Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS)

Multiple reaction monitoring (MRM) mass spectrometry coupled with stable isotope dilution (SID) and liquid chromatography (LC) is increasingly used in biological and clinical studies for precise and reproducible quantification of peptides and proteins in complex sample matrices. Robust LC-SID-MRM-MS-based assays that can be replicated across laboratories and ultimately in clinical laboratory settings require standardized protocols to demonstrate that the analysis platforms are performing adequately. We developed a system suitability protocol (SSP), which employs a predigested mixture of six proteins, to facilitate performance evaluation of LC-SID-MRM-MS instrument platforms, configured with nanoflow-LC systems interfaced to triple quadrupole mass spectrometers. The SSP was designed for use with low multiplex analyses as well as high multiplex approaches when software-driven scheduling of data acquisition is required. Performance was assessed by monitoring of a range of chromatographic and mass spectrometric metrics including peak width, chromatographic resolution, peak capacity, and the variability in peak area and analyte retention time (RT) stability. The SSP, which was evaluated in 11 laboratories on a total of 15 different instruments, enabled early diagnoses of LC and MS anomalies that indicated suboptimal LC-MRM-MS performance. The observed range in variation of each of the metrics scrutinized serves to define the criteria for optimized LC-SID-MRM-MS platforms for routine use, with pass/fail criteria for system suitability performance measures defined as peak area coefficient of variation <0.15, peak width coefficient of variation <0.15, standard deviation of RT <0.15 min (9 s), and the RT drift <0.5min (30 s). The deleterious effect of a marginally performing LC-SID-MRM-MS system on the limit of quantification (LOQ) in targeted quantitative assays illustrates the use and need for a SSP to establish robust and reliable system performance. Use of a SSP helps to ensure that analyte quantification measurements can be replicated with good precision within and across multiple laboratories and should facilitate more widespread use of MRM-MS technology by the basic biomedical and clinical laboratory research communities.

The Smartphone App Economy and App Ecosystems

This chapter gives an overview of the smartphone app economy and its various constituent ecosystems. It examines the role of the app store model and the proliferation of mobile apps in the shift from value chains controlled by network operators and handset manufacturers, to value networks – or ecosystems – focused around operating systems and apps. It outlines some of the benefits and disadvantages for developers of the app store model for remuneration and distribution. The chapter concludes with a discussion of recent research on the size and employment effects of the app economy.

Design and flight testing of an integrated solar powered UAV and WSN for remote gas sensing

This paper describes a generic and integrated solar powered remote Unmanned Air Vehicles (UAV) and Wireless Sensor Network (WSN) gas sensing system. The system uses a generic gas sensing system for CH4 and CO2 concentrations using metal oxide (MoX) and non-dispersive infrared sensors, and a new solar cell encapsulation method to power the UASs as well as a data management platform to store, analyse and share the information with operators and external users. The system was successfully field tested at ground and low altitudes, collecting, storing and transmitting data in real time to a central node for analysis and 3D mapping. The system can be used in a wide range of outdoor applications, especially in agriculture, bushfires, mining studies, opening the way to a ubiquitous low cost environmental monitoring. A video of the bench and flight test performed can be seen in the following link https://www.youtube.com/watch?v=Bwas7stYIxQ.

Creating a Sustainability Scorecard as a predictive tool for measuring the complex social, economic and environmental impacts of industries, a case study : assessing the viability and sustainability of the dairy industry

Sustainability is a key driver for decisions in the management and future development of industries. The World Commission on Environment and Development (WCED, 1987) outlined imperatives which need to be met for environmental, economic and social sustainability. Development of strategies for measuring and improving sustainability in and across these domains, however, has been hindered by intense debate between advocates for one approach fearing that efforts by those who advocate for another could have unintended adverse impacts. Studies attempting to compare the sustainability performance of countries and industries have also found ratings of performance quite variable depending on the sustainability indices used. Quantifying and comparing the sustainability of industries across the triple bottom line of economy, environment and social impact continues to be problematic. Using the Australian dairy industry as a case study, a Sustainability Scorecard, developed as a Bayesian network model, is proposed as an adaptable tool to enable informed assessment, dialogue and negotiation of strategies at a global level as well as being suitable for developing local solutions.

