Impact of the January 2012 solar proton event on polar mesospheric clouds

We use data from the Aeronomy of Ice in the Mesosphere mission and simulations using the Whole Atmosphere Community Climate Model to determine the impact of the 23–30 January 2012 solar proton event (SPE) on polar mesospheric clouds (PMCs) and mesospheric water vapor. We see a small heating and loss of ice mass on 26 January that is consistent with prior results but is not statistically significant. We also find a previously unreported but statistically significant ~10% increase in ice mass and in water vapor in the sublimation area in the model that occurs in the 7 to 14 days following the start of the event. The magnitude of the response to the January 2012 SPE is small compared to other sources of variability like gravity waves and planetary waves; however, sensitivity tests suggest that with larger SPEs this delayed increase in ice mass will increase, while there is little change in the loss of ice mass early in the event. The PMC response to SPEs in models is dependent on the gravity wave parameterization, and temperature anomalies from SPEs may be useful in evaluating and tuning gravity wave parameterizations

Middle atmospheric ozone, nitrogen dioxide and nitrogen trioxide in 2002-2011: SD-WACCM simulations compared to GOMOS observations

Most of our understanding of the atmosphere is based on observations and their comparison with model simulations. In middle atmosphere studies it is common practice to use an approach, where the model dynamics are at least partly based on temperature and wind fields from an external meteorological model. In this work we test how closely satellite measurements of a few central trace gases agree with this kind of model simulation. We use collocated vertical profiles where each satellite measurement is compared to the closest model data. We compare profiles and distributions of O3, NO2 and NO3 from the Global Ozone Monitoring by Occultation of Stars instrument (GOMOS) on the Envisat satellite with simulations by the Whole Atmosphere Community Climate Model (WACCM). GOMOS measurements are from nighttime. Our comparisons show that in the stratosphere outside the polar regions differences in ozone between WACCM and GOMOS are small, between 0 and 6%. The correlation of 5-day time series show a very high 0.9-0.95. In the tropical region 10° S-10° N below 10hPa WACCM values are up to 20% larger than GOMOS. In the Arctic below 6 hPa WACCM ozone values are up to 20% larger than GOMOS. In the mesosphere between 0.04 and 1hPa the WACCM is at most 20% smaller than GOMOS. Above the ozone minimum at 0.01hPa (or 80km) large differences are found between WACCM and GOMOS. The correlation can still be high, but at the second ozone peak the correlation falls strongly and the ozone abundance from WACCM is about 60% smaller than that from GOMOS. The total ozone columns (above 50hPa) of GOMOS and WACCM agree within ±2% except in the Arctic where WACCM is 10% larger than GOMOS. Outside the polar areas and in the validity region of GOMOS NO2 measurements (0.3-37 hPa) WACCM and GOMOS NO2 agree within -5 to +25% and the correlation is high (0.7-0.95) except in the upper stratosphere at the southern latitudes. In the polar areas, where solar particle precipitation and downward transport from the thermosphere enhance NO2 abundance, large differences up to -90% are found between WACCM and GOMOS NO2 and the correlation varies between 0.3 and 0.9. For NO3, we find that the WACCM and GOMOS difference is between -20 and 5% with a very high correlation of 0.7-0.95. We show that NO3 values strongly depend on temperature and the dependency can be fitted by the exponential function of temperature. The ratio of NO3 to O3 from WACCM and GOMOS closely follow the prediction from the equilibrium chemical theory. Abrupt temperature increases from sudden stratospheric warmings (SSWs) are reflected as sudden enhancements of WACCM and GOMOS NO3 values

Human resilience to Holocene climate changes inferred from rodent middens in drylands of northwestern Patagonia (Argentina)

