Buried refractive microlenses formed by selective oxidation of AlGaAs

Includes bibliographical references (page 1408).The authors demonstrate a novel method of fabricating buried refractive microlenses formed by selective oxidation of AlGaAs epitaxial layers on a GaAs substrate. By appropriate tailoring of the Al mole fraction in the vertical direction, a lens-shaped oxidation shape was achieved. Performance of the microlenses formed in this way was experimentally evaluated at 980nm, and modelled theoretically

The molecular basis of host specialization in bean pathovars of Pseudomonas syringae

Biotrophic phytopathogens are typically limited to their adapted host range. In recent decades, investigations have teased apart the general molecular basis of intraspecific variation for innate immunity of plants, typically involving receptor proteins that enable perception of pathogen-associated molecular patterns or avirulence elicitors from the pathogen as triggers for defense induction. However, general consensus concerning evolutionary and molecular factors that alter host range across closely related phytopathogen isolates has been more elusive. Here, through genome comparisons and genetic manipulations, we investigate the underlying mechanisms that structure host range across closely related strains of Pseudomonas syringae isolated from different legume hosts. Although type III secretionindependent virulence factors are conserved across these three strains, we find that the presence of two genes encoding type III effectors (hopC1 and hopM1) and the absence of another (avrB2) potentially contribute to host range differences between pathovars glycinea and phaseolicola. These findings reinforce the idea that a complex genetic basis underlies host range evolution in plant pathogens. This complexity is present even in host–microbe interactions featuring relatively little divergence among both hosts and their adapted pathogens

General N-and O-linked glycosylation of lipoproteins in mycoplasmas and role of exogenous oligosaccharide

The lack of a cell wall, flagella, fimbria, and other extracellular appendages and the possession of only a single membrane render the mycoplasmas structurally simplistic and ideal model organisms for the study of glycoconjugates. Most species have genomes of about 800 kb and code for few proteins predicted to have a role in glycobiology. The murine pathogens Mycoplasma arthritidis and Mycoplasma pulmonis have only a single gene annotated as coding for a glycosyltransferase but synthesize glycolipid, polysaccharide and glycoproteins. Previously, it was shown that M. arthritidis glycosylated surface lipoproteins through O-linkage. In the current study, O-linked glycoproteins were similarly found in M. pulmonis and both species of mycoplasma were found to also possess N-linked glycans at residues of asparagine and glutamine. Protein glycosylation occurred at numerous sites on surface-exposed lipoproteins with no apparent amino acid sequence specificity. The lipoproteins of Mycoplasma pneumoniae also are glycosylated. Glycosylation was dependent on the glycosidic linkages from host oligosaccharides. As far as we are aware, N-linked glycoproteins have not been previously described in Gram-positive bacteria, the organisms to which the mycoplasmas are phylogenetically related. The findings indicate that the mycoplasma cell surface is heavily glycosylated with implications for the modulation of mycoplasma-host interactions

Diffusion MR Characteristics Following Concurrent Radiochemotherapy Predicts Progression-Free and Overall Survival in Newly Diagnosed Glioblastoma.

The standard of care for newly diagnosed glioblastoma (GBM) is surgery, then radiotherapy (RT) with concurrent temozolomide (TMZ), followed by adjuvant TMZ. We hypothesized patients with low diffusivity measured using apparent diffusion coefficient (ADC) histogram analysis evaluated after RT+TMZ, prior to adjuvant TMZ, would have a significantly shorter progression-free (PFS) and overall survival (OS). To test this hypothesis we evaluated 120 patients with newly diagnosed GBM receiving RT+TMZ followed by adjuvant TMZ. MRI was performed after completion of RT+TMZ, prior to initiation of adjuvant TMZ. A double Gaussian mixed model was used to describe the ADC histograms within the enhancing tumor, where ADCL and ADCH were defined as the mean ADC value of the lower and higher Gaussian distribution, respectively. An ADCL value of 1.0 um2/ms and ADCH value of 1.6 um2/ms were used to stratify patients into high and low risk categories. Results suggest patients with low ADCL had significantly shorter PFS (Cox Hazard Ratio = 0.12, P = 0.0006). OS was significantly shorter with low ADCL tumors, showing a median OS of 407 vs. 644 days (Cox Hazard Ratio = 0.31, P = 0.047). ADCH was not predictive of PFS or OS when accounting for age and ADCL. In summary, newly diagnosed glioblastoma patients with low ADCL after completion of RT+TMZ are likely to progress and die earlier than patients with higher ADCL. Results suggest ADC histogram analysis may be useful for patient risk stratification following completion of RT+TMZ

