'Nothing exists for one cause' : putting biology back into evolution

The opening phrase of the title is from Charles Darwin’s notebooks (Schweber 1977). It is a double reminder, firstly that mainstream evolutionary theory is not just about describing nature but is particularly looking for mechanisms or ‘causes’, and secondly, that there will usually be several causes affecting any particular outcome. The second part of the title is our concern at the almost universal rejection of the idea that biological mechanisms are sufficient for macroevolutionary changes, thus rejecting a cornerstone of Darwinian evolutionary theory. Our primary aim here is to consider ways of making it easier to develop and to test hypotheses about evolution. Formalizing hypotheses can help generate tests. In an absolute sense, some of the discussion by scientists about evolution is little better than the lack of reasoning used by those advocating intelligent design. Our discussion here is in a Popperian framework where science is defined by that area of study where it is possible, in principle, to find evidence against hypotheses – they are in principle falsifiable. However, with time, the boundaries of science keep expanding. In the past, some aspects of evolution were outside the current boundaries of falsifiable science, but increasingly new techniques and ideas are expanding the boundaries of science and it is appropriate to re-examine some topics. It often appears that over the last few decades there has been an increasingly strong assumption to look first (and only) for a physical cause. This decision is virtually never formally discussed, just an assumption is made that some physical factor ‘drives’ evolution. It is necessary to examine our assumptions much more carefully. What is meant by physical factors ‘driving’ evolution, or what is an ‘explosive radiation’. Our discussion focuses on two of the six mass extinctions, the fifth being events in the Late Cretaceous, and the sixth starting at least 50,000 years ago (and is ongoing). Cretaceous/Tertiary boundary; the rise of birds and mammals. We have had a long-term interest (Cooper and Penny 1997) in designing tests to help evaluate whether the processes of microevolution are sufficient to explain macroevolution. The real challenge is to formulate hypotheses in a testable way. For example the numbers of lineages of birds and mammals that survive from the Cretaceous to the present is one test. Our first estimate was 22 for birds, and current work is tending to increase this value. This still does not consider lineages that survived into the Tertiary, and then went extinct later. Our initial suggestion was probably too narrow in that it lumped four models from Penny and Phillips (2004) into one model. This reduction is too simplistic in that we need to know about survival and ecological and morphological divergences during the Late Cretaceous, and whether Crown groups of avian or mammalian orders may have existed back into the Cretaceous. More recently (Penny and Phillips 2004) we have formalized hypotheses about dinosaurs and pterosaurs, with the prediction that interactions between mammals (and groundfeeding birds) and dinosaurs would be most likely to affect the smallest dinosaurs, and similarly interactions between birds and pterosaurs would particularly affect the smaller pterosaurs. There is now evidence for both classes of interactions, with the smallest dinosaurs and pterosaurs declining first, as predicted. Thus, testable models are now possible. Mass extinction number six: human impacts. On a broad scale, there is a good correlation between time of human arrival, and increased extinctions (Hurles et al. 2003; Martin 2005; Figure 1). However, it is necessary to distinguish different time scales (Penny 2005) and on a finer scale there are still large numbers of possibilities. In Hurles et al. (2003) we mentioned habitat modification (including the use of Geogenes III July 2006 31 fire), introduced plants and animals (including kiore) in addition to direct predation (the ‘overkill’ hypothesis). We need also to consider prey switching that occurs in early human societies, as evidenced by the results of Wragg (1995) on the middens of different ages on Henderson Island in the Pitcairn group. In addition, the presence of human-wary or humanadapted animals will affect the distribution in the subfossil record. A better understanding of human impacts world-wide, in conjunction with pre-scientific knowledge will make it easier to discuss the issues by removing ‘blame’. While continued spontaneous generation was accepted universally, there was the expectation that animals continued to reappear. New Zealand is one of the very best locations in the world to study many of these issues. Apart from the marine fossil record, some human impact events are extremely recent and the remains less disrupted by time.

Direct evaluation of IEC 61850-9-2 process bus network performance

This letter presents a technique to assess the overall network performance of sampled value process buses based on IEC 61850-9-2 using measurements from a single location in the network. The method is based upon the use of Ethernet cards with externally synchronized time stamping, and characteristics of the process bus protocol. The application and utility of the method is demonstrated by measuring latency introduced by Ethernet switches. Network latency can be measured from a single set of captures, rather than comparing source and destination captures. Absolute latency measures will greatly assist the design testing, commissioning and maintenance of these critical data networks.

