Introducing the H2020 AQUACROSS project: Knowledge, Assessment, and Management for AQUAtic Biodiversity and Ecosystem Services aCROSS EU policies

The AQUACROSS project was an unprecedented effort to unify policy concepts, knowledge, and management of freshwater, coastal, and marine ecosystems to support the cost-effective achievement of the targets set by the EU Biodiversity Strategy to 2020. AQUACROSS aimed to support EU efforts to enhance the resilience and stop the loss of biodiversity of aquatic ecosystems as well as to ensure the ongoing and future provision of aquatic ecosystem services. The project focused on advancing the knowledge base and application of Ecosystem-Based Management. Through elaboration of eight diverse case studies in freshwater and marine and estuarine aquatic ecosystem across Europe covering a range of environmental management problems including, eutrophication, sustainable fisheries as well as invasive alien species AQUACROSS demonstrated the application of a common framework to establish cost-effective measures and integrated Ecosystem-Based Management practices. AQUACROSS analysed the EU policy framework (i.e. goals, concepts, time frames) for aquatic ecosystems and built on knowledge stemming from different sources (i.e. WISE, BISE, Member State reporting within different policy processes, modelling) to develop innovative management tools, concepts, and business models (i.e. indicators, maps, ecosystem assessments, participatory approaches, mechanisms for promoting the delivery of ecosystem services) for aquatic ecosystems at various scales of space and time and relevant to different ecosystem types.

Tooth development disorders in infants of rat dams exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin and protective role of tocopherol and acetylsalicylic acid

Aryl hybrocardon receptor (AhR) activation plays a key role in the pathomechanism of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-induced defective spatial structure of teeth caused by disordered collagen synthesis. The aim of this study was to identify the influence of dioxins present in female Buffalo rats on the dental structure of their offspring's in the neonatal period and the potential of α-tocopherol and acetylsalicylic acid in curbing post-dioxin hard tissue defects. Research material consisted of molar teeth (n=40) of rat pups which had been given a single dose of TCDD and were then treated with tocopherol or acetylsalicylic acid for 3 weeks. In the offspring of rat dams exposed to TCDD, ameloblasts and odontoblasts were less developed in comparison with the control group and less dynamic angiogenesis in the area of dental papilla was observed. In the pups of TCDD-exposed mothers, a smaller number of AhR was found in amelogenic and odontoblastic cells, whereas in the pups of mothers exposed to TCDD followed by tocopherol and acetylsalicylic acid treatment, the expression of AhR in ameloblasts and odontoblasts increased. We conclude that tocopherol and acetylsalicylic acid treatment exerts a protective effect on the TCDD-induced structural defects of tooth tissue.

Side to side coaptation--new technic in peripherial nerve surgery--preliminary report

This study presents and evaluates side-to-side nerve repair techniques for their ability to induce collateral nerve sprouting. The coaptation of the ventral branches of spinal nerves C5 and C6 to C7 through an incision epineurium was used to repair the nerve. The number of myelinated fiber axons and G-ratio was evaluated. Preliminary results indicate the possibility of using side to side coaptation in brachial plexus nerve surgery.

Experimental osteoporosis in sheep – mechanical and histological approach

The implementation of new methods of osteoporotic therapy requires tests on animal model. The use of sheep as model has numerous advantages over other animals. The aim of this study was to describe the change in parameters in sheep with osteoporosis induced using steroids and ovariorectomy methods as opposed to the parameters in healthy sheep. The study was performed on female „merinos” breed sheep divided into the three groups: negative control (NC) - healthy animals, positive control (PC) - ovariorectomized animals and steroid control group (SC) - in which methylprednisolone was administered. This paper presents histological and ultrastructural examination with mechanical comparative tests for force/strength values as well as indentation tests of joint cartilage. The obtained results confirm the loss of bone mass associated with mineral composition content in bones, which has an influence on bone strength.

Gait analysis after neurorrhaphy in the brachial plexus

The gait is a form of human and animal locomotion on land by using limbs. The study assessed functional recovery after end to side and side to side neurorrhaphy the ventral branches of the C5 and C6 spinal nerves to the C7 spinal nerve on the rabbit brachial plexus. Gait statistical analysis showed significant differences between the control group versus the end-to-side and side to side neurorrhaphy groups, in opposite to the comparison between the two experimentals groups. Gait analysis results corresponded with the histomorphometric results. The results indicate the potential use of gait analysis for the assessment of the recovery of nerve function.

Seizures after single-agent overdose with pharmaceutical drugs: analysis of cases reported to a poison center

CONTEXT

Seizures during intoxications with pharmaceuticals are a well-known complication. However, only a few studies report on drugs commonly involved and calculate the seizure potential of these drugs.

OBJECTIVES

To identify the pharmaceutical drugs most commonly associated with seizures after single-agent overdose, the seizure potential of these pharmaceuticals, the age-distribution of the cases with seizures and the ingested doses.

METHODS

A retrospective review of acute single-agent exposures to pharmaceuticals reported to the Swiss Toxicological Information Centre (STIC) between January 1997 and December 2010 was conducted. Exposures which resulted in at least one seizure were identified. The seizure potential of a pharmaceutical was calculated by dividing the number of cases with seizures by the number of all cases recorded with that pharmaceutical. Data were analyzed using descriptive statistics.

