Dimeric procyanidins as modulators of airway inflammation in the context of allergic asthma : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy (PhD) in Human Physiology at Massey University, Manawatū, Palmerston North, New Zealand

Procyanidins are polyphenolic compounds that have come to be known as biologically active in the context of promoting human health. Epidemiological evidence suggests that populations that consume diets rich in procyanidins are less susceptible to inflammatory diseases. Allergic asthma is an inflammatory lung disease with an estimated 100 million affected individuals worldwide, with New Zealand having the world’s second highest rate. Inflammation at the airway epithelium and infiltration of immune cells, specifically eosinophils, into the lung tissue are two central characteristics of allergic asthma. Thymic stromal lymphopoietin (TSLP) and eotaxin isoforms, eotaxin-1 (CCL11) and eotaxin-3 (CCL26), are three biomarkers of airway inflammation produced by the epithelium. Cell culture models were successfully optimized for CCL11 and CCL26 production in A549 cells. Investigation of procyanidins effect on epithelial TSLP production was not possible because TSLP production in A549 cells was undetectable. Data suggests that dimeric A-type linked procyanidin A2, but not B-type linked procyanidin B1 or B2, is capable of inhibiting IL-4-induced CCL11 production when incubated on A549 cells prior to an inflammatory insult. Co-incubation of A549 cells with procyanidin A2 and procyanidin B2 demonstrated no evidence of a synergistic relationship for inhibiting cytokine- induced CCL11 production. Similarly, A549 cells exposed to procyanidin A2, and to a lesser extent procyanidin B2, had reduced production of cytokine-induced CCL26 production. An inhibition time course demonstrated procyanidin A2 had greatest inhibition efficacy on cytokine-induced CCL26 production when incubated for 2 h prior to an inflammatory insult. Comparison of procyanidin A2 inhibition to the known CCL26 inhibitor, IFN , demonstrated that procyanidin A2 and IFN did not share the same temporal inhibition patterns. Furthermore, experiments investigating concomitant incubation of procyanidin A2 and IFN demonstrated that procyanidin A2 could interfere with IFN –mediated CCL26 inhibition. Two possible mechanisms responsible for the procyanidin A–mediated inhibition of cytokine-induced CCL11 and CCL26 were investigated: the modulation of cytokine receptor expression, and modulation of plasma membrane fluidity. However, there was no evidence to support either of these modes of action. The data presented in this thesis collectively demonstrate the ability of procyanidin A2 to inhibit cytokine-induced eotaxin production from the lung epithelium in vitro and support further investigation of procyanidin A2 as a preventative approach for managing airway inflammation

MapSplice: Accurate Mapping of RNA-Seq Reads for Splice Junction Discovery

The accurate mapping of reads that span splice junctions is a critical component of all analytic techniques that work with RNA-seq data. We introduce a second generation splice detection algorithm, MapSplice, whose focus is high sensitivity and specificity in the detection of splices as well as CPU and memory efficiency. MapSplice can be applied to both short (\u3c75 bp) and long reads (≥75 bp). MapSplice is not dependent on splice site features or intron length, consequently it can detect novel canonical as well as non-canonical splices. MapSplice leverages the quality and diversity of read alignments of a given splice to increase accuracy. We demonstrate that MapSplice achieves higher sensitivity and specificity than TopHat and SpliceMap on a set of simulated RNA-seq data. Experimental studies also support the accuracy of the algorithm. Splice junctions derived from eight breast cancer RNA-seq datasets recapitulated the extensiveness of alternative splicing on a global level as well as the differences between molecular subtypes of breast cancer. These combined results indicate that MapSplice is a highly accurate algorithm for the alignment of RNA-seq reads to splice junctions. Software download URL: http://www.netlab.uky.edu/p/bioinfo/MapSplice

Maximizing oyster-reef growth supports green infrastructure with accelerating sea-level rise

Within intertidal communities, aerial exposure (emergence during the tidal cycle) generates strong vertical zonation patterns with distinct growth boundaries regulated by physiological and external stressors. Forecasted accelerations in sea-level rise (SLR) will shift the position of these critical boundaries in ways we cannot yet fully predict, but landward migration will be impaired by coastal development, amplifying the importance of foundation species’ ability to maintain their position relative to rising sea levels via vertical growth. Here we show the effects of emergence on vertical oyster-reef growth by determining the conditions at which intertidal reefs thrive and the sharp boundaries where reefs fail, which shift with changes in sea level. We found that oyster reef growth is unimodal relative to emergence, with greatest growth rates occurring between 20–40% exposure, and zero-growth boundaries at 10% and 55% exposures. Notably, along the lower growth boundary (10%), increased rates of SLR would outpace reef accretion, thereby reducing the depth range of substrate suitable for reef maintenance and formation, and exacerbating habitat loss along developed shorelines. Our results identify where, within intertidal areas, constructed or natural oyster reefs will persist and function best as green infrastructure to enhance coastal resiliency under conditions of accelerating SLR