Computational design of cyclic nitroxides as efficient redox mediators for dye-sensitized solar cells

Cyclic nitroxide radicals represent promising alternatives to the iodine-based redox mediator commonly used in dye-sensitized solar cells (DSSCs). To date DSSCs with nitroxide-based redox mediators have achieved energy conversion efficiencies of just over 5 % but efficiencies of over 15 % might be achievable, given an appropriate mediator. The efficacy of the mediator depends upon two main factors: it must reversibly undergo one-electron oxidation and it must possess an oxidation potential in a range of 0.600-0.850 V (vs. a standard hydrogen electrode (SHE) in acetonitrile at 25 °C). Herein, we have examined the effect that structural modifications have on the value of the oxidation potential of cyclic nitroxides as well as the reversibility of the oxidation process. These included alterations to the N-containing skeleton (pyrrolidine, piperidine, isoindoline, azaphenalene, etc.), as well as the introduction of different substituents (alkyl-, methoxy-, amino-, carboxy-, etc.) to the ring. Standard oxidation potentials were calculated using high-level ab initio methodology that was demonstrated to be very accurate (with a mean absolute deviation from experimental values of only 16 mV). An optimal value of 1.45 for the electrostatic scaling factor for UAKS radii in acetonitrile solution was obtained. Established trends in the values of oxidation potentials were used to guide molecular design of stable nitroxides with desired E° ox and a number of compounds were suggested for potential use as enhanced redox mediators in DSSCs. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An innovative approach to the assessment of nutrient intake in adults with type 2 diabetes : the development, trial and evaluation of a mobile phone photo/voice dietary record

