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Romancing the condition of england : making the academic novel work in the literary market place
(2002)
Two Hybrid cDNA Cloning
(2002)
Chitinase B (ChiB) from Serratia marcescens is a family 18 exochitinase whose catalytic domain has a TIM-barrel fold with a tunnel-shaped active site. We have solved structures of three ChiB complexes that reveal details of substrate binding, substrateassisted catalysis, and product displacement. The structure of an inactive ChiB mutant (E144Q) complexed with a pentameric substrate (binding in subsites 22 to 13) shows closure of the ''roof'' of the active site tunnel. It also shows that the sugar in the 21 position is distorted to a boat conformation, thus providing structural evidence in support of a previously proposed catalytic mechanism. The structures of the active enzyme complexed to Allosamidin (an analogue of a proposed reaction intermediate) and of the active enzyme soaked with pentameric substrate show events after cleavage of the glycosidic bond. The latter structure shows reopening of the roof of the active site tunnel and enzyme-assisted product displacement in the 11 and 12 sites, allowing a water molecule to approach the reaction center. Catalysis is accompanied by correlated structural changes in the core of the TIM barrel that involve conserved polar residues whose functions were hitherto unknown. These changes simultaneously contribute to stabilization of the reaction intermediate and alternation of the pKa of the catalytic acid during the catalytic cycle.
In this paper we report about the recently completed porting of GAMMA to the Netgear GA621 Gigabit Ethernet adapter, and provide a comparison among GAMMA, MPI/GAMMA, TCP/IP, and MPICH/TCP, based on the Netgear GA621 and the older Netgear GA620 network adapters and using different device drivers, in a Gigabit Ethernet cluster of PCs running Linux 2.4. GAMMA (the Genoa Active Message MAchine) is a lightweight messaging system based on an Active Message-like paradigm, originally designed for efficient exploitation of Fast Ethernet interconnects. The comparison includes simple latency/hspace{0pt}bandwidth evaluation of the messaging systems on both adapters, as well as performance comparisons based on the NAS NPB and an end-user fluid dynamics application called Modular Ocean Model (MOM). The analysis of results provides useful hints concerning the efficient use of Gigabit Ethernet with clusters of PCs. In particular, it emerges that GAMMA on the GA621 adapter, with a combination of low end-to-end latency (8.5 $mu$s) and high throughput (118.4 MByte/s), provides a performing, cost-effective alternative to proprietary high-speed networks, e.g.~Myrinet, for a wide range of cluster computing applications.
Over the past years, family 18 chitinases have been validated as potential targets for the design of drugs against human pathogens that contain or interact with chitin during their normal life cycles. Thus far, only one potent chitinase inhibitor has been described in detail, the pseudotrisaccharide allosamidin. Recently, however, two potent natural-product cyclopentapeptide chitinase inhibitors, argifin and argadin, were reported. Here, we describe high- resoln. crystal structures that reveal the details of the interactions of these cyclopeptides with a family 18 chitinase. The structures are examples of complexes of a carbohydrate-processing enzyme with high-affinity peptide-based inhibitors and show in detail how the peptide backbone and side chains mimic the interactions of the enzyme with chitooligosaccharides. Together with enzymol. characterization, the structures explain why argadin shows an order of magnitude stronger inhibition than allosamidin, whereas argifin shows weaker inhibition. The peptides bind to the chitinase in remarkably different ways, which may explain the differences in inhibition consts. The two complexes provide a basis for structure-based design of potent chitinase inhibitors, accessible by std. peptide chem.
Tomography of AM Herculis
(2002)
We present models for the complete life and death of a 60 Msolar star evolving in a close binary system, from the main-sequence phase to the formation of a compact remnant and fallback of supernova debris. After core hydrogen exhaustion, the star expands, loses most of its envelope by Roche lobe overflow, and becomes a Wolf-Rayet star. We study its post-mass transfer evolution as a function of the Wolf-Rayet wind mass-loss rate (which is currently not well constrained and will probably vary with the initial metallicity of the star). Varying this mass-loss rate by a factor of 6 leads to stellar masses at collapse that range from 3.1 up to 10.7 Msolar. Because of different carbon abundances left by core helium burning and nonmonotonic effects of the late shell-burning stages as function of the stellar mass, we find that, although the iron core masses at collapse are generally larger for stars with larger final masses, they do not depend monotonically on the final stellar mass or even the C/O core mass. We then compute the evolution of all models through collapse and bounce. The results range from strong supernova explosions (Ekin>1051ergs) for the lower final masses to the direct collapse of the star into a black hole for the largest final mass. Correspondingly, the final remnant masses, which were computed by following the supernova evolution and fallback of material for a timescale of about one year, are between 1.2 and 10 Msolar. We discuss the remaining uncertainties of this result and outline the consequences of our results for the understanding of the progenitor evolution of X-ray binaries and gamma-ray burst models.
