Development of a risk assessment for BSE in the aquatic environment

Bovine spongiform encephalopathy (BSE) is believed to be transmitted by the ingestion of proteinaceous agents called prions which accumulate in the brain and spinal cord of infected bovines. Concern has been expressed about the risks of transmission of BSE to humans through BSE prions discharged to the aquatic environment from rendering plants, abattoirs and landfills. The disease-related form of the prion protein is relatively resistant to degradation, and infectivity decays rather slowly in the environment. Levels of disinfection used for drinking water treatment would have little effect. This paper presents the assumptions which were used to model the risks from a rendering plant disposing of cull cattle carcasses in the catchment of a chalk aquifer which is used for a drinking water abstraction. The risk assessment approach focused on identifying the hydrogeological and physical barriers which would contribute to preventing BSE infectivity gaining entry to the aquifer. These barriers included inactivation of BSE agent by the rendering process, removal from the effluent by treatment at the plant, filtration and adsorption in the clay and chalk, and dilution in the ground water. The importance in environmental risk assessment of the cow-to-man species barrier is considered. Two key conclusions about the environmental behaviour of the BSE agent are that prion proteins are 'sticky' and bind to particulates, and that the millions of BSE prion molecules comprising a human oral ID₅₀ are subject to some degree of dispersion and hence dilution in the environment. Assuming the rendering plant processes 2000 cull cattle carcasses per week, the risks to drinking water consumers were estimated to be remote. Indeed, even using worst case assumptions an individual would have to consume 2 l d⁻¹ of tap water for 45 million years to have a 50% chance of infection through drinking water drawn from the aquifer.     

Sediment analysis for the assessment of risk from organic pollutants in lakes

Sediment analysis in three Italian subalpine lakes, very close to each other and exposed to different anthropogenic pressure, was used to assess the risk from organic pollutants, including some very persistent and widespread micropollutants (PCB, DDT, PAH) as well as known local pollutants. Additionally, a wide-spectrum characterization of organic compounds by GLC-MS analysis allowed the detection of other classes of chemicals. The contamination levels were related to long distance transport and to local sources of pollution in the watershed. PAH, PCB and organochlorine pesticide levels agree with the load calculated from atmospheric depositions. Local sources of pollution are responsible for the contamination by aliphatic hydrocarbons and tris(monochloroisopropyl)-phosphate (TCIPP); these compounds were found only in the two most urbanized basins. Heavy contamination by TCIPP was found in both water and sediments; water concentrations are considered hazardous for drinking purposes. This study shows that local contaminants, not yet included in any priority list, may single; out as a major environmental concern.     

Comparative proteomics as a new tool for exploring human mitochondrial tRNA disorders.

More than 70 different point mutations in human mitochondrial tRNA genes are correlated with severe disorders, including fatal cardiopathies, encephalopathies, myopathies, and others. So far, investigation of the molecular impact(s) of mutations has focused on the affected tRNA itself by seeking structural and/or functional perturbations capable of interfering with synthesis of the 13 mitochondrion-encoded subunits of respiratory chain complexes. Here, a proteomic approach was used to investigate whether such mutations would affect the pattern of mitochondrial proteins at a broader level. Analysis of several hundred mitochondrial proteins from sibling cybrid cell lines by two-dimensional electrophoresis, an approach that takes into account all regulatory steps of mitochondrial and nuclear gene expression, indeed reveals a number of up- and downregulated proteins when healthy and single-point-mutation-carrying mitochondria representative of either MELAS or MERRF syndrome were compared. Assignment by mass spectrometry of the two proteins which exhibit obvious large quantitative decreases in the levels of both pathologic mitochondria identified nuclear-encoded subunits of cytochrome c oxidase, a respiratory chain complex. This clearly shows a linkage between the effects of mutations in mitochondrial tRNA genes and the steady-state level of nuclear-encoded proteins in mitochondria. It opens new routes toward a large-scale exploration of potential proteic partners involved in the genotype-phenotype correlation of mitochondrial disorders.     

