Modifications at the C-Terminus To Improve Pyrrole−Imidazole Polyamide Activity in Cell Culture

Pyrrole−imidazole (Py-Im) hairpin polyamides are a class of small molecule DNA minor groove binding compounds that have been shown to modulate endogenous gene expression in cell culture. Gene regulation by polyamides requires efficient cellular uptake and nuclear localization properties for candidate compounds. To further optimize Py-Im polyamides for enhanced potency in cell culture, a focused library of polyamides possessing various modifications at the C-terminus was synthesized and tested. Comparison of polyamide biological activity in two cell lines revealed tolerance for structural modifications and agreement in activity trends between cell lines. The use of an oxime linkage between the polyamide and an aromatic functionality on the C-terminus resulted in a ~20-fold increase in the potency of polyamides targeted to the androgen response element (ARE) in LNCaP cells by measuring AR-activated PSA expression

Modulating hypoxia-inducible transcription by disrupting the HIF-1-DNA interface

Transcription mediated by hypoxia-inducible factor (HIF-1) contributes to tumor angiogenesis and metastasis but is also involved in activation of cell-death pathways and normal physiological processes. Given the complexity of HIF-1 signaling, it could be advantageous to target a subset of HIF-1 effectors rather than the entire pathway. We compare the genome-wide effects of three molecules that each interfere with the HIF-1–DNA interaction: a polyamide targeted to the hypoxia response element, small interfering RNA targeted to HIF-1α, and echinomycin, a DNA-binding natural product with a similar but less specific sequence preference than the polyamide. The polyamide affects a subset of hypoxia-induced genes consistent with its binding site preferences. For comparison, HIF-1α siRNA and echinomycin each affect the expression of nearly every gene induced by hypoxia. Remarkably, the total number of genes affected by either polyamide or HIF-1α siRNA over a range of thresholds is comparable. The data show that polyamides can be used to affect a subset of a pathway regulated by a transcription factor. In addition, this study offers a unique comparison of three complementary approaches towards exogenous control of endogenous gene expression

Non-invasive Cognitive Enhancement in Epilepsy

Epilepsy patients frequently experience cognitive difficulties, particularly in the domains of memory, attention, and executive function. Despite the frequency of these difficulties among epilepsy patients, current strategies to treat cognitive dysfunction are limited. We performed a systematic review of controlled trials of non-invasive cognitive enhancement in epilepsy. We identified studies examining the efficacy of pharmacological agents, namely the acetylcholinesterase inhibitors donepezil and galantamine, the NMDA non-competitive antagonist memantine, and the stimulant methylphenidate, as well as non-invasive non-pharmacological transcranial magnetic stimulation (TMS) and transcranial direct current stimulation (tDCS). We highlight the data currently available and the limitations of the current literature

Improved nuclear localization of DNA-binding polyamides

Regulation of endogenous genes by DNA-binding polyamides requires effective nuclear localization. Previous work employing confocal microscopy to study uptake of fluorophore-labeled polyamides has demonstrated the difficulty of predicting a priori the nuclear uptake of a given polyamide. The data suggest that dye identity influences uptake sufficiently such that a dye-conjugate cannot be used as a proxy for unlabeled analogs. Polyamides capable of nuclear localization unaided by fluorescent dyes are desirable due to size and other limitations of fluorophores. Recently, a polyamide-fluorescein conjugate targeted to the hypoxia response element (HRE) was found to inhibit vascular endothelial growth factor (VEGF) expression in cultured HeLa cells. The current study uses inhibition of VEGF expression as a biological read-out for effective nuclear localization of HRE-targeted polyamides. We synthesized a focused library of non-fluorescent, HRE-targeted polyamides in which the C-terminus ‘tail’ has been systematically varied. Members of this library bind the HRE with affinities comparable or superior to that of the fluorescein-labeled analog. Although most library members demonstrate modest or no biological activity, two non-fluorescent polyamides are reported with activity rivaling that of the previously reported fluorescein-labeled polyamide. We also show evidence that promoter occupancy by HIF-1, the transcription factor that binds the HRE, is inhibited by HRE-targeted polyamides

Modulating hypoxia-inducible transcription by disrupting the HIF-1-DNA interface

Transcription mediated by hypoxia-inducible factor (HIF-1) contributes to tumor angiogenesis and metastasis but is also involved in activation of cell-death pathways and normal physiological processes. Given the complexity of HIF-1 signaling, it could be advantageous to target a subset of HIF-1 effectors rather than the entire pathway. We compare the genome-wide effects of three molecules that each interfere with the HIF-1–DNA interaction: a polyamide targeted to the hypoxia response element, small interfering RNA targeted to HIF-1α, and echinomycin, a DNA-binding natural product with a similar but less specific sequence preference than the polyamide. The polyamide affects a subset of hypoxia-induced genes consistent with its binding site preferences. For comparison, HIF-1α siRNA and echinomycin each affect the expression of nearly every gene induced by hypoxia. Remarkably, the total number of genes affected by either polyamide or HIF-1α siRNA over a range of thresholds is comparable. The data show that polyamides can be used to affect a subset of a pathway regulated by a transcription factor. In addition, this study offers a unique comparison of three complementary approaches towards exogenous control of endogenous gene expression

Moderators of Wellbeing Interventions:Why Do Some People Respond More Positively Than Others?

