Laboratory Directed Research and Development Program FY 2007

Report on Ernest Orlando Lawrence Berkeley National Laboratory Laboratory Directed Research and Development Program FY 200

Nanoflow hydrodynamics

We show by nonequilibrium molecular dynamics simulations that the Navier-Stokes equation does not correctly describe water flow in a nanoscale geometry. It is argued that this failure reflects the fact that the coupling between the intrinsic rotational and translational degrees of freedom becomes important for nanoflows. The coupling is correctly accounted for by the extended Navier-Stokes equations that include the intrinsic angular momentum as an independent hydrodynamic degree of freedom

Silicon Drift Detector Readout Electronics for a Compton Camera

A prototype detector for Compton camera imaging is under development. A monolithic array of 19 channel Silicon drift detector with on-chip electronics is going to be used as a scatter detector for the prototype system. Custom designed analog and digital readout electronics for this detector was first tested by using a single cell Silicon drift detector. This paper describes the readout architecture and presents the results of the measurement.Comment: 10 pages, 9 figures, submitted to Nucl. Instr. Meth.

Extracellular Matrix Hydrogel Promotes Tissue Remodeling, Arteriogenesis, and Perfusion in a Rat Hindlimb Ischemia Model.

ObjectiveThis study aimed to examine acellular extracellular matrix based hydrogels as potential therapies for treating peripheral artery disease (PAD). We tested the efficacy of using a tissue specific injectable hydrogel, derived from decellularized porcine skeletal muscle (SKM), compared to a new human umbilical cord derived matrix (hUC) hydrogel, which could have greater potential for tissue regeneration because of its young tissue source age.BackgroundThe prevalence of PAD is increasing and can lead to critical limb ischemia (CLI) with potential limb amputation. Currently there are no therapies for PAD that effectively treat all of the underlying pathologies, including reduced tissue perfusion and muscle atrophy.MethodsIn a rodent hindlimb ischemia model both hydrogels were injected 1-week post-surgery and perfusion was regularly monitored with laser speckle contrast analysis (LASCA) to 35 days post-injection. Histology and immunohistochemistry were used to assess neovascularization and muscle health. Whole transcriptome analysis was further conducted on SKM injected animals on 3 and 10 days post-injection.ResultsSignificant improvements in hindlimb tissue perfusion and perfusion kinetics were observed with both biomaterials. End point histology indicated this was a result of arteriogenesis, rather than angiogenesis, and that the materials were biocompatible. Skeletal muscle fiber morphology analysis indicated that the muscle treated with the tissue specific, SKM hydrogel more closely matched healthy tissue morphology. Short term histology also indicated arteriogenesis rather than angiogenesis, as well as improved recruitment of skeletal muscle progenitors. Whole transcriptome analysis indicated that the SKM hydrogel caused a shift in the inflammatory response, decreased cell death, and increased blood vessel and muscle development.ConclusionThese results show the efficacy of an injectable ECM hydrogel alone as a potential therapy for treating patients with PAD. Our results indicate that the SKM hydrogel improved functional outcomes through stimulation of arteriogenesis and muscle progenitor cell recruitment

Identification of a bacteriocin and its cognate immunity factor expressed by Moraxella catarrhalis

<p>Abstract</p> <p>Background</p> <p>Bacteriocins are antimicrobial proteins and peptides ribosomally synthesized by some bacteria which can effect both intraspecies and interspecies killing.</p> <p>Results</p> <p><it>Moraxella catarrhalis </it>strain E22 containing plasmid pLQ510 was shown to inhibit the growth of <it>M. catarrhalis </it>strain O35E. Two genes (<it>mcbA </it>and <it>mcbB</it>) in pLQ510 encoded proteins predicted to be involved in the secretion of a bacteriocin. Immediately downstream from these two genes, a very short ORF (<it>mcbC</it>) encoded a protein which had some homology to double-glycine bacteriocins produced by other bacteria. A second very short ORF (<it>mcbI</it>) immediately downstream from <it>mcbC </it>encoded a protein which had no significant similarity to other proteins in the databases. Cloning and expression of the <it>mcbI </it>gene in <it>M. catarrhalis </it>O35E indicated that this gene encoded the cognate immunity factor. Reverse transcriptase-PCR was used to show that the <it>mcbA</it>, <it>mcbB</it>, <it>mcbC</it>, and <it>mcbI </it>ORFs were transcriptionally linked. This four-gene cluster was subsequently shown to be present in the chromosome of several <it>M. catarrhalis </it>strains including O12E. Inactivation of the <it>mcbA</it>, <it>mcbB</it>, or <it>mcbC </it>ORFs in <it>M. catarrhalis </it>O12E eliminated the ability of this strain to inhibit the growth of <it>M. catarrhalis </it>O35E. In co-culture experiments involving a <it>M. catarrhalis </it>strain containing the <it>mcbABCI </it>locus and one which lacked this locus, the former strain became the predominant member of the culture after overnight growth in broth.</p> <p>Conclusion</p> <p>This is the first description of a bacteriocin and its cognate immunity factor produced by <it>M. catarrhalis</it>. The killing activity of the McbC protein raises the possibility that it might serve to lyse other <it>M. catarrhalis </it>strains that lack the <it>mcbABCI </it>locus, thereby making their DNA available for lateral gene transfer.</p

