Validation of the first step of the heuristic refinement method for the derivation of solution structures of proteins from NMR data

A new method for the analysis of NMR data in terms of the solution structure of proteins has been developed. The method consists of two steps: first a systematic search of the conformational space to define the region allowed by the initial set of experimental constraints, and second, the narrowing of this region by the introduction of additional constraints and optional refinement procedures. The search of the conformational space is guided by heuristics to make it computationally feasible. The method is therefore called the heuristic refinement method and is coded in an expert system called PROTEAN. The paper describes the validation of the first step of the method using an artificial NMR data set generated from the known crystal structure of sperm whale carbon monoxymyoglobin. It is shown that the initial search procedure yields a low-resolution structure of the myoglobin molecule, accurately reproducing its main topological features, and that the precision of the structure depends on the quality of the initial data set.     

Causal inference and large-scale expert validation shed light on the drivers of SDM accuracy and variance

Aim

To develop a causal understanding of the drivers of Species distribution model (SDM) performance.

Location

United Kingdom (UK).

Methods

We measured the accuracy and variance of SDMs fitted for 518 species of invertebrate and plant in the UK. Our measure of variance reflects variation among replicate model fits, and taxon experts assessed model accuracy. Using directed acyclic graphs, we developed a causal model depicting plausible effects of explanatory variables (e.g. species' prevalence, sample size) on SDM accuracy and variance and quantified those effects using a multilevel piecewise path model.

Results

According to our model, sample size and niche completeness (proportion of a species' niche covered by sampling) directly affect SDM accuracy and variance. Prevalence and range completeness have indirect effects mediated by sample size. Challenging conventional wisdom, we found that the effect of prevalence on SDM accuracy is positive. This reflects the facts that sample size has a positive effect on accuracy and larger sample sizes are possible for widespread species. It is possible, however, that the omission of an unobserved confounder biased this effect. Previous studies, which reported negative correlations between prevalence and SDM accuracy, conditioned on sample size.

Main conclusions

Our model explicates the causal basis of previously reported correlations between SDM performance and species/data characteristics. It also suggests that niche completeness has similarly large effects on SDM accuracy and variance as sample size. Analysts should consider niche completeness, or proxies thereof, in addition to sample size when deciding whether modelling is worthwhile.     

Industrial enzymes--developments in production and application

The utilization of gene technology and of new production technologies have made industrial enzymes with improved properties or better cost performance available. This has in turn opened important new areas of enzyme applications. The benefits to the customers are considerable: cost savings in the application process, improved product quality, and in most cases also a significantly reduced impact on the environment.

Gene technology offers several benefits to the enzyme industry. This technology enables the use of safe, well-documented host organisms easy to cultivate, the microbial production of enzymes of animal and plant origin, the realization of enhanced efficiency and high product purity, and also the production of enzymes with improved stability and activity.

Developments in production technology include advanced control methods, the use of expert systems, and the application of large-scale crystallization.

As case stories the development of a lipase and of a cellulase is described. The effect on environment of enzyme application and production is discussed.     

A structured analysis of risk to important wildlife elements in three Australian Wildlife Conservancy sanctuaries

Where data and information are lacking, structured expert risk assessments can provide a powerful tool to progress natural resource planning. In many situations, practitioners make informal assessments of risk within small groups that typically constitute employees. In this study, we report on three small (in terms of experts) structured expert‐based risk assessment case studies conducted by expert employees of a not‐for‐profit organisation (Australian Wildlife Conservancy) to demonstrate the utility of the approach. The case studies were carried out for three wildlife sanctuaries managed by AWC: Faure Island, Karakamia and Paruna. The likelihood that a set of direct risk factors would cause management failure for sets of important wildlife elements in the three sanctuaries was elicited from the small group of ecological experts. The analysis was couched in terms of a management aim to not lose species from each wildlife element over the management period of 25 years with current management. The experts believed, in particular, that increasing temperature and decreasing water availability associated with climate change were likely to impact significantly upon the vegetation elements and water‐reliant fauna associated with the sanctuaries. Some vegetation elements were also thought likely to be at risk of over‐grazing, unsuitable fire regimes and, in some cases, disease. In addition to predation by exotic predators at one sanctuary, the experts identified additional direct risk factors for various fauna elements associated with expected changes to the vegetation elements, including reduction in food availability, nesting habitat, and generally important life media. From the risk analyses, a preliminary conceptual model was developed to underpin monitoring and to indicate areas for possible management intervention and research. The case studies demonstrate that even in a small workplace team, structured risk assessments can be efficiently accomplished and can provide expedient and transparent information that effectively captures and aggregates the views of the experts.     

Understanding the key characteristics and challenges of pine barrens restoration: insights from a Delphi survey of forest land managers and researchers

Pine barrens are open‐canopy ecological communities once prevalent on sandy soils across the northern Great Lakes Region of the United States and Canada, though fire suppression and plantation forestry have now reduced them to a few isolated areas. Efforts to restore pine barrens are underway on some public lands, but lack of knowledge on the social and ecological issues and challenges that affect these projects impedes fuller progress. As a precursor to designing a public preference survey for pine barrens restoration, we sought input from those with expert knowledge about pine barrens. Using a three‐round modified Delphi survey, forest land managers and researchers identified the key characteristics of pine barrens and important current and future management challenges. Key characteristics were related to fire, landscape structure, plant and animal species, soils, and social themes. Current and future challenges were related to landscape, invasive species, social, economic, climate change, and science themes. Four social issues (education, fire acceptance, fire risk, aesthetics) were rated among the top current challenges but none of them maintained prominence as future challenges. Potential explanations for this shift are that the experts felt these social concerns would be resolved in time or that other issues, such as development pressures and budgets for carrying out restoration, would become greater future challenges. Our approach can be used by managers and researchers to better understand the ecosystems they seek to restore and to communicate with public stakeholders about restoration efforts.     