Nutrition interventions in the form of both self-management education and individualised diet therapy are considered essential for the long-term management of type 2 diabetes mellitus (T2DM). The measurement of diet is essential to inform, support and evaluate nutrition interventions in the management of T2DM. Barriers inherent within health care settings and systems limit ongoing access to personnel and resources, while traditional prospective methods of assessing diet are burdensome for the individual and often result in changes in typical intake to facilitate recording. This thesis investigated the inclusion of information and communication technologies (ICT) to overcome limitations to current approaches in the nutritional management of T2DM, in particular the development, trial and evaluation of the Nutricam dietary assessment method (NuDAM) consisting of a mobile phone photo/voice application to assess nutrient intake in a free-living environment with older adults with T2DM. Study 1: Effectiveness of an automated telephone system in promoting change in dietary intake among adults with T2DM The effectiveness of an automated telephone system, Telephone-Linked Care (TLC) Diabetes, designed to deliver self-management education was evaluated in terms of promoting dietary change in adults with T2DM and sub-optimal glycaemic control. In this secondary data analysis independent of the larger randomised controlled trial, complete data was available for 95 adults (59 male; mean age(±SD)=56.8±8.1 years; mean(±SD)BMI=34.2±7.0kg/m2). The treatment effect showed a reduction in total fat of 1.4% and saturated fat of 0.9% energy intake, body weight of 0.7 kg and waist circumference of 2.0 cm. In addition, a significant increase in the nutrition self-efficacy score of 1.3 (p<0.05) was observed in the TLC group compared to the control group. The modest trends observed in this study indicate that the TLC Diabetes system does support the adoption of positive nutrition behaviours as a result of diabetes self-management education, however caution must be applied in the interpretation of results due to the inherent limitations of the dietary assessment method used. The decision to use a close-list FFQ with known bias may have influenced the accuracy of reporting dietary intake in this instance. This study provided an example of the methodological challenges experienced with measuring changes in absolute diet using a FFQ, and reaffirmed the need for novel prospective assessment methods capable of capturing natural variance in usual intakes. Study 2: The development and trial of NuDAM recording protocol The feasibility of the Nutricam mobile phone photo/voice dietary record was evaluated in 10 adults with T2DM (6 Male; age=64.7±3.8 years; BMI=33.9±7.0 kg/m2). Intake was recorded over a 3-day period using both Nutricam and a written estimated food record (EFR). Compared to the EFR, the Nutricam device was found to be acceptable among subjects, however, energy intake was under-recorded using Nutricam (-0.6±0.8 MJ/day; p<0.05). Beverages and snacks were the items most frequently not recorded using Nutricam; however forgotten meals contributed to the greatest difference in energy intake between records. In addition, the quality of dietary data recorded using Nutricam was unacceptable for just under one-third of entries. It was concluded that an additional mechanism was necessary to complement dietary information collected via Nutricam. Modifications to the method were made to allow for clarification of Nutricam entries and probing forgotten foods during a brief phone call to the subject the following morning. The revised recording protocol was evaluated in Study 4. Study 3: The development and trial of the NuDAM analysis protocol Part A explored the effect of the type of portion size estimation aid (PSEA) on the error associated with quantifying four portions of 15 single foods items contained in photographs. Seventeen dietetic students (1 male; age=24.7±9.1 years; BMI=21.1±1.9 kg/m2) estimated all food portions on two occasions: without aids and with aids (food models or reference food photographs). Overall, the use of a PSEA significantly reduced mean (±SD) group error between estimates compared to no aid (-2.5±11.5% vs. 19.0±28.8%; p<0.05). The type of PSEA (i.e. food models vs. reference food photograph) did not have a notable effect on the group estimation error (-6.7±14.9% vs. 1.4±5.9%, respectively; p=0.321). This exploratory study provided evidence that the use of aids in general, rather than the type, was more effective in reducing estimation error. Findings guided the development of the Dietary Estimation and Assessment Tool (DEAT) for use in the analysis of the Nutricam dietary record. Part B evaluated the effect of the DEAT on the error associated with the quantification of two 3-day Nutricam dietary records in a sample of 29 dietetic students (2 males; age=23.3±5.1 years; BMI=20.6±1.9 kg/m2). Subjects were randomised into two groups: Group A and Group B. For Record 1, the use of the DEAT (Group A) resulted in a smaller error compared to estimations made without the tool (Group B) (17.7±15.8%/day vs. 34.0±22.6%/day, p=0.331; respectively). In comparison, all subjects used the DEAT to estimate Record 2, with resultant error similar between Group A and B (21.2±19.2%/day vs. 25.8±13.6%/day; p=0.377 respectively). In general, the moderate estimation error associated with quantifying food items did not translate into clinically significant differences in the nutrient profile of the Nutricam dietary records, only amorphous foods were notably over-estimated in energy content without the use of the DEAT (57kJ/day vs. 274kJ/day; p<0.001). A large proportion (89.6%) of the group found the DEAT helpful when quantifying food items contained in the Nutricam dietary records. The use of the DEAT reduced quantification error, minimising any potential effect on the estimation of energy and macronutrient intake. Study 4: Evaluation of the NuDAM The accuracy and inter-rater reliability of the NuDAM to assess energy and macronutrient intake was evaluated in a sample of 10 adults (6 males; age=61.2±6.9 years; BMI=31.0±4.5 kg/m2). Intake recorded using both the NuDAM and a weighed food record (WFR) was coded by three dietitians and compared with an objective measure of total energy expenditure (TEE) obtained using the doubly labelled water technique. At the group level, energy intake (EI) was under-reported to a similar extent using both methods, with the ratio of EI:TEE was 0.76±0.20 for the NuDAM and 0.76±0.17 for the WFR. At the individual level, four subjects reported implausible levels of energy intake using the WFR method, compared to three using the NuDAM. Overall, moderate to high correlation coefficients (r=0.57-0.85) were found across energy and macronutrients except fat (r=0.24) between the two dietary measures. High agreement was observed between dietitians for estimates of energy and macronutrient derived for both the NuDAM (ICC=0.77-0.99; p<0.001) and WFR (ICC=0.82-0.99; p<0.001). All subjects preferred using the NuDAM over the WFR to record intake and were willing to use the novel method again over longer recording periods. This research program explored two novel approaches which utilised distinct technologies to aid in the nutritional management of adults with T2DM. In particular, this thesis makes a significant contribution to the evidence base surrounding the use of PhRs through the development, trial and evaluation of a novel mobile phone photo/voice dietary record. The NuDAM is an extremely promising advancement in the nutritional management of individuals with diabetes and other chronic conditions. Future applications lie in integrating the NuDAM with other technologies to facilitate practice across the remaining stages of the nutrition care process.

