An original phylogenetic approach identified mitochondrial haplogroup T1a1 as inversely associated with breast cancer risk in BRCA2 mutation carriers

Introduction: Individuals carrying pathogenic mutations in the BRCA1 and BRCA2 genes have a high lifetime risk of breast cancer. BRCA1 and BRCA2 are involved in DNA double-strand break repair, DNA alterations that can be caused by exposure to reactive oxygen species, a main source of which are mitochondria. Mitochondrial genome variations affect electron transport chain efficiency and reactive oxygen species production. Individuals with different mitochondrial haplogroups differ in their metabolism and sensitivity to oxidative stress. Variability in mitochondrial genetic background can alter reactive oxygen species production, leading to cancer risk. In the present study, we tested the hypothesis that mitochondrial haplogroups modify breast cancer risk in BRCA1/2 mutation carriers.

Methods: We genotyped 22,214 (11,421 affected, 10,793 unaffected) mutation carriers belonging to the Consortium of Investigators of Modifiers of BRCA1/2 for 129 mitochondrial polymorphisms using the iCOGS array. Haplogroup inference and association detection were performed using a phylogenetic approach. ALTree was applied to explore the reference mitochondrial evolutionary tree and detect subclades enriched in affected or unaffected individuals.

Results: We discovered that subclade T1a1 was depleted in affected BRCA2 mutation carriers compared with the rest of clade T (hazard ratio (HR) = 0.55; 95% confidence interval (CI), 0.34 to 0.88; P = 0.01). Compared with the most frequent haplogroup in the general population (that is, H and T clades), the T1a1 haplogroup has a HR of 0.62 (95% CI, 0.40 to 0.95; P = 0.03). We also identified three potential susceptibility loci, including G13708A/rs28359178, which has demonstrated an inverse association with familial breast cancer risk.

Conclusions: This study illustrates how original approaches such as the phylogeny-based method we used can empower classical molecular epidemiological studies aimed at identifying association or risk modification effects.

Derivatisable Cyanobactin Analogues: A Semisynthetic Approach

Many natural cyclic peptides have potent and potentially useful biological activities. Their use as therapeutic starting points is often limited by the quantities available, the lack of known biological targets and the practical limits on diversification to fine-tune their properties. We report the use of enzymes from the cyanobactin family to heterocyclise and macrocyclise chemically synthesised substrates so as to allow larger-scale syntheses and better control over derivatisation. We have made cyclic peptides containing orthogonal reactive groups, azide or dehydroalanine, that allow chemical diversification, including the use of fluorescent labels that can help in target identification. We show that the enzymes are compatible and efficient with such unnatural substrates. The combination of chemical synthesis and enzymatic transformation could help renew interest in investigating natural cyclic peptides with biological activity, as well as their unnatural analogues, as therapeutics.

Reactive power compensation by EPSO technique

This paper presents a methodology to address reactive power compensation using Evolutionary Particle Swarm Optimization (EPSO) technique programmed in the MATLAB environment. The main objective is to find the best operation point minimizing power losses with reactive power compensation, subjected to all operational constraints, namely full AC power flow equations, active and reactive power generation constraints. The methodology has been tested with the IEEE 14 bus test system demonstrating the ability and effectiveness of the proposed approach to handle the reactive power compensation problem.

Combined clonotyping and gene signatures of individual tumor-reactive CD8 T-cells define their functional relevance following peptide vaccination in melanoma patients