tAnGo: a randomised phase III trial of gemcitabine in paclitaxel-containing, epirubicin/cyclophosphamide-based, adjuvant chemotherapy for early breast cancer: a prospective pulmonary, cardiac and hepatic function evaluation

tAnGo is a large randomised trial assessing the addition of gemcitabine(G) to paclitaxel(T), following epirubicin(E) and cyclophosphamide(C) in women with invasive higher risk early breast cancer. To assess the safety and tolerability of adding G, a detailed safety substudy was undertaken. A total of 135 patients had cardiac, pulmonary and hepatic function assessed at (i) randomisation, (ii) mid-chemotherapy, (iii) immediately post-chemotherapy and (iv) 6 months post-chemotherapy. Skin toxicity was assessed during radiotherapy. No differences were detected in FEV1 or FVC levels between treatment arms or time points. Diffusion capacity (TLCO) reduced during treatment (P<0.0001), with a significantly lower drop in EC-GT patients (P=0.02). Most of the reduction occurred during EC and recovered by 6-months post treatment. There was no difference in cardiac function between treatment arms. Only 11 patients had echocardiography/MUGA results change from normal to abnormal during treatment, with only five having LVEF<50%. Transient transaminitis occurred in both treatment arms with significantly more in EC-GT patients post-chemotherapy (AST P=0.03, ALT P=0.003), although the majority was low grade. There was no correlation between transaminitis and other toxicities. Both treatment regimens reported temporary reductions in pulmonary functions and transient transaminitis levels. Despite these being greater with EC-GT, both regimens appear well tolerated

The Astropy Problem

The Astropy Project (http://astropy.org) is, in its own words, "a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages." For five years this project has been managed, written, and operated as a grassroots, self-organized, almost entirely volunteer effort while the software is used by the majority of the astronomical community. Despite this, the project has always been and remains to this day effectively unfunded. Further, contributors receive little or no formal recognition for creating and supporting what is now critical software. This paper explores the problem in detail, outlines possible solutions to correct this, and presents a few suggestions on how to address the sustainability of general purpose astronomical software

Trial outcomes and information for clinical decision-making: a comparative study of opinions of health professionals

Background: Trials are robust sources of data for clinical practice, however, trial outcomes may not reflect what is important to communicate for decision making. The study compared clinicians’ views of outcomes to include in a core outcome set for colorectal cancer (CRC) surgery, with what clinicians considered important information for clinical practice (core information). Methods: Potential outcomes/information domains were identified through systematic literature reviews, reviews of hospital information leaflets and interviews with patients. These were organized into 6 categories, and used to design a questionnaire survey that asked surgeons and nurses from a sample of CRC centers to rate the importance of each domain as an outcome or as information on a 9-point Likert scale. Respondents were re-surveyed (round 2) following group feedback (Delphi methods). Comparisons were made by calculating the difference in mean scores between the outcomes and information domains, and paired t-tests were used to explore the difference between mean scores of the 6 outcome/information categories. Results: Data sources identified 1216 outcomes/information of CRC surgery that informed a 94 item questionnaire. First round questionnaires were returned from 63/81 (78%) of centers. Clinicians rated 76/94 (84%) domains of higher importance to measure in trials than to information to communicate to patients in Round 1. This was reduced to 24/47 (51%) in Round 2. The greatest difference was evident in domains about survival, which was rated much more highly as a trial outcome than important piece of information for decision-making (mean difference 2.3, 95% CI 1.9-2.8, p<0.0001). Specific complications and quality-of-life domains were rated similarly (mean difference 0.18, 95% CI -0.1-0.4, p=0.2 and 0.2, 95% CI -0.1-0.5, p=0.2 respectively). Conclusions: Whilst clinicians want to measure key outcomes in trials, they rate these as less important to communicate in decision-making with patients. This discrepancy needs to be explored and addressed to maximize the impact of trials on clinical practice

Positional Cloning of a Type 2 Diabetes Quantitative Trait Locus; Tomosyn-2, a Negative Regulator of Insulin Secretion