RESULTS

We identified 15,441 single-agent exposures. Seizures occurred in 313 cases. The most prevalent pharmaceuticals were mefenamic acid (51 of the 313 cases), citalopram (34), trimipramine (27), venlafaxine (23), tramadol (15), diphenhydramine (14), amitriptyline (12), carbamazepine (11), maprotiline (10), and quetiapine (10). Antidepressants were involved in 136 cases. Drugs with a high seizure potential were bupropion (31.6%, seizures in 6 of 19 cases, 95% CI: 15.4-50.0%), maprotiline (17.5%, 10/57, 95% CI: 9.8-29.4%), venlafaxine (13.7%, 23/168, 95% CI: 9.3-19.7%), citalopram (13.1%, 34/259, 95% CI: 9.5-17.8%), and mefenamic acid (10.9%, 51/470, 95% CI: 8.4-14.0%). In adolescents (15-19y/o) 23.9% (95% CI: 17.6-31.7%) of the cases involving mefenamic acid resulted in seizures, but only 5.7% (95% CI: 3.3-9.7%) in adults (≥ 20y/o; p < 0.001). For citalopram these numbers were 22.0% (95% CI: 12.8-35.2%) and 10.9% (95% CI: 7.1-16.4%), respectively (p = 0.058). The probability of seizures with mefenamic acid, citalopram, trimipramine, and venlafaxine increased as the ingested dose increased.

CONCLUSIONS

Antidepressants were frequently associated with seizures in overdose, but other pharmaceuticals, as mefenamic acid, were also associated with seizures in a considerable number of cases. Bupropion was the pharmaceutical with the highest seizure potential even if overdose with bupropion was uncommon in our sample. Adolescents might be more susceptible to seizures after mefenamic acid overdose than adults. "Part of this work is already published as a conference abstract for the XXXIV International Congress of the European Association of Poisons Centres and Clinical Toxicologists (EAPCCT) 27-30 May 2014, Brussels, Belgium." Abstract 8, Clin Toxicol 2014;52(4):298.

Sewer deterioration modeling with condition data lacking historical records

Accurate predictions of future conditions of sewer systems are needed for efficient rehabilitation planning. For this purpose, a range of sewer deterioration models has been proposed which can be improved by calibration with observed sewer condition data. However, if datasets lack historical records, calibration requires a combination of deterioration and sewer rehabilitation models, as the current state of the sewer network reflects the combined effect of both processes. Otherwise, physical sewer lifespans are overestimated as pipes in poor condition that were rehabilitated are no longer represented in the dataset. We therefore propose the combination of a sewer deterioration model with a simple rehabilitation model which can be calibrated with datasets lacking historical information. We use Bayesian inference for parameter estimation due to the limited information content of the data and limited identifiability of the model parameters. A sensitivity analysis gives an insight into the model's robustness against the uncertainty of the prior. The analysis reveals that the model results are principally sensitive to the means of the priors of specific model parameters, which should therefore be elicited with care. The importance sampling technique applied for the sensitivity analysis permitted efficient implementation for regional sensitivity analysis with reasonable computational outlay. Application of the combined model with both simulated and real data shows that it effectively compensates for the bias induced by a lack of historical data. Thus, the novel approach makes it possible to calibrate sewer pipe deterioration models even when historical condition records are lacking. Since at least some prior knowledge of the model parameters is available, the strength of Bayesian inference is particularly evident in the case of small datasets.

Partial laser and gas nitriding of titanium components

Gas nitriding and laser gas nitriding processes were studied to produce thick and well adhering nitride layers on titanium alloys. A multitude of process parameters have been varied for the nitriding of Ti-6Al-4V substrates. The nitride layers were investigated with optical and electron microscopy, micro hardness testing and glow discharge optical emission spectroscopy. Gas nitriding resulted in strongly adherent nitride layers of up to 5 µm in thickness. Laser gas nitriding with high laser output resulted in very thick (> 500 µm) nitride layers with excellent surface adhesion. A partial melting of the surface during the process altered the surface contour; hence, a reshaping of the component may be necessary. A melting of the substrate surface was avoided through laser gas nitriding with low laser output and additional cooling. However, the up to 100 µm thick nitride layers showed cracks at the interfaces to the substrate.

Moving targets, long-lived infrastructure, and increasing needs for integration and adaptation in water management: an illustration from Switzerland

Switzerland provides an example of successful management of water infrastructure and water resources that was accomplished largely without integration across sectors. Limitations in this approach have become apparent; decisions that were formerly based only on technical and economic feasibility must now incorporate broader objectives such as ecological impact. In addition, current and emerging challenges relate to increasingly complex problems that are likely to demand more integrated approaches. If such integration is to be of benefit, it must be possible to redirect resources across sectors, and the synergies derived from integration must outweigh the additional cost of increased complexity.