Novel cancer vaccines are capableto efficiently induce and boost humantumor antigen specific T-cells. However,the properties of these CD8T-cells are only partially characterized.For in depth investigation ofT-cells following Melan-A/MART-1peptide vaccination in melanoma patients,we conducted a detailed prospectivestudy at the single cell level.We first sorted individual human naiveand effector CD8 T-cells from peripheralblood by flow cytometry, andtested a modified RT-PCR protocolincluding a global amplification ofexpressed mRNAs to obtain sufficientcDNAfromsingle cells.We successfullydetected the expression ofseveral specific genes of interest evendown to 106-fold dilution (equivalentto 10-5 cell). We then analyzed tumor-specific effector memory (EM)CD8T-cell subpopulations ex vivo, assingle cells from vaccinated melanomapatients. To elucidate the hallmarksof effective immunity the genesignatures were defined by a panel ofgenes related to effector functions(e.g. IFN-, granzyme B, perforin),and individual clonotypes were identifiedaccording to the expression ofdistinct T-cell receptors (TCR). Usingthis novel single cell analysis approach,we observed that T-cell differentiationis clonotype dependent,with a progressive restriction in TCRBV clonotype diversity from EMCD28pos to EMCD28neg subsets. However,the effector function gene imprintingis clonotype-independent,but dependent on differentiation,since it correlates with the subset oforigin (EMCD28pos or EMCD28neg). We also conducted a detailedcomparative analysis after vaccinationwith natural vs. analog Melan-Apeptide. We found that the peptideused for vaccination determines thefunctional outcome of individualT-cell clonotypes, with native peptideinducing more potent effector functions.Yet, selective clonotypic expansionwith differentiation was preservedregardless of the peptide usedfor vaccination. In summary, the exvivo single cell RT-PCR approach ishighly sensitive and efficient, andrepresents a reliable and powerfultool to refine our current view of molecularprocesses taking place duringT-cell differentiation.

A carbene insertion approach to functionalised poly(ethylene oxide)-based gels

Carbenes photogenerated from the novel bisdiazirine, 1, 3-bis(3-(trifluoromethyl)diazirin-3-yl) benzene 1, have been applied successfully to cross-linking of mono-methyl poly(ethylene oxide) (MePEO5000) in the presence of dichloromethane, leading to the simultaneous incorporation of alkylhalide functionalities. The PEO-based gels swell in a wide range of solvents with polarity index values varying from 3.1 to 9.0. Reaction of the alkylhalide functionalities present in the gels with 4-phenylazophenol provided loading capacities of up to 0.20 mmol g(-1) and demonstrated the potential of these materials for gel-phase synthesis applications. (C) 2008 Elsevier Ltd. All rights reserved.

Surface modification of nylon 6,6 using a carbene insertion approach

The diazirine functionalised fluorenone, 3-[3-(trifluoromethyl)diazirin-3-yl]phenyl-9-oxo-9H-fluorene-2-carboxyla te was synthesised to act as a model compound capable of modifying a wide variety of polymeric substrates. Photochemical activation of the diazirine moiety of the fluorenone derivative was utilised to afford highly reactive carbenes capable of insertion into or addition to a wide variety of functionalities. In this paper the photoinduced attachment of a fluorenone derivative to nylon 6,6 has been studied using UV-visible spectroscopic analysis. Incorporation of the fluorenone chromophore onto the backbone of nylon at different loading levels and after different coating cycles has been investigated and is detailed in this paper.

Targeting C-reactive protein for the treatment of cardiovascular disease

Complement-mediated inflammation exacerbates the tissue injury of ischaemic necrosis in heart attacks and strokes, the most common causes of death in developed countries. Large infarct size increases immediate morbidity and mortality and, in survivors of the acute event, larger non-functional scars adversely affect long-term prognosis. There is thus an important unmet medical need for new cardioprotective and neuroprotective treatments. We have previously shown that human C-reactive protein (CRP), the classical acute-phase protein that binds to ligands exposed in damaged tissue and then activates complement(1), increases myocardial and cerebral infarct size in rats subjected to coronary or cerebral artery ligation, respectively(2,3). Rat CRP does not activate rat complement, whereas human CRP activates both rat and human complement(4). Administration of human CRP to rats is thus an excellent model for the actions of endogenous human CRP2,3. Here we report the design, synthesis and efficacy of 1,6-bis(phosphocholine)-hexane as a specific small-molecule inhibitor of CRP. Five molecules of this palindromic compound are bound by two pentameric CRP molecules, crosslinking and occluding the ligand-binding B-face of CRP and blocking its functions. Administration of 1,6-bis(phosphocholine)-hexane to rats undergoing acute myocardial infarction abrogated the increase in infarct size and cardiac dysfunction produced by injection of human CRP. Therapeutic inhibition of CRP is thus a promising new approach to cardioprotection in acute myocardial infarction, and may also provide neuroprotection in stroke. Potential wider applications include other inflammatory, infective and tissue-damaging conditions characterized by increased CRP production, in which binding of CRP to exposed ligands in damaged cells may lead to complement-mediated exacerbation of tissue injury.

