Structural proteomics of minimal organisms: Conservation of protein fold usage and evolutionary implications

BACKGROUND: Determining the complete repertoire of protein structures for all soluble, globular proteins in a single organism has been one of the major goals of several structural genomics projects in recent years. RESULTS: We report that this goal has nearly been reached for several "minimal organisms" – parasites or symbionts with reduced genomes – for which over 95% of the soluble, globular proteins may now be assigned folds, overall 3-D backbone structures. We analyze the structures of these proteins as they relate to cellular functions, and compare conservation of fold usage between functional categories. We also compare patterns in the conservation of folds among minimal organisms and those observed between minimal organisms and other bacteria. CONCLUSION: We find that proteins performing essential cellular functions closely related to transcription and translation exhibit a higher degree of conservation in fold usage than proteins in other functional categories. Folds related to transcription and translation functional categories were also overrepresented in minimal organisms compared to other bacteria

Scalar Mediated FCNC at the First Muon Collider

In the most general two-Higgs doublet model (generally referred to as Model III), tree level flavor changing neutral couplings exist. It has been noted that the most natural value for such a coupling is of the order of the geometric mean of the Yukawa couplings of the two fermions. Bounds on those couplings that involve the second and third generations, from $\tau,B,D$ and $\mu$ physics, are very weak and are not sensitive to this "natural" value. In this paper, it is pointed out that the process \mu\mu ---> \mu\tau, at a muon collider tuned to the scalar resonance, will easily reach this sensitivity if the scalar mass is below 140 GeV. Hundreds of events are expected for an integrated luminosity of an inverse femtobarn, and there appears to be no background. Failure to observe this process, if the scalar is below 140 GeV, would effectively rule out Model III.Comment: Paragraph added and other wording changed in introduction, some wording changes in text. Calculation unaffected. Version to appear in Phys. Lett.

Phased Locked Laser Diode by Using Passive Array of Multi-Mode Interference Couplers

We report a phase locked laser diode based on a passive array of 1×2 multi-mode interference couplers and quantum well intermixing techniques which shows stable and clear coherence far field patters from both active and passive side up to at least 9 times threshold current

FO(FD): Extending classical logic with rule-based fixpoint definitions

We introduce fixpoint definitions, a rule-based reformulation of fixpoint constructs. The logic FO(FD), an extension of classical logic with fixpoint definitions, is defined. We illustrate the relation between FO(FD) and FO(ID), which is developed as an integration of two knowledge representation paradigms. The satisfiability problem for FO(FD) is investigated by first reducing FO(FD) to difference logic and then using solvers for difference logic. These reductions are evaluated in the computation of models for FO(FD) theories representing fairness conditions and we provide potential applications of FO(FD).Comment: Presented at ICLP 2010. 16 pages, 1 figur

Search for t->ch at e+e- Linear Colliders

We study the rare top-quark decay t->ch, where h is a generic Higgs boson, at a linear collider. If kinematically accessible, all models contain this decay at some level due to quark flavor mixing. Some models, such as Model III of the two-Higgs doublet model, have a tree-level top-charm-Higgs coupling, and the branching ratio is close to 0.5%. Others, such as the MSSM, have a coupling induced at one-loop, and can have a branching ratio in the range of 10^{-5} - 5x10^{-4}. We find that a linear collider of root(s) = 500 GeV and a luminosity of 500 fb^{-1} will begin to be sensitive to this range of the coupling.Comment: 12 pages, 5 figures, 2 table

Optimization of Protein-Protein Interaction Measurements for Drug Discovery Using AFM Force Spectroscopy

Increasingly targeted in drug discovery, protein-protein interactions challenge current high throughput screening technologies in the pharmaceutical industry. Developing an effective and efficient method for screening small molecules or compounds is critical to accelerate the discovery of ligands for enzymes, receptors and other pharmaceutical targets. Here, we report developments of methods to increase the signal-to-noise ratio (SNR) for screening protein-protein interactions using atomic force microscopy (AFM) force spectroscopy. We have demonstrated the effectiveness of these developments on detecting the binding process between focal adhesion kinases (FAK) with protein kinase B (Akt1), which is a target for potential cancer drugs. These developments include optimized probe and substrate functionalization processes and redesigned probe-substrate contact regimes. Furthermore, a statistical-based data processing method was developed to enhance the contrast of the experimental data. Collectively, these results demonstrate the potential of the AFM force spectroscopy in automating drug screening with high throughput