THE NATURE OF THE TOXIN-ANTITOXIN FLOCCULATION PHENOMENON

1. Animals immunized with the formalinized filtrates of young toxic cultures of B. botulinus produce an antitoxic serum poor in precipitins. 2. Animals immunized with the formalinized filtrates of old and partly autolyzed toxic cultures produce an antitoxic serum containing precipitins. 3. Animals immunized with toxin-free autolyzed bacteria produce a serum free from antitoxin but rich in specific precipitins. 4. Animals immunized with the filtrates of an atoxic variant produce a serum free from antitoxin but rich in precipitins for the homologous toxin. 5. Animals immunized with the washed bacteria of the atoxic variant produce a serum that contains no antitoxin, but is rich in precipitins for the homologous toxin. 6. Removal of the precipitins by flocculation with a non-toxic antigen does not materially reduce the antitoxic value of a serum. 7. Removal of the proteins of the antigen by add coagulation removes the specific precipitable substance. 8. All the sera that contain precipitins produce the specific flocculus when combined with homologous toxins, anatoxins, or with the filtrates of the atoxic variant. The flocculation is restricted within the type. The amount of the precipitate and the width of the zone vary approximately with the estimated amount of bacterial protein in the antigen that is used for the immunization of animals. We conclude, therefore, that the toxin-antitoxin flocculation is a specific bacterial precipitation phenomenon.

Mumps outbreak among the military in Luxembourg in 2008: epidemiology and evaluation of control measures

In the last quarter of 2008, an outbreak of mumps occurred in Luxembourg affecting initially 10 young adults at a military centre. Following a mass vaccination campaign, no further clinical cases were observed. 90% of 136 vaccine recipients were IgG positive one month after vaccination compared to 54% before vaccination. Until 31 December 2008, 19 mumps cases were also reported from the community. The outbreak strain belonged to genogroup G.

Mumps outbreak among the military in Luxembourg in 2008: epidemiology and evaluation of control measures

In the last quarter of 2008, an outbreak of mumps occurred in Luxembourg affecting initially 10 young adults at a military centre. Following a mass vaccination campaign, no further clinical cases were observed. 90% of 136 vaccine recipients were IgG positive one month after vaccination compared to 54% before vaccination. Until 31 December 2008, 19 mumps cases were also reported from the community. The outbreak strain belonged to genogroup G.

Update of Clostridium difficile infection due to PCR ribotype 027 in Europe, 2008

Outbreaks of Clostridium difficile infections (CDI) with increased severity, high relapse rate and significant mortality have been related to the emergence of a new, hypervirulent C. difficile strain in North America and Europe. This emerging strain is referred to as PCR ribotype 027 (Type 027). Since 2005, individual countries have developed surveillance studies about the spread of type 027. C. difficile Type 027 has been reported in 16 European countries. It has been responsible for outbreaks in Belgium, Germany, Finland, France, Ireland, Luxembourg, The Netherlands, Switzerland and the United Kingdom (England, Wales, Northern Ireland and Scotland). It has also been detected in Austria, Denmark, Sweden, Norway, Hungary, Poland and Spain. Three countries experienced imported patients with CDI due to Type 027 who acquired the infection abroad. The antimicrobial resistance pattern is changing, and outbreaks due to clindamycin-resistant ermB positive Type 027 strains have occurred in three European countries. Ongoing epidemiological surveillance of cases of CDI, with periodic characterisation of the strains involved, is required to detect clustering of cases in time and space and to monitor the emergence of new, highly virulent clones.

Update of Clostridium difficile infection due to PCR ribotype 027 in Europe, 2008

Outbreaks of Clostridium difficile infections (CDI) with increased severity, high relapse rate and significant mortality have been related to the emergence of a new, hypervirulent C. difficile strain in North America and Europe. This emerging strain is referred to as PCR ribotype 027 (Type 027). Since 2005, individual countries have developed surveillance studies about the spread of type 027.C. difficile Type 027 has been reported in 16 European countries. It has been responsible for outbreaks in Belgium, Germany, Finland, France, Ireland, Luxembourg, The Netherlands, Switzerland and the United Kingdom (England, Wales, Northern Ireland and Scotland). It has also been detected in Austria, Denmark, Sweden, Norway, Hungary, Poland and Spain. Three countries experienced imported patients with CDI due to Type 027 who acquired the infection abroad.The antimicrobial resistance pattern is changing, and outbreaks due to clindamycin-resistant ermB positive Type 027 strains have occurred in three European countries. Ongoing epidemiological surveillance of cases of CDI, with periodic characterisation of the strains involved, is required to detect clustering of cases in time and space and to monitor the emergence of new, highly virulent clones.

Update of Clostridium difficile-associated disease due to PCR ribotype 027 in Europe

Recent outbreaks of Clostridium difficile-associated diarrhoea (CDAD) with increased severity, high relapse rate and significant mortality have been related to the emergence of a new, hypervirulent C. difficile strain in North America, Japan and Europe. Definitions have been proposed by the European Centre of Disease Prevention and Control (ECDC) to identify severe cases of CDAD and to differentiate community-acquired cases from nosocomial CDAD (http://www.ecdc.europa.eu/documents/pdf/Cl_dif_v2.pdf). CDAD is mainly known as a healthcare-associated disease, but it is also increasingly recognised as a community-associated disease. The emerging strain is referred to as North American pulsed-field type 1 (NAP1) and PCR ribotype 027. Since 2005, individual countries have developed surveillance studies to monitor the spread of this strain. C. difficile type 027 has caused outbreaks in England and Wales, Ireland, the Netherlands, Belgium, Luxembourg, and France, and has also been detected in Austria, Scotland, Switzerland, Poland and Denmark. Preliminary data indicated that type 027 was already present in historical isolates collected in Sweden between 1997 and 2001.

