Thermal and pressure stability of myrosinase enzymes from black mustard (Brassica nigra L. W.D.J Koch. var. nigra), brown mustard (Brassica juncea L. Czern. var. juncea) and yellow mustard (Sinapsis alba L. Subsp Maire) seeds

This study investigates the effects of temperature and pressure on inactivation of myrosinase extracted from black, brown and yellow mustard seeds. Brown mustard had higher myrosinase activity (2.75 un/mL) than black (1.50 un/mL) and yellow mustard (0.63 un/mL). The extent of enzyme inactivation increased with pressure (600-800 MPa) and temperature (30-70 °C) for all the mustard seeds. However, at combinations of lower pressures (200-400 MPa) and high temperatures (60-80 °C), there was less inactivation. For example, application of 300 MPa and 70 °C for 10 minutes retained 20%, 80% and 65% activity in yellow, black and brown mustard, respectively, whereas the corresponding activity retentions when applying only heat (70 °C, 10min) were 0%, 59% and 35%. Thus, application of moderate pressures (200-400 MPa) can potentially be used to retain myrosinase activity needed for subsequent glucosinolate hydrolysis.

A functional genomics approach reveals novel quantitative trait loci associated with platelet signalling pathways

Platelet response to activation varies widely between individuals but shows interindividual consistency and strong heritability. The genetic basis of this variation has not been properly explored. We therefore systematically measured the effect on function of sequence variation in 97 candidate genes in the collagen and adenosine-diphosphate (ADP) signaling pathways. Resequencing of the genes in 48 European DNA samples nearly doubled the number of known single nucleotide polymorphisms (SNPs) and informed the selection of 1327 SNPs for genotyping in 500 healthy Northern European subjects with known platelet responses to collagen-related peptide (CRP-XL) and ADP. This identified 17 novel associations with platelet function (P < .005) accounting for approximately 46% of the variation in response. Further investigations with platelets of known genotype explored the mechanisms behind some of the associations. SNPs in PEAR1 associated with increased platelet response to CRP-XL and increased PEAR1 protein expression after platelet degranulation. The minor allele of a 3' untranslated region (UTR) SNP (rs2769668) in VAV3 was associated with higher protein expression (P = .03) and increased P-selectin exposure after ADP activation (P = .004). Furthermore the minor allele of the intronic SNP rs17786144 in ITPR1 modified Ca2+ levels after activation with ADP (P < .004). These data provide novel insights into key hubs within platelet signaling networks.

Verification and FPGA circuits of a block-2 fast path-based predictor

This paper formally derives a new path-based neural branch prediction algorithm (FPP) into blocks of size two for a lower hardware solution while maintaining similar input-output characteristic to the algorithm. The blocked solution, here referred to as B2P algorithm, is obtained using graph theory and retiming methods. Verification approaches were exercised to show that prediction performances obtained from the FPP and B2P algorithms differ within one mis-prediction per thousand instructions using a known framework for branch prediction evaluation. For a chosen FPGA device, circuits generated from the B2P algorithm showed average area savings of over 25% against circuits for the FPP algorithm with similar time performances thus making the proposed blocked predictor superior from a practical viewpoint.

Antioxidant activity of selected phenols and herbs used in diets for medical conditions.

The antioxidant capacity of some herbs used in dietology practice was determined by the DPPH free radical method, which was calibrated with ascorbic acid. Partially hydrophilic phenolic compounds are the most active compounds in plants, and therefore water was used as the extraction agent. Besides antioxidant capacity, the content of total phenolic compounds was also measured and a strong correlation between these two variables was found. The extracts of lemon balm (Melissa officinalis L.), peppermint (Mentha x piperita L.), oregano (Origanum vulgare L.), Greek oregano (Origanum heracleoticum L.), sage (Salvia officinalis L.) and winter savory (Satureja montana L.) showed very significant activity. It was comparable with the activity of green tea in the case of oregano and peppermint. Lower activity was observed in the case of rosemary (Rosmarinus officinalis L.), marjoram (Majorana hortensis), hyssop (Hyssopus officinalis L.), sweet basil (Ocimum basilicum), and lovage (Levisticum officinale Koch.). The inhibitory activity of the herb extracts was monitored also during the autooxidation of lard. Very high antioxidant capacity was observed mainly in sage samples, but also in marjoram and Greek oregano. The extracts of peppermint, oregano, rosemary, winter savory, lemon balm and hyssop showed middle activity comparable to that of alpha-tocopherol. The antioxidant capacity of sweet basil and lovage was insignificant.

