On itinerant water molecules and detectability of protein-protein interfaces through comparative analysis of homologues

We discuss the question of which residues are sufficiently important for protein-protein interaction to be under notable evolutionary pressure. Its interest stems from the applicability of this knowledge in the reverse direction, to detect a protein-protein interface on a single protomer, starting from the rate of mutation of participating residues. Using the analysis of trajectories produced by the molecular dynamics simulations, we suggest that, in the case of water soluble proteins, a large fraction of evolutionarily privileged residues can be found by considering the dynamic behavior of the protein interface and by looking for residues which exchange water molecules with the bulk of the solvent outstandingly slowly (tentatively termed "dry residues"). We show that the dry interface residues are better conserved across homologues than the generic "geometric footprint" and can be quite reliably detected through comparative analysis of protein homologues, without strong dependence on the choice of method. Furthermore, we show that dry residues distinguish themselves through a set of biophysical properties consistent with the known mechanisms of protein oligomerization: their compositional shift toward nonpolar, overlap, and co-location with residues exhibiting low mobility, their two- to threefold increased propensity over the rest of the geometric footprint to form hydrogen bonds, and four- to almost tenfold increased likelihood to participate in formation of salt bridges. These properties, consistently, help understand the observed increase in the evolutionary pressure that dry residues experience.     

Prediction of mean adult survival rates of southern African birds from demographic and ecological covariates

Estimates of annual survival rates of birds are valuable in a wide range of studies of population ecology and conservation. These include modelling studies to assess the impacts of climatic change or anthropogenic mortality for many species for which no reliable direct estimates of survival are available. We evaluate the performance of regression models in predicting adult survival rates of birds from values of demographic and ecological covariates available from textbooks and databases. We estimated adult survival for 67 species using dead recoveries of birds ringed in southern Africa and fitted regression models using five covariates: mean clutch size, mean body mass, mean age at first breeding, diet and migratory tendency. Models including these explanatory variables performed well in predicting adult survival in this set of species, both when phylogenetic relatedness of the species was taken into account using phylogenetic generalized least squares (51% of variation in logit survival explained) and when it was not (48%). Two independent validation tests also indicated good predictive power, as indicated by high correlations of observed with expected values in a leave‐one‐out cross validation test performed using data from the 67 species (35% of variation in logit survival explained), and when annual survival rates from independent mark–recapture studies of 38 southern African species were predicted from covariates and the regression using dead recoveries (48%). Clutch size and body mass were the most influential covariates, both with and without the inclusion of phylogenetic effects, and a regression model including only these two variables performed well in both of the validation tests (39 and 48% of variation in logit survival explained). Our regression models, including the version with only clutch size and body mass, are likely to perform well in predicting adult survival rate for southern African species for which direct survival estimates are not available.     

Antibodies against recombinant heat shock protein 65 of Tropheryma whipplei in patients with and without Whipple's disease.

Tropheryma whipplei is the causative agent of Whipple's disease (WD), a chronic, life-threatening infection. Laboratory diagnosis is mainly based on PCR and histopathological analysis in duodenal biopsies and other specimens requiring invasive procedures. We have examined the presence of antibodies to recombinant heat shock protein (Hsp65) of T. whipplei in patients with Whipple's disease as well as in control subjects by Western blot and enzyme-linked immunosorbent assay (ELISA). A recombinant plasmid carrying the entire T. whipplei hsp65 gene was constructed, and the expression yielded a 65-kDa histidine-tagged protein. Among four patients with Whipple's disease, two showed an IgG- and one an IgA-response, respectively, when analyzed by Western blotting, whereas from 10 patients without Whipple's disease, only two patients showed a positive IgG-response. The differences between the sera from patients and controls were thus not significant. Successful purification of the protein was achieved by Ni-NTA affinity chromatography. Quantitative analysis of serum antibodies by ELISA demonstrated that antibody levels in the sera of 14 patients were not significantly higher than in those of 89 control subjects. The established ELISA test is not useful to clinical diagnostics.     

BIODIVERSITY RESEARCH: Soil moisture limits foraging: a possible mechanism for the range dynamics of the hadeda ibis in southern Africa

