Comparison of bottom-up protein identification methods

With the rapid development of proteomics, a number of different methods appeared for the basic task of protein identification. We made a simple comparison between a common liquid chromatography-tandem mass spectrometry (LC-MS/MS) workflow using an ion trap mass spectrometer and a combined LC-MS and LC-MS/MS method using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry and accurate peptide masses. To compare the two methods for protein identification, we grew and extracted proteins from E. coli using established protocols. Cystines were reduced and alkylated, and proteins digested by trypsin. The resulting peptide mixtures were separated by reversed-phase liquid chromatography using a 4 h gradient from 0 to 50% acetonitrile over a C18 reversed-phase column. The LC separation was coupled on-line to either a Bruker Esquire HCT ion trap or a Bruker 7 tesla APEX-Qe Qh-FTICR hybrid mass spectrometer. Data-dependent Qh-FTICR-MS/MS spectra were acquired using the quadrupole mass filter and collisionally induced dissociation into the external hexapole trap. Proteins were in both schemes identified by Mascot MS/MS ion searches and the peptides identified from these proteins in the FTICR MS/MS data were used for automatic internal calibration of the FTICR-MS data, together with ambient polydimethylcyclosiloxane ions.

Land-atmosphere energy exchange in Arctic tundra and boreal forest: available data and feedbacks to climate

This paper summarizes and analyses available data on the surface energy balance of Arctic tundra and boreal forest. The complex interactions between ecosystems and their surface energy balance are also examined, including climatically induced shifts in ecosystem type that might amplify or reduce the effects of potential climatic change. High latitudes are characterized by large annual changes in solar input. Albedo decreases strongly from winter, when the surface is snow-covered, to summer, especially in nonforested regions such as Arctic tundra and boreal wetlands. Evapotranspiration (QE) of high-latitude ecosystems is less than from a freely evaporating surface and decreases late in the season, when soil moisture declines, indicating stomatal control over QE, particularly in evergreen forests. Evergreen conifer forests have a canopy conductance half that of deciduous forests and consequently lower QE and higher sensible heat flux (QH). There is a broad overlap in energy partitioning between Arctic and boreal ecosystems, although Arctic ecosystems and light taiga generally have higher ground heat flux because there is less leaf and stem area to shade the ground surface, and the thermal gradient from the surface to permafrost is steeper. Permafrost creates a strong heat sink in summer that reduces surface temperature and therefore heat flux to the atmosphere. Loss of permafrost would therefore amplify climatic warming. If warming caused an increase in productivity and leaf area, or fire caused a shift from evergreen to deciduous forest, this would increase QE and reduce QH. Potential future shifts in vegetation would have varying climate feedbacks, with largest effects caused by shifts from boreal conifer to shrubland or deciduous forest (or vice versa) and from Arctic coastal to wet tundra. An increase of logging activity in the boreal forests appears to reduce QE by roughly 50% with little change in QH, while the ground heat flux is strongly enhanced.

Modelling of urban sensible heat flux at multiple spatial scales : a demonstration using airborne hyperspectral imagery of Shanghai and a temperature–emissivity separation approach