Twists and turns: a tale of two shikimate-pathway enzymes

We are studying two enzymes from the shikimate pathway, dehydroquinate synthase (DHQS) and 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). Both enzymes have been the subject of numerous studies to elucidate their reaction mechanisms. Crystal structures of DHQS and EPSPS in the presence and absence of substrates, cofactors and/or inhibitors are now available. These structures reveal movements of domains, rearrangements of loops and changes in side-chain positions necessary for the formation of a catalytically competent active site. The potential for using complementary small-angle X-ray scattering (SAXS) studies to confirm the presence of these structural differences in solution has also been explored. Comparative analysis of crystal structures, in the presence and absence of ligands, has revealed structural features critical for substrate-binding and catalysis. We have also analysed these structures by generating GRID energy maps to detect favourable binding sites. The combination of X-ray crystallography, SAXS and computational techniques provides an enhanced analysis of structural features important for the function of these complex enzymes.

Transcription profiling in human platelets reveals LRRFIP1 as a novel protein regulating platelet function

Within the healthy population, there is substantial, heritable, and interindividual variability in the platelet response. We explored whether a proportion of this variability could be accounted for by interindividual variation in gene expression. Through a correlative analysis of genome-wide platelet RNA expression data from 37 subjects representing the normal range of platelet responsiveness within a cohort of 500 subjects, we identified 63 genes in which transcript levels correlated with variation in the platelet response to adenosine diphosphate and/or the collagen-mimetic peptide, cross-linked collagen-related peptide. Many of these encode proteins with no reported function in platelets. An association study of 6 of the 63 genes in 4235 cases and 6379 controls showed a putative association with myocardial infarction for COMMD7 (COMM domain-containing protein 7) and a major deviation from the null hypo thesis for LRRFIP1 [leucine-rich repeat (in FLII) interacting protein 1]. Morpholino-based silencing in Danio rerio identified a modest role for commd7 and a significant effect for lrrfip1 as positive regulators of thrombus formation. Proteomic analysis of human platelet LRRFIP1-interacting proteins indicated that LRRFIP1 functions as a component of the platelet cytoskeleton, where it interacts with the actin-remodeling proteins Flightless-1 and Drebrin. Taken together, these data reveal novel proteins regulating the platelet response.

Bounding the role of black carbon in the climate system: a scientific assessment

Black carbon aerosol plays a unique and important role in Earth’s climate system. Black carbon is a type of carbonaceous material with a unique combination of physical properties. This assessment provides an evaluation of black-carbon climate forcing that is comprehensive in its inclusion of all known and relevant processes and that is quantitative in providing best estimates and uncertainties of the main forcing terms: direct solar absorption; influence on liquid, mixed phase, and ice clouds; and deposition on snow and ice. These effects are calculated with climate models, but when possible, they are evaluated with both microphysical measurements and field observations. Predominant sources are combustion related, namely, fossil fuels for transportation, solid fuels for industrial and residential uses, and open burning of biomass. Total global emissions of black carbon using bottom-up inventory methods are 7500 Gg yr�-1 in the year 2000 with an uncertainty range of 2000 to 29000. However, global atmospheric absorption attributable to black carbon is too low in many models and should be increased by a factor of almost 3. After this scaling, the best estimate for the industrial-era (1750 to 2005) direct radiative forcing of atmospheric black carbon is +0.71 W m�-2 with 90% uncertainty bounds of (+0.08, +1.27)Wm�-2. Total direct forcing by all black carbon sources, without subtracting the preindustrial background, is estimated as +0.88 (+0.17, +1.48) W m�-2. Direct radiative forcing alone does not capture important rapid adjustment mechanisms. A framework is described and used for quantifying climate forcings, including rapid adjustments. The best estimate of industrial-era climate forcing of black carbon through all forcing mechanisms, including clouds and cryosphere forcing, is +1.1 W m�-2 with 90% uncertainty bounds of +0.17 to +2.1 W m�-2. Thus, there is a very high probability that black carbon emissions, independent of co-emitted species, have a positive forcing and warm the climate. We estimate that black carbon, with a total climate forcing of +1.1 W m�-2, is the second most important human emission in terms of its climate forcing in the present-day atmosphere; only carbon dioxide is estimated to have a greater forcing. Sources that emit black carbon also emit other short-lived species that may either cool or warm climate. Climate forcings from co-emitted species are estimated and used in the framework described herein. When the principal effects of short-lived co-emissions, including cooling agents such as sulfur dioxide, are included in net forcing, energy-related sources (fossil fuel and biofuel) have an industrial-era climate forcing of +0.22 (�-0.50 to +1.08) W m-�2 during the first year after emission. For a few of these sources, such as diesel engines and possibly residential biofuels, warming is strong enough that eliminating all short-lived emissions from these sources would reduce net climate forcing (i.e., produce cooling). When open burning emissions, which emit high levels of organic matter, are included in the total, the best estimate of net industrial-era climate forcing by all short-lived species from black-carbon-rich sources becomes slightly negative (�-0.06 W m�-2 with 90% uncertainty bounds of �-1.45 to +1.29 W m�-2). The uncertainties in net climate forcing from black-carbon-rich sources are substantial, largely due to lack of knowledge about cloud interactions with both black carbon and co-emitted organic carbon. In prioritizing potential black-carbon mitigation actions, non-science factors, such as technical feasibility, costs, policy design, and implementation feasibility play important roles. The major sources of black carbon are presently in different stages with regard to the feasibility for near-term mitigation. This assessment, by evaluating the large number and complexity of the associated physical and radiative processes in black-carbon climate forcing, sets a baseline from which to improve future climate forcing estimates.

