reviewed 5,854 distinct patients who visited an ophthalmology clinic within VA Connecticut from January 2006-December 2008. We randomly selected 98 of 138 distinct eAMD patients and 265 of 5,588 non-eAMD patients who did not receive ranibizumab. International Classification of Diseases, Ninth Revision, Clinical Modification coding of eAMD had an excellent positive predictive value of 97.8% (95% confidence interval (CI), 93.5-99.4%). The national Decision Support System (DSS) had an excellent positive predictive value of 100% (95% CI, 79.9-100%) for ranibizumab. However, the negative predictive value of the DSS dispensed ranibizumab decreased to 67.5 (95% CI, 62.1-72.4) because of a change in the way local values were stored that led to errors. Therefore, validation of clinical information over time in large databases is necessary.     

Estimation of the number of alpha-helical and beta-strand segments in proteins using circular dichroism spectroscopy

A simple approach to estimate the number of alpha-helical and beta-strand segments from protein circular dichroism spectra is described. The alpha-helix and beta-sheet conformations in globular protein structures, assigned by DSSP and STRIDE algorithms, were divided into regular and distorted fractions by considering a certain number of terminal residues in a given alpha-helix or beta-strand segment to be distorted. The resulting secondary structure fractions for 29 reference proteins were used in the analyses of circular dichroism spectra by the SELCON method. From the performance indices of the analyses, we determined that, on an average, four residues per alpha-helix and two residues per beta-strand may be considered distorted in proteins. The number of alpha-helical and beta-strand segments and their average length in a given protein were estimated from the fraction of distorted alpha-helix and beta-strand conformations determined from the analysis of circular dichroism spectra. The statistical test for the reference protein set shows the high reliability of such a classification of protein secondary structure. The method was used to analyze the circular dichroism spectra of four additional proteins and the predicted structural characteristics agree with the crystal structure data.