We reconstruct the Holocene vegetation, climate, and archaeological history for drylands of northwestern Patagonia, Argentina, based on multiproxy analysis (plant macrofossil, pollen, and parasites) of rodent middens integrated with a database of {14}^C dates associated with human occupations. The local scale corresponds to the Huenul paleoecological and archaeological locality, emplaced in north-western Patagonia (Neuquén Province, Argentina). The rodent midden record from the Huenul series reflects subtle vegetation changes driven by climatic variability at millennial timescale. Drier than present environmental conditions prevailed during the early Holocene (10,500–9400 cal yr BP), peaking during the mid-Holocene (9200–5500 cal yr BP), when wetter than present conditions established during the late Holocene (4400–2500 cal yr BP). These environmental and climatic dynamics agree with other paleoclimatic records from northern Patagonia, suggesting the winter precipitation dynamics related to the Southern Westerlies as a common driver. The diachronic distribution of anthropogenic radiocarbon dates from the western area of the South American Arid Diagonal between 32°–40°S conforms to a fitted exponential model of steady background population growth, not suggesting significant demographic changes that may have been the result of the impact of climate change. This record indicates that these human populations coped successfully with aridity, particularly during the mid-Holocene. These findings reinforce the need to integrate multi-scalar interdisciplinary analyses to assess the impact of climate change in human societies

Scallop swimming kinematics and muscle performance: modelling the effects of "within-animal" variation in temperature sensitivity

Escape behaviour was investigated in Queen scallops (Aequipecten opercularis) acclimated to 5, 10 or 15 degrees C and tested at their acclimation temperature. Scallops are active molluscs, able to escape from predators by jet-propelled swimming using a striated muscle working in opposition to an elastic hinge ligament. The first cycle of the escape response was recorded using high-speed video ( 250 Hz) and whole-animal velocity and acceleration determined. Muscle shortening velocity, force and power output were calculated using measurements of valve movement and jet area, and a simple biomechanical model. The average shortening speed of the adductor muscle had a Q(10) of 2.04, significantly reducing the duration of the jetting phase of the cycle with increased temperature. Muscle lengthening velocity and the overall duration of the clap cycle were changed little over the range 5 - 15 degrees C, as these parameters were controlled by the relatively temperature-insensitive, hinge ligament. Improvements in the average power output of the adductor muscle over the first clap cycle ( 222 vs. 139 W kg(-1) wet mass at 15 and 5 degrees C respectively) were not translated into proportional increases in overall swimming velocity, which was only 32% higher at 15 degrees C ( 0.37m s(-1)) than 5 degrees C (0.28 m s(-1))

Magnetic-local-time dependency of radiation belt electron precipitation: impact on ozone in the polar middle atmosphere

The radiation belts are regions in the near-Earth space where solar wind electrons are captured by the Earth's magnetic field. A portion of these electrons is continuously lost into the atmosphere where they cause ionization and chemical changes. Driven by the solar activity, the electron forcing leads to ozone variability in the polar stratosphere and mesosphere. Understanding the possible dynamical connections to regional climate is an ongoing research activity which supports the assessment of greenhouse-gas-driven climate change by a better definition of the solar-driven variability. In the context of the Coupled Model Intercomparison Project Phase 6 (CMIP6), energetic electron and proton precipitation is included in the solar-forcing recommendation for the first time. For the radiation belt electrons, the CMIP6 forcing is from a daily zonal-mean proxy model. This zonal-mean model ignores the well-known dependency of precipitation on magnetic local time (MLT), i.e. its diurnal variability. Here we use the Whole Atmosphere Community Climate Model with its lower-ionospheric-chemistry extension (WACCM-D) to study effects of the MLT dependency of electron forcing on the polar-ozone response. We analyse simulations applying MLT-dependent and MLT-independent forcings and contrast the resulting ozone responses in monthly-mean data as well as in monthly means at individual local times. We consider two cases: (1) the year 2003 and (2) an extreme, continuous forcing. Our results indicate that the ozone responses to the MLT-dependent and the MLT-independent forcings are very similar, and the differences found are small compared to those caused by the overall uncertainties related to the representation of electron forcing in climate simulations. We conclude that the use of daily zonal-mean electron forcing will provide an accurate ozone response in long-term climate simulations

D-region ion–neutral coupled chemistry (Sodankylä Ion Chemistry, SIC) within the Whole Atmosphere Community Climate Model (WACCM 4) – WACCM-SIC and WACCM-rSIC