Aerosol indirect effects – general circulation model intercomparison and evaluation with satellite data

Aerosol indirect effects continue to constitute one of the most important uncertainties for anthropogenic climate perturbations. Within the international AEROCOM initiative, the representation of aerosol-cloud-radiation interactions in ten different general circulation models (GCMs) is evaluated using three satellite datasets. The focus is on stratiform liquid water clouds since most GCMs do not include ice nucleation effects, and none of the model explicitly parameterises aerosol effects on convective clouds. We compute statistical relationships between aerosol optical depth (τa) and various cloud and radiation quantities in a manner that is consistent between the models and the satellite data. It is found that the model-simulated influence of aerosols on cloud droplet number concentration (Nd ) compares relatively well to the satellite data at least over the ocean. The relationship between �a and liquid water path is simulated much too strongly by the models. This suggests that the implementation of the second aerosol indirect effect mainly in terms of an autoconversion parameterisation has to be revisited in the GCMs. A positive relationship between total cloud fraction (fcld) and �a as found in the satellite data is simulated by the majority of the models, albeit less strongly than that in the satellite data in most of them. In a discussion of the hypotheses proposed in the literature to explain the satellite-derived strong fcld–�a relationship, our results indicate that none can be identified as a unique explanation. Relationships similar to the ones found in satellite data between �a and cloud top temperature or outgoing long-wave radiation (OLR) are simulated by only a few GCMs. The GCMs that simulate a negative OLR - �a relationship show a strong positive correlation between �a and fcld. The short-wave total aerosol radiative forcing as simulated by the GCMs is strongly influenced by the simulated anthropogenic fraction of �a, and parameterisation assumptions such as a lower bound on Nd . Nevertheless, the strengths of the statistical relationships are good predictors for the aerosol forcings in the models. An estimate of the total short-wave aerosol forcing inferred from the combination of these predictors for the modelled forcings with the satellite-derived statistical relationships yields a global annual mean value of −1.5±0.5Wm−2. In an alternative approach, the radiative flux perturbation due to anthropogenic aerosols can be broken down into a component over the cloud-free portion of the globe (approximately the aerosol direct effect) and a component over the cloudy portion of the globe (approximately the aerosol indirect effect). An estimate obtained by scaling these simulated clearand cloudy-sky forcings with estimates of anthropogenic �a and satellite-retrieved Nd–�a regression slopes, respectively, yields a global, annual-mean aerosol direct effect estimate of −0.4±0.2Wm−2 and a cloudy-sky (aerosol indirect effect) estimate of −0.7±0.5Wm−2, with a total estimate of −1.2±0.4Wm−2.

A review of measurement-based assessments of the aerosol direct radiative effect and forcing

