Fauna habitat modelling and mapping: A review and case study in the Lower Hunter Central Coast region of NSW

Abstract Habitat models are now broadly used in conservation planning on public lands. If implemented correctly, habitat modelling is a transparent and repeatable technique for describing and mapping biodiversity values, and its application in peri‐urban and agricultural landscape planning is likely to expand rapidly. Conservation planning in such landscapes must be robust to the scrutiny that arises when biodiversity constraints are placed on developers and private landholders. A standardized modelling and model evaluation method based on widely accepted techniques will improve the robustness of conservation plans. We review current habitat modelling and model evaluation methods and provide a habitat modelling case study in the New South Wales central coast region that we hope will serve as a methodological template for conservation planners. We make recommendations on modelling methods that are appropriate when presence‐absence and presence‐only survey data are available and provide methodological details and a website with data and training material for modellers. Our aim is to provide practical guidelines that preserve methodological rigour and result in defendable habitat models and maps. The case study was undertaken in a rapidly developing area with substantial biodiversity values under urbanization pressure. Habitat maps for seven priority fauna species were developed using logistic regression models of species‐habitat relationships and a bootstrapping methodology was used to evaluate model predictions. The modelled species were the koala, tiger quoll, squirrel glider, yellow‐bellied glider, masked owl, powerful owl and sooty owl. Models ranked sites adequately in terms of habitat suitability and provided predictions of sufficient reliability for the purpose of identifying preliminary conservation priority areas. However, they are subject to multiple uncertainties and should not be viewed as a completely accurate representation of the distribution of species habitat. We recommend the use of model prediction in an adaptive framework whereby models are iteratively updated and refined as new data become available.     

Design considerations for array CGH to oligonucleotide arrays.

BACKGROUND: Representational oligonucleotide microarray analysis has been developed for detection of single nucleotide polymorphisms and/or for genome copy number changes. In this process, the intensity of hybridization to oligonucleotides arrays is increased by hybridizing a polymerase chain reaction (PCR)-amplified representation of reduced genomic complexity. However, hybridization to some oligonucleotides is not sufficiently high to allow precise analysis of that portion of the genome. METHODS: In an effort to identify aspects of oligonucleotide hybridization affecting signal intensity, we explored the importance of the PCR product strand to which each oligonucleotide is homologous and the sequence of the array oligonucleotides. We accomplished this by hybridizing multiple PCR-amplified products to oligonucleotide arrays carrying two sense and two antisense 50-mer oligonucleotides for each PCR amplicon. RESULTS: In some cases, hybridization intensity depended more strongly on the PCR amplicon strand (i.e., sense vs. antisense) than on the detection oligonucleotide sequence. In other cases, the oligonucleotide sequence seemed to dominate. CONCLUSION: Oligonucleotide arrays for analysis of DNA copy number or for single nucleotide polymorphism content should be designed to carry probes to sense and antisense strands of each PCR amplicon to ensure sufficient hybridization and signal intensity.     

Dutch guidelines for interventional cardiology: institutional and operator competence and requirements for training

Interventional cardiology is an expanding field within cardiovascular medicine and today it is generally accepted that cardiologists require specific training, knowledge and skills. Hospitals where coronary interventions are performed must be properly equipped and able to provide specialised care. Percutaneous coronary interventions are frequently used for coronary revascularisation. The public should have confidence in the uniformity of high quality care. Therefore, such quality of care should be maintained by certification of the individual operators, general guidelines for institutional requirements and formal audits. The Netherlands Society of Cardiology (NVVC) will be implementing a new registration system for cardiologists with a subspecialisation that will include registration for interventional cardiology. The NVVC asked the Working Group of Interventional Cardiology (WIC) to update the 1994 Dutch guidelines on operator and institutional competence, and requirements for training in interventional cardiology in order to incorporate them into the official directives. The present guidelines represent the expert opinion of the Dutch interventional cardiology community and are in accordance with international regulations.After two rounds of discussion, the NVVC approved the guidelines in November 2004 during the autumn meeting.     

RNA isolation from yeast using silica matrices.

RNA isolation from yeast is complicated by the need to initially break the cell wall. While this can be accomplished by glass bead disruption or enzyme treatment, these approaches result in DNA contamination and/or the need for incubation periods. We have developed a protocol for the isolation of RNA samples from yeast that minimizes degradation by RNases and incorporates two purification steps: acid phenol extraction and binding to a silica matrix. The procedure requires no precipitation steps, facilitating automation, and can be completed in less than 90 min. The RNA quality is ideal for microarray analysis.     

Integrins in Head and Neck Squamous Cell Carcinoma (HNSCC): A Review of the Current Literature

Integrins are a family of adhesion molecules performing a major role in multiple cellular functions. Their contribution in carcinogenesis and metastatic process are the object of intense research activity worldwide during the last decades. This review focuses on the existing knowledge about integrin expression in head and neck squamous cell carcinoma (HNSCC) as it has been acquired mainly by immunohistochemical methods and by in vitro assays. The elucidation of the exact role of integrins and the study of expressive alterations of these molecules in cancer cells, may result in novel therapeutical approaches for useful applications in the clinical routine of HNSCC in the future.     

