Dual Beam FIB for Imaging, Nano-Sectioning and Sample Preparation of Spores: Initial Results.

Results from the first use of Focused Ion Beam (FIB) technology to section Bacillus spores at LLNL in a dual-beam (electron and ion) instrument is presented and discussed. With the use of a dual-beam instrument, high resolution imaging of single spores using low voltage scanning electron microscopy followed by FIB sectioning, SEM imaging of internal structure of the same spore is demonstrated to be possible. Additionally, FIB is shown to be able to precisely micro-machine spores thus potentially facilitating micro-scale experiments on single spores

Electrostatic Potentials and Fields in the Vicinity of Engineered Nanostructures

We have developed a method of calculation of the electrostatic potentials and fields in the vicinity of geometrically complex engineered nanostructures comprised of varying materials in electrolytes of arbitrary pH and ionic strength. The method involves direct summation of charged Debye-Hueckel spheres comprising the nanostructural surfaces and, by including charge redistribution on the surface of conducting materials held at constant potential, is applicable to mixed boundary conditions. The method is validated by comparison to analytical solutions for an infinite plane (Gouy-Chapman), an infinite cylinder (Bessel functions) and an infinite plane which contains a hole and which is held at constant potential. Excellent agreement between the potentials obtained by our numerical method and the closed form solutions is found for these conditions. The method is applied to the calculation of the electric field enhancement in the vicinity of a nanomembrane whose pore wall is held at constant charge and whose membrane surfaces are held at constant potential. The electric field is found to be enhanced by the charge buildup in the rim of the hole of the nanomembrane, which redistribution results from the potential being held constant in the conducting region. Ion concentrations are also calculated; positive ion rejection is found to be enhanced by this charge buildup in the region of the rim when a constant positive potential is applied

Spontaneous annihilation of high-density matter in the electroweak theory

In the presence of fermionic matter the topologically distinct vacua of the standard model are metastable and can decay by tunneling through the sphaleron barrier. This process annihilates one fermion per doublet due to the anomalous non-conservation of baryon and lepton currents and is accompanied by a production of gauge and Higgs bosons. We present a numerical method to obtain local bounce solutions which minimize the Euclidean action in the space of all configurations connecting two adjacent topological sectors. These solutions determine the decay rate and the configuration of the fields after the tunneling. We also follow the real time evolution of this configuration and analyze the spectrum of the created bosons. If the matter density exceeds some critical value, the exponentially suppressed tunneling triggers off an avalanche producing an enormous amount of bosons.Comment: 38 pages, 6 Postscript figure

Chemically Specific Cellular Imaging of Biofilm Formation

This document and the accompanying manuscripts summarize the technical accomplishments for our one-year LDRD-ER effort. Biofilm forming microbes have existed on this planet for billions of years and make up 60% of the biological mass on earth. Such microbes exhibit unique biochemical pathways during biofilm formation and play important roles in human health and the environment. Microbial biofilms have been directly implicated in, for example, product contamination, energy losses, and medical infection that cost the loss of human lives and billions of dollars. In no small part due to the lack of detailed understanding, biofilms unfortunately are resistant to control, inhibition, and destruction, either through treatment with antimicrobials or immunological defense mechanisms of the body. Current biofilm research has concentrated on the study of biofilms in the bulk. This is primarily due to the lack of analytical and physical tools to study biofilms non-destructively, in three dimensions, and on the micron or sub-micron scale. This has hindered the development of a clear understanding of either the early stage mechanisms of biofilm growth or the interactions of biofilms with their environment. Enzymatic studies have deduced a biochemical reaction that results in the oxidation of reduced sulfur species with the concomitant reduction of nitrate, a common groundwater pollutant, to dinitrogen gas by the bacterium, Thiobacillus denitrificans (TD). Because of its unique involvement in biologically relevant environmental pathways, TD is scheduled for genome sequencing in the near future by the DOE's Joint Genome Institute and is of interest to DOE's Genomes to Life Program. As our ecosystem is exposed to more and more nitrate contamination large scale livestock and agricultural practices, a further understanding of biofilm formation by organisms that could alleviate these problems is necessary in order to protect out biosphere. However, in order to study this complicated organism, we needed to first turn our attention to a well understood organism. Pseudomonas aeruginosa (PA) is a well-studied organism and will be used to compare our results with others. Then, we will turn our attention to TD. It is expected that the research performed will provide key data to validate biochemical studies of TD and result in high profile publications in leading journals. For this project, our ultimate goal was to combine both Magnetic Resonance Imaging (MRI) and Nuclear Magnetic Resonance (NMR) experimental analysis with computer simulations to provide unique 3D molecular structural, dynamics, and functional information on the order of microns for this DOE mission relevant microorganism, T. denitrificans. For FY05, our goals were to: (1) Determine proper media for optimal growth of PA; growth rate measurements in that media and characterization of metabolite signatures during growth via {sup 1}H and {sup 13}C NMR, (2) Determine and build mineral, metal, and implant material surfaces to support growth of PA, (3) Implementing new MRI sequences to image biofilms more efficiently and increase resolution with new hardware design, (4) Develop further diffusion and flow MRI measurements of biofilms and biofilm formation with different MRI pulse sequences and different hardware design, and (5) Develop a zero dimension model of the rate of growth and the metabolite profiles of PA. Our major accomplishments are discussed in the following text. However, the bulk of this work is described in the attached manuscript entitled, ''NMR Metabolomics of Planktonic and Biofilm Modes of Growth in Pseudomonas aeruginosa''. This paper will be submitted to the Journal of Bacteriology in coming weeks. In addition, this one-year effort has lead to our incorporation into the Enhanced Surveillance Campaign during FY05 for some proof-of-principle MRI measurements on polymers. We are currently using similar methods to evaluate these polymers. In addition, this work on MRI measurements on polymers has lead to a paper entitled, ''Characterization of local deformation in filled-silicone elastomers subject to high strain NMR MOUSE and Magnetic Resonance Imaging as a diagnostic tool for detection of inhomogeneities''

