Direct processing of clinically relevant large volume samples for the detection of sexually transmitted infectious agents from urine on a microfluidic device

Urine is a preferred specimen for nucleic acid-based detection of sexually transmitted infections (STIs) but represents a challenge for microfluidic devices due to low analyte concentrations. We present an extraction methodology enabling rapid on-chip nucleic acid purification directly from clinically relevant sample volumes up to 1 ml and subsequent PCR amplification detection.

Orphan DNA: Indigenous samples, ethical biovalue and postcolonial science in Australia

Thousands of blood samples taken from Australia’s indigenous people lie in institutional freezers of the global North, the legacy of a half-century of scientific research. Since those collections were assembled, standards of ethical research practice have changed dramatically, leaving some samples in a state of dormancy. While some European and American collections are still actively used for genetic research, this practice is viewed as unethical by most Australian genetic researchers, who have closer relationships with indigenous Australians and postcolonial politics. For collections to be used ethically, they require a ‘guardian’ who has an ongoing and documented relationship with the donors, so that consent to further studies on samples can be negotiated. This affective and bureaucratic network generates ‘ethical biovalue’ such that a research project can satisfy Australian ethical review. I propose in this article that without ethical biovalue, collections become ‘orphan’ DNA, divorced from a guardian and often difficult to trace to their sources. Such samples are both orphaned and functionally sterile, unable to produce data, scientific articles, knowledge or prestige. This article draws on an ethnographic study of genetic researchers who are working in indigenous communities across Australia. I present tales of researchers’ efforts to generate ethical biovalue and their fears for succession; fears that extend to threats to destroy samples rather than see them orphaned, or worse, fall into the wrong hands. Within these material and affective  networks, indigenous DNA morphs from biological sample to sacred object to political time bomb. 

Reliability of the pictorial scale of perceived movement skill competence in 2 diverse samples of young children

The purpose was to determine the reliability of an instrument designed to assess young children's perceived movement skill competence in two diverse samples.

International study to evaluate PCR methods for detection of Trypanosoma cruzi DNA in blood samples from Chagas disease patients.

A century after its discovery, Chagas disease still represents a major neglected tropical threat. Accurate diagnostics tools as well as surrogate markers of parasitological response to treatment are research priorities in the field. The purpose of this study was to evaluate the performance of PCR methods in detection of Trypanosoma cruzi DNA by an external quality evaluation.

IPA: Integrated predictive gene signature from gene expression based breast cancer patient samples

Background: Novel predictive markers are needed to accurately diagnose the breast cancer patients so they do not need to undergo any unnecessary aggressive therapies. Various gene expression studies based predictive gene signatureshave generated in the recent past to predict the binary estrogen-receptor subclass or to predict the therapy response subclass. However, the existing algorithms comes with many limitations, including low predictive performances over multiple cohorts of patients and non-significant or limited biological roles associated with thepredictive gene signatures. Therefore, the aim of this study is to develop novel predictive markers with improved performances.Methods: We propose a novel prediction algorithm called IPA to construct a predictive gene signature for performing multiple prediction tasks of predicting estrogen-receptor based binary subclass and predicting chemotherapy response (neoadjuvantly) based binary subclass. The constructed gene signature with considering multiple classification techniques was used to evaluate the algorithm performance on multiple cohorts of breast cancer patients.Results: The evaluation on multiple validation cohorts demonstrated that proposed algorithm achieved stable and high performance to perform prediction tasks, with consideration given to any classification techniques. We show that the predictive gene signature of our proposed algorithm reflects the mechanisms underlying the estrogen-receptors or response to therapy with significant greater biological interpretations, compared with the other existing algorithm.

DryLab® optimised two-dimensional high performance liquid chromatography for differentiation of ephedrine and pseudoephedrine based methamphetamine samples

In-silico optimised two-dimensional high performance liquid chromatographic (2D-HPLC) separations of a model methamphetamine seizure sample are described, where an excellent match between simulated and real separations was observed. Targeted separation of model compounds was completed with significantly reduced method development time. This separation was completed in the heart-cutting mode of 2D-HPLC where C18 columns were used in both dimensions taking advantage of the selectivity difference of methanol and acetonitrile as the mobile phases. This method development protocol is most significant when optimising the separation of chemically similar chemical compounds as it eliminates potentially hours of trial and error injections to identify the optimised experimental conditions. After only four screening injections the gradient profile for both 2D-HPLC dimensions could be optimised via simulations, ensuring the baseline resolution of diastereomers (ephedrine and pseudoephedrine) in 9.7 min. Depending on which diastereomer is present the potential synthetic pathway can be categorized.

