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.     

BioMove – an integrated platform simulating the dynamic response of species to environmental change

BioMove simulates plant species' geographic range shifts in response to climate, habitat structure and disturbance, at annual time steps. This spatially explicit approach integrates species' bioclimatic suitability and population‐level demographic rates with simulation of landscape‐level processes (dispersal, disturbance, species' response to dynamic dominant vegetation structure). Species population dynamics are simulated through matrix modelling that includes scaling demographic rates by climatic suitability. Dispersal functions simulate population spread. User‐specified plant functional types (PFTs) provide vegetation structure that determines resource competition and disturbance. PFTs respond annually through dispersal, inter‐PFT competition and demographic shifts. BioMove provides a rich framework for dynamic range simulations.     

Real-time on-line flow cytometry for bioprocess monitoring

As the understanding of variation is the key to a good process and product quality one should pay attention to dynamics on the single-cell level. The basic idea of this approach was to qualify and quantify variations on the single-cell level during bioreactor cultivations by monitoring the expression of an eGFP tagged target protein (human membrane protein) using fully automated real-time, flow injection flow cytometry (FI-FCM). The FI-FCM system consists of a sampling- and defoaming- as well as of a dilution-section. It allows a very short monitoring interval (5 min) and is able to dilute the reactor sample by a factor ranging up to more than 10,000.In bioreactor cultivations of recombinant Pichia pastoris expressing the eGFP tagged target protein, high correlations (R² ≥ 0.97) between the FI-FCM fluorescent signal and other, however, population-averaged fluorescence signals (off-line fluorescence, in situ fluorescence probe) were obtained. FI-FCM is the only method able to distinguish between few cells with high fluorescence and many cells with low fluorescence intensity and proved that cells differ significantly from each other within the population during bioreactor cultivations. Single-cell fluorescence was distributed over a broad range within the cell population. These distributions strongly suggest that (a) the AOX-I promoter is leaky and (b) a fraction of the population is able to express more protein of interest within shorter time and (c) a fraction of the population does not express the fusion protein at all. These findings can help in the selection of high producing, stable strains. To show the platform-independency of the system, it has successfully been tested during bioreactor cultivations of three different strains (P. pastoris, Saccharomyces cerevisiae, Escherichia coli).Along with its applications in PAT, the FI-FCM could be used as a platform-independent (prokaryotes and eukaryotes) method in various other applications; for example in the closed-loop-control of bioprocesses using different kinds of fluorescent reporters, (waste- and drinking-) water analysis, clone selection in combination with FACS or even for surgery applications.     

Effect of Antioxidant Supplementation on Exercise-Induced Cardiac Troponin Release in Cyclists: A Randomized Trial

Background

Cardiac troponin is the biochemical gold standard to diagnose acute myocardial infarction. Interestingly however, elevated cardiac troponin concentrations are also frequently observed during and after endurance-type exercise. Oxidative stress associated with prolonged exercise has been proposed to contribute to cardiac troponin release. Therefore, the aim of this study was to assess the effect of 4 week astaxanthin supplementation (a potent cartenoid antioxidant) on antioxidant capacity and exercise-induced cardiac troponin release in cyclists.

Methods

Thirty-two well-trained male cyclists (age 25±5, weight 73±7 kg, maximum O₂ uptake 60±5 mL·kg⁻¹·min⁻¹, W_max 5.4±0.5 W·kg⁻¹; mean ± SD) were repeatedly subjected to a laboratory based standardized exercise protocol before and after 4 weeks of astaxanthin (20 mg/day), or placebo supplementation in a double-blind randomized manner. Blood samples were obtained at baseline, at 60 min of cycling and immediately post-exercise (≈ 120 min).

Results

The pre-supplementation cycling trial induced a significant rise of median cardiac troponin T concentrations from 3.2 (IQR 3.0–4.2) to 4.7 ng/L (IQR 3.7–6.7), immediately post-exercise (p<0.001). Four weeks of astaxanthin supplementation significantly increased mean basal plasma astaxanthin concentrations from non-detectable values to 175±86 µg·kg⁻¹. However, daily astaxanthin supplementation had no effect on exercise-induced cardiac troponin T release (p = 0.24), as measured by the incremental area under the curve. Furthermore, the elevation in basal plasma astaxanthin concentrations was not reflected in changes in antioxidant capacity markers (trolox equivalent antioxidant capacity, uric acid, and malondialdehyde). Markers of inflammation (high-sensitivity C-reactive protein) and exercise-induced skeletal muscle damage (creatine kinase) were equally unaffected by astaxanthin supplementation.

Conclusion

Despite substantial increases in plasma astaxanthin concentrations, astaxanthin supplementation did not improve antioxidant capacity in well-trained cyclists. Accordingly, exercise-induced cardiac troponin T concentrations were not affected by astaxanthin supplementation.

Trial registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT01241877","term_id":"NCT01241877"}}NCT01241877     

Low bird diversity in the Fynbos plant diversity hotspot: Quaternary legacies in the current distributions of passerine birds

The Fynbos Biome or Cape Floristic Region is well‐known for its plant diversity. This diversity does not seem to carry over at higher trophic levels, and in particular in birds. Here, we analyzed the passerine bird assemblages of the Fynbos Biome at the quarter degree resolution with occupancy models and citizen science data. Multivariate analysis of distribution summary metrics revealed a gradient of specialist to generalist species, in which range‐restricted, specialist species responded positively to increases in number of competing species and included ancient lineages. Wide‐ranging, generalist species exhibited stronger affinities for the arid Karoo Biomes than for the other neighboring biome (Albany Thicket) and for the other mesic biomes in South Africa. Both results are explained by the Quaternary legacy hypothesis: the combined effects of habitat filtering, isolation by distance, and limited in situ diversification, acting throughout the Quaternary, and caused by the contrasting winter‐rainfall regime of the region and the low phylogenetic diversity and original adaptations of the plant assemblages.     

Entamoeba histolytica: cyst-like structures in vitro induction

The cyst of Entamoeba histolytica is responsible for amebiasis infection. However, no axenic in vitro system exists that promotes mass encystation for studying this process of this human-infecting parasite. Cyst-like structures of E. histolytica obtained in this work were induced using TYI-S-33 media in combination with enterobacterias Escherichia coli and Enterococcus faecalis conditioned media, high CO2 tension and histamine. Cyst-like structures showed the same characteristics of a typical E. histolytica cyst: aggregation, resistance to 0.15% sarcosyl for 10 min, high signal of fluorescence under UV light when stained with 10% calcofluor M2r and the surface topology showed a wrinkled wall. In addition these structures are multinucleated with condensed chromatin attached to nuclear membrane, contain big vacuoles and ribonucleoproteic helices in the cytoplasm and also present a thin cell wall. Last all characteristics are all the same as a typical of E. histolytica cyst.