How a Diverse Research Ecosystem Has Generated New Rehabilitation Technologies: Review of NIDILRR’s Rehabilitation Engineering Research Centers

Over 50 million United States citizens (1 in 6 people in the US) have a developmental, acquired, or degenerative disability. The average US citizen can expect to live 20% of his or her life with a disability. Rehabilitation technologies play a major role in improving the quality of life for people with a disability, yet widespread and highly challenging needs remain. Within the US, a major effort aimed at the creation and evaluation of rehabilitation technology has been the Rehabilitation Engineering Research Centers (RERCs) sponsored by the National Institute on Disability, Independent Living, and Rehabilitation Research. As envisioned at their conception by a panel of the National Academy of Science in 1970, these centers were intended to take a “total approach to rehabilitation”, combining medicine, engineering, and related science, to improve the quality of life of individuals with a disability. Here, we review the scope, achievements, and ongoing projects of an unbiased sample of 19 currently active or recently terminated RERCs. Specifically, for each center, we briefly explain the needs it targets, summarize key historical advances, identify emerging innovations, and consider future directions. Our assessment from this review is that the RERC program indeed involves a multidisciplinary approach, with 36 professional fields involved, although 70% of research and development staff are in engineering fields, 23% in clinical fields, and only 7% in basic science fields; significantly, 11% of the professional staff have a disability related to their research. We observe that the RERC program has substantially diversified the scope of its work since the 1970’s, addressing more types of disabilities using more technologies, and, in particular, often now focusing on information technologies. RERC work also now often views users as integrated into an interdependent society through technologies that both people with and without disabilities co-use (such as the internet, wireless communication, and architecture). In addition, RERC research has evolved to view users as able at improving outcomes through learning, exercise, and plasticity (rather than being static), which can be optimally timed. We provide examples of rehabilitation technology innovation produced by the RERCs that illustrate this increasingly diversifying scope and evolving perspective. We conclude by discussing growth opportunities and possible future directions of the RERC program

The 0.5MJ transiting exoplanet WASP-13b

We report the discovery of WASP-13b, a low-mass M_{\rm p} = 0.46 ^_~M_J transiting exoplanet with an orbital period of 4.35298 $\pm$ 0.00004 days. The transit has a depth of 9 mmag, and although our follow-up photometry does not allow us to constrain the impact parameter well (0 < b < 0.46), with radius in the range $R_{\rm p}$ ~ 1.06-1.21 RJ the location of WASP-13b in the mass-radius plane is nevertheless consistent with H/He-dominated, irradiated, low core mass and core-free theoretical models. The G1V host star is similar to the Sun in mass (M__ ~M_{\odot}) and metallicity ([M/H] = 0.0$\pm$0.2), but is possibly older ( 8.5^_{\rm -4.9} Gyr)

WASP-44b, WASP-45b and WASP-46b: three short-period, transiting extrasolar planets

We report the discovery of three extrasolar planets that transit their moderately bright (Vmag = 12-13) host stars. WASP-44b is a 0.89-MJup planet in a 2.42-day orbit around a G8V star. WASP-45b is a 1.03-MJup planet which passes in front of the limb of its K2V host star every 3.13 days. Weak Ca II H+K emission seen in the spectra of WASP-45 suggests the star is chromospherically active. WASP-46b is a 2.10-MJup planet in a 1.43-day orbit around a G6V star. Rotational modulation of the light curves of WASP-46 and weak Ca II H+K emission in its spectra show the star to be photospherically and chromospherically active. We imposed circular orbits in our analyses as the radial velocity data are consistent with (near-)circular orbits, as could be expected from both empirical and tidal-theory perspectives for such short-period, Jupiter-mass planets. We discuss the impact of fitting for eccentric orbits for such planets when not supported by the data. The derived planetary and stellar radii depend on the fitted eccentricity and these parameters inform intense theoretical efforts concerning tidal circularisation and heating, bulk planetary composition and the observed systematic errors in planetary and stellar radii. As such, we recommend exercising caution in fitting the orbits of short period, Jupiter-mass planets with an eccentric model when there is no evidence of non-circularity.Comment: 12 pages, 8 figures, 6 tables. As accepted for publication in MNRA