Aerosols affect the Earth's energy budget directly by scattering and absorbing radiation and indirectly by acting as cloud condensation nuclei and, thereby, affecting cloud properties. However, large uncertainties exist in current estimates of aerosol forcing because of incomplete knowledge concerning the distribution and the physical and chemical properties of aerosols as well as aerosol-cloud interactions. In recent years, a great deal of effort has gone into improving measurements and datasets. It is thus feasible to shift the estimates of aerosol forcing from largely model-based to increasingly measurement-based. Our goal is to assess current observational capabilities and identify uncertainties in the aerosol direct forcing through comparisons of different methods with independent sources of uncertainties. Here we assess the aerosol optical depth (τ), direct radiative effect (DRE) by natural and anthropogenic aerosols, and direct climate forcing (DCF) by anthropogenic aerosols, focusing on satellite and ground-based measurements supplemented by global chemical transport model (CTM) simulations. The multi-spectral MODIS measures global distributions of aerosol optical depth (τ) on a daily scale, with a high accuracy of ±0.03±0.05τ over ocean. The annual average τ is about 0.14 over global ocean, of which about 21%±7% is contributed by human activities, as estimated by MODIS fine-mode fraction. The multi-angle MISR derives an annual average AOD of 0.23 over global land with an uncertainty of ~20% or ±0.05. These high-accuracy aerosol products and broadband flux measurements from CERES make it feasible to obtain observational constraints for the aerosol direct effect, especially over global the ocean. A number of measurement-based approaches estimate the clear-sky DRE (on solar radiation) at the top-of-atmosphere (TOA) to be about -5.5±0.2 Wm-2 (median ± standard error from various methods) over the global ocean. Accounting for thin cirrus contamination of the satellite derived aerosol field will reduce the TOA DRE to -5.0 Wm-2. Because of a lack of measurements of aerosol absorption and difficulty in characterizing land surface reflection, estimates of DRE over land and at the ocean surface are currently realized through a combination of satellite retrievals, surface measurements, and model simulations, and are less constrained. Over the oceans the surface DRE is estimated to be -8.8±0.7 Wm-2. Over land, an integration of satellite retrievals and model simulations derives a DRE of -4.9±0.7 Wm-2 and -11.8±1.9 Wm-2 at the TOA and surface, respectively. CTM simulations derive a wide range of DRE estimates that on average are smaller than the measurement-based DRE by about 30-40%, even after accounting for thin cirrus and cloud contamination. A number of issues remain. Current estimates of the aerosol direct effect over land are poorly constrained. Uncertainties of DRE estimates are also larger on regional scales than on a global scale and large discrepancies exist between different approaches. The characterization of aerosol absorption and vertical distribution remains challenging. The aerosol direct effect in the thermal infrared range and in cloudy conditions remains relatively unexplored and quite uncertain, because of a lack of global systematic aerosol vertical profile measurements. A coordinated research strategy needs to be developed for integration and assimilation of satellite measurements into models to constrain model simulations. Enhanced measurement capabilities in the next few years and high-level scientific cooperation will further advance our knowledge.

An AeroCom assessment of black carbon in Arctic snow and sea ice

Though many global aerosols models prognose surface deposition, only a few models have been used to directly simulate the radiative effect from black carbon (BC) deposition to snow and sea ice. Here, we apply aerosol deposition fields from 25 models contributing to two phases of the Aerosol Comparisons between Observations and Models (AeroCom) project to simulate and evaluate within-snow BC concentrations and radiative effect in the Arctic. We accomplish this by driving the offline land and sea ice components of the Community Earth System Model with different deposition fields and meteorological conditions from 2004 to 2009, during which an extensive field campaign of BC measurements in Arctic snow occurred. We find that models generally underestimate BC concentrations in snow in northern Russia and Norway, while overestimating BC amounts elsewhere in the Arctic. Although simulated BC distributions in snow are poorly correlated with measurements, mean values are reasonable. The multi-model mean (range) bias in BC concentrations, sampled over the same grid cells, snow depths, and months of measurements, are −4.4 (−13.2 to +10.7) ng g−1 for an earlier phase of AeroCom models (phase I), and +4.1 (−13.0 to +21.4) ng g−1 for a more recent phase of AeroCom models (phase II), compared to the observational mean of 19.2 ng g−1. Factors determining model BC concentrations in Arctic snow include Arctic BC emissions, transport of extra-Arctic aerosols, precipitation, deposition efficiency of aerosols within the Arctic, and meltwater removal of particles in snow. Sensitivity studies show that the model–measurement evaluation is only weakly affected by meltwater scavenging efficiency because most measurements were conducted in non-melting snow. The Arctic (60–90° N) atmospheric residence time for BC in phase II models ranges from 3.7 to 23.2 days, implying large inter-model variation in local BC deposition efficiency. Combined with the fact that most Arctic BC deposition originates from extra-Arctic emissions, these results suggest that aerosol removal processes are a leading source of variation in model performance. The multi-model mean (full range) of Arctic radiative effect from BC in snow is 0.15 (0.07–0.25) W m−2 and 0.18 (0.06–0.28) W m−2 in phase I and phase II models, respectively. After correcting for model biases relative to observed BC concentrations in different regions of the Arctic, we obtain a multi-model mean Arctic radiative effect of 0.17 W m−2 for the combined AeroCom ensembles. Finally, there is a high correlation between modeled BC concentrations sampled over the observational sites and the Arctic as a whole, indicating that the field campaign provided a reasonable sample of the Arctic.