Evidence of gating in hundred nanometer diameter pores: an experimental and theoretical study

We report on the observation of an unexpected gating mechanism at the 100 nm scale on track-etched polycarbonate membranes. Transport measurements of methyl viologen performed by absorption spectroscopy under various pH conditions demonstrated that perfect gating was achieved for 100 nm diameter pores at pH 2, while the positively charged molecular ions moved through the membrane according to diffusion laws at pH 5. An oppositely charged molecular ion, naphthalene disulfonate, in the same membrane, showed the opposite trend: diffusion of the negative ion at pH 2 and perfect gating at pH 5. The influence of parameters such as ionic strength and membrane surface coating were also investigated. A theoretical study of the system shows that at this larger length scale the magnitude of the electric field in the vicinity of the pores is too small to account for the experimental observations, rather, it is the surface trapping of the mobile ion (Cl{sup -} or Na{sup +}) which gives rise to the gating phenomena. This surprising effect might have potential applications for high-throughput separation of large molecules and bio-organisms

Estudo multicêntrico comparativo de quatro diferentes tipos de sensores: atividade, acelerômetro, temperatura e período de pré-ejeçao

Recentemente diferentes princípios têm sido utilizados para estimular o coraçao na tentativa de recuperar o débito cardíaco. Neste estudo multicêntrico, foram comparadas as respostas à estimulaçao por 4 tipos de sensores, sendo 3 tipos de resposta de alça aberta (atividade física, acelerômetro e temperatura venosa central) implantados em 30 (SSIR-8 e DDDR-22), 9 (SSIR-5 -e DDDR-4) e 12 (SSIR) pacientes respectivamente. Um outro sensor do tipo alça fechada, sensível às variaçoes do sistema nervoso autônomo, foi implantado em 57 pacientes, todos no modo DDDR. Os resultados obtidos durante a realizaçao de atividade física diária, de teste ergométrico e de Holter de 24 horas foram comparados, sendo possível observar uma maior fidelidade na curva de resposta de freqüência frente a atividade física, nos pacientes submetidos à estimulaçao de alça fechada

Estudo multicêntrico comparativo de quatro diferentes tipos de sensores: atividade, acelerômetro, temperatura e período de pré-ejeçao

Recentemente diferentes princípios têm sido utilizados para estimular o coraçao na tentativa de recuperar o débito cardíaco. Neste estudo multicêntrico, foram comparadas as respostas à estimulaçao por 4 tipos de sensores, sendo 3 tipos de resposta de alça aberta (atividade física, acelerômetro e temperatura venosa central) implantados em 30 (SSIR-8 e DDDR-22), 9 (SSIR-5 -e DDDR-4) e 12 (SSIR) pacientes respectivamente. Um outro sensor do tipo alça fechada, sensível às variaçoes do sistema nervoso autônomo, foi implantado em 57 pacientes, todos no modo DDDR. Os resultados obtidos durante a realizaçao de atividade física diária, de teste ergométrico e de Holter de 24 horas foram comparados, sendo possível observar uma maior fidelidade na curva de resposta de freqüência frente a atividade física, nos pacientes submetidos à estimulaçao de alça fechada

SOCS2-Induced Proteasome-Dependent TRAF6 Degradation: A Common Anti-Inflammatory Pathway for Control of Innate Immune Responses

