High-throughput proteomics using matrix-assisted laser desorption/ ionization mass spectrometry

It has become evident that the mystery of life will not be deciphered just by decoding its blueprint, the genetic code. In the life and biomedical sciences, research efforts are now shifting from pure gene analysis to the analysis of all biomolecules involved in the machinery of life. One area of these postgenomic research fields is proteomics. Although proteomics, which basically encompasses the analysis of proteins, is not a new concept, it is far from being a research field that can rely on routine and large-scale analyses. At the time the term proteomics was coined, a gold-rush mentality was created, promising vast and quick riches (i.e., solutions to the immensely complex questions of life and disease). Predictably, the reality has been quite different. The complexity of proteomes and the wide variations in the abundances and chemical properties of their constituents has rendered the use of systematic analytical approaches only partially successful, and biologically meaningful results have been slow to arrive. However, to learn more about how cells and, hence, life works, it is essential to understand the proteins and their complex interactions in their native environment. This is why proteomics will be an important part of the biomedical sciences for the foreseeable future. Therefore, any advances in providing the tools that make protein analysis a more routine and large-scale business, ideally using automated and rapid analytical procedures, are highly sought after. This review will provide some basics, thoughts and ideas on the exploitation of matrix-assisted laser desorption/ ionization in biological mass spectrometry - one of the most commonly used analytical tools in proteomics - for high-throughput analyses.

Comparison of the euryarchaeal microbial community in guts and food-soil of the soil-feeding termite Cubitermes fungifaber across different soil types

Termites are an important component of tropical soil communities and have a significant affect on the structure and nutrient content of soil. Digestion in termites is related to gut structure, gut physico-chemical conditions and gut symbiotic microbiota. Here we describe the use of 16S rRNA gene sequencing and Terminal-restriction Fragment Length Polymorphism (T-RFLP) analysis to examine methanogenic Archaea (MA) in the guts and food-soil of the soil-feeder Cubitermes fungifaber Sjostedt across a range of soil types. If they are strictly vertically inherited, then MA in guts should be the same in all individuals even if the soils differ across sites. In contrast, gut MA should reflect what is present in soil if populations are merely a reflection of what is ingested as the insects forage. We show clear differences between the euryarchaeal communities in termite guts and in food-soils from five different sites. Analysis of 16S rRNA gene clones indicated little overlap between the gut and soil communities. Gut clones were related to a termite-derived Methanomicrobiales cluster, to Methanobrevibacter and, surprisingly, to the haloalkaliphile Natronococcus. Soil clones clustered with Methanosarcina, Methanomicrococcus or Rice Cluster I. T-RFLP analysis indicated that the archaeal communities in the soil samples differed from site to site, whereas those in termite guts were similar between sites. There was some overlap between the gut and soil communities but these may represent transient populations in either guts or soil. Our data does not support the hypothesis that termite gut MA are derived from their food soil but also does not support a purely vertical transmission of gut microflora.

High-throughput proteomics using matrix-assisted laser desorption/ionization mass spectrometry

It has become evident that the mystery of life will not be deciphered just by decoding its blueprint, the genetic code. In the life and biomedical sciences, research efforts are now shifting from pure gene analysis to the analysis of all biomolecules involved in the machinery of life. One area of these postgenomic research fields is proteomics. Although proteomics, which basically encompasses the analysis of proteins, is not a new concept, it is far from being a research field that can rely on routine and large-scale analyses. At the time the term proteomics was coined, a gold-rush mentality was created, promising vast and quick riches (i.e., solutions to the immensely complex questions of life and disease). Predictably, the reality has been quite different. The complexity of proteomes and the wide variations in the abundances and chemical properties of their constituents has rendered the use of systematic analytical approaches only partially successful, and biologically meaningful results have been slow to arrive. However, to learn more about how cells and, hence, life works, it is essential to understand the proteins and their complex interactions in their native environment. This is why proteomics will be an important part of the biomedical sciences for the foreseeable future. Therefore, any advances in providing the tools that make protein analysis a more routine and large-scale business, ideally using automated and rapid analytical procedures, are highly sought after. This review will provide some basics, thoughts and ideas on the exploitation of matrix-assisted laser desorption/ionization in biological mass spectrometry - one of the most commonly used analytical tools in proteomics - for high-throughput analyses.

Trichloro-mono-beta-diketonato oxorhenium(V) complexes: synthesis, characterization and crystal structure

Oxorhenium(V) complexes of beta-diketonate systems have been synthesized and isolated in pure form. The red complexes n-Bu4N[ReO(R1COCHCOR2)Cl-3] (acac, R-1=R-2=CH3; bzac, R-1=CH3 and R-2=C6H5; bzbz, R-1=R-2=C6H5) have been characterized by elemental analyses, spectroscopic and other physico-chemical tools. One complex, n-Bu4N[ReO(bzbz)Cl-3] (1c) has been subjected to single-crystal X-ray analysis. In the structure of the anion, the metal has a six-coordinate octahedral environment in which the bidentate -diketone ligand is cis and trans to the terminal oxygen.

