Combinatorial peptidomics: a generic approach for protein expression profiling

Traditional approaches to protein profiling were built around the concept of investigating one protein at a time and have long since reached their limits of throughput. Here we present a completely new approach for comprehensive compositional analysis of complex protein mixtures, capable of overcoming the deficiencies of current proteomics techniques. The Combinatorial methodology utilises the peptidomics approach, in which protein samples are proteolytically digested using one or a combination of proteases prior to any assay being carried out. The second fundamental principle is the combinatorial depletion of the crude protein digest (i.e. of the peptide pool) by chemical crosslinking through amino acid side chains. Our approach relies on the chemical reactivities of the amino acids and therefore the amino acid content of the peptides (i.e. their information content) rather than their physical properties. Combinatorial peptidomics does not use affinity reagents and relies on neither chromatography nor electrophoretic separation techniques. It is the first generic methodology applicable to protein expression profiling, that is independent of the physical properties of proteins and does not require any prior knowledge of the proteins. Alternatively, a specific combinatorial strategy may be designed to analyse a particular known protein on the basis of that protein sequence alone or, in the absence of reliable protein sequence, even the predicted amino acid translation of an EST sequence. Combinatorial peptidomics is especially suitable for use with high throughput micro- and nano-fluidic platforms capable of running multiple depletion reactions in a single disposable chip

Digitally enabled aged care and neurological rehabilitation to enhance outcomes with Activity and MObility UsiNg Technology (AMOUNT) in Australia: A randomised controlled trial

Background: Digitally enabled rehabilitation may lead to better outcomes but has not been tested in large pragmatic trials. We aimed to evaluate a tailored prescription of affordable digital devices in addition to usual care for people with mobility limitations admitted to aged care and neurological rehabilitation. Methods and findings: We conducted a pragmatic, outcome-assessor-blinded, parallel-group randomised trial in 3 Australian hospitals in Sydney and Adelaide recruiting adults 18 to 101 years old with mobility limitations undertaking aged care and neurological inpatient rehabilitation. Both the intervention and control groups received usual multidisciplinary inpatient and post-hospital rehabilitation care as determined by the treating rehabilitation clinicians. In addition to usual care, the intervention group used devices to target mobility and physical activity problems, individually prescribed by a physiotherapist according to an intervention protocol, including virtual reality video games, activity monitors, and handheld computer devices for 6 months in hospital and at home. Co-primary outcomes were mobility (performance-based Short Physical Performance Battery [SPPB]; continuous version; range 0 to 3; higher score indicates better mobility) and upright time as a proxy measure of physical activity (proportion of the day upright measured with activPAL) at 6 months. The dataset was analysed using intention-to-treat principles. The trial was prospectively registered with the Australian New Zealand Clinical Trials Registry (ACTRN12614000936628). Between 22 September 2014 and 10 November 2016, 300 patients (mean age 74 years, SD 14; 50% female; 54% neurological condition causing activity limitation) were randomly assigned to intervention (n = 149) or control (n = 151) using a secure online database (REDCap) to achieve allocation concealment. Six-month assessments were completed by 258 participants (129 intervention, 129 control). Intervention participants received on average 12 (SD 11) supervised inpatient sessions using 4 (SD 1) different devices and 15 (SD 5) physiotherapy contacts supporting device use after hospital discharge. Changes in mobility scores were higher in the intervention group compared to the control group from baseline (SPPB [continuous, 0–3] mean [SD]: intervention group, 1.5 [0.7]; control group, 1.5 [0.8]) to 6 months (SPPB [continuous, 0–3] mean [SD]: intervention group, 2.3 [0.6]; control group, 2.1 [0.8]; mean between-group difference 0.2 points, 95% CI 0.1 to 0.3; p = 0.006). However, there was no evidence of a difference between groups for upright time at 6 months (mean [SD] proportion of the day spent upright at 6 months: intervention group, 18.2 [9.8]; control group, 18.4 [10.2]; mean between-group difference −0.2, 95% CI −2.7 to 2.3; p = 0.87). Scores were higher in the intervention group compared to the control group across most secondary mobility outcomes, but there was no evidence of a difference between groups for most other secondary outcomes including self-reported balance confidence and quality of life. No adverse events were reported in the intervention group. Thirteen participants died while in the trial (intervention group: 9; control group: 4) due to unrelated causes, and there was no evidence of a difference between groups in fall rates (unadjusted incidence rate ratio 1.19, 95% CI 0.78 to 1.83; p = 0.43). Study limitations include 15%–19% loss to follow-up at 6 months on the co-primary outcomes, as anticipated; the number of secondary outcome measures in our trial, which may increase the risk of a type I error; and potential low statistical power to demonstrate significant between-group differences on important secondary patient-reported outcomes. Conclusions: In this study, we observed improved mobility in people with a wide range of health conditions making use of digitally enabled rehabilitation, whereas time spent upright was not impacted. Trial registration: The trial was prospectively registered with the Australian New Zealand Clinical Trials Register; ACTRN1261400093662