Metachronous, multicentric giant cell tumor of the sphenoid bone with histologic, CT, MR imaging, and positron-emission tomography/CT correlation

Giant cell tumor (GCT) of the sphenoid bone is a relatively rare entity and metachronous multicentric GCT of the sphenoid is even rarer; we are aware of only 3 previous cases in the literature. We describe here a tumor of the sphenoid bone that was identified 15 years after multiple resections of a GCT of the left inferior pubic ramus. Correlation is made between the histopathologic findings, MR imaging of the brain, CT of the head, and fusion positron-emission tomography (PET)/CT scan performed with fluorine-18 fluoro-2-deoxy-D-glucose (18F-FDG). This report is the first to describe the appearance of a GCT of the sphenoid bone on a fusion PET/CT examination. High metabolic activity in the base of the skull adjacent to the middle cranial fossa was demonstrated in a fashion similar to that of the known pelvic lesion. This case also demonstrates that the increased metabolic activity seen in a GCT of the sphenoid bone may be partially obscured by the adjacent physiologic high metabolic activity of the brain.

A standard interface between simulation programs and systems analysis software

A simple interface between simulation programs and systems analytical software is proposed. This interface is designed to facilitate linkage of environmental simulation programs with systems analytical software and thus can contribute to remedying the deficiency in applying systems analytical techniques to environmental modelling studies. The proposed concept, consisting of a text file interface combined with a batch mode simulation program call, is independent of model structure, operating system and programming language. It is open for implementation by academic and commercial simulation and systems analytical software developers and is very simple to implement. Its practicability is demonstrated by implementations for three environmental simulation packages (AQUASIM, SWAT and LEACHM) and two systems analytical program packages (UNCSIM, SUFI). The properties listed above and the demonstration of the ease of implementation of the approach are prerequisites for the stimulation of a widespread implementation of the proposed interface that would be beneficial for the dissemination of systems analytical techniques in the environmental and engineering sciences. Furthermore, such a development could stimulate the transfer of systems analytical techniques between different fields of application.

Validation of sperm sexing in the cattle (Bos taurus) by dual colour fluorescence in situ hybridization

Separation of X- and Y-bearing sperm cells, together with artificial insemination using sex-specific semen, makes it possible to pre-determine the sex of calves. This has the potential to considerably improve cattle breeding, genetic resource management and particularly the efficiency of dairy and meat production. However, the broad use of sexed semen will depend on availability, price, fertilizability and in particular the actual sorting purity of sperm doses. To validate the accuracy of sperm sexing in Bos taurus, we have developed a simple, fast and reliable dual colour fluorescence in situ hybridization (FISH) test, where Y-bearing spermatozoa are identified by a DNA fragment hybridizing to a large pericentromeric repetitive DNA block on the bovine Y chromosome (locus DYZI, Yp13-q12). To avoid an underestimation of Y signals, we used a second DNA probe identifying a large subcentromeric block of complex repetitive DNA on the bovine autosome 6 (locus D6Z1, 6q12-15) as a positive control. Bovine sperm were fixed with methanol:acetic acid and denatured by simply immersing in 3 M NaOH, yielding consistent hybridization results and good preservation of sperm morphology. The FISH protocol was evaluated on unsorted sperm as well as on sperm samples sexed using the Beltsville technology, which separates X- and Y-bearing spermatozoa by staining with Hoechst 33342 and flow sorting according to their DNA content (Johnson et al. 1987).

Fertility in heifers and cows after low dose insemination with sex-sorted and non-sorted sperm under field conditions

The present study was performed to test fertility after low dose insemination with sexed and non-sexed sperm in dairy cattle under field conditions in Switzerland. Spermatozoa were stained with Hoechst 33342 and sorted by flow cytometry. A total of 132 heifers and cows were inseminated with 2 x 10(6) X-bearing, frozen-thawed sperm (A) and 91 animals were inseminated with the same dose using non-sorted, frozen-thawed sperm (B). Pregnancy examination by ultrasound was performed twice, 30-40 days (PE1) and 70-90 days (PE2) after insemination. The pregnancy rates after PE1 were 33.3% (9/27) and 59.3% (16/27) in heifers (P=0.05) and 27.6% (29/105) and 28.1% (18/64) in cows (P>0.05) for groups A and B, respectively. Embryonic losses between PE1 and PE2 in heifers were 11.1% (1/9) and 0% (0/16) and in cows 17.2% (5/29) and 5.6% (1/18), the differences between groups A and B not being significant (P>0.05). Calving rates in heifers were 29.6% (8/27) and 57.8% (15/26), whereas in cows 22.1% (23/104) and 23.4% (16/63) gave birth to calves (for both groups P>0.05). The sex ratio was different (P<0.05) between A (85.3%) and B (58.6%). From our results it can be concluded that conception rates of sorted and non-sorted semen are similar using an insemination dose of 2 x 10(6). Fertility may be increased by improving sexing technology and animal management.

