A proteomic investigation of the heat stress response of the South African abalone haliotis midae

Includes bibliographical references.The abalone Haliotis midae has been fished to near-extinction on the South African coastline, primarily to satisfy a growing international market. In order to meet demands, H. midae has been produced in South Africa by aquaculture for several decades, and the South African abalone aquaculture industry continues to expand. Internationally, abalone aquaculture has been actively affected by the outbreak of bacterial and viral diseases, which spread rapidly and lead to high abalone mortality. There is evidence that environmental stresses on abalone farms may lead to immunosuppression, and thereby increase the severity of disease outbreaks. The water temperature on abalone farms fluctuates seasonally, and increased abalone mortality has been associated with warmer water during the summer months. However, the molecular mechanisms affecting the abalone during exposure to stress remain unclear. With advances in proteomics technology, it is possible to identify and quantify the expression of several hundred proteins simultaneously. This study therefore aimed to gain insight into the H. midae stress response by using proteomic tools to identify proteins that are differentially regulated in haemocytes during exposure to acute heat stress. Identifying which biochemical pathways are involved in the abalone stress response will give some insight into the molecular mechanism by which H. midae responds to heat stress

in silico verification and parallel reaction monitoring prevalidation of potential prostate cancer biomarkers

Purpose: Targeted proteomics of potential biomarkers is often challenging. Hence, we developed an intermediate workflow to streamline potential urinary biomarkers of prostate cancer (PCa). Materials & methods: Using previously discovered potential PCa biomarkers; we selected proteotypic peptides for targeted validation. Preliminary in silico immunohistochemical and single reaction monitoring (SRM) verification was performed. Successful PTPs were then prevalidated using parallel reaction monitoring (PRM) and reconfirmed in 15 publicly available databases. Results: Stringency-based targetable potential biomarkers were shortlisted following in silico screening. PRM reveals top 12 potential biomarkers including the top ranking seven in silico verification-based biomarkers. Database reconfirmation showed differential expression between PCa and benign/normal prostatic urine samples. Conclusion: The pragmatic penultimate screening step, described herein, would immensely improve targeted proteomics validation of ..

Identification of quantitative proteomic differences between Mycobacterium tuberculosis lineages with altered virulence

Evidence currently suggests that as a species Mycobacterium tuberculosis exhibits very little genomic sequence diversity. Despite limited genetic variability, members of the M. tuberculosis complex (MTBC) have been shown to exhibit vast discrepancies in phenotypic presentation in terms of virulence, elicited immune response and transmissibility. Here, we used qualitative and quantitative mass spectrometry tools to investigate the proteomes of seven clinically-relevant mycobacterial strains four M. tuberculosis strains, M. bovis, M. bovis BCG, and M. avium that show varying degrees of pathogenicity and virulence, in an effort to rationalize the observed phenotypic differences. Following protein preparation, liquid chromatography mass spectrometry (LC MS/MS) and data capture were carried out using an LTQ Orbitrap Velos. Data analysis was carried out using a novel bioinformatics strategy, which yielded high protein coverage and was based on high confidence peptides. Through this approach, we directly identified a total of 3788 unique M. tuberculosis proteins out of a theoretical proteome of 4023 proteins and identified an average of 3290 unique proteins for each of the MTBC organisms (representing 82% of the theoretical proteomes), as well as 4250 unique M. avium proteins (80% of the theoretical proteome). Data analysis showed that all major classes of proteins are represented in every strain, but that there are significant quantitative differences between strains. Targeted selected reaction monitoring (SRM) assays were used to quantify the observed differential expression of a subset of 23 proteins identified by comparison to gene expression data as being of particular relevance to virulence. This analysis revealed differences in relative protein abundance between strains for proteins which may promote bacterial fitness in the more virulent W. Beijing strain. These differences may contribute to this strain's capacity for surviving within the host and resisting treatment, which has contributed to its rapid spread. Through this approach, we have begun to describe the proteomic portrait of a successful mycobacterial pathogen. Data are available via ProteomeXchange with identifier PXDO04165

The design and construction of a simulated linac control area (SLCA) for Radiation Therapy