A Cross-Cultural Evaluation of the Personal Wellbeing Index – School Children in Samples of Australian and Portuguese Adolescents

The practice of comparing nations on subjective wellbeing (SWB) is becoming commonplace, with many countries ranked by economists and social scientists alike according to average levels of SWB based on survey responses. Such large, multi-national population surveys have the potential to generate insights into the causes and correlates of SWB within different cultural groups, as well as inform policy regarding how to improve the wellbeing of citizens. At the heart of these large-scale research endeavors are SWB measures that function equivalently between the various participating cultural groups. For this reason, it is concerning that their remains a paucity of research that supports measurement equivalence for many SWB instruments commonly employed. Thus, it remains unclear whether variations in SWB across cultures reflect true differences, or whether these differences reflect measurement biases (e.g., response bias inherent within a particular cultural group). The aim of this study was to examine the psychometric equivalence of the Personal Wellbeing Index–School Children (PWI-SC) in convenience samples of Australian and Portuguese adolescents using multiple-group confirmatory factor analysis. Participants comprising the Australian sample were 1104 Victorian high-school students aged between 12 and 19 years (M = 14.42, SD = 1.63). Participants comprising the Portuguese sample were 573 high-school students living in Portugal aged between 12 and 18 years (M = 14.32, SD = 1.72). The results demonstrated strict factorial invariance between both versions of the PWI-SC, suggesting that this scale measures the same underlying construct in both samples. Moreover, these findings provide preliminary support for quantitative comparisons between Australian and Portuguese adolescents on the SWB variable as valid.

Dietary salt intake and discretionary salt use in two general population samples in Australia: 2011 and 2014

The limited Australian measures to reduce population sodium intake through national initiatives targeting sodium in the food supply have not been evaluated. The aim was, thus, to assess if there has been a change in salt intake and discretionary salt use between 2011 and 2014 in the state of Victoria, Australia. Adults drawn from a population sample provided 24 h urine collections and reported discretionary salt use in 2011 and 2014. The final sample included 307 subjects who participated in both surveys, 291 who participated in 2011 only, and 135 subjects who participated in 2014 only. Analysis included adjustment for age, gender, metropolitan area, weekend collection and participation in both surveys, where appropriate. In 2011, 598 participants: 53% female, age 57.1(12.0)(SD) years and in 2014, 442 participants: 53% female, age 61.2(10.7) years provided valid urine collections, with no difference in the mean urinary salt excretion between 2011: 7.9 (7.6, 8.2) (95% CI) g/salt/day and 2014: 7.8 (7.5, 8.1) g/salt/day (p = 0.589), and no difference in discretionary salt use: 35% (2011) and 36% (2014) reported adding salt sometimes or often/always at the table (p = 0.76). Those that sometimes or often/always added salt at the table and when cooking had 0.7 (0.7, 0.8) g/salt/day (p = 0.0016) higher salt excretion. There is no indication over this 3-year period that national salt reduction initiatives targeting the food supply have resulted in a population reduction in salt intake. More concerted efforts are required to reduce the salt content of manufactured foods, together with a consumer education campaign targeting the use of discretionary salt.

Chemiluminescence detection of MDMA in street drug samples using tris (2,2'-bipyridine) ruthenium (III)

Tris(2,2'-bipyridine)ruthenium(II) chemiluminescence was investigated for the detection of 3,4-methylenedioxymethamphetamine (MDMA) and several related compounds in street drug samples. Optimization using flow injection analysis showed that the selectivity of the reagent can be targeted towards the detection of secondary amines by altering the pH of the reaction environment. The greater selectivity of this mode of detection, compared to UV-absorbance, reduces the probability of false positive results from interfering compounds. The detection limit for MDMA under these conditions was 0.48 μM. A HPLC method incorporating post-column tris(2,2'-bipyridine)ruthenium(II) chemiluminescence detection was applied to the determination of MDMA in five street drug samples. The results obtained were in good agreement with quantification performed using traditional UV-absorbance detection, which demonstrates the viability of this method for confirmatory analysis of drug samples. This is the first report of tris(2,2'-bipyridine)ruthenium(II) chemiluminescence for the detection of MDMA and related amphetamine derivatives.

A tandem liquid chromatography–mass spectrometry (LC–MS) method for profiling small molecules in complex samples

Liquid chromatography–mass spectrometry (LC–MS) methods using either aqueous normal phase (ANP) or reversed phase (RP) columns are routinely used in small molecule or metabolomic analyses. These stationary phases enable chromatographic fractionation of polar and non-polar compounds, respectively. The application of a single chromatographic stationary phase to a complex biological extract results in a significant proportion of compounds which elute in the non-retained fraction, where they are poorly detected because of a combination of ion suppression and the co-elution of isomeric compounds. Thus coverage of both polar and non-polar components of the metabolome generally involves multiple analyses of the same sample, increasing the analysis time and complexity. In this study we describe a novel tandem in-line LC–MS method, in which compounds from one injection are sequentially separated in a single run on both ANP and RP LC-columns. This method is simple, robust, and enables the use of independent gradients customized for both RP and ANP columns. The MS signal is acquired in a single chromatogram which reduces instrument time and operator and data analysis errors. This method has been used to analyze a range of biological extracts, from plant and animal tissues, human serum and urine, microbial cell and culture supernatants. Optimized sample preparation protocols are described for this method as well as a library containing the retention times and accurate masses of 127 compounds.