Binding affinities and geometries of various metal ligands in peptide deformylase inhibitors

Removal of the N-terminal formyl group from newly synthesized proteins by the enzyme peptide deformylase (PDF) is essential for normal growth of bacteria but not higher organisms. Recently, PDF has been explored as a target for novel antibiotics. Screening a collection of natural products for antimicrobial activity identified actinonin and two matlystatin analogs as potent PDF inhibitors. A number of synthetic analogs of these natural products were prepared and their inhibitory potency determined. Previous work has shown that PDF is an iron metalloproteinase also containing a catalytic glutamic acid residue. Ligation of the ferrous cation is an essential feature of potent inhibitors. The structures of actinonin, a matlystatin analog and a synthetic inhibitor complexed with PDF were determined by crystallography. A quantum mechanics/molecular mechanics (QM/MM) method was used to reproduce the geometry of known complexes, to predict the protonation state in the active site and to predict the geometry of additional complexes. The requirement for protonation of the active site glutamate anion is an important factor in understanding the potency of inhibitors with acidic iron-ligating groups such as hydroxamate and carboxylate. Even though potent inhibitors of PDF have been discovered, their bacteriostatic mechanism of action and the rapid development of resistance in vitro may limit their potential as antibacterial drugs.

Cutting edge: in vivo identification of TCR redistribution and polarized IL-2 production by naive CD4 T cells

TCR aggregation at the point of contact with an APC is thought to play an important role in T cell signal transduction. However, this potentially important phenomenon has never been documented during an immune response in vivo. Here we used immunohistology to show that the TCR on naive Ag-specific CD4 T cells in the lymph nodes of mice injected with Ag redistributed to one side of the cell. In cases where the APC could be identified, the TCR was concentrated on the side of the T cell facing the APC. In those T cells that produced IL-2, the TCR and IL-2 localized to the same side of the cell. In vivo IL-2 production depended on costimulatory signaling through CD28, whereas TCR redistribution did not. These results show that Ag-stimulated CD4 T cells produce IL-2 in a polarized fashion and undergo CD28-independent TCR redistribution in vivo.

Identifiability and uncertainty analysis of the river water quality model no. 1 (RWQM1)

State of the art models as used in activated sludge modelling and recently proposed for river water quality modelling integrate the knowledge in a certain field. If applied to data from a specific site, such models are nearly always overparameterised. This raises the question of how many parameters can be fitted in a given context and how to find identifiable parameter subsets given the experimental layout. This problem is addressed for the kinetic parameters of a simplified version of the recently published river water quality model no. 1 (RWQM1). The selection of practically identifiable parameter subsets is discussed for typical boundary conditions as a function of the measurement layout. Two methods for identifiable subset selection were applied and lead to nearly the same results. Assuming upstream and downstream measurements of dissolved substances to be available, only a few (5-8) model parameters appear to be identifiable. Extensive measurement campaigns with dedicated experiments seem to be required for successful calibration of RWQM1. The estimated prior uncertainties of the model parameters are used to estimate the uncertainty of model predictions. Finally an estimate is provided for the maximum possible decrease in prediction uncertainty achievable by a perfect determination of the values of the identifiable model parameters.

River Water Quality Model no. 1 (RWQM1): I. Modelling approach

Successful river water quality modelling requires the specification of an appropriate model structure and process formulation. Both must be related to the compartment structure of running water ecosystems including their longitudinal, vertical, and lateral zonation patterns. Furthermore, the temporal variability of abiotic boundary conditions may be important and must be incorporated by an appropriate choice of model parameters. A six-step decision procedure is proposed to achieve these objectives. The steps address the determination of the following model features: (1) temporal representation (dynamic or steady-state); (2) model dimensionality; (3) mixing; (4) advection; (5) reaction terms; and (6) boundary conditions. Numerical criteria based on process time constants and length scales provide a basis for these decisions.

River Water Quality Model no. 1 (RWQM1): II. Biochemical process equations

In this paper, biochemical process equations are presented as a basis for water quality modelling in rivers under aerobic and anoxic conditions. These equations are not new, but they summarise parts of the development over the past 75 years. The primary goals of the presentation are to stimulate communication among modellers and field-oriented researchers of river water quality and of wastewater treatment, to facilitate practical application of river water quality modelling, and to encourage the use of elemental mass balances for the derivation of stoichiometric coefficients of biochemical transformation processes. This paper is part of a series of three papers. In the first paper, the general modelling approach is described; in the present paper, the biochemical process equations of a complex model are presented; and in the third paper, recommendations are given for the selection of a reasonable submodel for a specific application.