Purpose Knowledge and skills needed by radiation therapists (therapeutic radiographers) in cutting edge radiation therapy are wide ranging – combining care for patients with high level technical and medical skills. In the UK pre-registration training takes place in both university and clinical departments. But increasing pressures on clinical departments means training time is limited; extending training into simulated environments has been proven to be highly effective [1] giving students more time to learn and develop, in a safe, non-clinical environment, using the same equipment, methods and discipline of the real clinic. This project aims to extend our simulation facilities to include a Linac control area, to complement students’ skills to safely and effectively ensure accurate and precise patient set-up and delivery of treatment. This paper describes the design and construction of such an area within our simulation centre. Methods Our aim was to create an SLCA with hardware and software components for patient selection, set-up, on-treatment image acquisition and registration and radiation delivery (with and without treatment interruptions). Using true-to-life components was as a high priority. The SLCA was designed around ARIA software, our Virtual Environment for RT (VERT) system, an indexed, flatbed motorised couch, a screened area to create a treatment bunker, a CCTV system, a real Linac function keypad with a specially designed MU counter/sound module, real controlled area/radiation on lighting panels and a simulated door interlock system. Results A schematic of the SLCA is shown in fig 1. All electronic components were built or assembled with documented specifications and design briefs. Screens create a ‘bunker’ so students set-up a patient in front of/using the VERT system and leave the room to the SLCA, as in a real bunker. The patient is visible all the time through the CCTV system. Patient and treatment plan can be selected on ARIA. CBCT acquisition and image registration is possible through the VERT system. The function keypad (from a decommissioned Elekta Linac) is interfaced to the MU counter and radiation-on light. MU are programmed into the counter and verified, before ‘beam-on’ is pressed, starting the MU counter, radiation-on sound (at realistic doserates) and radiation-on light. Conclusion All components have been designed and assembled; all work well as per design specification, enabling true-to-life patient set-up, patient selection and plan check, on-treatment CBCT verification and radiation-on effect with sound and light. The MU counter can be programmed with interruptions, so error scenarios can be simulated for training. The SLCA door interlock is being completed so simulated radiation cannot be initiated without a completed door interlock; and simulated radiation is interrupted when the door interlock is broken. Evaluation is on-going with clinical and university staff and UG/PG Radiation Therapy students. Ref: [1] S-J Ketterer et al. Simulated versus traditional therapeutic radiography placements: a randomized controlled trial. Radiog 2020;26:140-146. https://doi.org/10.1016/j.radi.2019.10.005 Keywords: Radiotherapy, Simulation, Lina

Computational modelling for decision-making: where, why, what, who and how

In order to deal with an increasingly complex world, we need ever more sophisticated computational models that can help us make decisions wisely and understand the potential consequences of choices. But creating a model requires far more than just raw data and technical skills: it requires a close collaboration between model commissioners, developers, users and reviewers. Good modelling requires its users and commissioners to understand more about the whole process, including the different kinds of purpose a model can have and the different technical bases. This paper offers a guide to the process of commissioning, developing and deploying models across a wide range of domains from public policy to science and engineering. It provides two checklists to help potential modellers, commissioners and users ensure they have considered the most significant factors that will determine success. We conclude there is a need to reinforce modelling as a discipline, so that misconstruction is less likely; to increase understanding of modelling in all domains, so that the misuse of models is reduced; and to bring commissioners closer to modelling, so that the results are more useful

Paedomorphic facial expressions give dogs a selective advantage

How wolves were first domesticated is unknown. One hypothesis suggests that wolves underwent a process of self-domestication by tolerating human presence and taking advantage of scavenging possibilities. The puppy-like physical and behavioural traits seen in dogs are thought to have evolved later, as a byproduct of selection against aggression. Using speed of selection from rehoming shelters as a proxy for artificial selection, we tested whether paedomorphic features give dogs a selective advantage in their current environment. Dogs who exhibited facial expressions that enhance their neonatal appearance were preferentially selected by humans. Thus, early domestication of wolves may have occurred not only as wolf populations became tamer, but also as they exploited human preferences for paedomorphic characteristics. These findings, therefore, add to our understanding of early dog domestication as a complex co-evolutionary process

A Human Lung Challenge Model to Evaluate the Safety and Immunogenicity of PPD and Live Bacillus Calmette-Guérin.

Rationale: A human model to better understand tuberculosis immunopathogenesis and facilitate vaccine development is urgently needed.Objectives: We evaluated the feasibility, safety, and immunogenicity of live bacillus Calmette-Guérin (BCG) in a lung-oriented controlled human infection model.Methods: We recruited 106 healthy South African participants with varying degrees of tuberculosis susceptibility. Live BCG, sterile PPD, and saline were bronchoscopically instilled into separate lung segments (n = 65). A control group (n = 34) underwent a single bronchoscopy without challenge. The primary outcome was safety. Cellular and antibody immune signatures were identified in BAL before and 3 days after challenge using flow cytometry, ELISA, RNA sequencing, and mass spectrometry.Measurements and Main Results: The frequency of adverse events was low (9.4%; n = 10), similar in the challenge versus control groups (P = 0.8), and all adverse events were mild and managed conservatively in an outpatient setting. The optimal PPD and BCG dose was 0.5 TU and 104 cfu, respectively, based on changes in BAL cellular profiles (P = 0.02) and antibody responses (P = 0.01) at incremental doses before versus after challenge. At 104 versus 103 cfu BCG, there was a significant increase in number of differentially expressed genes (367 vs. 3; P < 0.001) and dysregulated proteins (64 vs. 0; P < 0.001). Immune responses were highly setting specific (in vitro vs. in vivo) and compartment specific (BAL vs. blood) and localized to the challenged lung segments.Conclusions: A lung-oriented mycobacterial controlled human infection model using live BCG and PPD is feasible and safe. These data inform the study of tuberculosis immunopathogenesis and strategies for evaluation and development of tuberculosis vaccine candidates