Increase in prevalence of obesity and diabetes and decrease in plasma cholesterol in a central Australian Aboriginal community

Objective: To document change in prevalence of obesity, diabetes and other cardiovascular diease (CVD) risk factors, and trends in dietary macronutrient intake, over an eight-year period in a rural Aboriginal community in central Australia. Design: Sequential cross-sectional community surveys in 1987, 1991 and 1995. Subjects: All adults (15 years and over) in the community were invited to participate. In 1987, 1991 and 1995, 335 (87% of eligible adults), 331 (76%) and 304 (68%), respectively, were surveyed. Main outcome measures: Body mass index and waist : hip ratio; blood glucose level and glucose tolerance; fasting total and high density lipoprotein (HDL) cholesterol and triglyceride levels; and apparent dietary intake (estimated by the store turnover method). Intervention: A community-based nutrition awareness and healthy lifestyle program, 1988-1990. Results: At the eight-year follow-up, the odds ratios (95% CIs) for CVD risk factors relative to baseline were obesity, 1.84 (1.28-2.66); diabetes, 1.83 (1.11-3.03); hypercholesterolaemia, 0.29 (0.20-0.42); and dyslipidaemia (high triglyceride plus low HDL cholesterol level), 4.54 (2.84-7.29). In younger women (15-24 years), there was a trebling in obesity prevalence and a four- to fivefold increase in diabetes prevalence. Store turnover data suggested a relative reduction in the consumption of refined carbohydrates and saturated fats. Conclusion: Interventions targeting nutritional factors alone are unlikely to greatly alter trends towards increasing prevalences of obesity and diabetes. In communities where healthy food choices are limited, the role of regular physical activity in improving metabolic fitness may also need to be emphasised.

Review of the nutrition policy of the Arnhem Land Progress Association

The process of implementation and the effect of the nutrition policy of the Arnhem Land Progress Association (ALPA) were reviewed three years after implementation of the policy in five remote Aboriginal community retail stores in May 1990. In 1993, compliance with the policy varied among stores. Recommended foods were available regularly in most communities; however, promotional and educational components of the policy were not widely implemented. Dietary improvements were evident in those communities where stores most complied with the policy. Some aspects of the ALPA nutrition policy require modification, and renewed commitment to the policy is likely to improve further the diet in the Aboriginal communities involved. The ALPA nutrition policy is a potential model for the development of other local food and nutrition policies in remote Aboriginal communities.

DRB2 is required for microRNA biogenesis in Arabidopsis thaliana

Background The Arabidopsis thaliana (Arabidopsis) DOUBLE-STRANDED RNA BINDING (DRB) protein family consists of five members, DRB1 to DRB5. The biogenesis of two developmentally important small RNA (sRNA) species, the microRNAs (miRNAs) and trans-acting small interfering RNAs (tasiRNAs) by DICER-LIKE (DCL) endonucleases requires the assistance of DRB1 and DRB4 respectively. The importance of miRNA-directed target gene expression in plant development is exemplified by the phenotypic consequence of loss of DRB1 activity (drb1 plants). Principal Findings Here we report that the developmental phenotype of the drb235 triple mutant plant is the result of deregulated miRNA biogenesis in the shoot apical meristem (SAM) region. The expression of DRB2, DRB3 and DRB5 in wild-type seedlings is restricted to the SAM region. Small RNA sequencing of the corresponding tissue of drb235 plants revealed altered miRNA accumulation. Approximately half of the miRNAs detected remained at levels equivalent to those of wild-type plants. However, the accumulation of the remaining miRNAs was either elevated or reduced in the triple mutant. Examination of different single and multiple drb mutants revealed a clear association between the loss of DRB2 activity and altered accumulation for both the elevated and reduced miRNA classes. Furthermore, we show that the constitutive over-expression of DRB2 outside of its wild-type expression domain can compensate for the loss of DRB1 activity in drb1 plants. Conclusions/Significance Our results suggest that in the SAM region, DRB2 is both antagonistic and synergistic to the role of DRB1 in miRNA biogenesis, adding an additional layer of gene regulatory complexity in this developmentally important tissue.