Combined eDNA and Acoustic Analysis Reflects Diel Vertical Migration of Mixed Consortia in the Gulf of Mexico

Oceanic diel vertical migration (DVM) constitutes the daily movement of various mesopelagic organisms migrating vertically from depth to feed in shallower waters and return to deeper water during the day. Accurate classification of taxa that participate in DVM remains non-trivial, and there can be discrepancies between methods. DEEPEND consortium (www.deependconsortium.org) scientists have been characterizing the diversity and trophic structure of pelagic communities in the northern Gulf of Mexico (nGoM). Profiling has included scientific echosounders to provide accurate and quantitative estimates of organismal density and timing as well as quantitative net sampling of micronekton. The use of environmental DNA (eDNA) can detect uncultured microbial taxa and the remnants that larger organisms leave behind in the environment. eDNA offers the potential to increase understanding of the DVM and the organisms that participate. Here we used real-time shipboard echosounder data to direct the sampling of eDNA in seawater at various time-points during the ascending and descending DVM. This approach allowed the observation of shifts in eDNA profiles concurrent with the movement of organisms in the DVM as measured by acoustic sensors. Seawater eDNA was sequenced using a high-throughput metabarcoding approach. Additionally, fine-scale acoustic data using an autonomous multifrequency echosounder was collected simultaneously with the eDNA samples and changes in organism density in the water column were compared with changes in eDNA profiles. Our results show distinct shifts in eukaryotic taxa such as copepods, cnidarians, and tunicates, over short timeframes during the DVM. These shifts in eDNA track changes in the depth of sound scattering layers (SSLs) of organisms and the density of organisms around the CTD during eDNA sampling. Dominant taxa in eDNA samples were mostly smaller organisms that may be below the size limit for acoustic detection, while taxa such as teleost fish were much less abundant in eDNA data compared to acoustic data. Overall, these data suggest that eDNA, may be a powerful new tool for understanding the dynamics and composition of the DVM, yet challenges remain to reconcile differences among sampling methodologies

Exhaled breath hydrogen cyanide as a marker of early Pseudomonas aeruginosa infection in children with cystic fibrosis

Hydrogen cyanide is readily detected in the headspace above Pseudomonas aeruginosa cultures and in the breath of cystic fibrosis (CF) patients with chronic (P. aeruginosa) infection. We investigated if exhaled breath HCN is an early marker of P. aeruginosa infection. 233 children with CF who were free from P. aeruginosa infection were followed for 2 years. Their median (interquartile range) age was 8.0 (5.0–12.2) years. At each study visit, an exhaled breath sample was collected for hydrogen cyanide analysis. In total, 2055 breath samples were analysed. At the end of the study, the hydrogen cyanide concentrations were compared to the results of routine microbiology surveillance. P. aeruginosa was isolated from 71 children during the study with an incidence (95% CI) of 0.19 (0.15–0.23) cases per patient-year. Using a random-effects logistic model, the estimated odds ratio (95% CI) was 3.1 (2.6–3.6), which showed that for a 1- ppbv increase in exhaled breath hydrogen cyanide, we expected a 212% increase in the odds of P. aeruginosa infection. The sensitivity and specificity were estimated at 33% and 99%, respectively. Exhaled breath hydrogen cyanide is a specific biomarker of new P. aeruginosa infection in children with CF. Its low sensitivity means that at present, hydrogen cyanide cannot be used as a screening test for this infection

Lead Slowing-Down Spectrometry Time Spectral Analysis for Spent Fuel Assay: FY11 Status Report

