Advances in organometallic and protein chemistry

This thesis describes two areas of scientific investigation. The first contains a description of a study on the synthesis of biotinylated and fluoresceinylated bromomaleimide based reagents. Upon synthesis, the ability of these reagents to add reversibly to cysteine containing proteins is investigated by a series of LCMS experiments. A single point mutant (L111C) of the SH2 domain of the Grb2 adaptor protein, containing a single cysteine residue, is chosen as an ideal protein for study. Thus biotinylated and fluoresceinylated mono and dibromomaleimide reagents are added to Grb2 at 0°C, 21 °C and 37 °C for 2 h at pH 7 and 8 to give protected Grb2-bromomaleimide adducts in high yield and removed using 100 eq of beta-mecaptoethanol for 4 h to return original Grb2 protein intact. Reversibility is shown to be abolished by hydrolysis of the maleimide motif, a process more prevalent in the fluoresceinylated and dibrominated maleimide reagents than for the biotinylated and monobrominated reagents. LCMS is used to investigate the insertion of these reagents reversibly into the single disulfide bridge of somatostatin, a process shown to be complete within 1 h at 21 °C and pH 6. Reduction using 100 eq of beta-mecaptoethanol is shown to take place within 1 h. Additionally no hydrolysis is observed at pH 6, suggesting that with careful control of pH, reversibility of the bromomaleimide reagents can be switched on and off. The second part of the thesis contains a study on mechanistic aspects of organopalladium catalysis, particularly the factors affecting the final reductive elimination stage of the palladium catalysed alkyl amination reaction. DFT calculations have been used to obtain a number of energy level diagrams for the potential energy surface of Pd(IBu)(neopentyl)(morpholide), the three coordinate palladium complex believed to be the species from which reductive elimination takes place. From this it has been found that two different pathways are available; reductive elimination or morpholide promoted C-H activation of the neopentyl motif, the latter of which was favoured. The reaction pathway for reductive elimination from Pd(IBu)(neopentyl)(morpholide) is compared with Pd(IBu)(phenyl)(morpholide), Pd(PCyp3)(neopentyl)(morpholide) and Pd(IBu)(methyl)(morpholide), to show that the phenyl system is considerably lower in energy. The energy requirements for (i) reductive elimination, (ii) morpholide promoted C-H activation and (iii) β-hydride elimination from Pd(IBu)(2-dimethylpropyl)(morpholide) are compared, and shown to be in the order of energy (i)>(ii)>(iii). Additionally, the rate of reaction increases as the number of available reaction sites increases, again making reductive elimination the least favoured process. Offline ESI(+)-MS analysis have been used to monitor the reaction progress of Pd(IBu)(neopentyl)(morpholide) and Pd(IBu)(phenyl)(morpholide) three coordinate complexes. Whilst transient palladium-bound species can be observed for Pd(IBu)(phenyl)(morpholide), for Pd(IBu)(neopentyl)(morpholide) this is not the case, an artefact of the superiority of the sp2 phenyl system over the sp3 alkyl system

Practical Flapping Mechanisms for 20cm-span Micro Air Vehicles

[[abstract]]In the body of research relevant to high-performance flapping micro air vehicles (MAV), development of light-weight, compact and energy-efficient flapping mechanisms occupies a position of primacy due to its direct impact on the flight performance and mission capability. Realization of such versatile flapping mechanism with additional ability of producing thrust levels that fulfill requirements of cruising forward flight and vertical take-off and landing (VTOL) conditions demand extensive design validation and performance evaluation. This paper presents a concerted approach for mechanism development of a 20 cm span flapping MAV through an iterative design process and synergistic fabrication options involving electrical-discharge-wire-cutting (EDWC) and injection molding. Dynamic characterization of each mechanism is done through high speed photography, power take-off measurement, wind tunnel testing and proof-of-concept test flights. The research outcome represents best-in-class mechanism for a 20 cm span flapping MAV with desirable performance features of extra-large flapping stroke up to 100°, minimal transverse vibrations and almost no phase lag between the wings.[[notice]]補正完畢[[journaltype]]國外[[incitationindex]]SCI[[ispeerreviewed]]Y[[booktype]]紙本[[countrycodes]]US