M-solidity testing systems
(2002)
From the peak of a gravitational microlensing high-magnification event in the A component of QSO 2237+0305, which was accurately monitored by the Gravitational Lenses International Time Project collaboration, we derived new information on the nature and size of the optical V-band and R-band sources in the distant quasar. If the microlensing peak is caused by a microcaustic crossing, we first obtain that the standard accretion disk is a scenario more reliable/ feasible than other typical axially symmetric models. Moreover, the standard scenario fits both the V-band and R-band observations with reduced ?2 values very close to 1. Taking into account all these results, a standard accretion disk around a supermassive black hole is a good candidate for the optical continuum main source in QSO 2237+0305. Second, using the standard source model and a robust upper limit on the transverse galactic velocity, we infer that 90% of the V- band and R-band luminosities are emitted from a region with a radial size less than 1.2×10-2 pc (=3.7×1016 cm, at a 2 ? confidence level).
Citrate-capped gold nanoparticles as well as planar gold surfaces can be efficiently grafted with a covalently attached polymer monolayer a few nanometers thick, by simple contact of the metal surface with dilute aqueous solutions of hydrophilic polymers that are end-capped with disulfide moieties, as shown by UV/vis absorption, dynamic light scattering, and surface plasmon resonance studies. The hydrophilic polymer-coated gold colloids can be freeze-dried and stored as powders that can be subsequently dissolved to yield stable aqueous dispersions, even at very large concentrations. They allow for applying filtrations, gel permeation chromatography, or centrifugation. They do not suffer from undesirable nonspecific adsorption of proteins while allowing the diffusion of small species within the hydrogel surface coating. In addition, specific properties of the original hydrophilic polymers are retained such as a lower critical solution temperature. The latter feature could be useful to enhance optical responses of functionalized gold surfaces toward interaction with various substrates.
The influence of the charge density of polyelectrolytes on the growth of polyelectrolyte multilayers via layer- by-layer self-assembly from pure aqueous solutions was studied. Multilayers were built from strong polyanions, namely poly(styrenesulfonate) and an exfoliated synthetic hectorite, and cationic copolymers of diallyldimethylammonium chloride (DADMAC) with N-methyl-N-vinylformamide (NMVF) for which the composition and thus the charge density was varied systematically. The analysis of the system {cationic copolymer/poly(styrenesulfonate)} reveals that a critical linear charge density Ïc of 0.036 elementary charge/Å of contour length is necessary to obtain stable multilayer growth in pure water. Above Ïc, the increment of thickness/deposition cycle varies with the linear charge density of the cationic copolymers, in good agreement with current theories of polyelectrolyte solutions. As linear charge density increases, the system passes successively through a charge-dependent ?Debye-Hu ckel? regime and then through a chargeindependent ?strong-screening? regime where counterion condensation dominates the behavior. Analogous results were obtained for the variation of the basal spacing of internally structured hybrid multilayers {cationic copolymer/hectorite}. However, by contrast with the first system, no critical linear charge density was found for the hybrid system. This is explained by additional, nonelectrostatic interactions between the clay platelets and the formamide fragment.
The ralationship between early mother-infant interaction at 3 mo old, biological and psychosocial risks, and later social withdrawal was examined using a hierarchical logistics regression approach. A group of childeren (N=20; aged 4.5-8 yrs old) who were stabily socially withdrawn and a control group of healthy children (N=143) were formed. Variables were entered into the regression models in the follwing order: At first, biological and psychosocial risks and sex, followed by mother and child variables separately, while in a final regression model all of the variables were entered at once. The results show that child behaviors (smilling and gazing) as well as maternal behaviors (facial and motor responsiveness) significantly predict social withdrawal in middle childhood. Among the risks only biolgical risks significantly contribute to later child outcome. These results suggest that a dysfunctional interaction pattern between mother and infant may be a precursor of childhood social withdrawal.
We discuss the evolution of white dwarf containing binaries, in particular such systems consisting of a white dwarf and a main sequence star which have the potential to produce a Type Ia supernova. After investigating current problems in connecting observations of supersoft X-ray sources with such systems, we consider two major problems which theoretical models encounter to produce Chandrasekhar-mass white dwarfs: the helium shell burning instability and the white dwarf spin-up. We conclude by suggesting that the formation of Chandrasekhar-mass white dwarfs may be easier when these two problem are considered simultaneously.
Based on NMR spectroscopic information about the allosamidin-hevamine complex, ab initio MO calcns. of the ring current effect of the arom. moieties of Trp255, Tyr183 and Tyr6 of hevamine were carried out to investigate the role of these amino acid residues in binding interactions with allosamidin in soln. In addn., the intermol. steric compression effect on the 13C chem. shifts of the allosamizoline carbon atoms and the hydrogen bonding to Glu127 was identified. It can be inferred that the binding forces are strongest in the allosamizoline moiety of allosamidin.
We present a data set of images of the gravitationally lensed quasar Q2237+0305, that was obtained at the Apache Point Observatory (APO) between June 1995 and January 1998. Although the images were taken under variable, often poor seeing conditions and with coarse pixel sampling, photometry is possible for the two brighter quasar images A and B with the help of exact quasar image positions from HST observations. We obtain a light curve with 73 data points for each of the images A and B. There is evidence for a long (ga 100 day) brightness peak in image A in 1996 with an amplitude of about 0.4 to 0.5 mag (relative to 1995), which indicates that microlensing has been taking place in the lensing galaxy. Image B does not vary much over the course of the observation period. The long, smooth variation of the light curve is similar to the results from the OGLE monitoring of the system (Wozniak et al. cite{Wozniak00}). Based on observations obtained with the Apache Point Observatory 3.5-meter telescope, which is owned and operated by the Astrophysical Research Consortium.