We previously mapped a type 2 diabetes (T2D) locus on chromosome 16 (Chr 16) in an F2 intercross from the BTBR T (+) tf (BTBR) Lepob/ob and C57BL/6 (B6) Lepob/ob mouse strains. Introgression of BTBR Chr 16 into B6 mice resulted in a consomic mouse with reduced fasting plasma insulin and elevated glucose levels. We derived a panel of sub-congenic mice and narrowed the diabetes susceptibility locus to a 1.6 Mb region. Introgression of this 1.6 Mb fragment of the BTBR Chr 16 into lean B6 mice (B6.16BT36–38) replicated the phenotypes of the consomic mice. Pancreatic islets from the B6.16BT36–38 mice were defective in the second phase of the insulin secretion, suggesting that the 1.6 Mb region encodes a regulator of insulin secretion. Within this region, syntaxin-binding protein 5-like (Stxbp5l) or tomosyn-2 was the only gene with an expression difference and a non-synonymous coding single nucleotide polymorphism (SNP) between the B6 and BTBR alleles. Overexpression of the b-tomosyn-2 isoform in the pancreatic β-cell line, INS1 (832/13), resulted in an inhibition of insulin secretion in response to 3 mM 8-bromo cAMP at 7 mM glucose. In vitro binding experiments showed that tomosyn-2 binds recombinant syntaxin-1A and syntaxin-4, key proteins that are involved in insulin secretion via formation of the SNARE complex. The B6 form of tomosyn-2 is more susceptible to proteasomal degradation than the BTBR form, establishing a functional role for the coding SNP in tomosyn-2. We conclude that tomosyn-2 is the major gene responsible for the T2D Chr 16 quantitative trait locus (QTL) we mapped in our mouse cross. Our findings suggest that tomosyn-2 is a key negative regulator of insulin secretion

Core Outcomes for Colorectal Cancer Surgery: A Consensus Study

Background: Colorectal cancer (CRC) is a major cause of worldwide morbidity and mortality. Surgical treatment is common, and there is a great need to improve the delivery of such care. The gold standard for evaluating surgery is within well-designed randomized controlled trials (RCTs); however, the impact of RCTs is diminished by a lack of coordinated outcome measurement and reporting. A solution to these issues is to develop an agreed standard “core” set of outcomes to be measured in all trials to facilitate cross-study comparisons, meta-analysis, and minimize outcome reporting bias. This study defines a core outcome set for CRC surgery. Methods and Findings: The scope of this COS includes clinical effectiveness trials of surgical interventions for colorectal cancer. Excluded were nonsurgical oncological interventions. Potential outcomes of importance to patients and professionals were identified through systematic literature reviews and patient interviews. All outcomes were transcribed verbatim and categorized into domains by two independent researchers. This informed a questionnaire survey that asked stakeholders (patients and professionals) from United Kingdom CRC centers to rate the importance of each domain. Respondents were resurveyed following group feedback (Delphi methods). Outcomes rated as less important were discarded after each survey round according to predefined criteria, and remaining outcomes were considered at three consensus meetings; two involving international professionals and a separate one with patients. A modified nominal group technique was used to gain the final consensus. Data sources identified 1,216 outcomes of CRC surgery that informed a 91 domain questionnaire. First round questionnaires were returned from 63 out of 81 (78%) centers, including 90 professionals, and 97 out of 267 (35%) patients. Second round response rates were high for all stakeholders (>80%). Analysis of responses lead to 45 and 23 outcome domains being retained after the first and second surveys, respectively. Consensus meetings generated agreement on a 12 domain COS. This constituted five perioperative outcome domains (including anastomotic leak), four quality of life outcome domains (including fecal urgency and incontinence), and three oncological outcome domains (including long-term survival). Conclusion: This study used robust consensus methodology to develop a core outcome set for use in colorectal cancer surgical trials. It is now necessary to validate the use of this set in research practice

Urbanisation generates multiple trait syndromes for terrestrial animal taxa worldwide

Cities can host significant biological diversity. Yet, urbanisation leads to the loss of habitats, species, and functional groups. Understanding how multiple taxa respond to urbanisation globally is essential to promote and conserve biodiversity in cities. Using a dataset encompassing six terrestrial faunal taxa (amphibians, bats, bees, birds, carabid beetles and reptiles) across 379 cities on 6 continents, we show that urbanisation produces taxon-specific changes in trait composition, with traits related to reproductive strategy showing the strongest response. Our findings suggest that urbanisation results in four trait syndromes (mobile generalists, site specialists, central place foragers, and mobile specialists), with resources associated with reproduction and diet likely driving patterns in traits associated with mobility and body size. Functional diversity measures showed varied responses, leading to shifts in trait space likely driven by critical resource distribution and abundance, and taxon-specific trait syndromes. Maximising opportunities to support taxa with different urban trait syndromes should be pivotal in conservation and management programmes within and among cities. This will reduce the likelihood of biotic homogenisation and helps ensure that urban environments have the capacity to respond to future challenges. These actions are critical to reframe the role of cities in global biodiversity loss.info:eu-repo/semantics/publishedVersio