Negative space and positive environment : mapping opportunities for urban resilience

Cities have long held a fascination for people – as they grow and develop, there is a desire to know and understand the intricate interplay of elements that makes cities ‘live’. In part, this is a need for even greater efficiency in urban centres, yet the underlying quest is for a sustainable urban form. In order to make sense of the complex entities that we recognise cities to be, they have been compared to buildings, organisms and more recently machines. However the search for better and more elegant urban centres is hardly new, healthier and more efficient settlements were the aim of Modernism’s rational sub-division of functions, which has been translated into horizontal distribution through zoning, or vertical organisation thought highrise developments. However both of these approaches have been found to be unsustainable, as too many resources are required to maintain this kind or urbanisation and social consequences of either horizontal or vertical isolation must also be considered. From being absolute consumers of resources, of energy and of technology, cities need to change, to become sustainable in order to be more resilient and more efficient in supporting culture, society as well as economy. Our urban centres need to be re-imagined, re-conceptualised and re-defined, to match our changing society. One approach is to re-examine the compartmentalised, mono-functional approach of urban Modernism and to begin to investigate cities like ecologies, where every element supports and incorporates another, fulfilling more than just one function. This manner of seeing the city suggests a framework to guide the re-mixing of urban settlements. Beginning to understand the relationships between supporting elements and the nature of the connecting ‘web’ offers an invitation to investigate the often ignored, remnant spaces of cities. This ‘negative space’ is the residual from which space and place are carved out in the Contemporary city, providing the link between elements of urban settlement. Like all successful ecosystems, cities need to evolve and change over time in order to effectively respond to different lifestyles, development in culture and society as well as to meet environmental challenges. This paper seeks to investigate the role that negative space could have in the reorganisation of the re-mixed city. The space ‘in-between’ is analysed as an opportunity for infill development or re-development which provides to the urban settlement the variety that is a pre-requisite for ecosystem resilience. An analysis of the urban form is suggested as an empirical tool to map the opportunities already present in the urban environment and negative space is evaluated as a key element in achieving a positive development able to distribute diverse environmental and social facilities in the city.

Nangkha Nangdrik in the land of the thunder dragon

- The Kingdom of Bhutan is a country on the move - In July 2008, Bhutan transitioned from an absolute monarchy to a constitutional monarchy - The Constitution and a number of pieces of national legislation make specific reference to alternative dispute resolution. - An alternative dispute resolution Bill will come before the Bhutanese parliament in early 2012.

Concentration and oxidative potential of on-road particle emissions and their relationship with traffic composition : Relevance to exposure assessment

Particles emitted by vehicles are known to cause detrimental health effects, with their size and oxidative potential among the main factors responsible. Therefore, understanding the relationship between traffic composition and both the physical characteristics and oxidative potential of particles is critical. To contribute to the limited knowledge base in this area, we investigated this relationship in a 4.5 km road tunnel in Brisbane, Australia. On-road concentrations of ultrafine particles (<100 nm, UFPs), fine particles (PM2.5), CO, CO2 and particle associated reactive oxygen species (ROS) were measured using vehicle-based mobile sampling. UFPs were measured using a condensation particle counter and PM2.5 with a DustTrak aerosol photometer. A new profluorescent nitroxide probe, BPEAnit, was used to determine ROS levels. Comparative measurements were also performed on an above-ground road to assess the role of emission dilution on the parameters measured. The profile of UFP and PM2.5 concentration with distance through the tunnel was determined, and demonstrated relationships with both road gradient and tunnel ventilation. ROS levels in the tunnel were found to be high compared to an open road with similar traffic characteristics, which was attributed to the substantial difference in estimated emission dilution ratios on the two roadways. Principal component analysis (PCA) revealed that the levels of pollutants and ROS were generally better correlated with total traffic count, rather than the traffic composition (i.e. diesel and gasoline-powered vehicles). A possible reason for the lack of correlation with HDV, which has previously been shown to be strongly associated with UFPs especially, was the low absolute numbers encountered during the sampling. This may have made their contribution to in-tunnel pollution largely indistinguishable from the total vehicle volume. For ROS, the stronger association observed with HDV and gasoline vehicles when combined (total traffic count) compared to when considered individually may signal a role for the interaction of their emissions as a determinant of on-road ROS in this pilot study. If further validated, this should not be overlooked in studies of on- or near-road particle exposure and its potential health effects.