Developing a method for the accurate, direct, and independent assay of the fissile isotopes in bulk materials (such as used fuel) from next-generation domestic nuclear fuel cycles is a goal of the Office of Nuclear Energy, Fuel Cycle R&D, Material Protection and Control Technology (MPACT) Campaign. To meet this goal, MPACT supports a multi-institutional collaboration, of which PNNL is a part, to study the feasibility of Lead Slowing Down Spectroscopy (LSDS). This technique is an active nondestructive assay method that has the potential to provide independent, direct measurement of Pu and U isotopic masses in used fuel with an uncertainty considerably lower than the approximately 10% typical of today's confirmatory assay methods. This document is a progress report for FY2011 PNNL analysis and algorithm development. Progress made by PNNL in FY2011 continues to indicate the promise of LSDS analysis and algorithms applied to used fuel. PNNL developed an empirical model based on calibration of the LSDS to responses generated from well-characterized used fuel. The empirical model, which accounts for self-shielding effects using empirical basis vectors calculated from the singular value decomposition (SVD) of a matrix containing the true self-shielding functions of the used fuel assembly models. The potential for the direct and independent assay of the sum of the masses of 239Pu and 241Pu to within approximately 3% over a wide used fuel parameter space was demonstrated. Also, in FY2011, PNNL continued to develop an analytical model. Such efforts included the addition of six more non-fissile absorbers in the analytical shielding function and the non-uniformity of the neutron flux across the LSDS assay chamber. A hybrid analytical-empirical approach was developed to determine the mass of total Pu (sum of the masses of 239Pu, 240Pu, and 241Pu), which is an important quantity in safeguards. Results using this hybrid method were of approximately the same accuracy as the pure empirical approach. In addition, total Pu with much better accuracy with the hybrid approach than the pure analytical approach. In FY2012, PNNL will continue efforts to optimize its empirical model and minimize its reliance on calibration data. In addition, PNNL will continue to develop an analytical model, considering effects such as neutron-scattering in the fuel and cladding, as well as neutrons streaming through gaps between fuel pins in the fuel assembly

Diel Variation in the Vertical Distribution of Deep-Water Scattering Layers in the Gulf of Mexico

Sound scattering layers (SSLs) are important components of oceanic ecosystems with ubiquitous distribution throughout the world\u27s oceans. This vertical movement is an important mechanism for exchanging organic matter from the surface to the deep ocean, as many of the organisms comprising SSLs serve as prey resources for linking the lower trophic levels to larger predators. Variations in abundance and taxonomic composition of mesopelagic organisms were quantified using repeated discrete net sampling and acoustics over a 30-h survey, performed during 26–27 June 2011 at single site (27°28’51”N and 88°27’54”W) in the northern Gulf of Mexico. We acoustically classified the mesopelagic SSL into four broad taxonomic categories, crustacean and small non-swimbladdered fish (CSNSBF), large non-swimbladdered fish (LNSBF), swimbladdered fish (SBF) and unclassified and we quantified the abundance of mesopelagic organisms over three discrete depth intervals; epipelagic (0–200 m); upper mesopelagic (200–600 m) and lower mesopelagic (600–1000 m). Irrespective of the acoustic categories at dusk part of the acoustic energy redistributed from the mesopelagic into the upper epipelagic (shallower than 100 m) remaining however below the thermocline depth. At night higher variability in species composition was observed between 100 and 200 m suggested that a redistribution of organisms may also occur within the upper portion of the water column. Along the upper mesopelagic backscatter spectra from CSNSBF migrated between 400 and 460 m while spectra from the other categories moved to shallower depths (300 and 350 m), resulting in habitat separation from CSNSBF. Relatively small vertical changes in both acoustic backscatter and center of mass metrics of the deep mesopelagic were observed for CNSBF and LNSBF suggesting that these animals may be tightly connected to deeper (below 1000 m) mesopelagic habitats, and do not routinely migrate into the epipelagic

A proteinaceous organic matrix regulates carbonate mineral production in the marine teleost intestine

Marine teleost fish produce CaCO(3) in their intestine as part of their osmoregulatory strategy. This precipitation is critical for rehydration and survival of the largest vertebrate group on earth, yet the molecular mechanisms that regulate this reaction are unknown. Here, we isolate and characterize an organic matrix associated with the intestinal precipitates produced by Gulf toadfish (Opsanus beta). Toadfish precipitates were purified using two different methods, and the associated organic matrix was extracted. Greater than 150 proteins were identified in the isolated matrix by mass spectrometry and subsequent database searching using an O. beta transcriptomic sequence library produced here. Many of the identified proteins were enriched in the matrix compared to the intestinal fluid, and three showed no substantial homology to any previously characterized protein in the NCBI database. To test the functionality of the isolated matrix, a micro-modified in vitro calcification assay was designed, which revealed that low concentrations of isolated matrix substantially promoted CaCO(3) production, where high concentrations showed an inhibitory effect. High concentrations of matrix also decreased the incorporation of magnesium into the forming mineral, potentially providing an explanation for the variability in magnesium content observed in precipitates produced by different fish species