This study presents a new ion–neutral chemical model coupled into the Whole Atmosphere Community Climate Model (WACCM). The ionospheric D-region (altitudes ∼  50–90 km) chemistry is based on the Sodankylä Ion Chemistry (SIC) model, a one-dimensional model containing 307 ion–neutral and ion recombination, 16 photodissociation and 7 photoionization reactions of neutral species, positive and negative ions, and electrons. The SIC mechanism was reduced using the simulation error minimization connectivity method (SEM-CM) to produce a reaction scheme of 181 ion–molecule reactions of 181 ion–molecule reactions of 27 positive and 18 negative ions. This scheme describes the concentration profiles at altitudes between 20 km and 120 km of a set of major neutral species (HNO3, O3, H2O2, NO, NO2, HO2, OH, N2O5) and ions (O2+, O4+, NO+, NO+(H2O), O2+(H2O), H+(H2O), H+(H2O)2, H+(H2O)3, H+(H2O)4, O3−, NO2−, O−, O2, OH−, O2−(H2O), O2−(H2O)2, O4−, CO3−, CO3−(H2O), CO4−, HCO3−, NO2−, NO3−, NO3−(H2O), NO3−(H2O)2, NO3−(HNO3), NO3−(HNO3)2, Cl−, ClO−), which agree with the full SIC mechanism within a 5 % tolerance. Four 3-D model simulations were then performed, using the impact of the January 2005 solar proton event (SPE) on D-region HOx and NOx chemistry as a test case of four different model versions: the standard WACCM (no negative ions and a very limited set of positive ions); WACCM-SIC (standard WACCM with the full SIC chemistry of positive and negative ions); WACCM-D (standard WACCM with a heuristic reduction of the SIC chemistry, recently used to examine HNO3 formation following an SPE); and WACCM-rSIC (standard WACCM with a reduction of SIC chemistry using the SEM-CM method). The standard WACCM misses the HNO3 enhancement during the SPE, while the full and reduced model versions predict significant NOx, HOx and HNO3 enhancements in the mesosphere during solar proton events. The SEM-CM reduction also identifies the important ion–molecule reactions that affect the partitioning of odd nitrogen (NOx), odd hydrogen (HOx) and O3 in the stratosphere and mesosphere

Sequential therapy of anti-Nogo-A antibody treatment and treadmill training leads to cumulative improvements after spinal cord injury in rats

Intense training is the most clinically successful treatment modality following incomplete spinal cord injuries (SCIs). With the advent of plasticity enhancing treatments, understanding how treatments might interact when delivered in combination becomes critical. Here, we investigated a rational approach to sequentially combine treadmill locomotor training with antibody mediated suppression of the fiber growth inhibitory protein Nogo-A. Following a large but incomplete thoracic lesion, rats were immediately treated with either anti-Nogo-A or control antibody (2 weeks) and then either left untrained or step-trained starting 3 weeks after injury for 8 weeks. It was found that sequentially combined therapy improved step consistency and reduced toe dragging and climbing errors, as seen with training and anti-Nogo-A individually. Animals with sequential therapy also adopted a more parallel paw position during bipedal walking and showed greater overall quadrupedal locomotor recovery than individual treatments. Histologically, sequential therapy induced the greatest corticospinal tract sprouting caudally into the lumbar region and increased the number of serotonergic synapses onto lumbar motoneurons. Increased primary afferent sprouting and synapse formation onto lumbar motoneurons observed with anti-Nogo-A antibody were reduced by training. Animals with sequential therapy also showed the highest reduction of lumbar interneuronal activity associated with walking (c-fos expression). No treatment effects for thermal nociception, mechanical allodynia, or lesion volume were observed. The results demonstrate that sequential administration of anti-Nogo-A antibody followed in time with intensive locomotor training leads to superior recovery of lost locomotor functions, which is probably mediated by changes in the interaction between descending sprouting and local segmental networks after SCI