Evaluation of the iPhone with an acrylic sleeve versus the Scoliometer for rib hump measurement in scoliosis

Background. Vertebral rotation found in structural scoliosis contributes to trunkal asymmetry which is commonly measured with a simple Scoliometer device on a patient's thorax in the forward flexed position. The new generation of mobile 'smartphones' have an integrated accelerometer, making accurate angle measurement possible, which provides a potentially useful clinical tool for assessing rib hump deformity. This study aimed to compare rib hump angle measurements performed using a Smartphone and traditional Scoliometer on a set of plaster torsos representing the range of torsional deformities seen in clinical practice. Methods. Nine observers measured the rib hump found on eight plaster torsos moulded from scoliosis patients with both a Scoliometer and an Apple iPhone on separate occasions. Each observer repeated the measurements at least a week after the original measurements, and were blinded to previous results. Intra-observer reliability and inter-observer reliability were analysed using the method of Bland and Altman and 95% confidence intervals were calculated. The Intra-Class Correlation Coefficients (ICC) were calculated for repeated measurements of each of the eight plaster torso moulds by the nine observers. Results. Mean absolute difference between pairs of iPhone/Scoliometer measurements was 2.1 degrees, with a small (1 degrees) bias toward higher rib hump angles with the iPhone. 95% confidence intervals for intra-observer variability were +/- 1.8 degrees (Scoliometer) and +/- 3.2 degrees (iPhone). 95% confidence intervals for inter-observer variability were +/- 4.9 degrees (iPhone) and +/- 3.8 degrees (Scoliometer). The measurement errors and confidence intervals found were similar to or better than the range of previously published thoracic rib hump measurement studies. Conclusions. The iPhone is a clinically equivalent rib hump measurement tool to the Scoliometer in spinal deformity patients. The novel use of plaster torsos as rib hump models avoids the variables of patient fatigue and discomfort, inconsistent positioning and deformity progression using human subjects in a single or multiple measurement sessions.

Single-subject analysis reveals variation in knee mechanics during step landing

Introduction: Evidence concerning the alteration of knee function during landing suffers from a lack of consensus. This uncertainty can be attributed to methodological flaws, particularly in relation to the statistical analysis of variable human movement data. Aim: The aim of this study was to compare single-subject and group analysis in quantifying alterations in the magnitude and within-participant variability of knee mechanics during a step landing task. Methods: A group of healthy men (N = 12) stepped-down from a knee-high platform for 60 consecutive trials, each trial separated by a 1-minute rest. The magnitude and within-participant variability of sagittal knee stiffness and coordination of the landing leg during the immediate postimpact period were evaluated. Coordination of the knee was quantified in the sagittal plane by calculating the mean absolute relative phase of sagittal shank and thigh motion (MARP1) and between knee rotation and knee flexion (MARP2). Changes across trials were compared between both group and single-subject statistical analyses. Results: The group analysis detected significant reductions in MARP1 magnitude. However, the single-subject analyses detected changes in all dependent variables, which included increases in variability with task repetition. Between-individual variation was also present in the timing, size and direction of alterations to task repetition. Conclusion: The results have important implications for the interpretation of existing information regarding the adaptation of knee mechanics to interventions such as fatigue, footwear or landing height. It is proposed that a familiarisation session be incorporated in future experiments on a single-subject basis prior to an intervention.

The impact of temperature on years of life lost in Brisbane, Australia

Temperature is an important determinant of health. A better knowledge of how temperature affects population health is important not only to the scientific community, but also to the decision-makers who develop and implement early warning systems and intervention strategies to mitigate the health effects of extreme temperatures. The temperature–health relationship is also of growing interest as climate change is projected to shift the overall temperature distribution higher. Previous studies have examined the relative risks of temperature-related mortality, but the absolute measure of years of life lost is also useful as it combines the number of deaths with life expectancy. Here we use years of life lost to provide a novel measure of the impact of temperature on mortality in Brisbane, Australia. We also project the future temperature-related years of life lost attributable to climate change. We show that the association between temperature and years of life lost is U-shaped, with increased years of life lost for cold and hot temperatures. The temperature-related years of life lost will worsen greatly if future climate change goes beyond a 2 �C increase and without any adaptation to higher temperatures. This study highlights that public health adaptation to climate change is necessary.

