An in silico approach to the ß-defensin structure-activity problem

ß-defensins are a family of cationic, cysteine-rich antimicrobial peptide (AMP) components of the innate immune response to infection. They are expressed both inducibly and constitutively within vertebrates, insects and plants and antimicrobial action is observed against (both gram positive and gram negative) bacteria and a subset of enveloped viruses. The antimicrobial phenomenon is thought to result from membrane permeablisation that depends on key, electrostatic binding events between defensin and pathogen cell surface. This thesis tackles, in silico, two components of this structure-activity problem: That of rationally predicting ß-defensin structure, and that of elucidating the first (presumed) binding events between ß-defensin and pathogen cell surface. Preliminary results suggest that successful in silico folding requires a mobile disulphide bond strategy to circumvent kinetic trapping of intermediate states, and that the mechanism of pathogenic binding involves a complex interplay of hydrogen bonding, as well as productive electrostatic interactions

The complexity of selection at the major primate β-defensin locus

BACKGROUND: We have examined the evolution of the genes at the major human β-defensin locus and the orthologous loci in a range of other primates and mouse. For the first time these data allow us to examine selective episodes in the more recent evolutionary history of this locus as well as the ancient past. We have used a combination of maximum likelihood based tests and a maximum parsimony based sliding window approach to give a detailed view of the varying modes of selection operating at this locus. RESULTS: We provide evidence for strong positive selection soon after the duplication of these genes within an ancestral mammalian genome. Consequently variable selective pressures have acted on β-defensin genes in different evolutionary lineages, with episodes both of negative, and more rarely positive selection, during the divergence of primates. Positive selection appears to have been more common in the rodent lineage, accompanying the birth of novel, rodent-specific β-defensin genes. These observations allow a fuller understanding of the evolution of mammalian innate immunity. In both the rodent and primate lineages, sites in the second exon have been subject to positive selection and by implication are important in functional diversity. A small number of sites in the mature human peptides were found to have undergone repeated episodes of selection in different primate lineages. Particular sites were consistently implicated by multiple methods at positions throughout the mature peptides. These sites are clustered at positions predicted to be important for the specificity of the antimicrobial or chemoattractant properties of β-defensins. Surprisingly, sites within the prepropeptide region were also implicated as being subject to significant positive selection, suggesting previously unappreciated functional significance for this region. CONCLUSIONS: Identification of these putatively functional sites has important implications for our understanding of β-defensin function and for novel antibiotic design

BED Estimates of HIV Incidence: Resolving the Differences, Making Things Simpler

Objective: Develop a simple method for optimal estimation of HIV incidence using the BED capture enzyme immunoassay. Design: Use existing BED data to estimate mean recency duration, false recency rates and HIV incidence with reference to a fixed time period, T. Methods: Compare BED and cohort estimates of incidence referring to identical time frames. Generalize this approach to suggest a method for estimating HIV incidence from any cross-sectional survey. Results: Follow-up and BED analyses of the same, initially HIV negative, cases followed over the same set time period T, produce estimates of the same HIV incidence, permitting the estimation of the BED mean recency period for cases who have been HIV positive for less than T. Follow-up of HIV positive cases over T, similarly, provides estimates of the false-recent rate appropriate for T. Knowledge of these two parameters for a given population allows the estimation of HIV incidence during T by applying the BED method to samples from cross-sectional surveys. An algorithm is derived for providing these estimates, adjusted for the false-recent rate. The resulting estimator is identical to one derived independently using a more formal mathematical analysis. Adjustments improve the accuracy of HIV incidence estimates. Negative incidence estimates result from the use of inappropriate estimates of the false-recent rate and/or from sampling error, not from any error in the adjustment procedure

Sustainability of Nutraceuticals and Functional Foods

Sustainability challenges and issues in nutraceuticals and functional foods arena have influenced both consumers and the industrial sector. Though the present day can be termed as an era of nutraceuticals and functional foods, the knowledge on sustainability among the people involved is limited in the pharma‐food industry. In this chapter, we provide a general overview of this subject, followed by discussion on the four pillars of sustainability and how these relate to the agricultural system, food safety and food security. Examples of nutraceuticals products, health benefits incurred, consumer trends and food choices as well as market values are all examined

E-cigarettes and urologic health: a collaborative review of toxicology, epidemiology, and potential risks

Context: Use of electronic cigarettes (ECs) is on the rise in most high-income countries. Smoking conventional cigarettes is a known risk factor for urologic malignancy incidence, progression, and mortality, as well as for other urologic health indicators. The potential impact of EC use on urologic health is therefore of clinical interest to the urology community. Objective: To review the available data on current EC use, including potential benefits in urologic patients, potential issues linked to toxicology of EC constituents, and how this might translate into urologic health risks. Evidence acquisition: A Medline search was carried out in August 2016 for studies reporting urologic health outcomes and EC use. Snowballing techniques were also used to identify relevant studies from recent systematic reviews. A narrative synthesis of data around EC health outcomes, toxicology, and potential use in smoking cessation and health policy was carried out. Evidence synthesis: We found no studies to date that have been specifically designed to prospectively assess urologic health risks, even in an observational setting. Generating such data would be an important contribution to the debate on the role of ECs in public health and clinical practice. There is evidence from a recent Cochrane review of RCTs that ECs can support smoking cessation. There are emerging data indicating that potentially harmful components of ECs such as tobacco-specific nitrosamines, polyaromatic hydrocarbons, and heavy metals could be linked to possible urologic health risks. Conclusions: ECs might be a useful tool to encourage cessation of conventional cigarette smoking. However, data collection around the specific impact of ECs on urologic health is needed to clarify the possible patient benefits, outcomes, and adverse events. Patient summary: While electronic cigarettes might help some people to stop smoking, their overall impact on urologic health is not clear. While electronic cigarettes might help some people to stop smoking, it is not clear if they may be bad for urologic health

