Symposium introduction: The importance of scale in ecology

Abstract Conceptual issues about scale, both spatial and temporal, have had considerable influence on the way in which ecologists view populations, communities and ecosystems. Scale includes two aspects: the extent over which a community or ecosystem is studied, and the resolution or ‘grain’ at which measurements or experiments are conducted. We illustrate the influence of extent and grain on perceptions of ecological patterns and processes, derived from fundamental measurements, field experiments and theory and modelling. These concepts provide background for a series of subsequent papers that were presented at a symposium on spatial and temporal scaling in freshwater systems. These papers conclude that multi-scale measurements and experiments plus novel methodologies for analysing large-scale surveys and manipulations should be priorities for future research in freshwater systems.     

Evaluating Land-Use Impacts: Selection of Surface Area Metrics for Life-Cycle Assessment of Mining

Land use is an increasingly important component of sustainability evaluations, and numerous performance metrics have evolved to meet this need. The selection of appropriate land-use metrics for decision makers, however, remains an ongoing challenge. Additionally, life-cycle practitioners often struggle to provide meaningful impact assessment because of challenges associated with traditional land-use impact metrics. This article is intended to assist decision makers and life-cycle practitioners who wish to more effectively measure and evaluate one aspect of land use: surface area occupation. Existing performance metrics are discussed, and the specific circumstances under which each is appropriate are identified. Building on leading-edge research and analysis in the field of life-cycle impact assessment, a modified methodology for evaluating surface area occupation is proposed. This approach is demonstrated for a series of mining practices including three individual gold mines, a bauxite mine, and a copper mine. The specific data requirements and resulting equivalency factors for each mine are discussed. Results indicate that equivalency factors for gold (average of 700 acre-yr/ton) are expected to be several orders of magnitude higher than for either bauxite (0.004 acre-yr/ ton) or copper (0.03 acre-yr/ton). These dramatic differences in results demonstrate that equivalency factors are appropriate and necessary for including land-use impact potential as part of a life-cycle assessment that includes several different minerals or material requirements.     

Morphological variation of species through time

Ten measurements, taken from each of 700 shells or four biologically distinct shallow marine gastropod species, were used to define the appropriate phenotypes in multidimensional space. Canonical discriminant analysis was performed on the data and a set of allocatory rules was derived. These allocatory rules, derived from extant specimens, were than applied to 644 fossil specimens of three of these biological species. Fossil individuals occupy the appropriate phenotypic space as defined by their modern descendants. The variation of fossil sample means about the modern means is illustrated. This variation is in the form of oscillations around the modern mean values and is correlated with climate. The distinction between taxonomic and biological species is discussed. The results of a number of previous studies are re-examined in the light of this discussion. It is argued that biological groupings can only be reliably determined when the appropriate data are available for extant organisms. Extant organisms, which have good fossil records, should therefore from the basis of paleontological evolutionary studies.     

Oxygenation measurement by multi‐wavelength oxygen‐dependent phosphorescence and delayed fluorescence: catchment depth and application in intact heart

Oxygen delivery and metabolism represent key factors for organ function in health and disease. We describe the optical key characteristics of a technique to comprehensively measure oxygen tension (PO₂) in myocardium, using oxygen‐dependent quenching of phosphorescence and delayed fluorescence of porphyrins, by means of Monte Carlo simulations and ex vivo experiments. Oxyphor G2 (microvascular PO₂) was excited at 442 nm and 632 nm and protoporphyrin IX (mitochondrial PO₂) at 510 nm. This resulted in catchment depths of 161 (86) µm, 350 (307) µm and 262 (255) µm respectively, as estimated by Monte Carlo simulations and ex vivo experiments (brackets). The feasibility to detect changes in oxygenation within separate anatomical compartments is demonstrated in rat heart in vivo.

Schematic of ex vivo measurements.     

Dual lifetime referencing enables pH‐control for oxidoreductions in hydrogel‐stabilized biphasic reaction systems

pH‐shifts are a serious challenge in cofactor dependent biocatalytic oxidoreductions. Therefore, a pH control strategy was developed for reaction systems, where the pH value is not directly measurable. Such a reaction system is the biphasic aqueous‐organic reaction system, where the oxidoreduction of hydrophobic substrates in organic solvents is catalysed by hydrogel‐immobilized enzymes, and enzyme‐coupled cofactor regeneration is accomplished via formate dehydrogenase, leading to a pH‐shift. Dual lifetime referencing (DLR), a fluorescence spectroscopic method, was applied for online‐monitoring of the pH‐value within the immobilizates during the reaction, allowing for a controlled dosage of formic acid. It could be shown that by applying trisodium 8‐hydroxypyrene‐1, 3, 6‐trisulfonate as pH indicator and Ru(II) tris(4, 7‐diphenyl‐1, 10‐phenantroline) (Ru[dpp]) as a reference luminophore the control of the pH‐value in a macroscopic gel‐bead‐stabilized aqueous/organic two phase system in a range of pH 6.5 to 8.0 is possible. An experimental proof of concept could maintain a stable pH of 7.5 ± 0.15 during the reaction for at least 105 h. With these results, it could be shown that DLR is a powerful tool for pH‐control within reaction systems with no direct access for conventional pH‐measurement.     