An objective, niche-based approach to indicator species selection

1. Species-based indices are frequently employed as surrogates for wider biodiversity health and measures of environmental condition. Species selection is crucial in determining an indicators metric value and hence the validity of the interpretation of ecosystem condition and function it provides, yet an objective process to identify appropriate indicator species is frequently lacking. 2. An effective indicator needs to (i) be representative, reflecting the status of wider biodiversity; (ii) be reactive, acting as early-warning systems for detrimental changes in environmental conditions; (iii) respond to change in a predictable way. We present an objective, niche-based approach for species' selection, founded on a coarse categorisation of species' niche space and key resource requirements, which ensures the resultant indicator has these key attributes. 3. We use UK farmland birds as a case study to demonstrate this approach, identifying an optimal indicator set containing 12 species. In contrast to the 19 species included in the farmland bird index (FBI), a key UK biodiversity indicator that contributes to one of the UK Government's headline indicators of sustainability, the niche space occupied by these species fully encompasses that occupied by the wider community of 62 species. 4. We demonstrate that the response of these 12 species to land-use change is a strong correlate to that of the wider farmland bird community. Furthermore, the temporal dynamics of the index based on their population trends closely matches the population dynamics of the wider community. However, in both analyses, the magnitude of the change in our indicator was significantly greater, allowing this indicator to act as an early-warning system. 5. Ecological indicators are embedded in environmental management, sustainable development and biodiversity conservation policy and practice where they act as metrics against which progress towards national, regional and global targets can be measured. Adopting this niche-based approach for objective selection of indicator species will facilitate the development of sensitive and representative indices for a range of taxonomic groups, habitats and spatial scales.

A multi-level analytical approach for detection and visualization of intracellular NO production and nitrosation events using diaminofluoresceins

Diaminofluoresceins are widely used probes for detection and intracellular localization of NO formation in cultured/isolated cells and intact tissues. The fluorinated derivative, 4-amino-5-methylamino-2′,7′-difluorofluorescein (DAF-FM), has gained increasing popularity in recent years due to its improved NO-sensitivity, pH-stability, and resistance to photo-bleaching compared to the first-generation compound, DAF-2. Detection of NO production by either reagent relies on conversion of the parent compound into a fluorescent triazole, DAF-FM-T and DAF-2-T, respectively. While this reaction is specific for NO and/or reactive nitrosating species, it is also affected by the presence of oxidants/antioxidants. Moreover, the reaction with other molecules can lead to the formation of fluorescent products other than the expected triazole. Thus additional controls and structural confirmation of the reaction products are essential. Using human red blood cells as an exemplary cellular system we here describe robust protocols for the analysis of intracellular DAF-FM-T formation using an array of fluorescence-based methods (laser-scanning fluorescence microscopy, flow cytometry and fluorimetry) and analytical separation techniques (reversed-phase HPLC and LC-MS/MS). When used in combination, these assays afford unequivocal identification of the fluorescent signal as being derived from NO and are applicable to most other cellular systems without or with only minor modifications.

APOE genotype influences triglyceride and C-reactive protein responses to altered dietary fat intake in UK adults

Background: The response of plasma lipids to dietary fat manipulation is highly heterogeneous, with some indications that APOE genotype may be important. Objective: The objective was to use a prospective recruitment approach to determine the effect of dietary fat quantity and composition on both lipid and nonlipid cardiovascular disease biomarkers according to APOE genotype. Design: Participants had a mean (±SD) age of 51 ± 9 y and a BMI (in kg/m2) of 26.0 ± 3.8 (n = 44 E3/E3, n = 44 E3/E4) and followed a sequential dietary intervention (the SATgenϵ study) in which they were assigned to a low-fat diet, a high-fat high-SFA (HSF) diet, and the HSF diet with 3.45 g DHA/d (HSF-DHA), each for 8 wk. Fasting blood samples were collected at the end of each intervention arm. Results: An overall diet effect was evident for all cholesterol fractions (P < 0.01), with no significant genotype × diet interactions observed. A genotype × diet interaction (P = 0.033) was evident for plasma triglycerides, with 17% and 30% decreases in APOE3/E3 and APOE3/E4 individuals after the HSF-DHA diet relative to the low-fat diet. A significant genotype × diet interaction (P = 0.009) was also observed for C-reactive protein (CRP), with only significant increases in concentrations after the HSF and HSF-DHA diets relative to the low-fat diet in the APOE3/E4 group (P < 0.015). Conclusions: Relative to the wild-type APOE3/E3 group, our results indicate a greater sensitivity of fasting triglycerides and CRP to dietary fat manipulation in those with an APOE3/E4 genotype (25% population), with no effect of this allelic profile on cholesterol concentrations. The SATgenϵ study was registered at clinicaltrials.gov as NCT01384032.