Nuclear gene silencing directs reception of long-distance mRNA silencing in Arabidopsis

In plants, silencing of mRNA can be transmitted from cell to cell and also over longer distances from roots to shoots. To investigate the long-distance mechanism, WT and mutant shoots were grafted onto roots silenced for an mRNA. We show that three genes involved in a chromatin silencing pathway, NRPD1a encoding RNA polymerase IVa, RNA-dependent RNA polymerase 2 (RDR2), and DICER-like 3 (DCL3), are required for reception of long-distance mRNA silencing in the shoot. A mutant representing a fourth gene in the pathway, argonaute4 (ago4), was also partially compromised in the reception of silencing. This pathway produces 24-nt siRNAs and resulted in decapped RNA, a known substrate for amplification of dsRNA by RDR6. Activation of silencing in grafted shoots depended on RDR6, but no 24-nt siRNAs were detected in mutant rdr6 shoots, indicating that RDR6 also plays a role in initial signal perception. After amplification of decapped transcripts, DCL4 and DCL2 act hierarchically as they do in antiviral resistance to produce 21- and 22-nt siRNAs, respectively, and these guide mRNA degradation. Several dcl genotypes were also tested for their capacity to transmit the mobile silencing signal from the rootstock. dcl1-8 and a dcl2 dcl3 dcl4 triple mutant are compromised in micro-RNA and siRNA biogenesis, respectively, but were unaffected in signal transmission. © 2007 by The National Academy of Sciences of the USA.

DRB2, DRB3 and DRB5 function in a non-canonical microRNA pathway in Arabidopsis thaliana

DOUBLE-STRANDED RNA BIN DIN G (DRB) proteins have been functionally characterized in viruses, prokaryotes and eukaryotes and are involved in all aspects of RNA biology. Arabidopsis thaliana (Arabidopsis) encodes five closely related DRB proteins, DRB1 to DRB5. DRB1 and DRB4 are required by DICER-LIKE (DCL) proteins DCL1 and DCL4 to accurately and efficiently process structurally distinct double-stranded RNA (dsRNA) precursor substrates in the microRNA (miRNA) and trans-acting small-interfering RNA (tasiRNA) biogenesis pathways respectively. We recently reported that DRB2 is also involved in the biogenesis of specific miRNA subsets. Furthermore, the severity of the developmental phenotype displayed by the drb235 triple mutant plant, compared with those expressed by either drb2, drb3 and drb5 single mutants, or double mutant combinations thereof, indicates that DRB3 and DRB5 function in the same non-canonical miRNA pathway as DRB2. Through the use of our artificial miRNA (amiRNA) plant expression vector, pBlueGreen 2,3 we demonstrate here that unlike DRB2, DRB3 and DRB5 are not involved in the dsRNA processing stages of the miRNA biogenesis pathway, but are required to mediate RNA silencing of target genes of DRB2-associated miRNA s. © 2012 Landes Bioscience.

Genus Umbravirus

The practical need to partition the world of viruses into distinguishable, universally agreed upon entities is the ultimate justification for developing a virus classification system. The Author of this Book is Andrew MQ King, Elliot Lefkowitz, Eric B. Carstens, Michael J. Adams Since 1971, the International Committee on Taxonomy of Viruses (ICTV) operating on behalf of the world community of virologists has taken on the task of developing a single, universal taxonomic scheme for all viruses infecting animals (vertebrate, invertebrates, and protozoa), plants (higher plants and algae), fungi, bacteria, and archaea.

Fine tuning of elasticity via crosslinking collagen-based materials to mediate mechanotransduction and stability using corona treatment

The common goal of tissue engineering is to develop substitutes that can closely mimic the structure of extracellular matrix (ECM). However, similarly important is the intensive material properties which have often been overlooked, in particular, for soft tissues that are not to bear load assumingly. The mechanostructural properties determine not only the structural stability of biomaterials but also their physiological functionality by directing cellular activity and regulating cell fate decision. The aim here is to emphasize that cells could sense intensive material properties like elasticity and reside, proliferate, migrate and differentiate accordinglyno matter if the construct is from a natural source like cartilage, skin etc. or of synthetic one. Meanwhile, the very objective of this work is to provide a tunable scheme for manipulating the elasticity of collagen-based constructs to be used to demonstrate how to engineer cell behavior and regulate mechanotransduction. Articular cartilage was chosen as it represents one of the most complex hierarchical arrangements of collagen meshwork in both connective tissues and ECM-like biomaterials. Corona discharge treatment was used to produce constructs with varying density of crosslinked collagen and stiffness accordingly. The results demonstrated that elastic modulus increased up to 33% for samples treated up to one minute as crosslink density was found to increase with exposure time. According to the thermal analysis, longer exposure to corona increased crosslink density as the denaturation enthalpy increased. However the spectroscopy results suggested that despite the stabilization of the collagen structure the integrity of the triple helical structure remained intact. The in vitro superficial culture of heterologous chondrocytes also determined that the corona treatment can modulate migration with increased focal adhesion of cells due to enhanced stiffness, without cytotoxicity effects, and providing the basis for reinforcing three-dimensional collagen-based biomaterials in order to direct cell function and mediate mechanotransduction.

