Phytophthora ramorum

Phytophthora ramorum is a recently emerged plant pathogen and causal agent of one of the most destructive and devastating diseases currently affecting US horticulture and forests (Rizzo et al. 2002, 2005). This oomycete pathogen was discovered in Marin County, California, in the mid-1990s, causing sudden oak death on coast live oak (Quercus agrifolia) and tanoak (Notholithocarpus densiflorus) and simultaneously discovered in Europe causing foliar blight on Rhododendron and Viburnum (Rizzo et al. 2002; Werres et al. 2001). It is now known to affect more than 100 plant species, including economically important nursery and forest host species (Frankel 2008; Rizzo et al. 2005; Tooley et al. 2004; Tooley and Kyde 2007)

Electromechanical Piezoresistive Sensing in Suspended Graphene Membranes

Monolayer graphene exhibits exceptional electronic and mechanical properties, making it a very promising material for nanoelectromechanical (NEMS) devices. Here, we conclusively demonstrate the piezoresistive effect in graphene in a nano-electromechanical membrane configuration that provides direct electrical readout of pressure to strain transduction. This makes it highly relevant for an important class of nano-electromechanical system (NEMS) transducers. This demonstration is consistent with our simulations and previously reported gauge factors and simulation values. The membrane in our experiment acts as a strain gauge independent of crystallographic orientation and allows for aggressive size scalability. When compared with conventional pressure sensors, the sensors have orders of magnitude higher sensitivity per unit area.Comment: 20 pages, 3 figure

CSO and CARMA Observations of L1157. I. A Deep Search for Hydroxylamine (NH2_2OH)

A deep search for the potential glycine precursor hydroxylamine (NH$_2$OH) using the Caltech Submillimeter Observatory (CSO) at $\lambda = 1.3$ mm and the Combined Array for Research in Millimeter-wave Astronomy (CARMA) at $\lambda = 3$ mm is presented toward the molecular outflow L1157, targeting the B1 and B2 shocked regions. We report non-detections of NH$_2$OH in both sources. We a perform non-LTE analysis of CH$_3$OH observed in our CSO spectra to derive kinetic temperatures and densities in the shocked regions. Using these parameters, we derive upper limit column densities of NH$_2$OH of $\leq1.4 \times 10^{13}$~cm$^{-2}$ and $\leq1.5 \times 10^{13}$~cm$^{-2}$ toward the B1 and B2 shocks, respectively, and upper limit relative abundances of $N_{NH_2OH}/N_{H_2} \leq1.4 \times 10^{-8}$ and $\leq1.5 \times 10^{-8}$, respectively.Comment: Accepted in the Astrophysical Journa

CSO and CARMA Observations of L1157. II. Chemical Complexity in the Shocked Outflow

L1157, a molecular dark cloud with an embedded Class 0 protostar possessing a bipolar outflow, is an excellent source for studying shock chemistry, including grain-surface chemistry prior to shocks, and post-shock, gas-phase processing. The L1157-B1 and B2 positions experienced shocks at an estimated ~2000 and 4000 years ago, respectively. Prior to these shock events, temperatures were too low for most complex organic molecules to undergo thermal desorption. Thus, the shocks should have liberated these molecules from the ice grain-surfaces en masse, evidenced by prior observations of SiO and multiple grain mantle species commonly associated with shocks. Grain species, such as OCS, CH3OH, and HNCO, all peak at different positions relative to species that are preferably formed in higher velocity shocks or repeatedly-shocked material, such as SiO and HCN. Here, we present high spatial resolution (~3") maps of CH3OH, HNCO, HCN, and HCO+ in the southern portion of the outflow containing B1 and B2, as observed with CARMA. The HNCO maps are the first interferometric observations of this species in L1157. The maps show distinct differences in the chemistry within the various shocked regions in L1157B. This is further supported through constraints of the molecular abundances using the non-LTE code RADEX (Van der Tak et al. 2007). We find the east/west chemical differentiation in C2 may be explained by the contrast of the shock's interaction with either cold, pristine material or warm, previously-shocked gas, as seen in enhanced HCN abundances. In addition, the enhancement of the HNCO abundance toward the the older shock, B2, suggests the importance of high-temperature O-chemistry in shocked regions.Comment: Accepted for publication in the Astrophysical Journa

Impact of reactive surfaces on the abiotic reaction between nitrite and ferrous iron and associated nitrogen and oxygen isotope dynamics