Urbanization related alterations to the surface energy balance impact urban warming (‘heat islands’), the growth of the boundary layer, and many other biophysical processes. Traditionally, in situ heat flux measures have been used to quantify such processes, but these typically represent only a small local-scale area within the heterogeneous urban environment. For this reason, remote sensing approaches are very attractive for elucidating more spatially representative information. Here we use hyperspectral imagery from a new airborne sensor, the Operative Modular Imaging Spectrometer (OMIS), along with a survey map and meteorological data, to derive the land cover information and surface parameters required to map spatial variations in turbulent sensible heat flux (QH). The results from two spatially-explicit flux retrieval methods which use contrasting approaches and, to a large degree, different input data are compared for a central urban area of Shanghai, China: (1) the Local-scale Urban Meteorological Parameterization Scheme (LUMPS) and (2) an Aerodynamic Resistance Method (ARM). Sensible heat fluxes are determined at the full 6 m spatial resolution of the OMIS sensor, and at lower resolutions via pixel aggregation and spatial averaging. At the 6 m spatial resolution, the sensible heat flux of rooftop dominated pixels exceeds that of roads, water and vegetated areas, with values peaking at ∼ 350 W m− 2, whilst the storage heat flux is greatest for road dominated pixels (peaking at around 420 W m− 2). We investigate the use of both OMIS-derived land surface temperatures made using a Temperature–Emissivity Separation (TES) approach, and land surface temperatures estimated from air temperature measures. Sensible heat flux differences from the two approaches over the entire 2 × 2 km study area are less than 30 W m− 2, suggesting that methods employing either strategy maybe practica1 when operated using low spatial resolution (e.g. 1 km) data. Due to the differing methodologies, direct comparisons between results obtained with the LUMPS and ARM methods are most sensibly made at reduced spatial scales. At 30 m spatial resolution, both approaches produce similar results, with the smallest difference being less than 15 W m− 2 in mean QH averaged over the entire study area. This is encouraging given the differing architecture and data requirements of the LUMPS and ARM methods. Furthermore, in terms of mean study QH, the results obtained by averaging the original 6 m spatial resolution LUMPS-derived QH values to 30 and 90 m spatial resolution are within ∼ 5 W m− 2 of those derived from averaging the original surface parameter maps prior to input into LUMPS, suggesting that that use of much lower spatial resolution spaceborne imagery data, for example from Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) is likely to be a practical solution for heat flux determination in urban areas.

Multi-scale sensible heat fluxes in the urban environment from large aperture scintillometry and eddy covariance

Sensible heat fluxes (QH) are determined using scintillometry and eddy covariance over a suburban area. Two large aperture scintillometers provide spatially integrated fluxes across path lengths of 2.8 km and 5.5 km over Swindon, UK. The shorter scintillometer path spans newly built residential areas and has an approximate source area of 2-4 km2, whilst the long path extends from the rural outskirts to the town centre and has a source area of around 5-10 km2. These large-scale heat fluxes are compared with local-scale eddy covariance measurements. Clear seasonal trends are revealed by the long duration of this dataset and variability in monthly QH is related to the meteorological conditions. At shorter time scales the response of QH to solar radiation often gives rise to close agreement between the measurements, but during times of rapidly changing cloud cover spatial differences in the net radiation (Q*) coincide with greater differences between heat fluxes. For clear days QH lags Q*, thus the ratio of QH to Q* increases throughout the day. In summer the observed energy partitioning is related to the vegetation fraction through use of a footprint model. The results demonstrate the value of scintillometry for integrating surface heterogeneity and offer improved understanding of the influence of anthropogenic materials on surface-atmosphere interactions.

Saccharomyces cerevisiae coq10 null mutants are responsive to antimycin A

Deletion of COQ10 in Saccharomyces cerevisiae elicits a respiratory defect characterized by the absence of cytochrome c reduction, which is correctable by the addition of exogenous diffusible coenzyme Q(2). Unlike other coq mutants with hampered coenzyme Q(6) (Q(6)) synthesis, coq10 mutants have near wild-type concentrations of Q(6). In the present study, we used Q-cycle inhibitors of the coenzyme QH(2)-cytochrome c reductase complex to assess the electron transfer properties of coq10 cells. Our results show that coq10 mutants respond to antimycin A, indicating an active Q-cycle in these mutants, even though they are unable to transport electrons through cytochrome c and are not responsive to myxothiazol. EPR spectroscopic analysis also suggests that wild-type and coq10 mitochondria accumulate similar amounts of Q(6) semiquinone, despite a lower steady-state level of coenzyme QH(2)-cytochrome c reductase complex in the coq10 cells. Confirming the reduced respiratory chain state in coq10 cells, we found that the expression of the Aspergillus fumigatus alternative oxidase in these cells leads to a decrease in antimycin-dependent H(2)O(2) release and improves their respiratory growth.