An assessment of actinobacterial diversity in the marine environment

The 16S rRNA gene sequence diversity within the Phylum Actinobacteria was assessed from four sources: PCR-generated V6 sequence tags derived from seawater samples, metagenomic data from the Global Ocean Sampling (GOS) expedition, marine-derived sequences maintained in the Ribosomal Database Project (RDP), and select cultured strains for which sequence data is not yet available in the RDP. This meta-analysis revealed remarkable levels of phylogenetic diversity and confirms the existence of major, deeply rooted, and as of yet uncharacterized lineages within the phylum. A dramatic incongruence among cultured strains and those detected using culture-independent techniques was also revealed. Redundancy among the actinobacteria detected using culture-independent techniques suggests that greater sequence coverage or improved DNA extraction efficiencies may be required to detect the rare phylotypes that can be readily cultured from marine samples. Conversely, new strategies need to be developed for the cultivation of frequently observed but yet to be cultured marine actinobacteria.     

Primary poisoning risk for encapsulated sodium nitrite,a new tool for pest control

ABSTRACT

Acute toxicity of sodium nitrite (NaNO₂) was assessed in chickens (Gallus gallus domesticus) and domestic mallard ducks (Anas platyrhynchos domestica) by oral gavage and in free-feeding trials with chickens, domestic mallard ducks, pigeons (Columba livia f. domestica), budgerigars (Melopsittacus undulates) and wētā (Family: Rhaphidophoridae). Free-feeding trials involved the presentation of toxic paste and pellet baits containing encapsulated NaNO₂ developed for the control of common brushtail possums (Trichosurus vulpecula) and feral pigs (Sus scrofa). The oral gavage LD₅₀ value for NaNO₂ in solution was approximately 68.50?mg/kg (95% CI 55.00–80.00?mg/kg) for both chickens and ducks. In feeding trials, six out of 12 chickens consumed toxic paste bait and four of these birds consumed a lethal dose. When chickens consumed toxic paste bait, the LD₅₀ value was approximately 254.6?mg/kg (95% CI 249.1–260.2?mg/kg). Of the other three species of birds presented with toxic baits only one duck consumed a lethal dose of paste bait. There was no evidence of wētā feeding on toxic baits.     

Protecting our environment,a motivating outdoor game for proteomics!

The global Earth ecosystem faces many intertwined threats, primarily anthropogenic pollution, drastic reduction of wild spaces, faster spread of pathogens, and global climate warming. Ecotoxicology, the integration of toxicology and ecology, aims to describe the effects of toxicants on organisms, whether at the level of the population, the community, the ecosystem, or the biosphere. Sentinel species are employed to assess threats to life, giving advance warning of danger. In this issue of Proteomics, Wilde and collaborators (Proteomics 2022, 22, https://doi.org/10.1002/pmic.202100289 ) present a comprehensive coverage of the proteome of the crustacean Daphnia magna, a species used to evaluate aquatic pollution. This study illustrates how current shotgun proteomics technology allows straightforward quantitation of any protein for whole animals or dissected organs, making global molecular phenotyping a reality for animals. Tandem mass spectrometry operated in data-independent acquisition can be used to compare the response of sentinels to various environmental conditions. The current low number of well-annotated animal or plant genomes, the high diversity of genetic backgrounds of each species, and the paucity of knowledge about protein functions for most of the relevant sentinels pose huge challenges for data interpretation. As a result, ecology and ecotoxicology today constitute an exceptional field for proteomics.     