Aim Climate limits the ranges of many animals, but the mechanism whereby it does so remains poorly understood. One explanation is that climate (e.g. temperature or rainfall) affects energy expenditure, eventually limiting where a species can occur. We propose that climate can also affect energy uptake through its effect on foraging efficiency. We examined this idea for the case of the hadeda ibis (Bostrychia hagedash) which has considerably expanded its range in southern Africa over the past 80 years. Hadedas forage mainly by extracting earthworms and other invertebrates from soft soil. Soil moisture, in the absence of irrigation largely determined by climate and soil composition, may therefore be a factor limiting feeding efficiency in hadedas. Location We tested this hypothesis by observing foraging hadedas in Cape Town, South Africa. Results We found that soil moisture limited the rate at which hadedas caught prey items, with an optimum on relatively moist ground. We further measured the energy content of the hadedas’ main prey, earthworms. Using published physiological relationships, we estimated that hadedas need to forage for about 6.3 h to meet their daily energy requirements under optimal soil moisture conditions. On dry soils, they need to forage for >12 h, thus showing that soil moisture has the potential to limit the range of this species. Main conclusions Hadedas originally only occurred in the wettest parts of South Africa, but gradually colonized drier areas, and are now absent only from the driest parts of the country. Our results support the view that climate (determining soil moisture) originally limited the hadedas range and that irrigation has been an important factor facilitating their range expansion. The hadeda is an example for a species whose range expansion is driven by interactions between climate and land‐use change.     

Application of ribotyping for differentiating aeromonads isolated from clinical and environmental sources.

We have investigated the usefulness of ribotyping for the differentiation of aeromonads isolated from five patients with gastroenteritis and from the source water, treatment plant, and distribution system of a small public water supply. Aeromonas hydrophila and Aeromonas caviae were isolated from fecal specimens preserved in Cary-Blair transport medium by using blood ampicillin agar or alkaline peptone water (pH 8.4) subcultured to blood ampicillin agar plates. A. hydrophila, Aeromonas sobria, and A. caviae were isolated from duplicate 100-ml water samples by the membrane filter technique by using ampicillin dextrin agar for quantitative determination of growth and alkaline peptone water enrichment for detection of the presence or absence of aeromonads below the detection limit of the membrane filter method. In addition, free chlorine residuals and pH values were determined for all water samples and heterotrophic plate counts and total and fecal coliform analyses were performed on them. Ribotyping patterns of aeromonads recovered from well 1, detention basin, sand filter, softener, and distribution samples were compared with those of the five clinical isolates. All patient strains were unique; however, identical ribotypes of A. hydrophila and A. sobria isolated from multiple sites in the water system indicated colonization of a well, sand filters, and the softener, with the potential for sporadic contamination of distribution water. Plant operational deficiencies were noted and corrected. Ribotyping can effectively differentiate otherwise indistinguishable strains of bacteria, thus providing a powerful tool for investigation of waterborne diseases and bacteriological problems within water treatment plants and distribution systems.     

ICDs at higher age and clinical risk factors

Background

The implantable cardioverter defibrillator (ICD) is effective in preventing sudden cardiac death. However, in elderly patients (aged 75 years or older) the role of ICDs is still not well-defined and controversial.

Methods

We retrospectively analysed all clinical and survival data of all ICD patients who were ≥75 years at the date of implantation in the Erasmus MC, Rotterdam, the Netherlands and the University Hospital, Basel, Switzerland. Kaplan-Meier survival analysis was performed, and mortality predictors were identified. Mortality of the cohort was compared with a random sample of patients aged 60–70 years originating from the same database and to an age- and sex-matched cohort of Dutch persons.

Results

The study cohort consisted of 179 patients aged 75 years or older who were implanted between February 1999 and July 2008. The median follow-up time was 2.0 (IQR 2.8) years. Survival rates after 1, 2 and 3 years were 87, 82, 75 %, respectively. Survival was similar for primary and secondary prevention. Mortality in this study population could be predicted by combining four clinical risk factors: QRS duration >120 ms, NYHA class > II, renal failure and atrial fibrillation (AF). Survival was worse compared with the group of ICD patients aged 60–70 years and to the age- and sex-matched group of elderly persons. However, survival was not significantly worse when comparing elderly ICD patients without additional risk factors to the general population.

Conclusions

Elderly patients still have an acceptable survival probability independent of prevention indication, certainly if there are no additional clinical risk factors. The presence or absence of additional clinical risk factors should be taken into account when making the decision for implantation, since they strongly correlate with survival.     

Rapid detection and species identification of Mycobacterium spp. using real-time PCR and DNA-microarray

Infections with mycobacteria are an important issue in public health care. Here we present a "proof-of-principle" concept for the identification of 37 different Mycobacterium species using 5' exonuclease real-time PCR and DNA microarray based on the region upstream of the 65 kDa heat shock protein. With our two PCR probes, one complementary to all mycobacteria species, the other specific for the M. tbc-complex, 34 species were properly classified by real-time PCR. After reamplification and hybridization to a DNA microarray, all species showed a specific pattern. All 10 blindly tested positive cultures revealed a positive real-time PCR signal with the genus probe. After reamplification and hybridization, six samples could unambiguously be identified. One sample showed a mixture of presumably three species-specific patterns and sequencing the 16S rRNA confirmed the presence of a mixture. The hybridization results of three specimens could not be interpreted because the signal to background ratio was not sufficient. Two samples considered as negative controls (LAL Reagent Water (Cambrex) and DNA of Candida albicans) gave neither a genus nor a M. tbc-complex positive PCR signal. Based on these results we consider our method to be a promising tool for the rapid identification of different mycobacteria species, with the advantage of possible identification of mixed infections or contaminations.     