Fludarabine modulates composition and function of the T cell pool in patients with chronic lymphocytic leukaemia

The combination of cytotoxic treatment with strategies for immune activation represents an attractive strategy for tumour therapy. Following reduction of high tumour burden by effective cytotoxic agents, two major immune-stimulating approaches are being pursued. First, innate immunity can be activated by monoclonal antibodies triggering antibody-dependent cellular cytotoxicity. Second, tumour-specific T cell responses can be generated by immunization of patients with peptides derived from tumour antigens and infused in soluble form or loaded onto dendritic cells. The choice of cytotoxic agents for such combinatory regimens is crucial since most substances such as fludarabine are considered immunosuppressive while others such as cyclophosphamide can have immunostimulatory activity. We tested in this study whether fludarabine and/or cyclophosphamide, which represent a very effective treatment regimen for chronic lymphocytic leukaemia, would interfere with a therapeutic strategy of T cell activation. Analysis of peripheral blood samples from patients prior and during fludarabine/cyclophosphamide therapy revealed rapid and sustained reduction of tumour cells but also of CD4+ and CD8+ T cells. This correlated with a significant cytotoxic activity of fludarabine/cyclophosphamide on T cells in vitro. Unexpectedly, T cells surviving fludarabine/cyclophosphamide treatment in vitro had a more mature phenotype, while fludarabine-treated T cells were significantly more responsive to mitogenic stimulation than their untreated counterparts and showed a shift towards TH1 cytokine secretion. In conclusion, fludarabine/cyclophosphamide therapy though inducing significant and relevant T cell depletion seems to generate a micromilieu suitable for subsequent T cell activation

Australia's relations with Iran and the Australia-US Alliance, 1979-2005

Australia has been a close ally of the US for over five decades. Strategic alignment with Washington has been, and remains, a central tenet of Australian strategic thinking and the US alliance continues to serve as an ideational framework for the formulation of Australian foreign policy. In contrast, Australia's relations with Iran since the 1979 Iranian Revolution have been at the lower end of the scale of importance, and based principally upon a trade relationship that has been dominated by the export of Australian agricultural commodities. Considered together, these two very different international relationships present an interesting problem, on two levels, for the study of Australian foreign policy. First, the extreme animosity between Washington and Tehran highlights a particular problem for Australian foreign policy-how to manage a potential clash of interests with a superpower ally. Second, the Australia-Iran relationship has been dominated by trade interests, while Canberra's interests in supporting the US alliance are predominantly strategic. Thus, the foreign policy challenges that have at times arisen because of Australia's relations with Iran in the context of the US alliance reflect the problem of balancing trade and strategic interests in Australian foreign policy. For most of the period between 1979 and 2005 Australia has managed these two relationships through a policy of non-linkage between strategic and international trade interests. This thesis presents an analytical framework that explains Australian policies of non-linkage in terms of the impact of domestic political dynamics on the foreign policy formulation process. The framework employs the concept of an issue area to analyse how domestic political and economic interests coalesce around specific foreign policy concerns, and demonstrates that the interaction between interests associated with strategic and international trade issue areas has determined whether Australia pursues policies of linkage or non-linkage with respect to its relations with Iran and the US. This thesis contributes to the study of Australian foreign policy by offering a framework that: 1) organises the plurality of foreign policy interests in the domestic political domain into issue areas, 2) explains the domestic political dynamics that determine the capacity of each issue area to shape the formulation of foreign policy within Cabinet. It contributes to the broader field of Foreign Policy Analysis by demonstrating that the application of issue area analysis provides new perspectives on, and insights into, the relationship between domestic politics and foreign policy

Premier Digit and Progardes Desmanthus compete effectively for applied phosphorus under mixed sward conditions

Grasses generally dominate the pastures of northern Australia. This may be associated, in part, with varietal differences in critical phosphorus (P) requirements that influence the competitive ability and persistence of the legume component. However, the effect of plant competition on shoot yield responses to soil P supply remain unquantified in tropical pasture swards. Micro-swards of Premier Digit and Progardes Desmanthus were grown, both as monocultures and mixed plantings, in soil amended with five rates of P fertiliser to determine the influence of sward conditions on shoot yield and tissue P. The shoot yield and tissue P concentrations of both species increased in response to soil P supply, with the shoot yield of Progardes Desmanthus in mixed plantings representing between 33–47% of the total yield of Digit and Desmanthus combined. The critical external P requirements of Progardes Desmanthus were generally equal to or lower than that of Premier Digit, yet both species competed effectively for applied P. Therefore, Premier Digit and Progardes Desmanthus may be suitable companion pasture species for establishment in the low-P soils of northern Australia