Randomly amplified polymorphic DNA PCR as a tool for assessment of marine viral richness

Recent discoveries have uncovered considerable genetic diversity among aquatic viruses and raised questions about the variability of this diversity within and between environments. Studies of the temporal and spatial dynamics of aquatic viral assemblages have been hindered by the lack of a common genetic marker among viruses for rapid diversity assessments. Randomly amplified polymorphic DNA (RAPD) PCR bypasses this obstacle by sampling at the genetic level without requiring viral isolation or previous sequence knowledge. In this study, the utility of RAPD-PCR for assessing DNA viral richness within Chesapeake Bay water samples was evaluated. RAPD-PCR using single 10-mer oligonucleotide primers successfully produced amplicons from a variety of viral samples, and banding patterns were highly reproducible, indicating that each band likely represents a single amplicon originating from viral template DNA. In agreement with observations from other community profiling techniques, resulting RAPD-PCR banding patterns revealed more temporal than spatial variability in Chesapeake Bay virioplankton assemblages. High-quality hybridization probes and sequence information were also easily generated from single RAPD-PCR products or whole reactions. Thus, the RAPD-PCR technique appears to be practical and efficient for routine use in high-resolution viral diversity studies by providing assemblage comparisons through fingerprinting, probing, or sequence information.     

The Hirsch-index: a simple, new tool for the assessment of scientific output of individual scientists

In this brief paper we explore the Hirsch-index together with a couple of other bibliometric parameters for the assessment of the scientific output of 29 Dutch professors in clinical cardiology. It appears that even within such a homogeneous group there is large interindividual variability. Although the differences are quite remarkable, it remains undetermined what they mean; at least it is premature to interpret them as differences in scientific quality. It goes without saying that even more prudence is required when different fields of medicine and life sciences are compared (for example within University Medical Centres). Recent efforts to produce an amalgam of scientific ‘productivity’, ‘relevance’ and ‘viability’ as a surrogate parameter for the assessment of scientific quality, as for example performed in the AMC in Amsterdam, should be discouraged in the absence of a firm scientific base. Unfortunately for politicians and ‘managers of science’ only reading papers and studying are suitable for quality assessment of scientific output. Citations analyses can't substitute that. (Neth Heart J 2009;17:145–54.)     

Olfactory assessment of predation risk in the aquatic environment

The aquatic environment is well suited for the transmission of chemical information. Aquatic animals have evolved highly sensitive receptors for detecting these cues. Here, I review behavioural evidence for the use of chemical cues by aquatic animals for the assessment of predation risk. Chemical cues are released during detection, attack, capture and ingestion of prey. The nature of the cue released depends on the stage of the predation sequence in which cues are released. Predator odours, disturbance pheromones, injury-released chemical cues and dietary cues all convey chemical information to prey Prey use these cues to minimize their probability of being taken on to the next stage of the sequence. The evolution of specialized epidermal alarm substance cells in fishes in the superorder Ostariophysi represent an amplification of this general phenomenon. These cells carry a significant metabolic cost. The cost is offset by the fitness benefit of the chemical attraction of predators. Attempts of piracy by secondary predators interrupt predation events allowing prey an opportunity for escape. In conclusion, chemical cues are widely used by aquatic prey for risk assessment and this has resulted in the evolution of specialized structures among some taxa.     

Critical assessment of the automated AutoDock as a new docking tool for virtual screening

A major problem in virtual screening concerns the accuracy of the binding free energy between a target protein and a putative ligand. Here we report an example supporting the outperformance of the AutoDock scoring function in virtual screening in comparison to the other popular docking programs. The original AutoDock program is in itself inefficient to be used in virtual screening because the grids of interaction energy have to be calculated for each putative ligand in chemical database. However, the automation of the AutoDock program with the potential grids defined in common for all putative ligands leads to more than twofold increase in the speed of virtual database screening. The utility of the automated AutoDock in virtual screening is further demonstrated by identifying the actual inhibitors of various target enzymes in chemical databases with accuracy higher than the other docking tools including DOCK and FlexX. These results exemplify the usefulness of the automated AutoDock as a new promising tool in structure-based virtual screening.     