The role of apolipoprotein N-acyl transferase, Lnt, in the lipidation of factor H binding protein of Neisseria meningitidis strain MC58 and its potential as a drug target

BACKGROUND AND PURPOSE The level of cell surface expression of the meningococcal vaccine antigen, Factor H binding protein (FHbp) varies between and within strains and this limits the breadth of strains that can be targeted by FHbp-based vaccines. The molecular pathway controlling expression of FHbp at the cell surface, including its lipidation, sorting to the outer membrane and export, and the potential regulation of this pathway have not been investigated until now. This knowledge will aid our evaluation of FHbp vaccines. EXPERIMENTAL APPROACH A meningococcal transposon library was screened by whole cell immuno-dot blotting using an anti-FHbp antibody to identify a mutant with reduced binding and the disrupted gene was determined. KEY RESULTS In a mutant with markedly reduced binding, the transposon was located in the lnt gene which encodes apolipoprotein N-acyl transferase, Lnt, responsible for the addition of the third fatty acid to apolipoproteins prior to their sorting to the outer membrane. We provide data indicating that in the Lnt mutant, FHbp is diacylated and its expression within the cell is reduced 10 fold, partly due to inhibition of transcription. Furthermore the Lnt mutant showed 64 fold and 16 fold increase in susceptibility to rifampicin and ciprofloxacin respectively. CONCLUSION AND IMPLICATIONS We speculate that the inefficient sorting of diacylated FHbp in the meningococcus results in its accumulation in the periplasm inducing an envelope stress response to down-regulate its expression. We propose Lnt as a potential novel drug target for combination therapy with antibiotics

Solar Neutrino Constraints on the BBN Production of Li

Using the recent WMAP determination of the baryon-to-photon ratio, 10^{10} \eta = 6.14 to within a few percent, big bang nucleosynthesis (BBN) calculations can make relatively accurate predictions of the abundances of the light element isotopes which can be tested against observational abundance determinations. At this value of \eta, the Li7 abundance is predicted to be significantly higher than that observed in low metallicity halo dwarf stars. Among the possible resolutions to this discrepancy are 1) Li7 depletion in the atmosphere of stars; 2) systematic errors originating from the choice of stellar parameters - most notably the surface temperature; and 3) systematic errors in the nuclear cross sections used in the nucleosynthesis calculations. Here, we explore the last possibility, and focus on possible systematic errors in the He3(\alpha,\gamma)Be7 reaction, which is the only important Li7 production channel in BBN. The absolute value of the cross section for this key reaction is known relatively poorly both experimentally and theoretically. The agreement between the standard solar model and solar neutrino data thus provides additional constraints on variations in the cross section (S_{34}). Using the standard solar model of Bahcall, and recent solar neutrino data, we can exclude systematic S_{34} variations of the magnitude needed to resolve the BBN Li7 problem at > 95% CL. Additional laboratory data on He3(\alpha,\gamma)Be7 will sharpen our understanding of both BBN and solar neutrinos, particularly if care is taken in determining the absolute cross section and its uncertainties. Nevertheless, it already seems that this ``nuclear fix'' to the Li7 BBN problem is unlikely; other possible solutions are briefly discussed.Comment: 21 pages, 3 ps figure