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Visser, A., Wankel, S. D., Niklaus, P. A., Byrne, J. M., Kappler, A. A., & Lehmann, M. F. Impact of reactive surfaces on the abiotic reaction between nitrite and ferrous iron and associated nitrogen and oxygen isotope dynamics. Biogeosciences, 17(16), (2020): 4355-4374, doi:10.5194/bg-17-4355-2020.Anaerobic nitrate-dependent Fe(II) oxidation (NDFeO) is widespread in various aquatic environments and plays a major role in iron and nitrogen redox dynamics. However, evidence for truly enzymatic, autotrophic NDFeO remains limited, with alternative explanations involving the coupling of heterotrophic denitrification with the abiotic oxidation of structurally bound or aqueous Fe(II) by reactive intermediate nitrogen (N) species (chemodenitrification). The extent to which chemodenitrification is caused (or enhanced) by ex vivo surface catalytic effects has not been directly tested to date. To determine whether the presence of either an Fe(II)-bearing mineral or dead biomass (DB) catalyses chemodenitrification, two different sets of anoxic batch experiments were conducted: 2 mM Fe(II) was added to a low-phosphate medium, resulting in the precipitation of vivianite (Fe3(PO4)2), to which 2 mM nitrite (NO−2) was later added, with or without an autoclaved cell suspension (∼1.96×108 cells mL−1) of Shewanella oneidensis MR-1. Concentrations of nitrite (NO−2), nitrous oxide (N2O), and iron (Fe2+, Fetot) were monitored over time in both set-ups to assess the impact of Fe(II) minerals and/or DB as catalysts of chemodenitrification. In addition, the natural-abundance isotope ratios of NO−2 and N2O (δ15N and δ18O) were analysed to constrain the associated isotope effects. Up to 90 % of the Fe(II) was oxidized in the presence of DB, whereas only ∼65 % of the Fe(II) was oxidized under mineral-only conditions, suggesting an overall lower reactivity of the mineral-only set-up. Similarly, the average NO−2 reduction rate in the mineral-only experiments (0.004±0.003 mmol L−1 d−1) was much lower than in the experiments with both mineral and DB (0.053±0.013 mmol L−1 d−1), as was N2O production (204.02±60.29 nmol L−1 d−1). The N2O yield per mole NO−2 reduced was higher in the mineral-only set-ups (4 %) than in the experiments with DB (1 %), suggesting the catalysis-dependent differential formation of NO. N-NO−2 isotope ratio measurements indicated a clear difference between both experimental conditions: in contrast to the marked 15N isotope enrichment during active NO−2 reduction (15εNO2=+10.3 ‰) observed in the presence of DB, NO−2 loss in the mineral-only experiments exhibited only a small N isotope effect (<+1 ‰). The NO−2-O isotope effect was very low in both set-ups (18εNO2 <1 ‰), which was most likely due to substantial O isotope exchange with ambient water. Moreover, under low-turnover conditions (i.e. in the mineral-only experiments as well as initially in experiments with DB), the observed NO−2 isotope systematics suggest, transiently, a small inverse isotope effect (i.e. decreasing NO−2 δ15N and δ18O with decreasing concentrations), which was possibly related to transitory surface complexation mechanisms. Site preference (SP) of the 15N isotopes in the linear N2O molecule for both set-ups ranged between 0 ‰ and 14 ‰, which was notably lower than the values previously reported for chemodenitrification. Our results imply that chemodenitrification is dependent on the available reactive surfaces and that the NO−2 (rather than the N2O) isotope signatures may be useful for distinguishing between chemodenitrification catalysed by minerals, chemodenitrification catalysed by dead microbial biomass, and possibly true enzymatic NDFeO.This research has been supported by the Deutsche Forschungsgemeinschaft (DFG; grant no. GRK 1708, “Molecular principles of bacterial survival strategies”) and the University of Basel, Switzerland

Impact of reactive surfaces on the abiotic reaction between nitrite and ferrous iron and associated nitrogen and oxygen isotope dynamics

Anaerobic nitrate-dependent Fe(II) oxidation (NDFeO) is widespread in various aquatic environments and plays a major role in iron and nitrogen redox dynamics. However, evidence for truly enzymatic, autotrophic NDFeO remains limited, with alternative explanations involving the coupling of heterotrophic denitrification with the abiotic oxidation of structurally bound or aqueous Fe(II) by reactive intermediate nitrogen (N) species (chemodenitrification). The extent to which chemodenitrification is caused (or enhanced) by ex vivo surface catalytic effects has not been directly tested to date. To determine whether the presence of either an Fe(II)-bearing mineral or dead biomass (DB) catalyses chemodenitrification, two different sets of anoxic batch experiments were conducted: 2 mM Fe(II) was added to a low-phosphate medium, resulting in the precipitation of vivianite (Fe3(PO4)2), to which 2 mM nitrite (NO−2) was later added, with or without an autoclaved cell suspension (∼1.96×108 cells mL−1) of Shewanella oneidensis MR-1. Concentrations of nitrite (NO−2), nitrous oxide (N2O), and iron (Fe2+, Fetot) were monitored over time in both set-ups to assess the impact of Fe(II) minerals and/or DB as catalysts of chemodenitrification. In addition, the natural-abundance isotope ratios of NO−2 and N2O (δ15N and δ18O) were analysed to constrain the associated isotope effects. Up to 90 % of the Fe(II) was oxidized in the presence of DB, whereas only ∼65 % of the Fe(II) was oxidized under mineral-only conditions, suggesting an overall lower reactivity of the mineral-only set-up. Similarly, the average NO−2 reduction rate in the mineral-only experiments (0.004±0.003 mmol L−1 d−1) was much lower than in the experiments with both mineral and DB (0.053±0.013 mmol L−1 d−1), as was N2O production (204.02±60.29 nmol L−1 d−1). The N2O yield per mole NO−2 reduced was higher in the mineral-only set-ups (4 %) than in the experiments with DB (1 %), suggesting the catalysis-dependent differential formation of NO. N-NO−2 isotope ratio measurements indicated a clear difference between both experimental conditions: in contrast to the marked 15N isotope enrichment during active NO−2 reduction (15εNO2=+10.3 ‰) observed in the presence of DB, NO−2 loss in the mineral-only experiments exhibited only a small N isotope effect (<+1 ‰). The NO−2-O isotope effect was very low in both set-ups (18εNO2 <1 ‰), which was most likely due to substantial O isotope exchange with ambient water. Moreover, under low-turnover conditions (i.e. in the mineral-only experiments as well as initially in experiments with DB), the observed NO−2 isotope systematics suggest, transiently, a small inverse isotope effect (i.e. decreasing NO−2 δ15N and δ18O with decreasing concentrations), which was possibly related to transitory surface complexation mechanisms. Site preference (SP) of the 15N isotopes in the linear N2O molecule for both set-ups ranged between 0 ‰ and 14 ‰, which was notably lower than the values previously reported for chemodenitrification. Our results imply that chemodenitrification is dependent on the available reactive surfaces and that the NO−2 (rather than the N2O) isotope signatures may be useful for distinguishing between chemodenitrification catalysed by minerals, chemodenitrification catalysed by dead microbial biomass, and possibly true enzymatic NDFeO

