Application of label-free mass spectrometry-based proteomics to biomarker discovery

Mass spectrometry is an analytical technique which is used extensively in the fields of chemistry and physics. Developments in the field over the last two decades have permitted the analysis of a wide variety of biological molecules from a range of sources. The term proteomics relates to the study of the protein complement of a cell or organism with particular interest in the identification and quantification of these analytes. A biomarker is a characteristic that can be measured and evaluated to give an indication of normal, biological processes, or pharmacological responses to a therapeutic intervention. Bodily fluids are a rich source of potential biomarkers as they can be obtained in reasonable quantity and their extraction is generally minimally invasive. The plasma proteome, which contains many thousands of analytes spanning a dynamic range greater than 10 orders of magnitude, reflects the status of the many tissues and organs in the body serving as an ideal medium for potential biomarker discovery. The analytical challenges posed by the plasma proteome are significant. Depletion of the highly abundant proteins is usually a prerequisite of any biomarker study and no technique has the dynamic range to study all of the proteins present. Comprehensive characterisation of the plasma proteome requires significant experimental effort and cost. Use of pooled samples in biomarker studies is widespread and the majority of biomarkers, which have been identified in the discovery phase, have not passed clinical validation. A data independent, label-free quantitative approach has been evaluated for the study of depleted maternal plasma proteomes taken in the first trimester. Plasma was characterised from individual and groups of patients from three obstetric conditions using single and multi-dimensional chromatography. Potential biomarkers from each source were identified and evaluated. Multi-dimensional chromatography was used to simplify the complexity of the analytes introduced to the mass spectrometer and the benefits and limitations of the approach in terms of biomarker discovery have been demonstrated

Standardised method for reporting exercise programmes : protocol for a modified Delphi study

Introduction Exercise is integral to health across the lifespan and important for people with chronic health conditions. A systematic review of exercise trials for chronic conditions reported suboptimal descriptions of the evaluated interventions and concluded that this hinders interpretation and replication. The aim of this project is to develop a standardised method for reporting essential exercise programme details being evaluated in clinical trials. Methods and analysis A modified Delphi technique will be used to gain consensus among international exercise experts. We will use three sequential rounds of anonymous online questionnaires to refine a standardised checklist. A draft checklist of potentially relevant items was developed based on the results of a systematic review of exercise systematic reviews. An international panel of experts was identified by exercise systematic review authorship, established international profile in exercise research and practice and by peer referral. In round 1, the international panel of experts will be asked to rate the importance of each draft item and provide additional suggestions for revisions or new items. Consensus will be considered reached if at least 70% of the panel strongly agree/disagree that an item should be included or excluded. Where agreement is not reached or there are suggestions for altered or new items, these will be taken to round 2 together with an aggregated summary of round 1 responses. Following the second round, a ranking of item importance will be made to rationalise the number of items. The final template will be distributed to panel members for approval. Ethics and dissemination Ethics approval was received from The Cabrini Institute Ethics Committee, Melbourne, Australia (HREC 02-07-04-14). We plan to use a stepwise process to develop and refine a standardised and internationally agreed template for explicit reporting of exercise programmes. The template will be generalisable across all types of exercise interventions. The findings will be disseminated through peer-reviewed publications and conference presentations

Exercise and progressive supranuclear palsy : the need for explicit exercise reporting

Background Progressive Supranuclear Palsy (PSP) is the most frequent form of atypical Parkinsonism. Although there is preliminary evidence for the benefits of gait rehabilitation, balance training and oculomotor exercises in PSP, the quality of reporting of exercise therapies appears mixed. The current investigation aims to evaluate the comprehensiveness of reporting of exercise and physical activity interventions in the PSP literature. Methods Two independent reviewers used the Consensus on Exercise Reporting Template (CERT) to extract all exercise intervention data from 11 studies included in a systematic review. CERT items covered: ‘what’ (materials), ‘who’ (instructor qualifications), ‘how’ (delivery), ‘where’ (location), ‘when’, ‘how much’ (dosage), ‘tailoring’ (what, how), and ‘how well’ (fidelity) exercise delivery complied with the protocol. Each exercise item was scored ‘1’ (adequately reported) or ‘0’ (not adequately reported or unclear). The CERT score was calculated, as well as the percentage of studies that reported each CERT item. Results The CERT scores ranged from 3 to 12 out of 19. No PSP studies adequately described exercise elements that would allow exact replication of the interventions. Well-described items included exercise equipment, exercise settings, exercise therapy scheduling, frequency and duration. Poorly described items included decision rules for exercise progression, instructor qualifications, exercise adherence, motivation strategies, safety and adverse events associated with exercise therapies. Discussion The results revealed variability in the reporting of physical therapies for people living with PSP. Future exercise trials need to more comprehensively describe equipment, instructor qualifications, exercise and physical activity type, dosage, setting, individual tailoring of exercises, supervision, adherence, motivation strategies, progression decisions, safety and adverse events. Conclusion Although beneficial for people living with PSP, exercise and physical therapy interventions have been inadequately reported. It is recommended that evidence-based reporting templates be utilised to comprehensively document therapeutic exercise design, delivery and evaluation

“RIPSSL”: A New Reflective Inquiry Protocol to Lift the Lid on Students’ Significant Extra-Curricular Learning Outcomes from Study Abroad

Education abroad generally has no overarching curriculum outside the formal study component. This paper presents the Reflective Inquiry Protocol for Surfacing Significant Learning (RIPSSL), a new approach for understanding and articulating significant learning from education abroad. Tests of RIPSSL show education abroad students use it to move beyond “it was great” when considering learning from their experiences. Our findings are important for educators and students as they work to recognize and articulate the value of education abroad. RIPSSL provides a reflective educational approach to evidence learning from life experiences by surfacing students’ significant learning in their own words