Rat Heterotopic Abdominal Heart/Single-lung Transplantation in a Volume-loaded Configuration

Herein, we describe a novel technique for heterotopic abdominal heart-lung transplantation (HAHLT) in rats. The configuration of the transplant graft involves anastomosis of donor inferior vena cava (IVC) to recipient IVC, and donor ascending aorta (Ao) to recipient abdominal Ao. The right upper and middle lung lobes are preserved and function as conduits for blood flow from right heart to left heart.There are several advantages to using this technique, and it lends itself to a broad range of applications. Because the graft is transplanted in a configuration that allows for dyamic volume-loading, cardiac function may be directly assessed in vivo. The use of pressure-volume conductance catheters permits characterization of load-dependent and load-independent hemodynamic parameters. The graft may be converted to a loaded configuration by applying a clamp to the recipient’s infra-hepatic IVC. We describe modified surgical techniques for both donor and recipient operations, and an ideal myocardial protection strategy. Depending on the experimental aim, this model may be adapted for use in both acute and chronic studies of graft function, immunologic status, and variable ventricular loading conditions. The conducting airways to the transplanted lung are preserved, and allow for acute lung re-ventilation. This facilitates analysis of the effects of the mixed venous and arterial blood providing coronary perfusion to the graft.A limitation of this model is its technical complexity. There is a significant learning curve for new operators, who should ideally be mentored in the technique. A surgical training background is advantageous for those wishing to apply this model. Despite its complexity, we aim to present the model in a clear and easily applicable format. Because of the physiologic similarity of this model to orthotopic transplantation, and its broad range of study applications, the effort invested in learning the technique is likely to be worthwhile.     

A Novel Experimental and Analytical Approach to the Multimodal Neural Decoding of Intent During Social Interaction in Freely-behaving Human Infants

Understanding typical and atypical development remains one of the fundamental questions in developmental human neuroscience. Traditionally, experimental paradigms and analysis tools have been limited to constrained laboratory tasks and contexts due to technical limitations imposed by the available set of measuring and analysis techniques and the age of the subjects. These limitations severely limit the study of developmental neural dynamics and associated neural networks engaged in cognition, perception and action in infants performing “in action and in context”. This protocol presents a novel approach to study infants and young children as they freely organize their own behavior, and its consequences in a complex, partly unpredictable and highly dynamic environment. The proposed methodology integrates synchronized high-density active scalp electroencephalography (EEG), inertial measurement units (IMUs), video recording and behavioral analysis to capture brain activity and movement non-invasively in freely-behaving infants. This setup allows for the study of neural network dynamics in the developing brain, in action and context, as these networks are recruited during goal-oriented, exploration and social interaction tasks.     

Comparison of three common DNA concentration measurement methods

Accurate measurement of DNA concentration is important for DNA-based biological applications. DNA concentration is usually determined by the ultraviolet (UV) absorption, fluorescence staining, and diphenylamine reaction methods. However, the best method for quality assurance of measurements is unknown. Here, we comprehensively compared these methods using different types of samples. We found that all three methods accurately determined the concentrations of high-purity DNA solutions. After digestion of DNA samples, concentration measurements revealed that the PicoGreen dye method was very sensitive to the degradation of DNA. The three methods displayed different anti-jamming ability when contaminants such as transfer RNA (tRNA), protein, and organic chemicals were included in DNA solutions. The diphenylamine reaction method gave the highest accuracy, with an average error of approximately 10% between measured and true values. The PicoGreen dye method was influenced by tRNA and protein, and the UV absorption method was susceptible to all kinds of impurities. Overall, the diphenylamine reaction method gave the most accurate results when DNA was mixed with contaminants, the PicoGreen dye method was most suitable for degraded DNA samples or DNA extracted from processed products, and the UV absorbance method was best for evaluating the impurities in DNA solutions.     

Determination of aqueous two-phase system phase-forming components in the presence of bovine serum albumin

In the current work, the quantification of different poly(ethylene glycol) (PEG)–potassium phosphate/sodium citrate aqueous two-phase system (ATPS) phase-forming components was investigated by using conductivity and refractive index measurements. For this purpose, refractive index and conductivity calibration curves were obtained for ATPS at different pH values in the presence of different bovine serum albumin (BSA) concentrations. Whereas BSA had no effect on the conductivity, it had a considerable effect on the refractive index. Finally, a convenient dilution of the samples prior to the ATPS constituent determination is needed to ensure no significant influence from BSA.