Interventions rarely have a universal effect on all individuals. Reasons ranging from participant characteristics, context and fidelity of intervention completion could cause some people to respond more positively than others. Understanding these individual differences in intervention response may provide clues to the mechanisms behind the intervention, as well as inform future designs to make interventions maximally beneficial for all. Here we focus on an intervention designed to improve adolescent wellbeing, and explore potential moderators using a representative and well-powered sample. 16-year old participants (N = 932) in the Twins Wellbeing Intervention Study logged online once a week to complete control and wellbeing-enhancing activities consecutively. Throughout the study participants also provided information about a range of potential moderators of intervention response including demographics, seasonality, personality, baseline characteristics, activity fit, and effort. As expected, some individuals gained more from the intervention than others; we used multi-level modelling to test for moderation effects that could explain these individual differences. Of the 15 moderators tested, none significantly explained individual differences in intervention response in the intervention and follow-up phases. Self-reported effort and baseline positive affect had a notable effect in moderating response in the control phase, during which there was no overall improvement in wellbeing and mental health. Our results did not replicate the moderation effects that have been suggested by previous literature and future work needs to reconcile these differences. They also show that factors that have previously been shown to influence baseline wellbeing do not also influence an individual's ability to benefit from a wellbeing intervention. Although future research should continue to explore potential moderators of intervention efficacy, our results suggest that the beneficial effect of positive activities in adolescents were universal across such factors as sex and socioeconomic status, bolstering claims of the scalability of positive activities to increase adolescent wellbeing

Identifying Trends in Masterplanning: A Typological Classification System

This document is the Accepted Manuscript version of the following article: Robert Adam, and Claire Jamieson, ‘Identifying trends in masterplanning: A typological classification system’, URBAN DESIGN International, Vol. 19 (4): 274-290, December 2014. The final publication is available at Springer via https://doi.org/10.1057/udi.2013.24.This article reports research carried out to develop a new typological method for the analysis of masterplans. This quantitative method of analysis can be used to produce comparative data that will help in the comparison of urban design typologies and their development over time. This article sets out the research to date, describing how the initial aims have developed from simple analysis to the creation of an analytical tool with wide applications. Comprising a detailed taxonomy of urban design features gathered from a wide database of recent and emerging masterplans, the system provides opportunities for further study such as trends, qualitative comparison against quantitative measurement, and comparison of aims and outcomes. This article will describe the methodology and process of research, while elaborating on the potential of the tool.Peer reviewedFinal Accepted Versio

Internet-based randomised controlled trials for the evaluation of complementary and alternative medicines: probiotics in spondyloarthropathy

<b>Background</b> The clinical effectiveness of complementary and alternative medicines (CAMs) is widely debated because of a lack of clinical trials. The internet may provide an effective and economical approach for undertaking randomised controlled trials (RCTs) of low-risk interventions. We investigated whether the internet could be used to perform an internet-based RCT of a CAM fulfilling the revised CONSORT (Consolidated Standards of Reporting Trials) statement quality checklist for reporting of RCTs. A secondary aim was to examine the effect of probiotics compared to placebo in terms of well-being over 12 weeks.<p></p> <b>Methods</b> People aged ≥18 years with confirmed spondyloarthropathy living in the United Kingdom with internet access were invited to participate in an internet-based RCT of probiotic compared to placebo for improving well-being and bowel symptoms. The intervention was a probiotic containing 4 strains of live bacteria or identical placebo taken by mouth daily for 3 months. The primary outcome measure was the performance of the trial according to the revised CONSORT statement.<p></p> <b>Results</b> 147 people were randomised into the trial. The internet-based trial of the CAM fulfilled the revised CONSORT statement such as efficient blinding, allocation concealment, intention to treat analysis and flow of participants through the trial. Recruitment of the required number of participants was completed in 19 months. Sixty-five percent (96/147) completed the entire 3 months of the trial. The trial was low cost and demonstrated that in an intention to treat analysis, probiotics did not improve well-being or bowel symptoms.<p></p> <b>Conclusion</b> The internet-based RCT proved to be a successful and economical method for examining this CAM intervention. Recruitment, adherence and completion rate were all similar to those reported with conventional RCTs but at a fraction of the cost. Internet-based RCTs can fulfil all the criteria of the revised CONSORT statement and are an appropriate method for studying low-risk interventions