Pattern recognition receptors and receptors for pro-inflammatory cytokines provide critical signals to drive the development of protective immunity to infection. Therefore, counter-regulatory pathways are required to ensure that overwhelming inflammation harm host tissues. Previously, we showed that lipoxins modulate immune response during infection, restraining inflammation during infectious diseases in an Aryl hydrocarbon receptor (AhR)/suppressors of cytokine signaling (SOCS)2-dependent-manner. Recently, Indoleamine-pyrrole 2,3- dioxygenase (IDO)-derived tryptophan metabolites, including L-kynurenine, were also shown to be involved in several counter-regulatory mechanisms. Herein, we addressed whether the intracellular molecular events induced by lipoxins mediating control of innate immune signaling are part of a common regulatory pathway also shared by L-kynurenine exposure. We demonstrate that Tumor necrosis factor receptor-associated factor (TRAF)6 – member of a family of adapter molecules that couple the TNF receptor and interleukin-1 receptor/Toll-like receptor families to intracellular signaling events essential for the development of immune responses – is targeted by both lipoxins and L-kynurenine via an AhR/SOCS2-dependent pathway. Furthermore, we show that LXA4- and L-kynurenine-induced AhR activation, its subsequent nuclear translocation, leading SOCS2 expression and TRAF6 Lys47-linked poly-ubiquitination and proteosome-mediated degradation of the adapter proteins. The in vitro consequences of such molecular interactions included inhibition of TLR- and cytokine receptor-driven signal transduction and cytokine production. Subsequently, in vivo proteosome inhibition led to unresponsiveness to lipoxins, as well as to uncontrolled pro-inflammatory reactions and elevated mortality during toxoplasmosis. In summary, our results establish proteasome degradation of TRAF6 as a key molecular target for the anti-inflammatory pathway triggered by lipoxins and L-kynurenine, critical counter-regulatory mediators in the innate and adaptive immune systems

The drivers and impacts of Amazon forest degradation

Approximately 2.5 × 10 6 square kilometers of the Amazon forest are currently degraded by fire, edge effects, timber extraction, and/or extreme drought, representing 38% of all remaining forests in the region. Carbon emissions from this degradation total up to 0.2 petagrams of carbon per year (Pg C year −1 ), which is equivalent to, if not greater than, the emissions from Amazon deforestation (0.06 to 0.21 Pg C year −1 ). Amazon forest degradation can reduce dry-season evapotranspiration by up to 34% and cause as much biodiversity loss as deforestation in human-modified landscapes, generating uneven socioeconomic burdens, mainly to forest dwellers. Projections indicate that degradation will remain a dominant source of carbon emissions independent of deforestation rates. Policies to tackle degradation should be integrated with efforts to curb deforestation and complemented with innovative measures addressing the disturbances that degrade the Amazon forest

The drivers and impacts of Amazon forest degradation

BACKGROUND: Most analyses of land-use and land-cover change in the Amazon forest have focused on the causes and effects of deforestation. However, anthropogenic disturbances cause degradation of the remaining Amazon forest and threaten their future. Among such disturbances, the most important are edge effects (due to deforestation and the resulting habitat fragmentation), timber extraction, fire, and extreme droughts that have been intensified by human-induced climate change. We synthesize knowledge on these disturbances that lead to Amazon forest degradation, including their causes and impacts, possible future extents, and some of the interventions required to curb them. ADVANCES: Analysis of existing data on the extent of fire, edge effects, and timber extraction between 2001 and 2018 reveals that 0.36 ×106 km2 (5.5%) of the Amazon forest is under some form of degradation, which corresponds to 112% of the total area deforested in that period. Adding data on extreme droughts increases the estimate of total degraded area to 2.5 ×106 km2, or 38% of the remaining Amazonian forests. Estimated carbon loss from these forest disturbances ranges from 0.05 to 0.20 Pg C year−1 and is comparable to carbon loss from deforestation (0.06 to 0.21 Pg C year−1). Disturbances can bring about as much biodiversity loss as deforestation itself, and forests degraded by fire and timber extraction can have a 2 to 34% reduction in dry-season evapotranspiration. The underlying drivers of disturbances (e.g., agricultural expansion or demand for timber) generate material benefits for a restricted group of regional and global actors, whereas the burdens permeate across a broad range of scales and social groups ranging from nearby forest dwellers to urban residents of Andean countries. First-order 2050 projections indicate that the four main disturbances will remain a major threat and source of carbon fluxes to the atmosphere, independent of deforestation trajectories. OUTLOOK: Whereas some disturbances such as edge effects can be tackled by curbing deforestation, others, like constraining the increase in extreme droughts, require additional measures, including global efforts to reduce greenhouse gas emissions. Curbing degradation will also require engaging with the diverse set of actors that promote it, operationalizing effective monitoring of different disturbances, and refining policy frameworks such as REDD+. These will all be supported by rapid and multidisciplinary advances in our socioenvironmental understanding of tropical forest degradation, providing a robust platform on which to co-construct appropriate policies and programs to curb it