Spatial Controls of Pre–Euro-American Wind and Fire Disturbance in Northern Wisconsin (USA) Forest Landscapes

We elucidate spatial controls of wind and fire disturbance across northern Wisconsin (USA), where climatic and topographic gradients are not strong, using data from the original US Public Land Survey (PLS) notes. These records contain information on the location and extent of heavy windthrows and stand-replacing fires prior to Euro-American settlement. The spatial patterns of windthrow and fire were spatially clustered at all scales in this historical environment, with stronger associations at local than regional scales. Logistic regression shows environmental variables to have a strong influence on this pattern. In the case of heavy windthrow, environmental drivers of disturbance pattern are fairly consistent across the region. The effects of climate and vegetation are predominant at all scales, but effects are often indirect, with strong interactions between them. Interactions between these two drivers and soil characteristics are also sometimes present. In contrast, models of stand-replacing fire show simple and direct control within and across fire-prone landscapes of historical northern Wisconsin, with climate and physiography as the main factors explaining the distribution of fire disturbance. This simple and direct control is lost at the regional scale, where climate, physiographic, soil, and vegetation variables, along with interactions between them, are significant factors. Contrary to other regions, the topographic effects are generally not important in predicting either wind or fire disturbance. Our work suggests that, in landscapes that lack strong environmental patterning, climate maintains its role as a primary driver of these natural disturbances, but topography is replaced by interactions and feedbacks with other forms of environmental heterogeneity.     

An Exploratory Framework for the Empirical Measurement of Resilience

Deliberate progress towards the goal of long-term sustainability depends on understanding the dynamics of linked social and ecological systems. The concept of social-ecological resilience holds promise for interdisciplinary syntheses. Resilience is a multifaceted concept that as yet has not been directly operationalized, particularly in systems for which our ignorance is such that detailed, parameter-rich simulation models are difficult to develop. We present an exploratory framework as a step towards the operationalization of resilience for empirical studies. We equate resilience with the ability of a system to maintain its identity, where system identity is defined as a property of key components and relationships (networks) and their continuity through space and time. Innovation and memory are also fundamental to understanding identity and resilience. By parsing our systems into the elements that we subjectively consider essential to identity, we obtain a small set of specific focal variables that reflect changes in identity. By assessing the potential for changes in identity under specified drivers and perturbations, in combination with a scenario-based approach to considering alternative futures, we obtain a surrogate measure of the current resilience of our study system as the likelihood of a change in system identity under clearly specified conditions, assumptions, drivers and perturbations. Although the details of individual case studies differ, the concept of identity provides a level of generality that can be used to compare measure of resilience across cases. Our approach will also yield insights into the mechanisms of change and the potential consequences of different policy and management decisions, providing a level of decision support for each case study area.     

Rapid evolution and the convergence of ecological and evolutionary time

Recent studies have documented rates of evolution of ecologically important phenotypes sufficiently fast that they have the potential to impact the outcome of ecological interactions while they are underway. Observations of this type go against accepted wisdom that ecological and evolutionary dynamics occur at very different time scales. While some authors have evaluated the rapidity of a measured evolutionary rate by comparing it to the overall distribution of measured evolutionary rates, we believe that ecologists are mainly interested in rapid evolution because of its potential to impinge on ecological processes. We therefore propose that rapid evolution be defined as a genetic change occurring rapidly enough to have a measurable impact on simultaneous ecological change. Using this definition we propose a framework for decomposing rates of ecological change into components driven by simultaneous evolutionary change and by change in a non‐evolutionary factor (e.g. density dependent population dynamics, abiotic environmental change). Evolution is judged to be rapid in this ecological context if its contribution to ecological change is large relative to the contribution of other factors. We provide a worked example of this approach based on a theoretical predator–prey interaction [ Abrams, P. & Matsuda, H. (1997) . Evolution, 51, 1740], and find that in this system the impact of prey evolution on predator per capita growth rate is 63% that of internal ecological dynamics. We then propose analytical methods for measuring these contributions in field situations, and apply them to two long‐term data sets for which suitable ecological and evolutionary data exist. For both data sets relatively high rates of evolutionary change have been found when measured as character change in standard deviations per generation (haldanes). For Darwin's finches evolving in response to fluctuating rainfall [ Grant, P.R. & Grant, B.R. (2002) . Science, 296, 707], we estimate that evolutionary change has been more rapid than ecological change by a factor of 2.2. For a population of freshwater copepods whose life history evolves in response to fluctuating fish predation [ Hairston, N.G. Jr & Dillon, T.A. (1990) . Evolution, 44, 1796], we find that evolutionary change has been about one quarter the rate of ecological change – less than in the finch example, but nevertheless substantial. These analyses support the view that in order to understand temporal dynamics in ecological processes it is critical to consider the extent to which the attributes of the system under investigation are simultaneously changing as a result of rapid evolution.