Evolutionary trace report_maker: a new type of service for comparative analysis of proteins

: Evolutionary trace report_maker offers a new type of service for researchers investigating the function of novel proteins. It pools, from different sources, information about protein sequence, structure and elementary annotation, and to that background superimposes inference about the evolutionary behavior of individual residues, using real-valued evolutionary trace method. As its only input it takes a Protein Data Bank identifier or UniProt accession number, and returns a human-readable document in PDF format, supplemented by the original data needed to reproduce the results quoted in the report.     

Life Cycle Assessment of the Mobile Communication System UMTS: Towards Eco-efficient Systems (12 pp)

Goal, Scope and Background Goal of this study is an evaluation of the environmental sustainability of the UMTS mobile communication system in Switzerland by means of a Life Cycle Assessment (LCA). A baseline environmental impact profile across the full life cycle of the UMTS (Universal Mobile Telecommunication System) and its predecessor, the GSM (Global System for Mobile Communication) is presented. The baseline assessment was a necessary first step to evaluate the environmental impacts of the mobile communication systems use and growth, thus permitting the evaluation of its environmental sustainability. Main Features Two functional units are defined: a data set of 1 Gbit (1.000.000 kbit), and the yearly mobile communication of an average customer. In the UMTS, both data packages and calls can be conveyed. In order to be able to standardize the results, an equivalence between these two kinds of transmission is formed. Two different options are defined, which represent different ways of transferring the data: mobile phone to mobile phone, and mobile phone to fixed network. All components of the UMTS network like the mobile phones, base stations, antennae, switching systems and the components of the landline like cable system and switching centers, are assessed. The environmental impacts are assessed taking into account all major life cycle phases like raw material extraction, manufacturing, use, disassembly and disposal of the product and the needed infrastructure. Electronic components like printed wiring boards and integrated circuits are assessed using a simple model based on the size (for IC) or number of layers (for PWB), respectively. Mining of precious metals (gold, silver) is included. The study was carried out by ESU-services, Motorola, Swisscom and Deutsche Telekom. Thanks to the industrial partners it can rely on primary data for the production of mobile phone and base station, and for the operation of the networks. As the UMTS network is still being built, no actual data of network operation is available. Data from the GSM (Global System for Mobile Communication) were used in case of data gaps. Results and Conclusions About 25 kg CO2 are emitted and 800 MJ-eq (non-renewable) primary energy are required for the transfer of 1 Gbit information from mobile phone to mobile phone in the UMTS network. For a transfer from mobile to fixed network, these values are 20 kg CO2 and 640 MJ-eq, respectively. On the other hand, the fixed network requires more resources like copper (0.07 kg for the mobile to mobile option vs. 0.12 kg for mobile to fixed network). From an environmental point of view, the mobile telephone is the most important element of the mobile communication network (UMTS and GSM). The short service life of the mobile phone plays a substantial role. Increasing the utilization period of the mobile phone (e.g. by leasing, re-use, extension of the innovation cycles, etc.) could thus represent a large potential for its improvement. The second most important components are the base stations. In the assessment mainly the use phase proved to be important. The lower environmental impact (per Gbit data transfer) as compared to the mobile phone can be explained by the longer service life (around factor 8). Main impacts are caused by the electricity consumption, in particular the energy needed for cooling the base stations. By choosing an environmentally benign electricity mix and/or by increasing the portion of renewable sources of energy, the network operators have a substantial potential of lower the environmental impacts (in particular the greenhouse gas emissions) of mobile telecommunication. Furthermore, the manufacturing of electronic components, the life time of the appliances and energy consumption are key parameters influencing the environmental profile of the networks most. Given its larger data transfer rate, the UMTS is ecologically more favorable in terms of data transfer rate than its predecessor, the GSM system. The higher energy consumption and the more complex production of the devices in the UMTS system are compensated by the faster data transmission rate. Per customer, the result is inverse, however, since the higher efficiency is compensated by the higher data communication per user in the UMTS system. The UMTS network in its state of 2004 according to the 2001 planning and with the accordingly calculated number of customers and data transfer causes 2.1 times more CO2 emissions and requires 2.4 times more (non-renewable) primary energy per customer than for the GSM system in its current state. It must be noted, however, that the UMTS technology supports other services than the GSM system. The development of the UMTS is accompanied with an increased consumption of resources and emissions of pollutants and greenhouse gases regarding the entire system for mobile telephone communication. The GSM system is a mature technology, while the UMTS is still at the beginning of its learning curve. Thus, it can be safely assumed that large improvement potentials are still present for the UMTS network components concerning expenditures and emissions both at production and by the use of the devices. This study provides the necessary information where such improvements are most effective in environmental terms.