Synthesis and catalytic epoxidation potentiality of oxodiperoxo molybdenum(VI) complexes with pyridine-2-carboxaldoxime and pyridine-2-carboxylate: the crystal structure of PMePh3[MoO(O-2)(2)(PyCO)]

[MoO(O-2)(2)(PyCOXH)(H2O)] and PMePh3[MoO(O-2)(2)(PyCO)] (PyCOXH = Pyridine-2-carboxaldoxime and PyCOH = Pyridine-2-carboxylic acid) have been synthesized. Both complexes have been characterized by physico-chemical and spectroscopic methods; in addition, the carboxylate complex has been structurally characterized by X-ray crystallography. The carboxylate complex is a more efficient catalyst than the oxime complex for epoxidation of olefins and shows excellent catalytic activity for the substrates: cyclooctene, cinnamyl alcohol, allyl alcohol and 1-hexene.

Synthesis, crystal structure and reactivity of copper(II) complexes of tetradentate N2S2 donor ligands

Two new hexa-coordinated mononuclear copper(II) complexes of two ligands L-1 and L-2 containing NSSN donor sets formulated as [Cu(L)(H2O)(2)](NO3)(2) [1a, L = 1,2-bis(2-pyridylmethylthio)ethane (L-1), 1b L = 1,3-bis(2-pyridyl-methylthio)propane (L-2)] were synthesized and characterized by physico-chemical and spectroscopic methods. In 1a the single crystal X-ray crystallography analysis showed a distorted octahedral geometry about copper(II) ion. The crystal packing evidences pairs of complexes arranged about a center of symmetry and connected through a H-bond occurring between aquo ligands and nitrate anions. On reaction with chloride and pseudohalides (N-3(-) and SCN-), in acetonitrile at ambient temperature. complexes 1 changed to monocationic penta-coordinated mononuclear copper(H) species formulated as [Cu(L)(Cl)]NO3 (2), [Cu(L)(N-3)]NO3 (3). and [Cu(L)(SCN)]NO3 (4). These copper(II) complexes have been isolated in pure form from the reaction mixtures and characterized by physico-chemical and spectroscopic tools. The solid-state structure of 2a, established by X-ray crystallography, shows a trigonal bipyramidal geometry about the metal ion with a trigonality index (tau) of 0.561. (C) 2009 Elsevier B.V. All rights reserved.

Fine root condition relates to visible crown damage in Norway spruce on acidified soils

Allochthonous Norway spruce stands in the Kysucké Beskydy Mts. (north-western Slovakia) have been exposed to substantial acid deposition in the recent past and grow in acidified soil conditions with mean pH of about 4.0 in the topsoil. We selected 90 spruce trees representing 30 triples of different crown status: healthy, stressed and declining to assess the relationship between crown and fine root status. Sequential coring and in-growth bags were applied to each triplet to investigate fine root biomass and growth in the soil depths of 0-10 and 10-20 cm. Fine root quantity (biomass and necromass), turnover (production over standing stock), morphological features (specific root length, root tip density) and chemical properties (Ca:Al molar ratio) were compared among the abovementioned health status categories. Living fine root biomass decreased with increasing stress, while the ratio of living to dead biomass increased. Annual fine root production decreased and specific root length increased in stressed trees when compared to healthy or declining trees, a situation which may be related to the position of trees in the canopy (healthy and declining – dominant, stressed – co-dominant). The Ca:Al ratio decreased with increasing crown damage, indicating a decreased ability to filter out aluminium. In conclusion, fine root status appears to be linked to visible crown damage and can be used as a tree health indicator.

Boundary layer dynamics over London, UK, as observed using Doppler lidar during REPARTEE-II

Urban boundary layers (UBLs) can be highly complex due to the heterogeneous roughness and heating of the surface, particularly at night. Due to a general lack of observations, it is not clear whether canonical models of boundary layer mixing are appropriate in modelling air quality in urban areas. This paper reports Doppler lidar observations of turbulence profiles in the centre of London, UK, as part of the second REPARTEE campaign in autumn 2007. Lidar-measured standard deviation of vertical velocity averaged over 30 min intervals generally compared well with in situ sonic anemometer measurements at 190 m on the BT telecommunications Tower. During calm, nocturnal periods, the lidar underestimated turbulent mixing due mainly to limited sampling rate. Mixing height derived from the turbulence, and aerosol layer height from the backscatter profiles, showed similar diurnal cycles ranging from c. 300 to 800 m, increasing to c. 200 to 850 m under clear skies. The aerosol layer height was sometimes significantly different to the mixing height, particularly at night under clear skies. For convective and neutral cases, the scaled turbulence profiles resembled canonical results; this was less clear for the stable case. Lidar observations clearly showed enhanced mixing beneath stratocumulus clouds reaching down on occasion to approximately half daytime boundary layer depth. On one occasion the nocturnal turbulent structure was consistent with a nocturnal jet, suggesting a stable layer. Given the general agreement between observations and canonical turbulence profiles, mixing timescales were calculated for passive scalars released at street level to reach the BT Tower using existing models of turbulent mixing. It was estimated to take c. 10 min to diffuse up to 190 m, rising to between 20 and 50 min at night, depending on stability. Determination of mixing timescales is important when comparing to physico-chemical processes acting on pollutant species measured simultaneously at both the ground and at the BT Tower during the campaign. From the 3 week autumnal data-set there is evidence for occasional stable layers in central London, effectively decoupling surface emissions from air aloft.