River Water Quality Model no. 1 (RWQM1): case study II. Oxygen and nitrogen conversion processes in the River Glatt (Switzerland)

Various simplifications of the river water quality model no. 1 are applied to data sets from the river Glatt in Switzerland. In a first application, the biomass responsible for nitrogen and oxygen conversion processes is quantified based on known reaeration rates, measured concentrations of ammonia, nitrite and oxygen and assumed growth parameters of algae and bacteria. In a second application, the model is extended to calculate chemical equilibria of inorganic carbon compounds dissolved in the water and daily variations in pH. The influence of partially unknown inflow concentrations and of calcite precipitation on fluctuations in electrical conductivity and pH are discussed. In the last model, the processes of growth of sessile algae and bacteria, detachment of algae, and grazing by benthic organisms are introduced. Due to lack of data for quantifying these processes, this last model application is speculative. Nevertheless, it is interesting because it shows a direction to which river water quality modelling would have to proceed in order to increase its predictive capabilities.

River Water Quality Model no. 1 (RWQM1): case study. I. Compartmentalisation approach applied to oxygen balances in the River Lahn (Germany)

A case study on the application of the River Water Quality Model No. 1 (RWQM1) is presented in order to illustrate the importance of modelling a sediment compartment for an ecologically meaningful assessment of the impact of wastewater effluents and combined sewer overflows. The focus of this case study is on the compartmentalisation approach of the RWQM1 that makes such a description possible. In contrast to this, a strongly simplified biochemical submodel is used that considers only oxygen and dissolved substrate. The object of the case study is the River Lahn, a moderately polluted 5th order stream in Germany, for which the connectivity of surface/subsurface flows and mass fluxes within river sediments have been intensively investigated. The hyporheic flow between a downwelling and upwelling zone of a riffle-pool sequence has been studied with the aid of tracer experiments and continuous records of water constituents. High diurnal fluctuations of oxygen travelled to considerable depth of the sediment and oxygen in the interstitial water decreased considerably while travelling through the riffle. Starting with the implementation of a strongly simplified version of the biochemical part of the RWQM1, but with the consideration of a sediment pore water compartment in addition to the water column compartment, a calibration procedure is performed using tracer data from the water column and the sediment. The calibrated model is then used to study the system response to wastewater treatment plant effluent and combined sewer overflow emissions. The modelling approach makes it possible to quantify the sediment oxygen demand and the spatial and temporal extent of sediment zones with oxygen depletion. However, the spatially averaged approach does not account for inhomogeneities in the sediment. It is shown that for this river with its alluvial coarse sediments even moderate emissions from sewerage systems may be high enough to drop sediment oxygen concentrations to low levels while those in the surface flow remain close to saturation. Similarly, it is demonstrated that combined sewer overflows may cause anoxic sediment oxygen conditions for extended time periods. The implications for ecologically sound river water quality modelling and for specific quality objectives are discussed.

River Water Quality Model no. 1 (RWQM1): III. Biochemical submodel selection

The new River Water Quality Model no. 1 introduced in the two accompanying papers by Shanahan et al. and Reichert et al. is comprehensive. Shanahan et al. introduced a six-step decision procedure to select the necessary model features for a certain application. This paper specifically addresses one of these steps, i.e. the selection of submodels of the comprehensive biochemical conversion model introduced in Reichert et al. Specific conditions for inclusion of one or the other conversion process or model component are introduced, as are some general rules that can support the selection. Examples of simplified models are presented.

Molecular views of viral polyprotein processing revealed by the crystal structure of the hepatitis C virus bifunctional protease-helicase

BACKGROUND

Hepatitis C virus (HCV) currently infects approximately 3% of the world's population. HCV RNA is translated into a polyprotein that during maturation is cleaved into functional components. One component, nonstructural protein 3 (NS3), is a 631-residue bifunctional enzyme with protease and helicase activities. The NS3 serine protease processes the HCV polyprotein by both cis and trans mechanisms. The structural aspects of cis processing, the autoproteolysis step whereby the protease releases itself from the polyprotein, have not been characterized. The structural basis for inclusion of protease and helicase activities in a single polypeptide is also unknown.

RESULTS

We report here the 2.5 A resolution structure of an engineered molecule containing the complete NS3 sequence and the protease activation domain of nonstructural protein 4A (NS4A) in a single polypeptide chain (single chain or scNS3-NS4A). In the molecule, the helicase and protease domains are segregated and connected by a single strand. The helicase necleoside triphosphate and RNA interaction sites are exposed to solvent. The protease active site of scNS3-NS4A is occupied by the NS3 C terminus, which is part of the helicase domain. Thus, the intramolecular complex shows one product of NS3-mediated cleavage at the NS3-NS4A junction of the HCV polyprotein bound at the protease active site.

CONCLUSIONS

The scNS3-NS4A structure provides the first atomic view of polyprotein cis processing. Both local and global structural rearrangements follow the cis cleavage reaction, and large segments of the polyprotein can be folded prior to proteolytic processing. That the product complex of the cis cleavage reaction exists in a stable molecular conformation suggests autoinhibition and substrate-induced activation mechanisms for regulation of NS3 protease activity.

