Conserved Amino Acids in Each Subunit of the Heteroligomeric tRNA m\u3csup\u3e1\u3c/sup\u3eA58 Mtase from \u3cem\u3eSaccharomyces cerevisiae\u3c/em\u3e Contribute to tRNA Binding

In Saccharomyces cerevisiae, a two-subunit methyltransferase (Mtase) encoded by the essential genes TRM6 and TRM61 is responsible for the formation of 1-methyladenosine, a modified nucleoside found at position 58 in tRNA that is critical for the stability of . The crystal structure of the homotetrameric m1A58 tRNA Mtase from Mycobacterium tuberculosis, TrmI, has been solved and was used as a template to build a model of the yeast m1A58 tRNA Mtase heterotetramer. We altered amino acids in TRM6 and TRM61 that were predicted to be important for the stability of the heteroligomer based on this model. Yeast strains expressing trm6 and trm61 mutants exhibited growth phenotypes indicative of reduced m1A formation. In addition, recombinant mutant enzymes had reduced in vitro Mtase activity. We demonstrate that the mutations introduced do not prevent heteroligomer formation and do not disrupt binding of the cofactor S-adenosyl-l-methionine. Instead, amino acid substitutions in either Trm6p or Trm61p destroy the ability of the yeast m1A58 tRNA Mtase to bind , indicating that each subunit contributes to tRNA binding and suggesting a structural alteration of the substrate-binding pocket occurs when these mutations are present

A Compact Microchip-Based Atomic Clock Based on Ultracold Trapped Rb Atoms

We propose a compact atomic clock based on ultracold Rb atoms that are magnetically trapped near the surface of an atom microchip. An interrogation scheme that combines electromagnetically-induced transparency (EIT) with Ramsey's method of separated oscillatory fields can achieve atomic shot-noise level performance of 10^{-13}/sqrt(tau) for 10^6 atoms. The EIT signal can be detected with a heterodyne technique that provides noiseless gain; with this technique the optical phase shift of a 100 pW probe beam can be detected at the photon shot-noise level. Numerical calculations of the density matrix equations are used to identify realistic operating parameters at which AC Stark shifts are eliminated. By considering fluctuations in these parameters, we estimate that AC Stark shifts can be canceled to a level better than 2*10^{-14}. An overview of the apparatus is presented with estimates of duty cycle and power consumption.Comment: 15 pages, 11 figures, 5 table

Combined visible and near-infrared OPA for wavelength scaling experiments in strong-field physics

We report the operation of an optical parametric amplifier (OPA) capable of producing gigawatt peak-power laser pulses with tunable wavelength in either the visible or near-infrared spectrum. The OPA has two distinct operation modes (i) generation of >350 uJ, sub 100 fs pulses, tunable between 1250 - 1550 nm; (ii) generation of >190 uJ, sub 150 fs pulses tunable between 490 - 530 nm. We have recorded high-order harmonic spectra over a wide range of driving wavelengths. This flexible source of femtosecond pulses presents a useful tool for exploring the wavelength-dependence of strong-field phenomena, in both the multi-photon and tunnel ionization regimes.Comment: 14 pages, 9 figures, This paper was published in Proceedings of SPIE 10088, Nonlinear Frequency Generation and Conversion: Materials and Devices XVI, doi 10.1117/12.225077

Efficient Immunization Strategies for Computer Networks and Populations

We present an effective immunization strategy for computer networks and populations with broad and, in particular, scale-free degree distributions. The proposed strategy, acquaintance immunization, calls for the immunization of random acquaintances of random nodes (individuals). The strategy requires no knowledge of the node degrees or any other global knowledge, as do targeted immunization strategies. We study analytically the critical threshold for complete immunization. We also study the strategy with respect to the susceptible-infected-removed epidemiological model. We show that the immunization threshold is dramatically reduced with the suggested strategy, for all studied cases.Comment: Revtex, 5 pages, 4 ps fig

A Mesoscopic Resonating Valence Bond system on a triple dot

We introduce a mesoscopic pendulum from a triple dot. The pendulum is fastened through a singly-occupied dot (spin qubit). Two other strongly capacitively islands form a double-dot charge qubit with one electron in excess oscillating between the two low-energy charge states (1,0) and (0,1); this embodies the weight of the pendulum. The triple dot is placed between two superconducting leads as shown in Fig. 1. Under well-defined conditions, the main proximity effect stems from the injection of resonating singlet (valence) bonds on the triple dot. This gives rise to a Josephson current that is charge- and spin-dependent. Consequences in a SQUID-geometry are carefully investigated.Comment: final version to appear in PR

A new approach for performing contamination control bakeouts in JPL thermal vacuum test chambers

Contamination control requirements for the Wide Field/Planetary Camera II (WF/PC II) are necessarily stringent to protect against post-launch contamination of the sensitive optical surfaces, particularly the cold charge coupled device (CCD) imaging surfaces. Typically, thermal vacuum test chambers have employed a liquid nitrogen (LN2) cold trap to collect outgassed contaminants. This approach has the disadvantage of risking recontamination of the test article from shroud offgassing during post-test warmup of the chamber or from any shroud warming of even a few degrees during the bakeout process. By using an enclave, essentially a chamber within a chamber, configured concentrically and internally within an LN2 shroud, a method was developed, based on a design concept by Taylor, for preventing recontamination of test articles during bakeouts and subsequent post-test warmup of the vacuum chamber. Enclaves for testing WF/PC II components were designed and fabricated, then installed in three of JPL's Environmental Test Lab chambers. The design concepts, operating procedures, and test results of this development are discussed

Spreading of Persistent Infections in Heterogeneous Populations

Up to now, the effects of having heterogeneous networks of contacts have been studied mostly for diseases which are not persistent in time, i.e., for diseases where the infectious period can be considered very small compared to the lifetime of an individual. Moreover, all these previous results have been obtained for closed populations, where the number of individuals does not change during the whole duration of the epidemics. Here, we go one step further and analyze, both analytically and numerically, a radically different kind of diseases: those that are persistent and can last for an individual's lifetime. To be more specific, we particularize to the case of Tuberculosis' (TB) infection dynamics, where the infection remains latent for a period of time before showing up and spreading to other individuals. We introduce an epidemiological model for TB-like persistent infections taking into account the heterogeneity inherent to the population structure. This sort of dynamics introduces new analytical and numerical challenges that we are able to sort out. Our results show that also for persistent diseases the epidemic threshold depends on the ratio of the first two moments of the degree distribution so that it goes to zero in a class of scale-free networks when the system approaches the thermodynamic limit.Comment: 12 pages and 2 figures. Revtex format. Submitted for publication