Elucidating Ribosomes-Genetic Studies of the ATPase Uup and the Ribosomal Protein L1.

The ribosome is comprised of two subunits, formed from three ribosomal RNAs and many ribosomal proteins. The two subunits come together around a messenger RNA during initiation, and catalyze the addition of sequential amino acids to a growing polypeptide chain as directed by the messenger RNA during elongation. While much of the ribosome is a relatively rigid molecular machine, there are two flexible protrusions comprised of rRNA and ribosomal proteins. One of these protrusions is the L1 arm where deacylated tRNAs leave the ribosome. The contributions of the L1 stalk and associating factors are unclear. In this work, I report that loss of the protein L1 results in changes in translation accuracy and perturbation of the ribosome profile. I also find that proteins involved in RpoS regulation/regulon, proteins affecting the structure of the ribosome in the vicinity of the active site, and proteins affecting DNA replication are able to suppress, when at high copy, the previously-­‐reported slow growth the of ΔrplA (encoding L1) mutant. Recent studies have revealed that translation factors act on the L1 arm side of the ribosome. I have characterized Uup, an E. coli ABCF protein that shares many of the residues involved in binding to tRNAfMet and ribosomal protein L1 in the closely related E. coli ABCF protein EttA. Exogenous Uup suppresses many phenotypes caused by deletion of tthe elongation family GTPase BipA, including a growth-­dependent ribosome profile defect. Both translation of reporter plasmids and translating ribosomes are reduced in Δuup. While Δuup and ΔettA show different phenotypes in multiple assays, each can suppress defects resulting from loss of the other. I propose that Uup, as shown for EttA, can promote formation of the first peptide bond in the elongation phase of translation. This adds to the short but rapidly growing list of translation factors regulating translation at the E­‐site.PHDMolecular, Cellular and Developmental BiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/116786/1/katharyn_1.pd

Microstructural Evolution and Phase Formation in Rapidly Solidified Ni-25.3 At. Pct Si Alloy

The drop-tube technique was used to solidify droplets of the Ni-25.3 at. pct Si alloy at high cooling rates. XRD, SEM, and TEM analysis revealed that the metastable phase, Ni25Si9, formed as the dominant phase in all ranges of the droplets, with γ-Ni31Si12 and β 1-Ni3Si also being present. Three different microstructures were observed: the regular and anomalous eutectic structures and near single-phase structure containing small inclusions of a second phase, termed here as heteroclite structure. Both eutectic structures comprise alternating lamellae of Ni25Si9 and β 1-Ni3Si, which, we conjecture, is a consequence of an unobserved eutectic reaction between the Ni25Si9 and β 1-Ni3Si phases. The matrix of the heteroclite structure is also identified as the metastable phase Ni25Si9, in which twined growth is observed in the TEM. As the cooling rate is increased (particle size decreased), the proportion of droplets displaying the entire heteroclite structure tends to increase, with its fraction increasing from 13.91 pct (300 to 500 µm) to 40.10 pct (75 to 106 µm). The thermodynamic properties of the Ni25Si9 phase were also studied by in-situ heating during XRD analysis and by DTA. This showed the decomposition of Ni25Si9 to β 1 and γ-Ni31Si12 for temperatures in excess of 790 K (517 °C)

Maximal entanglement of squeezed vacuum states via swapping with number-phase measurement

We propose a method to refine entanglement via swapping from a pair of squeezed vacuum states by performing the Bell measurement of number sum and phase difference. The resultant states are maximally entangled by adjusting the two squeezing parameters to the same value. We then describe the teleportation of number states by using the entangled states prepared in this way.Comment: 4 pages, 1 PS figure, RevTe