Correction to: Microbial function and genital inflammation in young South African women at high risk of HIV infection

Correction to: Microbiome 8, 165 (2020) https://doi.org/10.1186/s40168-020-00932-

The design and construction of a simulated linac control area (SLCA) for Radiation Therapy

Purpose Knowledge and skills needed by radiation therapists (therapeutic radiographers) in cutting edge radiation therapy are wide ranging – combining care for patients with high level technical and medical skills. In the UK pre-registration training takes place in both university and clinical departments. But increasing pressures on clinical departments means training time is limited; extending training into simulated environments has been proven to be highly effective [1] giving students more time to learn and develop, in a safe, non-clinical environment, using the same equipment, methods and discipline of the real clinic. This project aims to extend our simulation facilities to include a Linac control area, to complement students’ skills to safely and effectively ensure accurate and precise patient set-up and delivery of treatment. This paper describes the design and construction of such an area within our simulation centre. Methods Our aim was to create an SLCA with hardware and software components for patient selection, set-up, on-treatment image acquisition and registration and radiation delivery (with and without treatment interruptions). Using true-to-life components was as a high priority. The SLCA was designed around ARIA software, our Virtual Environment for RT (VERT) system, an indexed, flatbed motorised couch, a screened area to create a treatment bunker, a CCTV system, a real Linac function keypad with a specially designed MU counter/sound module, real controlled area/radiation on lighting panels and a simulated door interlock system. Results A schematic of the SLCA is shown in fig 1. All electronic components were built or assembled with documented specifications and design briefs. Screens create a ‘bunker’ so students set-up a patient in front of/using the VERT system and leave the room to the SLCA, as in a real bunker. The patient is visible all the time through the CCTV system. Patient and treatment plan can be selected on ARIA. CBCT acquisition and image registration is possible through the VERT system. The function keypad (from a decommissioned Elekta Linac) is interfaced to the MU counter and radiation-on light. MU are programmed into the counter and verified, before ‘beam-on’ is pressed, starting the MU counter, radiation-on sound (at realistic doserates) and radiation-on light. Conclusion All components have been designed and assembled; all work well as per design specification, enabling true-to-life patient set-up, patient selection and plan check, on-treatment CBCT verification and radiation-on effect with sound and light. The MU counter can be programmed with interruptions, so error scenarios can be simulated for training. The SLCA door interlock is being completed so simulated radiation cannot be initiated without a completed door interlock; and simulated radiation is interrupted when the door interlock is broken. Evaluation is on-going with clinical and university staff and UG/PG Radiation Therapy students. Ref: [1] S-J Ketterer et al. Simulated versus traditional therapeutic radiography placements: a randomized controlled trial. Radiog 2020;26:140-146. https://doi.org/10.1016/j.radi.2019.10.005 Keywords: Radiotherapy, Simulation, Lina

Quantitative label-free proteomic analysis of human urine to identify novel candidate protein biomarkers for schistosomiasis

<div><p>Background</p><p>Schistosomiasis is a chronic neglected tropical disease that is characterized by continued inflammatory challenges to the exposed population and it has been established as a possible risk factor in the aetiology of bladder cancer. Improved diagnosis of schistosomiasis and its associated pathology is possible through mass spectrometry to identify biomarkers among the infected population, which will influence early detection of the disease and its subtle morbidity.</p><p>Methodology</p><p>A high-throughput proteomic approach was used to analyse human urine samples for 49 volunteers from Eggua, a schistosomiasis endemic community in South-West, Nigeria. The individuals were previously screened for <i>Schistosoma haematobium</i> and structural bladder pathologies via microscopy and ultrasonography respectively. Samples were categorised into schistosomiasis, schistosomiasis with bladder pathology, bladder pathology, and a normal healthy control group. These samples were analysed to identify potential protein biomarkers.</p><p>Results</p><p>A total of 1306 proteins and 9701 unique peptides were observed in this study (FDR = 0.01). Fifty-four human proteins were found to be potential biomarkers for schistosomiasis and bladder pathologies due to schistosomiasis by label-free quantitative comparison between groups. Thirty-six (36) parasite-derived potential biomarkers were also identified, which include some existing putative schistosomiasis biomarkers that have been previously reported. Some of these proteins include Elongation factor 1 alpha, phosphopyruvate hydratase, histone H4 and heat shock proteins (HSP 60, HSP 70).</p><p>Conclusion</p><p>These findings provide an in-depth analysis of potential schistosoma and human host protein biomarkers for diagnosis of chronic schistosomiasis caused by <i>Schistosoma haematobium</i> and its pathogenesis.</p></div