Evaluation of economic impact of external eauivalent models used in reactive OPF studies for interconnected systems

Reactive-optimisation procedures are responsible for the minimisation of online power losses in interconnected systems. These procedures are performed separately at each control centre and involve external network representations. If total losses can be minimised by the implementation of calculated local control actions, the entire system benefits economically, but such control actions generally result in a certain degree of inaccuracy, owing to errors in the modelling of the external system. Since these errors are inevitable, they must at least be maintained within tolerable limits by external-modelling approaches. Care must be taken to avoid unrealistic loss minimisation, as the local-control actions adopted can lead the system to points of operation which will be less economical for the interconnected system as a whole. The evaluation of the economic impact of the external modelling during reactive-optimisation procedures in interconnected systems, in terms of both the amount of losses and constraint violations, becomes important in this context. In the paper, an analytical approach is proposed for such an evaluation. Case studies using data from the Brazilian South-Southeast system (810 buses) have been carried out to compare two different external-modelling approaches, both derived from the equivalent-optimal-power-flow (EOPF) model. Results obtained show that, depending on the external-model representation adopted, the loss representation can be flawed. Results also suggest some modelling features that should be adopted in the EOPF model to enhance the economy of the overall system.

A heuristic method for reactive power planning

An approach for solving reactive power planning problems is presented, which is based on binary search techniques and the use of a special heuristic to obtain a discrete solution. Two versions were developed, one to run on conventional (sequential) computers and the other to run on a distributed memory (hypercube) machine. This latter parallel processing version employs an asynchronous programming model. Once the set of candidate buses has been defined, the program gives the location and size of the reactive sources needed(if any) in keeping with operating and security constraints.

New concepts of the power received by ideal energy storage elements: the instantaneous complex power approach

This paper presents some definitions and concepts of the Instantaneous Complex Power Theory [1] which is a new approach for the Akagi's Instantaneous Reactive Power Theory [2].The powers received by an ideal inductor are interpreted and the knowledge of the actual nature of these powers may lead to changes of the conventional electrical power concepts.

Incorporating voltage/reactive representation to short-term generation scheduling models

This paper proposes a methodology to incorporate voltage/reactive representation to Short Term Generation Scheduling (STGS) models, which is based on active/reactive decoupling characteristics of power systems. In such approach STGS is decoupled in both Active (AGS) and Reactive (RGS) Generation Scheduling models. AGS model establishes an initial active generation scheduling through a traditional dispatch model. The scheduling proposed by AGS model is evaluated from the voltage/reactive points of view, through the proposed RGS model. RGS is formulated as a sequence of T nonlinear OPF problems, solved separately but taking into account load tracking between consecutive time intervals. This approach considerably reduces computational effort to perform the reactive analysis of the RGS problem as a whole. When necessary, RGS model is capable to propose active generation redispatches, such that critical reactive problems (in which all reactive variables have been insufficient to control the reactive problems) can be overcome. The formulation and solution methodology proposed are evaluated in the IEEE30 system in two case studies. These studies show that the methodology is robust enough to incorporate reactive aspects to STGS problem.

Comparison of Reactive Power Support in Distribution Networks Provided by Capacitor Banks and Distributed Generators

This paper presents a comparison of reactive power support in distribution networks provided by switched Capacitor Banks (CBs) and Distributed Generators (DGs). Regarding switched CBs, a Tabu Search metaheuristic algorithm is developed to determine their optimal operation with the objective of reducing the power losses in the lines on the system, while meeting network constraints. on the other hand, the optimal operation of DGs is analyzed through an evolutionary Multi-Objective (MO) programming approach. The objectives of such approach are the minimization of power losses and operation cost of the DGs. The comparison of the reactive power support provided by switched CBs and DGs is carried out using a modified IEEE 34 bus distribution test system.