ECOSYSTEM APPROACH TO FISHERIES MANAGEMENT IN THE SOUTHERN BENGUELA: A WORKSHOP OVERVIEW

A workshop was held in Cape Town in December 2002 to introduce the concept of an ecosystem approach to fisheries (EAF) management in the southern Benguela, and to examine the options for implementing an EAF in South Africa. The workshop considered alternative modelling approaches that may have potential for an ecosystem approach to fisheries. Consensus was that an EAF should be implemented in South Africa through an incremental process, starting immediately. Ecosystem models can be used to provide guidance on reference points and broader management objectives still currently set on the basis of single-species assessments. Such additional information would be incorporated into the decision-making process, and comments received at a management level would also feed back to the modelling process. It was suggested that, at the scientific level, an ecosystem modelling perspective could be incorporated into existing single-species management recommendations by testing them with ecosystem models. Compilation of an “ecosystem considerations” document was recommended to initiate the process. It was proposed that a dedicated EAF working group be established in South Africa to advise on the process of implementing an EAF in the various fisheries, and to provide overarching guidance and to ensure consistency in integrating existing data and information for informing the management process

Using ultra-thin parylene films as an organic gate insulator in nanowire field-effect transistors

We report the development of nanowire field-effect transistors featuring an ultra-thin parylene film as a polymer gate insulator. The room temperature, gas-phase deposition of parylene is an attractive alternative to oxide insulators prepared at high temperatures using atomic layer deposition. We discuss our custom-built parylene deposition system, which is designed for reliable and controlled deposition of <100 nm thick parylene films on III-V nanowires standing vertically on a growth substrate or horizontally on a device substrate. The former case gives conformally-coated nanowires, which we used to produce functional $\Omega$-gate and gate-all-around structures. These give sub-threshold swings as low as 140 mV/dec and on/off ratios exceeding $10^3$ at room temperature. For the gate-all-around structure, we developed a novel fabrication strategy that overcomes some of the limitations with previous lateral wrap-gate nanowire transistors. Finally, we show that parylene can be deposited over chemically-treated nanowire surfaces; a feature generally not possible with oxides produced by atomic layer deposition due to the surface `self-cleaning' effect. Our results highlight the potential for parylene as an alternative ultra-thin insulator in nanoscale electronic devices more broadly, with potential applications extending into nanobioelectronics due to parylene's well-established biocompatible properties

Evaluating antibiotics for use in medicine using a poloxamer biofilm model

BACKGROUND: Wound infections, due to biofilms, are a constant problem because of their recalcitrant nature towards antibiotics. Appropriate antibiotic selection for the treatment of these biofilm infections is important. The traditional in vitro disc diffusion method for antibiotic selection uses bacterial cultures grown on agar plates. However, the form of bacterial growth on agar is not representative of how bacteria grow in wounds and other tissue sites as here bacteria grow naturally in a biofilm. The aim of this research was to test a more appropriate method for testing antimicrobial efficacy on biofilms and compare with the standard methods used for antibiotic sensitivity testing. METHODS: Outer Membrane Protein analysis was performed on E.coli, Staphylococcus aureus, Pseudomonas aeruginosa, Proteus mirabilis and Acinetobacter juni when grown on Mueller Hinton agar ('quasi-biofilm state') and 30% Poloxamer hydrogel ('true- biofilm state). Susceptibility to antibiotics on 28 clinical isolates was determined using the modified Kirby Bauer disc diffusion method, on agar and 30% Poloxamer. RESULTS: Similar outer membrane proteins [OMPs] were identified in bacteria grown in a biofilm state and on a 30% poloxamer hydrogel, which were very different to the OMPs identified in bacteria grown on Mueller-Hinton agar and broth. There was a significant difference between the means of the clearance zones around the antibiotic discs on standard agar and poloxamer gels [P < 0.05]. The zones of clearance were generally smaller for poloxamer-grown bacteria than those grown on standard agar. Diffusion distances of various antibiotics through agar and 30% poloxamer showed no significant difference [P > 0.05]. CONCLUSION: The findings of this experiment suggest that poloxamer gel could be used as an appropriate medium on which to conduct biofilm antibiotic susceptibility tests as it enables bacteria to be grown in a state representative of the infected surface from which the culture was taken