Principle and implementations of a refracto-nephelo-turbidimeter for seawater measurements

International audienceSalinity and turbidity are two important seawater properties in physical oceanography. The study of physical oceanography requires a compact high-resolution in-situ salino-turbidimeter to measure these two parameters in different ocean zones. Refractometry has proved to be an effective method to measure seawater salinity with a high resolution. Previous studies have shown that the transmission and scattering of light in a turbid medium impact the light beam deviation measurements, which makes the combination of salinity and turbidity measurements with the same sample mandatory. In this paper, we analyze the requirements and challenges of a refracto-turbidimeter design from their measurement principles and correlations. According to these requirements, we propose a miniature refracto-nephelo-turbidimeter with a CCD, providing a salinity measurement resolution of 2 mg.kg-1 and a turbidity measurement resolution of 1 % of the measurement range. Based on this refracto-nephelo-turbidimeter, different embodiments are discussed to meet the different requirements for different ocean zones

The Anomalous Magnetic Moment of the Muon and Higgs-Mediated Flavor Changing Neutral Currents

In the two-Higgs doublet extension of the standard model, flavor-changing neutral couplings arise naturally. In the lepton sector, the largest such coupling is expected to be $\mu-\tau-\phi#. We consider the effects of this coupling on the anomalous magnetic moment of the muon. The resulting bound on the coupling, unlike previous bounds, is independent of the value of other unknown couplings. It will be significantly improved by the upcoming E821 experiment at Brookhaven National Lab.Comment: 7 pages Latex, 2 figure

Fourth Generation b-prime decays into b + Higgs

If a fourth generation quark exists whose mass is below 255 GeV, then the only two-body charged current decay, b'-->cW, is doubly-Cabibbo suppressed. For this reason, CDF has searched for the one-loop neutral current decay b' --> bZ, assuming that the branching ratio into bZ is 100%; an analysis giving the bounds on m_b' for smaller branching ratios is in preparation. In this Report, we examine the neutral current decay b' --> bH, which will occur if the Higgs mass is less than m_b'-m_b. Four different cases are examined: the sequential case, the non-chiral isosinglet case, the non-chiral isodoublet case, and a two-Higgs model with flavor-changing neutral currents. In the first three of these, the rates for b' --> bZ and b' --> bH are comparable, assuming comparable phase space factors; in the fourth, b' --> bH is completely dominant. Thus, we emphasize the importance of giving b' mass bounds as a function of the branching ratio into bZ, since the assumption of a 100% branching ratio for b' --> bZ may only be valid if the Higgs mass is near or above the b' mass.Comment: Minor typos fixed, reference added, sentence changed in experimental discussion. Conclusions unchange

Nanoparticles Supported on Sub-Nanometer Oxide Films : Scaling Model Systems to Bulk Materials

Ultrathin layers of oxides deposited on atomically flat metal surfaces have been shown to significantly influence the electronic structure of the underlying metal, which in turn alters the catalytic performance. Upscaling of the specifically designed architectures as required for technical utilization of the effect has yet not been achieved. Here, we apply liquid crystalline phases of fluorohectorite nanosheets to fabricate such architectures in bulk. Synthetic sodium fluorohectorite, a layered silicate, when immersed into water spontaneously and repulsively swells to produce nematic suspensions of individual negatively charged nanosheets separated to more than 60 nm, while retaining parallel orientation. Into these galleries oppositely charged palladium nanoparticles were intercalated whereupon the galleries collapse. Individual and separated Pd nanoparticles were thus captured and sandwiched between nanosheets. As suggested by the model systems, the resulting catalyst performed better in the oxidation of carbon monoxide than the same Pd nanoparticles supported on external surfaces of hectorite or on a conventional Al2O3 support. XPS confirmed a shift of Pd 3d electrons to higher energies upon coverage of Pd nanoparticles with nanosheets to which we attribute the improved catalytic performance. DFT calculations showed increasing positive charge on Pd weakened CO adsorption and this way damped CO poisoning