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.     

Heavy Metals in Sediments of the Gold Mining Impacted Pra River Basin,Ghana, West Africa

Total concentrations of Hg, Al, Fe, As, Pb, Cu, Cr, Ni, Mn, Co, V, and Zn were determined in surface sediments collected from 21 locations within the gold mining impacted Pra River basin in southwestern Ghana. Samples were collected during both the rainy and dry seasons. We hypothesized that in the rural southwestern portion of Ghana, the lack of industrial activities makes artisanal gold mining (AGM) by Hg amalgamation the main source of water resource contamination with heavy metals. Therefore, metals showing concentration trends similar to that of Hg in the studied system are likely impacted by AGM. We found that total-Hg (THg) concentrations in riverine sediments are rather low as compared to other aquatic systems that are impacted by similar mining activities. Measured THg concentrations ranged from 0.018 to 2.917 mg/kg in samples collected in the rainy season and from about 0.01 to 0.043 mg/kg in those collected during the dry season. However, the determination of the enrichment factor (EF) calculated using shale data as reference background values showed signs of severe contamination in most of the sampled sites. In the dry season, THg concentrations correlated positively and significantly to the concentrations of As (r = 0.864, p < 0.01), Cu (r = 0.691, p < 0.05), and Ni (r = 0.579, p < 0.05). Based on our previously stated hypothesis, this could then be an indication of the impact of AGM on ambient levels of these 3 elements. However, the determined concentrations of Cu, and Ni co-varied significantly with Al, suggesting that natural sources do account for the observed levels. Accordingly, both AGM and metal inputs from weathered natural deposits are likely co-responsible for the observed levels of Cu and Ni. In contrast, the lack of correlation between As and Al tends to suggest an impact of AGM on As levels. Overall, our data suggest that besides Hg and to some extent As, the impact of AGM on ambient levels of investigated metals in the gold mining impacted Pra River remains negligible. Finally, the increase in metal concentrations from the dry to the rainy season underlines the impact of changes in hydrologic conditions on levels and fate of metals in this tropical aquatic system.     

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.     

Plant invasions in treeless vegetation of the Australian Alps

A total of 128 invasive plant species have been recorded in treeless vegetation in the Australian Alps. Most of these are forbs and most are uncommon. Cover of invasive species is generally minimal unless there has been gross disturbance to natural vegetation and soils. Although there is a significantly positive correlation between invasive and native species diversity, suggesting that conditions that allow numerous native species to co-exist also permit more plant invasions, altitude is the most important determinant of invasive species diversity. Only 22 of the 128 species have been recorded above 1800 m. Some plant communities (e.g. those with high pH or relatively nutrient-rich soils), however, seem to be vulnerable to invasions regardless of altitude. Most invasive species appear to have been introduced unintentionally (e.g. as seed attached to vehicles, animals and humans) but a few were introduced to assist with revegetation of disturbed soils and for amenity plantings in ski resorts, and have subsequently established in native vegetation. Treeless communities in the Australian Alps are likely to face increasing pressure from invasive species as a result of global warming and continued introduction of non-native plants to ski resort gardens. Whilst it may be difficult to prevent invasive species of low elevations migrating to higher elevations as temperatures rise, the risk of invasion from garden plants could be minimised through regulation. Non-native plants in ski resort gardens pose a far greater risk than most invasive species currently present in the Alps because they have been chosen for their capacity to survive at high altitudes.