Sustainability of a successful health and nutrition program in a remote Aboriginal community

OBJECTIVE: To assess the long term effect of a nutrition program in a remote Aboriginal community (Minjilang). DESIGN: Evaluation of nutritional outcomes over the three years before and the three years after a health and nutrition program that ran from June 1989 to June 1990. Turnover of food items at the community store was used as a measure of dietary intake at Minjilang and a comparison community. SETTING: A community of about 150 Aboriginal people live at Minjilang on Croker Island, 240 km north-east of Darwin. A similar community of about 300 people on another island was used as the comparison. RESULTS: The program produced lasting improvements in dietary intake of most target foods (including fruit, vegetables and wholegrain bread) and nutrients (including folate, ascorbic acid and thiamine). Sugar intake fell in both communities before the program, but the additional decrease in sugar consumption during the program at Minjilang "rebounded" in the next year. Dietary improvements in the comparison community were delayed and smaller than at Minjilang. CONCLUSIONS: The success of the program at Minjilang was linked to an ongoing process of social change, which in turn provided a stimulus for dietary improvement in the comparison community. When Aboriginal people themselves control and maintain ownership of community-based intervention programs, nutritional improvements can be initiated and sustained.

Measuring dietary intake in remote Australian Aboriginal communities

This paper reports a comparison of the practicality, acceptability and face validity of five dietary intake methods in two remote Australian Aboriginal communities: weighed dietary intake, 24‐hour recall, ‘store‐turnover’, diet history and food frequency methods. The methods used to measure individual dietary intake were poorly accepted by the communities. Quantitative data were obtained only from the first three methods. The 24‐hour recall method tended to produce higher nutrient intakes than the weighed intake method and certain foods appeared to be selectively recalled according to perceived nutritional desirability. The ‘store‐turnover’ method was most acceptable to the communities and had less potential for bias than the other methods. It was also relatively objective, non‐intrusive, rapid, easy and inexpensive. However, food distribution patterns within the communities could not be assessed by this method. Nevertheless, other similarly isolated communities may benefit by use of the ‘store‐turnover’ method.

Survival tucker : improved diet and health indicators in an Aboriginal community

The poor nutritional status of Aboriginal Australians is a serious and complex public health concern. We describe an unusually successful health and nutrition project initiated by the people of Minjilang, which was developed, implemented and evaluated with the community. Apparent community dietary intake, assessed by the ‘store-turnover’ method, and biochemical, anthropometric and haematological indicators of health and nutritional status were measured before intervention and at three-monthly intervals during the intervention year. Following intervention, there was a significant decrease in dietary intake of sugar and saturated fat, an increase in micronutrient density, corresponding improvements in biochemical indices (for example, a 12 per cent decrease in mean serum cholesterol, increases in serum and red cell folate, serum vitamin B6 and plasma ascorbic acid), decrease in mean systolic and diastolic blood pressures, a normalisation of body mass index, and a normalisation of haematologic indices. The success of this project demonstrates that Aboriginal communities can bring about improvements in their generally poor nutritional status, and that the store-turnover method provides a valid, inexpensive and noninvasive method for evaluating the resultant changes in community diet. Although the project was undoubtedly effective in the short term, further work is in progress to assess individual strategies with respect to sustainability, cost-effectiveness and generalisability.

Apparent dietary intake in remote Aboriginal communities

Apparent per capita food and nutrient intake in six remote Australian Aboriginal communities using the ‘store-turnover’ method is described. The method is based on the analysis of community-store food invoices. The face validity of the method supports the notion that, under the unique circumstances of remote Aboriginal communities, the turnover of foodstuffs from the community store is a useful measure of apparent dietary intake for the community as a whole. In all Aboriginal communities studied, the apparent intake of energy, sugars and fat was excessive, while the apparent intake of dietary fibre and several nutrients, including folic acid, was low. White sugar, flour, bread and meat provided in excess of 50 per cent of the apparent total energy intake. Of the apparent high fat intake, fatty meats contributed nearly 40 per cent in northern coastal communities and over 60 per cent in central desert communities. Sixty per cent of the apparent high intake of sugars was derived from sugar per se in both regions. Compared with national Australian apparent consumption data, intakes of sugar, white flour and sweetened carbonated beverages were much higher in Aboriginal communities, and intakes of wholemeal bread, fruit and vegetables were much lower. Results of the store-turnover method have important implications for community-based nutrition intervention programs.