Ketogenic diet improves behaviors in a maternal immune activation model of autism spectrum disorder

Prenatal factors influence autism spectrum disorder (ASD) incidence in children and can increase ASD symptoms in offspring of animal models. These may include maternal immune activation (MIA) due to viral or bacterial infection during the first trimesters. Unfortunately, regardless of ASD etiology, existing drugs are poorly effective against core symptoms. For nearly a century a ketogenic diet (KD) has been used to treat seizures, and recent insights into mechanisms of ASD and a growing recognition that immune/inflammatory conditions exacerbate ASD risk has increased interest in KD as a treatment for ASD. Here we studied the effects of KD on core ASD symptoms in offspring exposed to MIA. To produce MIA, pregnant C57Bl/6 mice were injected with the viral mimic polyinosinic-polycytidylic acid; after weaning offspring were fed KD or control diet for three weeks. Consistent with an ASD phenotype of a higher incidence in males, control diet-fed MIA male offspring were not social and exhibited high levels of repetitive self-directed behaviors; female offspring were unaffected. However, KD feeding partially or completely reversed all MIA-induced behavioral abnormalities in males; it had no effect on behavior in females. KD-induced metabolic changes of reduced blood glucose and elevated blood ketones were quantified in offspring of both sexes. Prior work from our laboratory and others demonstrate KDs improve relevant behaviors in several ASD models, and here we demonstrate clear benefits of KD in the MIA model of ASD. Together these studies suggest a broad utility for metabolic therapy in improving core ASD symptoms, and support further research to develop and apply ketogenic and/or metabolic strategies in patients with ASD

Mixed-conducting oxygen permeable ceramic membranes for the carbon dioxide reforming of methane

This is the published version. Copyright 2007 Royal Society of ChemistryDue to the high economic, environmental, and safety costs associated with pure oxygen, mixed-conducting oxygen-permeable ceramic membranes are being explored as an alternative oxygen source for hydrocarbon conversion reactors. This work reports a dramatic improvement in catalyst performance when an oxygen-permeable SrFeCo0.5Ox ceramic membrane is used in conjunction with a conventional powder Pt/ZrO2 catalyst for the CO2 reforming of CH4. Experiments comparing catalyst performance with up to 2% co-fed oxygen to catalyst performance with oxygen from the ceramic membrane demonstrated a conversion three times higher with the membrane than with any amount of co-fed oxygen. The results suggest that membrane oxygen is more beneficial for catalyst activity and stability than molecular gas-phase oxygen

Site specific genetic incorporation of azidophenylalanine in Schizosaccharomyces pombe

The diversity of protein functions is impacted in significant part by the chemical properties of the twenty amino acids, which are used as building blocks for nearly all proteins. The ability to incorporate unnatural amino acids (UAA) into proteins in a site specific manner can vastly expand the repertoire of protein functions and also allows detailed analysis of protein function. In recent years UAAs have been incorporated in a site-specific manner into proteins in a number of organisms. In nearly all cases, the amber codon is used as a sense codon, and an orthogonal tRNA/aminoacyl-tRNA synthetase (RS) pair is used to generate amber suppressing tRNAs charged with the UAA. In this work, we have developed tools to incorporate the cross-linking amino acid azido-phenylalanine (AzF) through the use of bacterial tRNATyr and a modified version of TyrRS, AzFRS, in Schizosaccharomyces pombe, which is an attractive model organism for the study of cell behavior and function. We have incorporated AzF into three different proteins. We show that the majority of AzF is modified to amino-phenyl alanine, but protein cross-linking was still observed. These studies set the stage for exploitation of this new technology for the analysis of S. pombe proteins

Self-Hypnosis for Intrapartum Pain management (SHIP) in pregnant nulliparous women: a randomised controlled trial of clinical effectiveness

Abstract Objective: (Primary): to establish the effect of antenatal group self-hypnosis for nulliparous women on intra-partum epidural use Design: Multi-method RCT Setting: Three NHS Trusts Population: Nulliparous women not planning elective caesarean, without medication for hypertension and without psychological illness. Methods: Randomisation at 28-32 weeks gestation to usual care, or to usual care plus brief self-hypnosis training (two x 90 minute groups at around 32 and 35 weeks gestation; daily audio self-hypnosis CD). Follow up at two and six weeks postnatal. Main outcome measures:- Primary: epidural analgesia Secondary: associated clinical and psychological outcomes; economic analysis. Results: 680 women were randomised. There was no statistically significant difference in epidural use: 27.9% (intervention), 30.3% (control), odds ratio (OR) 0.89 (95% confidence interval (CI): 0.64 to 1.24), or in 27 of 29 pre-specified secondary clinical and psychological outcomes. Women in the intervention group had lower actual than anticipated levels of fear and anxiety between baseline and two weeks post natal (anxiety: OR -0.72, 95% CI -1.16 to -0.28, P= 0.001); fear (OR -0.62, 95% CI -1.08 to -0.16, p = 0.009) Postnatal response rates were 67% overall at two weeks. The additional cost of the intervention per woman was £4.83 (CI -£257.93 to £267.59). Conclusions: Allocation to two third-trimester group self-hypnosis training sessions did not significantly reduce intra-partum epidural analgesia use or a range of other clinical and psychological variables. The impact of women’s anxiety and fear about childbirth needs further investigation. Trial registration: ISRCTN27575146 http://www.controlled-trials.com/ISRCTN2757514