SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution

Background  

General protein evolution models help determine the baseline expectations for the evolution of sequences, and they have been extensively useful in sequence analysis and for the computer simulation of artificial sequence data sets.     

Vertical transmission in feather mites: insights into its adaptive value

1. The consequences of symbiont transmission strategies are better understood than their adaptive causes. 2. Feather mites are permanent ectosymbionts of birds assumed to be transmitted mainly vertically from parents to offspring. The transmission of Proctophyllodes doleophyes Gaud (Astigmata, Proctophyllodidae) was studied in two European populations of pied flycatchers, Ficedula hypoleuca Pallas (Passeriformes, Muscicapidae). 3. The vertical transmission of this mite species is demonstrated here with an acaricide experiment. This study also compared (for two distant populations during 4 years) patterns in reductions in mite intensity in adult birds, from egg incubation to chick‐rearing periods, with the predictions of three hypotheses on how host survival prospects and mite intraspecific competition might drive feather mites' transmission strategy. 4. The results are in agreement with previous studies and show that feather mites transmit massively from parents to chicks. 5. The magnitude of the transmission was closer to that predicted by the hypothesis based on intraspecific competition, while a bet‐hedging strategy is also partially supported.     

Escape from natural enemies during climate-driven range expansion: a case study

Abstract.  1. A major, and largely unexplored, uncertainty in projecting the impact of climate change on biodiversity is the consequence of altered interspecific interactions, for example between parasitoids and their hosts. The present study investigated parasitism in the Brown Argus butterfly, Aricia agestis ; a species that has expanded northward in Britain during the last 30  years in association with climate warming.
2.  Aricia agestis larvae suffered lower mortality from parasitoids in newly colonised areas compared with long-established populations. This result was consistent over four consecutive generations (2 years) when comparing one population of each type, and also when several populations within the historical and recently colonised range of the species were compared within a single year. Thus, A. agestis appears to be partially escaping from parasitism as it expands northwards.
3. Reduced parasitism occurred despite the fact that several of the parasitoid species associated with A. agestis were already present in the newly colonised areas, supported predominantly by an alternative host species, the Common Blue butterfly, Polyommatus icarus .
4. As the species expand their distributions into areas of increased climatic suitability, invasion fronts may escape from natural enemies, enhancing rates of range expansion. The results suggest that the decoupling of interspecific interactions may allow some species to exploit a wider range of environments and to do so more rapidly than previously thought possible.     

Conformational properties of the disease-causing Z variant of α1-antitrypsin revealed by theory and experiment

The human serine protease inhibitor (serpin) α-1 antitrypsin (α1-AT) protects tissues from proteases of inflammatory cells. The most common disease-causing mutation in α1-AT is the Z-mutation (E342K) that results in an increased propensity of α1-AT to polymerize in the ER of hepatocytes, leading to a lack of secretion into the circulation. The structural consequences of this mutation, however, remain elusive. We report a comparative molecular dynamics investigation of the native states of wild-type and Z α1-AT, revealing a striking contrast between their structures and dynamics in the breach region at the top of β-sheet A, which is closed in the wild-type simulations but open in the Z form. Our findings are consistent with experimental observations, notably the increased solvent exposure of buried residues in the breach region in Z, as well as polymerization via domain swapping, whereby the reactive center loop is rapidly inserted into an open A-sheet before proper folding of the C-terminal β-strands, allowing C-terminal domain swapping with a neighboring molecule. Taken together, our experimental and simulation data imply that mutations at residue 342 that either stabilize an open form of the top of β-sheet A or increase the local flexibility in this region, may favor polymerization and hence aggregation.     

Water Balance in Cucumis Plants, Measured by Nuclear Magnetic Resonance, II

Nuclear magnetic resonance (NMR) was used to investigate theeffects of changes in root temperature, of changes in the areaof root in contact with culture solution and of day/night rhythmon the water balance of a cucumber and a gherkin plant. Resultsare discussed in terms of water potential, flow rate and resistanceusing a previously presented model of water balance. As longas water uptake alone is varied, flow rate and water content(or potential) will change in the same direction. In contrast,from that model it is predicted that changes in transpirationwill affect flow rate and water content in opposite ways. Anexperimental verification of this prediction was given in theprevious paper. Results obtained by the NMR method are comparedto those determined using a dendrometer. The results demonstratethat the NMR method is a valuable tool to study plant waterbalance and that it can serve as a technique for discriminatingbetween changes in plant water balance that are due to changesin water uptake by roots and those due to changes in transpiration. Key words: Water balance model, Cucumis satious L., flow, water content, NMR, water balance measurement     

<Emphasis Type="Italic">In vivo</Emphasis> assessment of the impedance ratio method used in electronic foramen locators

Background  

The results of an in vivo study on the "ratio method" used in electronic foramen locators (EFL) are presented. EFLs are becoming widely used in the determination of the working length (WL) during the root canal treatment. The WL is the distance from a coronal reference point to the point at which canal preparation and filling should terminate. The "ratio method" was assessed by many clinicians with the aim of determining its ability to locate the apical foramen (AF). Nevertheless, in vivo studies to assess the method itself and to explain why the "ratio method" is able to locate the apical foramen and is unable to determine intermediate distances were not published so far.     

Predicting deleterious nsSNPs: an analysis of sequence and structural attributes

Background  

There has been an explosion in the number of single nucleotide polymorphisms (SNPs) within public databases. In this study we focused on non-synonymous protein coding single nucleotide polymorphisms (nsSNPs), some associated with disease and others which are thought to be neutral. We describe the distribution of both types of nsSNPs using structural and sequence based features and assess the relative value of these attributes as predictors of function using machine learning methods. We also address the common problem of balance within machine learning methods and show the effect of imbalance on nsSNP function prediction. We show that nsSNP function prediction can be significantly improved by 100% undersampling of the majority class. The learnt rules were then applied to make predictions of function on all nsSNPs within Ensembl.     

Aspergillus terreus and its toxic metabolites as a food contaminant in some Egyptian Bakery products and grains

A. terreus isolates isolated from some bakery products, corn and rice were found to be able to produce territrems. 90% of theA. terreus isolated from bakery products were able to produce territrem A, with a mean of 0.09 ppm, while 80% ofA. terreus isolates produce territrem B with a mean of 0.24 ppm. On the other hand 31.8% of the isolates ofA. terreus from corn were able to produce territrem A with a mean of 0.44 ppm. ConcerningA. terreus isolates from rice, 66.7% were found to produce territrem A, with a mean of 5.28 ppm, and 77.8% of the isolates produced territrem B with a mean of 1.79 ppm.