Role for protein–protein interaction databases in human genetics

Proteomics and the study of protein–protein interactions are becoming increasingly important in our effort to understand human diseases on a system-wide level. Thanks to the development and curation of protein-interaction databases, up-to-date information on these interaction networks is accessible and publicly available to the scientific community. As our knowledge of protein–protein interactions increases, it is important to give thought to the different ways that these resources can impact biomedical research. In this article, we highlight the importance of protein–protein interactions in human genetics and genetic epidemiology. Since protein–protein interactions demonstrate one of the strongest functional relationships between genes, combining genomic data with available proteomic data may provide us with a more in-depth understanding of common human diseases. In this review, we will discuss some of the fundamentals of protein interactions, the databases that are publicly available and how information from these databases can be used to facilitate genome-wide genetic studies.     

Development of an expert system for the integration of biomarker responses in mussels into an animal health index

Biomarkers on sentinel organisms are utilised worldwide in biomonitoring programs. However, the lack of effective interpretational capacity has hampered their uptake for use for assessment of risk in environmental management. The aim of the present study was to develop and test an objective decision-support or expert system capable of integrating biomarker results into a five-level health-status index. The expert system is based on a set of rules derived from available data on responses to natural and contaminant-induced stress of marine mussels. Integration of parameters includes: level of biological organization; biological significance; mutual inter-relationship; and qualitative trends in a stress gradient. The system was tested on a set of biomarker data obtained from the field and subsequently validated with data from previous studies. The results demonstrate that the expert system can effectively quantify the biological effects of different levels of pollution. The system represents a simple tool for risk assessment of the harmful impact of contaminants by providing a clear indication of the degree of stress syndrome induced by pollutants in mussels.     

Homelessness and dog ownership: an investigation into animal empathy,attachment, crime,drug use,health and public opinion

Abstract

A sample of 51 homeless people in Cambridge, UK completed a questionnaire featuring adapted Animal Empathy and Companion Animal Bonding Scales. Concepts of crime, drug use, and health matters amongst the homeless, both dog owning and non-dog owning, were investigated, as well. Ninety members of the general public completed a similar questionnaire which sought their opinions on homeless people who own dogs. There was a highly significant difference (p < 0.01) between the homeless and the securely housed on their animal empathy and attachment scores, with the homeless sample displaying higher values. Gender and dog ownership status had no effect on these scores. A near significant result (U = 2, n₁ = 13, n₂ = 58, p = 0.06) was revealed for animal empathy scores of those who gave money to dog-owning homeless people and those who gave to non-dog owning homeless people. Of the public respondents, women were significantly more likely to show concern for a homeless person's dog's welfare than men (X²₍₁₎ = 8.5, p < 0.01), and of the homeless respondents, non-dog owners were significantly more likely than dog owners to believe that having a dog helped initiate conversations with the public (X²₍₁₎ = 4.0, p < 0.05). Highly significant differences (U = 10, n₁ = 31, n₂ = 20, p < 0.01) were found for medical care use between the dog-owning and non-dog owning homeless, and health scores showed a reversed trend compared to that expected for the general population, with dog owners scoring lower than non-dog owners.     

A risk‐based inventory of invasive plant species of Queensland,Australia: Regional,ecological and floristic insights

Invasive alien plant species threaten agriculture and biodiversity globally and require ongoing management to minimise impacts. However, the large number of invasive species means that a risk‐based approach to prioritisation is needed, taking into account the spatial scale of management decisions and myriad of available information. Here, we developed a risk‐based inventory of invasive plants in Queensland, Australia, using both current species distribution/abundance and the severity of their impacts. Our assessment followed a comprehensive data collection process including a scoping of local government pest management plans, herbarium records, the published literature and structured elicitation of expert knowledge during a series of regional stakeholder workshops. From ~300 plant species that were identified as established and/or emerging invaders in the State, only one‐third were considered by practitioners to pose significant risks across regions to be considered management priorities. We aggregated regional species lists into a statewide priority list and analysed the data set (107 species) for historical, geographical, floristic and ecological patterns. Regions on the mainland eastern seaboard of the State share similar invasive plant communities, suggesting that these regions may form a single management unit, unlike the western/inland and the extreme far north (Torres Strait Islands) regions, which share fewer invasive plant species. Positive correlations were detected between invasiveness and time since introduction for some but not all plant life forms. Stakeholders identified research and management priorities for the invasive plant list, including biological control options, public awareness/education, effective herbicide use, ecology/taxonomy and risk analysis. In the course of the exercise, a statewide invasive plant priority list of high‐, medium‐ and low‐impact scores for policy, research and management was compiled. Finally, our approach to invasive plant species prioritisation highlighted that planning and policy documents are not necessarily reflected at the grass‐root level in terms of species identity and management priorities.