About Bianchi I with VSL

In this paper we study how to attack, through different techniques, a perfect fluid Bianchi I model with variable G,c and Lambda, but taking into account the effects of a $c$-variable into the curvature tensor. We study the model under the assumption,div(T)=0. These tactics are: Lie groups method (LM), imposing a particular symmetry, self-similarity (SS), matter collineations (MC) and kinematical self-similarity (KSS). We compare both tactics since they are quite similar (symmetry principles). We arrive to the conclusion that the LM is too restrictive and brings us to get only the flat FRW solution. The SS, MC and KSS approaches bring us to obtain all the quantities depending on \int c(t)dt. Therefore, in order to study their behavior we impose some physical restrictions like for example the condition q<0 (accelerating universe). In this way we find that $c$ is a growing time function and Lambda is a decreasing time function whose sing depends on the equation of state, w, while the exponents of the scale factor must satisfy the conditions $\sum_{i=1}^{3}\alpha_{i}=1$ and $\sum_{i=1}^{3}\alpha_{i}^{2}<1,$ $\forall\omega$, i.e. for all equation of state$,$ relaxing in this way the Kasner conditions. The behavior of $G$ depends on two parameters, the equation of state $\omega$ and $\epsilon,$ a parameter that controls the behavior of $c(t),$ therefore $G$ may be growing or decreasing.We also show that through the Lie method, there is no difference between to study the field equations under the assumption of a $c-$var affecting to the curvature tensor which the other one where it is not considered such effects.Nevertheless, it is essential to consider such effects in the cases studied under the SS, MC, and KSS hypotheses.Comment: 29 pages, Revtex4, Accepted for publication in Astrophysics & Space Scienc

Evolutionary life history theory as an organising framework for cohort studies: insights from the Cebu Longitudinal Health and Nutrition Survey

By tracking a group of individuals through time, cohort studies provide fundamental insights into the developmental time course and causes of health and disease. Evolutionary life history theory seeks to explain patterns of growth, development, reproduction and senescence, and inspires a range of hypotheses that are testable using the longitudinal data from cohort studies. Here we review two decades of life history theory-motivated work conducted in collaboration with the Cebu Longitudinal Health and Nutrition Survey (CLHNS), a birth cohort study that enrolled more than 3000 pregnant women in the Philippines in 1983 and has since followed these women, their offspring and grandoffspring. This work has provided evidence that reproduction carries “costs” to cellular maintenance functions, potentially speeding senescence, and revealed an unusual form of genetic plasticity in which the length of telomeres inherited across generations is influenced by reproductive timing in paternal ancestors. Men in Cebu experience hormonal and behavioural changes in conjunction with changes in relationship and fatherhood status that are consistent with predictions based upon other species that practice bi-parental care. The theoretical expectation that early life cues of mortality or environmental unpredictability will motivate a “fast” life history strategy are confirmed for behavioural components of reproductive decision making, but not for maturational tempo, while our work points to a broader capacity for early life developmental calibration of systems like immunity, reproductive biology and metabolism. Our CLHNS findings illustrate the power of life history theory as an integrative, lifecourse framework to guide longitudinal studies of human populations

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Jet size dependence of single jet suppression in lead-lead collisions at sqrt(s(NN)) = 2.76 TeV with the ATLAS detector at the LHC

Measurements of inclusive jet suppression in heavy ion collisions at the LHC provide direct sensitivity to the physics of jet quenching. In a sample of lead-lead collisions at sqrt(s) = 2.76 TeV corresponding to an integrated luminosity of approximately 7 inverse microbarns, ATLAS has measured jets with a calorimeter over the pseudorapidity interval |eta| < 2.1 and over the transverse momentum range 38 < pT < 210 GeV. Jets were reconstructed using the anti-kt algorithm with values for the distance parameter that determines the nominal jet radius of R = 0.2, 0.3, 0.4 and 0.5. The centrality dependence of the jet yield is characterized by the jet "central-to-peripheral ratio," Rcp. Jet production is found to be suppressed by approximately a factor of two in the 10% most central collisions relative to peripheral collisions. Rcp varies smoothly with centrality as characterized by the number of participating nucleons. The observed suppression is only weakly dependent on jet radius and transverse momentum. These results provide the first direct measurement of inclusive jet suppression in heavy ion collisions and complement previous measurements of dijet transverse energy imbalance at the LHC.Comment: 15 pages plus author list (30 pages total), 8 figures, 2 tables, submitted to Physics Letters B. All figures including auxiliary figures are available at http://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/HION-2011-02