Stepwise quantitative risk assessment as a tool for characterization of microbiological food safety

This paper describes a system for the microbiological quantitative risk assessment for food products and their production processes. The system applies a stepwise risk assessment, allowing the main problems to be addressed before focusing on less important problems. First, risks are assessed broadly, using order of magnitude estimates. Characteristic numbers are used to quantitatively characterize microbial behaviour during the production process. These numbers help to highlight the major risk-determining phenomena, and to find negligible aspects. Second, the risk-determining phenomena are studied in more detail. Both general and/or specific models can be used for this and varying situations can be simulated to quantitatively describe the risk-determining phenomena. Third, even more detailed studies can be performed where necessary, for instance by using stochastic variables. The system for quantitative risk assessment has been implemented as a decision supporting expert system called SIEFE: Stepwise and Interactive Evaluation of Food safety by an Expert System. SIEFE performs bacterial risk assessments in a structured manner, using various information sources. Because all steps are transparent, every step can easily be scrutinized. In the current study the effectiveness of SIEFE is shown for a cheese spread. With this product, quantitative data concerning the major risk-determining factors were not completely available to carry out a full detailed assessment. However, this did not necessarily hamper adequate risk estimation. Using ranges of values instead helped identifying the quantitatively most important parameters and the magnitude of their impact. This example shows that SIEFE provides quantitative insights into production processes and their risk-determining factors to both risk assessors and decision makers, and highlights critical gaps in knowledge.     

Multidisciplinary rapid assessment of coastal areas as a tool for the design and management of marine protected areas

A method is described for rapid multidisciplinary environmental assessment of coastal areas within the conceptual framework of comprehensive management of Marine Protected Areas (MPAs). The aim is to provide tools for the selection, design and management of coastal MPAs when time, budget or potential human pressures, either alone or in combination, create an urgent need for prioritisation. Maximising results and minimising cost and time is the goal, using a methodology that re evaluates existing information on the area, allows use of physical, environmental and socio-economic indicators, and finally integrates information in a Geographic Information System capable of generating outputs in the form of thematic maps to support managers.The final products obtained inform planners and managers about the study areas, across multiple aspects that all need to be considered in integrated coastal management. Although originally proposed for widespread use in the Mediterranean, this methodology can be flexibly adapted, with minor modifications in the selection of indicators, for its use in other regions. The results show its potential for merging and synthesising information not only as a tool in Rapid Assessment Programs but also as a tool for facing management of wide coastal areas as social-ecological ecosystems.     

Anti-sulfonylbenzoate antibodies as a tool for the detection of nucleotide-binding proteins for functional proteomics

Proteins that bind ATP and GTP are important cellular components. We developed an immunological approach to selectively tag nucleotide-binding proteins based on the use of 5'-[4-(fluorosulfonyl)benzoyl]adenosine and 5'-[4-(fluorosulfonyl)benzoyl]guanosine affinity tags and an antibody against 4-(sulfonyl)benzoate. Detection follows affinity labeling, gel electrophoresis, and ester bond cleavage to expose the epitope. Trial analyses of labeled proteins from lymphoid cells identified multiple ATP-binding proteins, including chaperones, actin, kinases, an RNA splicing factor, a membrane ATPase, and ATP synthase.     

Medical simulation: the new tool for training and skill assessment

Medical simulation is a new method to facilitate skill training and assessment. Simulation has achieved a high degree of sophistication in aviation and other fields. However, the complexity of health care, the numerous stakeholders, and the lack of central control of medical education have been barriers to the development and broad implementation of medical simulation. Acceptance by the medical community is growing, with the publication of scientific validation studies, the development of economic models and funding, and the integration of simulation into existing curricula and training programs. The major forces for implementing simulation will most likely come from the medical device industry and from institutions with mandates to improve the quality of health care and enhance patient safety. Certification boards are expected to increase their utilization of simulation technology to objectively assess proficiency of skills relevant to physicians and the health care system. Medical simulation has made the transition from an experimental technology to the clinical world, and the next five to 10 years may be viewed as the golden age of medical simulation.