Estudo da influência de compostos recalcitrantes na remoção de matéria orgânica biodegradável no tratamento de efluente de refinarias de petróleo

Petroleum Refinery wastewaters (PRW) have hart-to-degrade compounds, such as: phenols, ammonia, cyanides, sulfides, oils and greases and the mono and polynuclear aromatic hydrocarbons: benzene, toluene and xylene (BTX), acenaphthene, nitrobenzene and naphtalene. It is known that the microrganisms activity can be reduced in the presence of certain substances, adversely affecting the biological process of wastewater treatment. This research was instigated due the small number of studies regarding to this specific topic in the avaiable literature. This body of work ims to evaluate the effect of toxic substances on the biodegradability of the organic material found in PRW. Glucose was chosen as the model substrate due to its biodegradable nature. This study was divided into three parts: i) a survey of recalcitants compounds and the removal of phenol by using both biological and photochemical-biological processes; ii) biomass aclimation and iii) evaluation of the inhibitory effect certain compounds have on glucose biodegradation. The phenol degradation experiments were carried out in an activity sludge system and in a photochemical reactor. The results showed the photochemical-biological process to be more effective on phenol degradation, suggesting the superioruty of a combined photochemical-biological treatment when compared with a simple biological process for phenol removal from industry wastewaters. For the acclimation step, was used an activated sludge from industrial wastewaters. A rapid biomass aclimation to a synthetic solution composed of the main inhibitory compouns fpund in a PRW was obtained using the following operation condition: (pH = 7,0; DO ≥ 2,0 mg/L; RS = 20 days e qH = 31,2 and 20,4 hours), The last part was consisted of using respirometry evaluation toxicity effects of selected compounds over oxygen uptake rate to adaptated and non adaptated biomass in the presence of inhibitory compounds. The adaptated sludge showed greater degration capacity, with lower sensibility to toxic effects. The respirometry has proved to be very practical, as the techiniques used were simple and rapid, such as: Chemical Oxygen Demand (COD), Dissolved Oxygen (DO), and Volatile Suspended Solids (VSS). Using the latter it is possible to perform sludge selection to beggingthe process; thus allowing its use for aerobic treatment system`s behacior prediction

Prevalência de equinos quarto de milha portadores das mutações causadoras da miopatia por acúmulo de polissacarídeo tipo 1, paralisia periódica hipercalêmica e hipertermia maligna no Brasil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Prevalência da mutação causadora da paralisia periódica hipercalêmica em equinos da raça Quarto de Milha no Brasil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Carga de trabalho de equinos da raça Quarto de Milha monitorados com Sistema de Posicionamento Global (GPS) e monitor cardíaco durante exercício de Três Tambores

Pós-graduação em Biotecnologia Animal - FMVZ

Estrutura populacional e parâmetros genéticos da característica classe de tempo em corridas de equinos da raça Quarto de Milha

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Benthic and planktonic foraminifera of sediment core GIK17957-2

A detailed age model for core 17957-2 of the southern South China Sea was developed based on delta18O, coarse fraction, magnetostratigraphy, and biostratigraphy for the last 1500 kyr. The delta18O record has clear ~100-kyr cycles after the Mid-Pleistocene Revolution (MPR) at the entrance of marine isotopic stage (MIS) 22. Planktonic foraminifera responded to the MPR immediately, showing the increased sea surface temperature (SST) and dissolution after the MPR. Benthic foraminifera did not respond to it until the Brunhes/Matuyama boundary. Since the MPR, the depth of thermocline gradually became shallower until MISs 6-5. This major change within MISs 6-5 was also reflected in the decreased SSTs and increased productivity and Deep Water Mass. Thus two major Pleistocene paleoceanographic changes were found: One was around the MPR; the other occurred within MISs 6-5, which speculatively might be ascribed to the reorganization of surface and deep circulation, possibly induced by tectonic forces.