Structural characterization of nitric oxide synthase isoforms reveals striking active-site conservation

Crystal structures of human endothelial nitric oxide synthase (eNOS) and human inducible NOS (iNOS) catalytic domains were solved in complex with the arginine substrate and an inhibitor S-ethylisothiourea (SEITU), respectively. The small molecules bind in a narrow cleft within the larger active-site cavity containing heme and tetrahydrobiopterin. Both are hydrogen-bonded to a conserved glutamate (eNOS E361, iNOS E377). The active-site residues of iNOS and eNOS are nearly identical. Nevertheless, structural comparisons provide a basis for design of isozyme-selective inhibitors. The high-resolution, refined structures of eNOS (2.4 A resolution) and iNOS (2.25 A resolution) reveal an unexpected structural zinc situated at the intermolecular interface and coordinated by four cysteines, two from each monomer.

Zinc mediated dimer of human interferon-alpha 2b revealed by X-ray crystallography

BACKGROUND

The human alpha-interferon (huIFN-alpha) family displays broad spectrum antiviral, antiproliferative and immunomodulatory activities on a variety of cell types. The diverse biological activities of the IFN-alpha's are conveyed to cells through specific interactions with cell-surface receptors. Despite considerable effort, no crystal structure of a member of this family has yet been reported, because the quality of the protein crystals have been unsuitable for crystallographic studies. Until now, structural models of the IFN-alpha's have been based on the structure of murine IFN-beta (muIFN-beta). These models are likely to be inaccurate, as the amino acid sequence of muIFN-beta differs significantly from the IFN-alpha's at proposed receptor-binding sites. Structural information on a huIFN-alpha subtype would provide an improved basis for modeling the structures of the entire IFN-alpha family.

RESULTS

The crystal structure of recombinant human interferon-alpha 2b (huIFN-alpha 2b) has been determined at 2.9 A resolution. HuIFN-alpha 2b exists in the crystal as a noncovalent dimer, which associates in a novel manner. Unlike other structurally characterized cytokines, extensive interactions in the dimer interface are mediated by a zinc ion (Zn2+). The overall fold of huIFN-alpha 2b is most similar to the structure of muIFN-beta. Unique to huIFN-alpha 2b is a 3(10) helix in the AB loop which is held to the core of the molecule by a disulfide bond.

CONCLUSIONS

The structure of huIFN-alpha 2b provides an accurate model for analysis of the > 15 related type 1 interferon molecules. HuIFN-alpha 2b displays considerable structural similarity with muIFN-beta, interleukin-10 and interferon-gamma, which also bind related class 2 cytokine receptors. From these structural comparisons and numerous studies on the effects of mutations on biological activity, we have identified protein surfaces that appear to be important in receptor activation. This study also reveals the potential biological importance of the huIFN-alpha 2b dimer.

Indirect calorimetry in the nutritional management of eating disorders

The caloric prescription, a key component of the nutritional therapy of anorexia nervosa (AN) and bulimia nervosa (BN), may be empirically prescribed, or based on predicted resting energy expenditure (REE), yet adaptive changes in the metabolic rate may render both methods unreliable. Indirect calorimetry measurement of fasting REE was obtained in 32 patients with AN (n = 21) or BN (n = 11). Predicted REE was calculated according to the Harris-Benedict equation, and empiric caloric prescriptions were made by experienced physicians. In the AN group, mean measured REE was significantly lower than predicted REE (p = .00). The empiric caloric prescription was, as intended, significantly higher than the measured REE, but the two methods correlated significantly (r = .53, p < .05). The predicted REE overestimated caloric needs but was also highly correlated with measured REE (r = .69, p < .001). By regression analysis, measured REE could be calculated from predicted REE as follows: measured REE (Kcal/day) = (1.84 x Harris-Benedict predicted REE) - 1,435. In the BN group, mean measured REE was not significantly different from the empiric caloric prescription (p = .09) but was significantly lower than the Harris-Benedict predicted REE (p = .022). Neither correlated with measured REE in BN. Therefore, in BN indirect calorimetry is the only reliable method for determining caloric needs. In AN indirect calorimetry remains the preferred method, but when not available, we recommend the above equation to determine resting energy requirements.

Liver anatomy applied to the placement of transjugular intrahepatic portosystemic shunts

PURPOSE

To study the vascular and biliary liver anatomy and its relevance to the creation of a transjugular intrahepatic portosystemic shunt (TIPS).

MATERIALS AND METHODS

Acrylic casts of 25 normal human livers (necropsy specimens) were obtained. The anatomy of the hepatic veins, portal vein, hepatic artery, and bile ducts and the relationship of structures of the portal triad were evaluated. Diameters of the vessels and distances and relative position of the structures were recorded. Special attention was given to the puncture path used for TIPS.

RESULTS

One right hepatic vein (RHV) was seen in 16 cases, two RHVs in one, and an accessory RHV in six. All were posterior to the portal bifurcation. The mean distance between the RHV and the portal bifurcation was 4.4 cm. In 13 cases, the path for TIPS puncture was free of major vascular and biliary structures. In 12 cases, portal, biliary, and/or arterial structures were seen in the puncture path.

CONCLUSION

TIPS puncture should be performed in the postero-inferior aspect of the right portal trunk or at the posterior aspect of the bifurcation of the portal vein. Knowledge of the vascular liver anatomy is imperative to create the TIPS safely.