Warm Greenland during the last interglacial: the role of regional changes in sea ice cover

The last interglacial, also known as the Eemian, is characterized by warmer than present conditions at high latitudes. This is implied by various Eemian proxy records as well as by climate model simulations, though the models mostly underestimate the warming with respect to proxies. Simulations of Eemian surface air temperatures (SAT) in the Northern Hemisphere extratropics further show large variations between different climate models, and it has been hypothesized that this model spread relates to diverse representations of the Eemian sea ice cover. Here we use versions 3 and 4 of the Community Climate System Model (CCSM3 and CCSM4) to highlight the crucial role of sea ice and sea surface temperatures changes for the Eemian climate, in particular in the North Atlantic sector and in Greenland. A substantial reduction in sea ice cover results in an amplified atmospheric warming and thus a better agreement with Eemian proxy records. Sensitivity experiments with idealized lower boundary conditions reveal that warming over Greenland is mostly due to a sea ice retreat in the Nordic Seas. In contrast, sea ice changes in the Labrador Sea have a limited local impact. Changes in sea ice cover in either region are transferred to the overlying atmosphere through anomalous surface energy fluxes. The large-scale spread of the warming resulting from a Nordic Seas sea ice retreat is mostly explained by anomalous heat advection rather than by radiation or condensation processes. In addition, the sea ice perturbations lead to changes in the hydrological cycle. Our results consequently imply that both temperature and snow accumulation records from Greenland ice cores are sensitive to sea ice changes in the Nordic Seas but insensitive to sea ice changes in the Labrador Sea. Moreover, the simulations suggest that the uncertainty in the Eemian sea ice cover accounts for 1.6 °C of the Eemian warming at the NEEM ice core site. The estimated Eemian warming of 5 °C above present day based on the NEEM δ15N record can be reconstructed by the CCSM4 model for the scenario of a substantial sea ice retreat in the Nordic Seas combined with a reduced Greenland ice sheet

Optical fibers for endoscopic high-power Er:YAG laserosteotomy

ignificance: The highest absorption peaks of the main components of bone are in the mid-infrared region, making Er:YAG and CO2 lasers the most efficient lasers for cutting bone. Yet, studies of deep bone ablation in minimally invasive settings are very limited, as finding suitable materials for coupling high-power laser light with low attenuation beyond 2  μm is not trivial. Aim: The first aim of this study was to compare the performance of different optical fibers in terms of transmitting Er:YAG laser light with a 2.94-μm wavelength at high pulse energy close to 1 J. The second aim was to achieve deep bone ablation using the best-performing fiber, as determined by our experiments. Approach: In our study, various optical fibers with low attenuation (λ  =  2.94  μm) were used to couple the Er:YAG laser. The fibers were made of germanium oxide, sapphire, zirconium fluoride, and hollow-core silica, respectively. We compared the fibers in terms of transmission efficiency, resistance to high Er:YAG laser energy, and bending flexibility. The best-performing fiber was used to achieve deep bone ablation in a minimally invasive setting. To do this, we adapted the optimal settings for free-space deep bone ablation with an Er:YAG laser found in a previous study. Results: Three of the fibers endured energy per pulse as high as 820 mJ at a repetition rate of 10 Hz. The best-performing fiber, made of germanium oxide, provided higher transmission efficiency and greater bending flexibility than the other fibers. With an output energy of 370 mJ per pulse at 10 Hz repetition rate, we reached a cutting depth of 6.82  ±  0.99  mm in sheep bone. Histology image analysis was performed on the bone tissue adjacent to the laser ablation crater; the images did not show any structural damage. Conclusions: The findings suggest that our prototype could be used in future generations of endoscopic devices for minimally invasive laserosteotomy