Turbulent flux and meteorological measurements during ARCTEX-2006 campaign

This dataset present result from the DFG- funded Arctic-Turbulence-Experiment (ARCTEX-2006) performed by the University of Bayreuth on the island of Svalbard, Norway, during the winter/spring transition 2006. From May 5 to May 19, 2006 turbulent flux and meteorological measurements were performed on the monitoring field near Ny-Ålesund, at 78°55'24'' N, 11°55'15'' E Kongsfjord, Svalbard (Spitsbergen), Norway. The ARCTEX-2006 campaign site was located about 200 m southeast of the settlement on flat snow covered tundra, 11 m to 14 m above sea level. The permanent sites used for this study consisted of the 10 m meteorological tower of the Alfred Wegener Institute for Polar- and Marine Research (AWI), the international standardized radiation measurement site of the Baseline Surface Radiation Network (BSRN), the radiosonde launch site and the AWI tethered balloon launch sites. The temporary sites - set up by the University of Bayreuth - were a 6 m meteorological gradient tower, an eddy-flux measurement complex (EF), and a laser-scintillometer section (SLS). A quality assessment and data correction was applied to detect and eliminate specific measurement errors common at a high arctic landscape. In addition, the quality checked sensible heat flux measurements are compared with bulk aerodynamic formulas that are widely used in atmosphere-ocean/land-ice models for polar regions as described in Ebert and Curry (1993, doi:10.1029/93JC00656) and Launiainen and Cheng (1995). These parameterization approaches easily allow estimation of the turbulent surface fluxes from routine meteorological measurements. The data show: - the role of the intermittency of the turbulent atmospheric fluctuation of momentum and scalars, - the existence of a disturbed vertical temperature profile (sharp inversion layer) close to the surface, - the relevance of possible free convection events for the snow or ice melt in the Arctic spring at Svalbard, and - the relevance of meso-scale atmospheric circulation pattern and air-mass advection for the near-surface turbulent heat exchange in the Arctic spring at Svalbard. Recommendations and improvements regarding the interpretation of eddy-flux and laser-scintillometer data as well as the arrangement of the instrumentation under polar distinct exchange conditions and (extreme) weather situations could be derived.

Fluxes and meteorological observations on Spitsbergen

Arctic permafrost may be adversely affected by climate change in a number of ways, so that establishing a world-wide monitoring program seems imperative. This thesis evaluates possibilities for permafrost monitoring at the example of a permafrost site on Svalbard, Norway. An energy balance model for permafrost temperatures is developed that evaluates the different components of the surface energy budget in analogy to climate models. The surface energy budget, consisting of radiation components, sensible and latent heat fluxes as well as the ground heat flux, is measured over the course of one year, which has not been accomplished for arctic land areas so far. A considerable small-scale heterogeneity of the summer surface temperature is observed in long-term measurements with a thermal imaging system, which can be reproduced in the energy balance model. The model can also simulate the impact of different snow depths on the soil temperature, that has been documented in field measurements. Furthermore, time series of terrestrial surface temperature measurements are compared to satellite-borne measurements, for which a significant cold-bias is observed during winter. Finally, different possibilities for a world-wide monitoring scheme are assessed. Energy budget models can incorporate different satellite data sets as training data sets for parameter estimation, so that they may constitute an alternative to purely satellite-based schemes.

Water chemistry and heat budget of the Churchill River estuary region

A conceptual scheme for the transition from winter to spring is developed for a small Arctic estuary (Churchill River, Hudson Bay) using hydrological, meteorological and oceanographic data together with models of the landfast ice. Observations within the Churchill River estuary and away from the direct influence of the river plume (Button Bay), between March and May 2005, show that both sea ice (production and melt) and river water influence the region's freshwater budget. In Button Bay, ice production in the flaw lead or polynya of NW Hudson Bay result in salinization through winter until the end of March, followed by a gradual freshening of the water column through April-May. In the Churchill Estuary, conditions varied abruptly throughout winter-spring depending on the physical interaction among river discharge, the seasonal landfast ice, and the rubble zone along the seaward margin of the landfast ice. Until late May, the rubble zone partially impounded river discharge, influencing the surface salinity, stratification, flushing time, and distribution and abundance of nutrients in the estuary. The river discharge, in turn, advanced and enhanced sea ice ablation in the estuary by delivering sensible heat. Weak stratification, the supply of riverine nitrogen and silicate, and a relatively long flushing time (~6 days) in the period preceding melt may have briefly favoured phytoplankton production in the estuary when conditions were still poor in the surrounding coastal environment. However, in late May, the peak flow and breakdown of the ice-rubble zone around the estuary brought abrupt changes, including increased stratification and turbidity, reduced marine and freshwater nutrient supply, a shorter flushing time, and the release of the freshwater pool into the interior ocean. These conditions suppressed phytoplankton productivity while enhancing the inventory of particulate organic matter delivered by the river. The physical and biological changes observed in this study highlight the variability and instability of small frozen estuaries during winter-spring transition, which implies sensitivity to climate change.