Retinal and choroidal thickness in myopic anisometropia

PURPOSE: To examine the foveal retinal thickness (RT) and subfoveal choroidal thickness (ChT) between the fellow eyes of myopic anisometropes. METHODS: Twenty-two young (mean age 23 ± 5 years), healthy myopic anisometropes (≥ 1 D spherical equivalent [SEq] anisometropia) without amblyopia or strabismus were recruited. Spectral domain optical coherence tomography (SD-OCT) was used to capture images of the retina and choroid. Customised software was used to register, align and average multiple foveal OCT B-Scan images from each subject in order to enhance image quality. Two independent masked observers then manually determined the RT and ChT at the centre of the fovea from each SD-OCT image, which were then averaged. Axial length was measured using optical low coherence biometry during relaxed accommodation. RESULTS: The mean absolute SEq anisometropia was 1.74 ± 0.95 D and the mean interocular difference in axial length was 0.58 ± 0.41 mm. There was a strong correlation between SEq anisometropia and the interocular difference in axial length (r = 0.90, p < 0.001). Measures of RT and ChT were highly correlated between the two observers (r = 0.99 and 0.97 respectively) and in close agreement (mean inter-observer difference: RT 1.3 ± 2.2 µm, ChT 1.5 ± 13.7 µm). There was no significant difference in RT between the more (218 ± 18 µm) and less myopic eyes (215 ± 18 µm) (p > 0.05). However, the mean subfoveal ChT was significantly thinner in the more myopic eye (252 ± 46 µm) compared to the fellow, less myopic eye (286 ± 58 µm) (p < 0.001). There was a moderate correlation between the interocular difference in ChT and the interocular difference in axial length (r = -0.50, p < 0.01). CONCLUSIONS: Foveal RT was similar between the fellow eyes of myopic anisometropes; however, the subfoveal choroid was significantly thinner in the more myopic (longer) eye of our anisometropic cohort. The interocular difference in ChT correlated with the magnitude of axial anisometropia.

Standardising practices improves ambulatory diabetic foot management and reduces amputations : the Queensland Diabetic Foot Innovation Project, 2006 – 2009

Background Diabetic foot complications are recognised as the most common reason for diabetic related hospitalisation and lower extremity amputations. Multi-faceted strategies to reduce diabetic foot hospitalisation and amputation rates have been successful. However, most diabetic foot ulcers are managed in ambulatory settings where data availability is poor and studies limited. The project aimed to develop and evaluate strategies to improve the management of diabetic foot complications in three diverse ambulatory settings and measure the subsequent impact on ospitalisation and amputation. Methods Multifaceted strategies were implemented in 2008, including: multi-disciplinary teams, clinical pathways and training, clinical indicators, telehealth support and surveys. A retrospective audit of consecutive patient records from July 2006 – June 2007 determined baseline clinical indicators (n = 101). A clinical pathway teleform was implemented as a clinical record and clinical indicator analyser in all sites in 2008 (n = 327) and followed up in 2009 (n = 406). Results Prior to the intervention, clinical pathways were not used and multi-disciplinary teams were limited. There was an absolute improvement in treating according to risk of 15% in 2009 and surveillance of the high risk population of 34% and 19% in 2008 and 2009 respectively (p < 0.001). Improvements of 13 – 66% (p < 0.001) were recorded in 2008 for individual clinical activities to a performance > 92% in perfusion, ulcer depth, infection assessment and management, offloading and education. Hospitalisation impacts recorded reductions of up to 64% in amputation rates / 100,000 population (p < 0.001) and 24% average length of stay (p < 0.001) Conclusion These findings support the use of multi-faceted strategies in diverse ambulatory services to standardise practice, improve diabetic foot complications management and positively impact on hospitalisation outcomes. As of October 2010, these strategies had been rolled out to over 25 ambulatory sites, representing 66% of Queensland Health districts, managing 1,820 patients and 13,380 occasions of service, including 543 healed ulcer patients. It is expected that this number will rise dramatically as an incentive payment for the use of the teleform is expanded.