On the relative roles of dynamics and chemistry governing the abundance and diurnal variation of low latitude thermospheric nitric oxide

We use data from two NASA satellites, the Thermosphere Ionosphere Energetics and Dynamics (TIMED) and the Aeronomy of Ice in the Mesosphere (AIM) satellites in conjunction with model simulations from the Thermosphere-Ionosphere-Mesosphere-Electrodynamics General Circulation Model (TIME-GCM) to elucidate the key dynamical and chemical factors governing the abundance and diurnal variation of nitric oxide (NO) at near solar minimum conditions and low latitudes. This analysis was enabled by the recent orbital precession of the AIM satellite which caused the solar occultation pattern measured by the Solar Occultation for Ice Experiment (SOFIE) to migrate down to low and mid latitudes for specific periods of time. We use a month of NO data collected in January 2017 to compare with two versions of the TIME-GCM, one driven solely by climatological tides and analysis-derived planetary waves at the lower boundary and free running at all other altitudes, while the other is constrained by a high-altitude analysis from the Navy Global Environmental Model (NAVGEM)up to the mesopause. We also compare SOFIE data with a NO climatology from the Nitric Oxide Empirical Model (NOEM). Both SOFIE and NOEM yield peak NO abundances of around 4×107cm−3; however, the SOFIE profile peaks about 6-8 km lower than NOEM. We show that this difference is likely a local time effect; SOFIE being a dawn measurement and NOEM representing late morning/near noon. The constrained version of TIME-GCM exhibits a low altitude dawn peak while the model that is forced solely at the lower boundary and free running above does not. We attribute this difference due to a phase change in the semi-diurnal tide in the NAVGEM-constrained model causing descent of high NO mixing ratio air near dawn. This phase difference between the two models arises due to differences in the mesospheric zonal mean zonal winds. Regarding the absolute NO abundance, all versions of the TIME-GCM overestimate this. Tuning the model to yield calculated atomic oxygen in agreement with TIMED data helps, but is insufficient. Further, the TIME-GCM underestimates the electron density [e-] as compared with the International Reference Ionosphere empirical model. This suggests a potential conflict with the requirements of NO modeling and [e-] modeling since one solution typically used to increase model [e-] is to increase the solar soft X ray flux which would, in this case, worsen the NO model/data discrepancy

Engineering Archeal Surrogate Systems for the Development of Protein-Protein Interaction Inhibitors against Human RAD51

Protein-protein interactions (PPIs) are increasingly important targets for drug discovery. Efficient fragment-based drug discovery approaches to tackle PPIs are often stymied by difficulties in the production of stable, unliganded target proteins. Here, we report an approach that exploits protein engineering to "humanise" thermophilic archeal surrogate proteins as targets for small-molecule inhibitor discovery and to exemplify this approach in the development of inhibitors against the PPI between the recombinase RAD51 and tumour suppressor BRCA2. As human RAD51 has proved impossible to produce in a form that is compatible with the requirements of fragment-based drug discovery, we have developed a surrogate protein system using RadA from $\textit{Pyrococcus furiosus}$. Using a monomerised RadA as our starting point, we have adopted two parallel and mutually instructive approaches to mimic the human enzyme: firstly by mutating RadA to increase sequence identity with RAD51 in the BRC repeat binding sites, and secondly by generating a chimeric archaeal human protein. Both approaches generate proteins that interact with a fourth BRC repeat with affinity and stoichiometry comparable to human RAD51. Stepwise humanisation has also allowed us to elucidate the determinants of RAD51 binding to BRC repeats and the contributions of key interacting residues to this interaction. These surrogate proteins have enabled the development of biochemical and biophysical assays in our ongoing fragment-based small-molecule inhibitor programme and they have allowed us to determine hundreds of liganded structures in support of our structure-guided design process, demonstrating the feasibility and advantages of using archeal surrogates to overcome difficulties in handling human proteins.Wellcome Trust Translational (Grant ID: 080083/Z/06/Z) and Seeding Drug Discovery Initiative (Grant ID: 91050/Z/10/Z) award