Effects of fluoxetine on functional outcomes after acute stroke (FOCUS): a pragmatic, double-blind, randomised, controlled trial

Background Results of small trials indicate that fluoxetine might improve functional outcomes after stroke. The FOCUS trial aimed to provide a precise estimate of these effects. Methods FOCUS was a pragmatic, multicentre, parallel group, double-blind, randomised, placebo-controlled trial done at 103 hospitals in the UK. Patients were eligible if they were aged 18 years or older, had a clinical stroke diagnosis, were enrolled and randomly assigned between 2 days and 15 days after onset, and had focal neurological deficits. Patients were randomly allocated fluoxetine 20 mg or matching placebo orally once daily for 6 months via a web-based system by use of a minimisation algorithm. The primary outcome was functional status, measured with the modified Rankin Scale (mRS), at 6 months. Patients, carers, health-care staff, and the trial team were masked to treatment allocation. Functional status was assessed at 6 months and 12 months after randomisation. Patients were analysed according to their treatment allocation. This trial is registered with the ISRCTN registry, number ISRCTN83290762. Findings Between Sept 10, 2012, and March 31, 2017, 3127 patients were recruited. 1564 patients were allocated fluoxetine and 1563 allocated placebo. mRS data at 6 months were available for 1553 (99·3%) patients in each treatment group. The distribution across mRS categories at 6 months was similar in the fluoxetine and placebo groups (common odds ratio adjusted for minimisation variables 0·951 [95% CI 0·839–1·079]; p=0·439). Patients allocated fluoxetine were less likely than those allocated placebo to develop new depression by 6 months (210 [13·43%] patients vs 269 [17·21%]; difference 3·78% [95% CI 1·26–6·30]; p=0·0033), but they had more bone fractures (45 [2·88%] vs 23 [1·47%]; difference 1·41% [95% CI 0·38–2·43]; p=0·0070). There were no significant differences in any other event at 6 or 12 months. Interpretation Fluoxetine 20 mg given daily for 6 months after acute stroke does not seem to improve functional outcomes. Although the treatment reduced the occurrence of depression, it increased the frequency of bone fractures. These results do not support the routine use of fluoxetine either for the prevention of post-stroke depression or to promote recovery of function. Funding UK Stroke Association and NIHR Health Technology Assessment Programme

Cellular redox poise modulation; the role of coenzyme Q10, gene and metabolic regulation

In this communication, the concept is developed that coenzyme Q10 has a toti-potent role in the regulation of cellular metabolism. The redox function of coenzyme Q10 leads to a number of outcomes with major impacts on sub-cellular metabolism and gene regulation. Coenzyme Q10's regulatory activities are achieved in part, through the agency of its localization in the various sub-cellular membrane compartments. Its fluctuating redox poise within these membranes reflects the cell's metabolic micro-environments. As an integral part of this process, H2O2 is generated as a product of the normal electron transport systems to function as a mitogenic second messenger informing the nuclear and mitochondrial (chloroplast) genomes on a real-time basis of the status of the sub-cellular metabolic micro-environments and the needs of that cell. Coenzyme Q10 plays a major role both in energy conservation, and energy dissipation as a component of the uncoupler protein family. Coenzyme Q10 is both an anti-oxidant and a pro-oxidant and of the two the latter is proposed as its more important cellular function. Coenzyme Q10 has been reported, to be of therapeutic benefit in the treatment of a wide range of age related degenerative systemic diseases and mitochondrial disease. Our over-arching hypotheses on the central role played by coenzyme Q10 in redox poise changes, the generation of H2O2, consequent gene regulation and metabolic flux control may account for the wide ranging therapeutic benefits attributed to coenzyme Q10. Copyright © 2004 Published by Elsevier B.V

Cellular redox regulation and prooxidant signaling systems: A new perspective on the free radical theory of aging

The overarching role of coenzyme Q10 in gene regulation, bioenergy formation, cellular redox poise regulation, and hydrogen peroxide formation is presented. Coenzyme Q10 has a central role acting as a prooxidant in the generation of H2O2. Contrary to the dogma that superoxide and H2O2 formation are highly deleterious to cell survival this premise is rejected. Data are discussed that continuous superoxide and hydrogen peroxide formation are essential for normal cell function and that they play a major role in subcellular redox state modulation. It is the prooxidant activity of the so-called antioxidants that may be responsible for previously claimed benefits for high doses of oxido-reduction nutritional supplements such as alpha lipoic acid and coenzyme Q10. Oxygen-free radical formation is essential for the biological function and is not a direct causation of the mammalian aging process; aging is a multisystem stochastic process. © 2006 New York Academy of Science