Knee extensor strength differences in obese and healthy-weight 10-13 year olds

The purpose of this study was to investigate if obese children have reduced knee extensor (KE) strength and to explore the relationship between adiposity and KE strength. An observational case-control study was conducted in three Australian states, recruiting obese [n=107 (51 female, 56 male)] and healthy-weight [n=132 (56 female, 76 male)] 10–13 year old children. Body mass index, body composition (dual energy X-ray absorptiometry), isokinetic/isometric peak KE torques (dynamometry) and physical activity (accelerometry) were assessed. Results revealed that compared with their healthy-weight peers, obese children had higher absolute KE torques (P≤0.005), equivocal KE torques when allometrically normalized for fat-free mass (FFM) (P≥0.448) but lower relative KE torques when allometrically normalized for body mass (P≤0.008). Adjustments for maternal education, income and accelerometry had little impact on group differences, except for isometric KE torques relative to body mass which were no longer significantly lower in obese children (P≥0.013, not significant after controlling for multiple comparisons). Percent body fat was inversely related to KE torques relative to body mass (r= -0.22 to -0.35, P≤0.002), irrespective of maternal education, income or accelerometry. In conclusion, while obese children have higher absolute KE strength and FFM, they have less functional KE strength (relative to mass) available for weight-bearing activities than healthy-weight children. The finding that FFM-normalized KE torques did not differ suggests that the intrinsic contractile properties of the KE muscles are unaffected by obesity. Future research is needed to see if deficits in KE strength relative to mass translate into functional limitations in weight-bearing activities.

Prostate cancer biomarkers and the emerging proteomic techniques used in biomarker research

Prostate cancer (CaP) is the second leading cause of cancer-related deaths in North American males and the most common newly diagnosed cancer in men world wide. Biomarkers are widely used for both early detection and prognostic tests for cancer. The current, commonly used biomarker for CaP is serum prostate specific antigen (PSA). However, the specificity of this biomarker is low as its serum level is not only increased in CaP but also in various other diseases, with age and even body mass index. Human body fluids provide an excellent resource for the discovery of biomarkers, with the advantage over tissue/biopsy samples of their ease of access, due to the less invasive nature of collection. However, their analysis presents challenges in terms of variability and validation. Blood and urine are two human body fluids commonly used for CaP research, but their proteomic analyses are limited both by the large dynamic range of protein abundance making detection of low abundance proteins difficult and in the case of urine, by the high salt concentration. To overcome these challenges, different techniques for removal of high abundance proteins and enrichment of low abundance proteins are used. Their applications and limitations are discussed in this review. A number of innovative proteomic techniques have improved detection of biomarkers. They include two dimensional differential gel electrophoresis (2D-DIGE), quantitative mass spectrometry (MS) and functional proteomic studies, i.e., investigating the association of post translational modifications (PTMs) such as phosphorylation, glycosylation and protein degradation. The recent development of quantitative MS techniques such as stable isotope labeling with amino acids in cell culture (SILAC), isobaric tags for relative and absolute quantitation (iTRAQ) and multiple reaction monitoring (MRM) have allowed proteomic researchers to quantitatively compare data from different samples. 2D-DIGE has greatly improved the statistical power of classical 2D gel analysis by introducing an internal control. This chapter aims to review novel CaP biomarkers as well as to discuss current trends in biomarker research from two angles: the source of biomarkers (particularly human body fluids such as blood and urine), and emerging proteomic approaches for biomarker research.

Identification of long intergenic region sequences involved in maize streak virus replication

The main cis-acting control regions for replication of the single-stranded DNA genome of maize streak virus (MSV) are believed to reside within an approximately 310 nt long intergenic region (LIR). However, neither the minimum LIR sequence required nor the sequence determinants of replication specificity have been determined experimentally. There are iterated sequences, or iterons, both within the conserved inverted-repeat sequences with the potential to form a stem-loop structure at the origin of virion-strand replication, and upstream of the rep gene TATA box (the rep-proximal iteron or RPI). Based on experimental analyses of similar iterons in viruses from other geminivirus genera and their proximity to known Rep-binding sites in the distantly related mastrevirus wheat dwarf virus, it has been hypothesized that the iterons may be Rep-binding and/or -recognition sequences. Here, a series of LIR deletion mutants was used to define the upper bounds of the LIR sequence required for replication. After identifying MSV strains and distinct mastreviruses with incompatible replication-specificity determinants (RSDs), LIR chimaeras were used to map the primary MSV RSD to a 67 nt sequence containing the RPI. Although the results generally support the prevailing hypothesis that MSV iterons are functional analogues of those found in other geminivirus genera, it is demonstrated that neither the inverted-repeat nor RPI sequences are absolute determinants of replication specificity. Moreover, widely divergent mastreviruses can trans-replicate one another. These results also suggest that sequences in the 67 nt region surrounding the RPI interact in a sequence-specific manner with those of the inverted repeat.