Isolation and characterization of a resistant core peptide of recombinant human granulocyte-macrophage colony-stimulating factor (GM-CSF); confirmation of the GM-CSF amino acid sequence by mass spectrometry

A trypsin-resistant core peptide of recombinant human granulocyte-macrophage colony-stimulating factor (rhGM-CSF) was isolated and analyzed by high-energy Cs+ liquid secondary-ion (LSI) mass spectrometric analysis. This analysis provided successful detection of the high-mass disulfide-linked core peptide as well as information confirming the existence of disulfide pairing. Similarly, LSI mass spectrometric analysis of the peptide fragments isolated chromatographically from a Staphylococcus aureus V8 protease digest of rhGM-CSF provided rapid confirmation of the cDNA-derived sequence and determination of the existing disulfide bonds between cysteine residues 54-96 and 88-121. Electrospray ionization mass spectrometry was employed to measure the molecular weight of the intact protein and to determine the number of the disulfide bonds in the protein molecule by comparative analysis of the protein before and after reduction with beta-mercaptoethanol.

A homology model of human interferon alpha-2

An atomic coordinate five alpha-helix three-dimensional model is presented for human interferon alpha-2 (HuIFN alpha 2). The HuIFN alpha 2 structure was constructed from murine interferon beta (MuIFN beta) by homology modeling using the STEREO and IMPACT programs. The HuIFN alpha 2 model is consistent with its known biochemical and biophysical properties including epitope mapping. Lysine residues predicted to be buried in the model were primarily unreactive with succinimidyl-7-amino-4-methylcoumarin-3-acetic acid (AMCA-NHS), a lysine modification agent, as shown by mass spectrometric analysis of tryptic digests. N-terminal sequence analysis of polypeptides generated by limited digestion of HuIFN alpha 2 with endoproteinase Lys-C demonstrated rapid cleavage at K31, which is consistent with the presence of this residue in a loop in the proposed HuIFN alpha 2 model. Based on this model structure potential receptor binding sites are identified.

Application of electrospray mass spectrometry in probing protein-protein and protein-ligand noncovalent interactions

A novel mass spectrometry-based methodology using electrospray ionization (ESI) is described for the detection of protein-protein [interferon (IFN)-γ dimer] and protein-ligand [ras-guanosine diphosphate (GDP)] noncovalent interactions. The method utilizes ESI from aqueous solution at appropriate pH. The presence of the noncovalent complex of the IFN-γ dimer was confirmed by the observed average molecular weight of 33,819 Da. The key to the detection of the IFN-γ dimer is the use of an alkaline solution (pH ≈ 9) for sample preparation and for mass spectrornetry analysis. The effect of the declustering energy in the region of the ion sampling orifice and focusing quadrupole on the preservation of the gas-phase noncovalent complex (IFN-γ dimer) was also studied. The effect of the declustering energy on complex dissociation was further extended to probe the noncovalent protein-ligand association of ras-GDP. It was found that little energy is required to dissociate the IFN-γ dimer, whereas a substantial amount of energy is required to dissociate the gas-phase ras-GDP complex.

Crystal structure of recombinant human interleukin-4

The crystal structure of recombinant human interleukin-4 (rhuIL-4) was initially determined at 3.5-A resolution by multiple isomorphous replacement techniques and subsequently refined to a resolution of 2.35 A by simulated annealing. The final crystallographic R-factor, based on all data in the range 6.0-2.35 A (7470 reflections), is 0.232. Bond lengths and bond angles in the molecule have root mean square deviations from ideal values of 0.016 A and 2.4 degrees, respectively. The overall structure is highly compact and globular with a predominantly hydrophobic core. The main structural feature of rhuIL-4 is a four alpha-helix bundle, which composes approximately 58% of the structure. The helices are arranged in a left-handed antiparallel bundle with two overhand connections. Within these connections is a two-stranded antiparallel beta-sheet. Both the tertiary and secondary structures of rhuIL-4 are similar to those of human granulocyte-macrophage colony-stimulating factor. Critical regions for receptor binding are proposed.

Utility of phenomenological models for describing temperature dependence of bacterial growth

We compared three unstructured mathematical models, the master reaction, the square root, and the damage/repair models, for describing the relationship between temperature and the specific growth rates of bacteria. The models were evaluated on the basis of several criteria: applicability, ease of use, simple interpretation of model parameters, problem-free determination of model parameters, statistical evaluation of goodness of fit (chi 2 test), and biological relevance. Best-fit parameters for the master reaction model could be obtained by using two consecutive nonlinear least-square fits. The damage/repair model proved to be unsuited for the data sets considered and was judged markedly overparameterized. The square root model allowed nonproblematical parameter estimation by a nonlinear least-square procedure and, together with the master reaction model, was able to describe the temperature dependence of the specific growth rates of Klebsiella pneumoniae NCIB 418, Escherichia coli NC3, Bacillus sp. strain NCIB 12522, and the thermotolerant coccobacillus strain NA17. The square root and master reaction models were judged to be equally valid and superior to the damage/repair model, even though the square root model is devoid of a conceptual basis.