Production and dissolution rates of earthworm-secreted calcium carbonate

Earthworms secrete granules of calcium carbonate. These are potentially important in soil biogeochemical cycles and are routinely recorded in archaeological studies of Quaternary soils. Production rates of calcium carbonate granules by the earthworm Lumbricus terrestris L. were determined over 27 days in a range of soils with differing chemical properties (pH, organic matter content, water holding capacity, bulk composition, cation exchange capacity and exchangeable cations). Production rate varied between soils, lay in the range 0–0.043 mmolCaCO3 (0–4.3 mg) earthworm−1 d−1 with an average rate of 8 × 10−3 mmolCaCO3 (0.8 mg) earthworm−1 d−1 and was significantly correlated (r = 0.68, P ≤ 0.01) with soil pH. In a second experiment lasting 315 days earthworms repeatedly (over periods of 39–57 days) produced comparable masses of granules. Converting individual earthworm granule production rates into fluxes expressed on per hectare of land per year basis depends heavily on estimates of earthworm numbers. Using values of 10–20 L. terrestris m−2 suggests a rate of 18– 3139 molCaCO3 ha−1 yr−1. Data obtained from flow-through dissolution experiments suggest that at near neutral pH, granule geometric surface areanormalised dissolution rates are similar to those for other biogenic and inorganic calcium carbonate. Fits of the data to the dissolution relationship r = k(1 − ˝)n where r = dissolution rate, k = a rate constant, ˝ = relative saturation and n = the reaction order gave values of k = 1.72 × 10−10 mol cm−2 s−1 and n = 1.8 for the geometric surface area-normalised rates and k = 3.51 × 10−13 mol cm−2 s−1 and n = 1.8 for the BET surface area-normalised rates. In 196 day leaching column experiments trends in granule dissolution rate referenced to soil chemistry corresponded to predictions made by the SLIM model for dissolution of limestone in soil. If soil solution approaches saturation with respect to calcium carbonate granule dissolution will slow or even stop and granules be preserved indefinitely. Granules have the potential to be a small but significant component of the biogeochemical cycling of C and Ca in soil.

Nickel(II) and copper(II) complexes of Schiff base ligands containing N4O2 and N4S2 donors with pyrrole terminal binding groups: synthesis, characterization, X-ray structures, DFT and electrochemical studies

A series of hexadentate ligands, H2Lm (m = 1−4), [1H-pyrrol-2-ylmethylene]{2-[2-(2-{[1H-pyrrol-2-ylmethylene]amino}phenoxy)ethoxy]phenyl}amine (H2L1), [1H-pyrrol-2-ylmethylene]{2-[4-(2-{[1H-pyrrol-2-ylmethylene]amino}phenoxy)butoxy]phenyl}amine (H2L2), [1H-pyrrol-2-ylmethylene][2-({2-[(2-{[1H-pyrrol-2-ylmethylene]amino}phenyl)thio]ethyl}thio)phenyl]amine (H2L3) and [1H-pyrrol-2-ylmethylene][2-({4-[(2-{[1H-pyrrol-2-lmethylene]amino}phenyl)thio]butyl}thio) phenyl]amine (H2L4) were prepared by condensation reaction of pyrrol-2-carboxaldehyde with {2-[2-(2-aminophenoxy)ethoxy]phenyl}amine, {2-[4-(2-aminophenoxy)butoxy]phenyl}amine, [2-({2-[(2-aminophenyl)thio]ethyl}thio)phenyl]amine and [2-({4-[(2-aminophenyl)thio]butyl}thio)phenyl]amine respectively. Reaction of these ligands with nickel(II) and copper(II) acetate gave complexes of the form MLm (m = 1−4), and the synthesized ligands and their complexes have been characterized by a variety of physico-chemical techniques. The solid and solution states investigations show that the complexes are neutral. The molecular structures of NiL3 and CuL2, which have been determined by single crystal X-ray diffraction, indicate that the NiL3 complex has a distorted octahedral coordination environment around the metal while the CuL2 complex has a seesaw coordination geometry. DFT calculations were used to analyse the electronic structure and simulation of the electronic absorption spectrum of the CuL2 complex using TDDFT gives results that are consistent with the measured spectroscopic behavior of the complex. Cyclic voltammetry indicates that all copper complexes are electrochemically inactive but the nickel complexes with softer thioethers are more easily oxidized than their oxygen analogs.

Nanoscale zerovalent iron alters soil bacterial community structure and inhibits chloroaromatic biodegradation potential in Aroclor 1242-contaminated soil

Nanoscale zerovalent iron (nZVI) has potential for the remediation of organochlorine-contaminated environments. Environmental safety concerns associated with in situ deployment of nZVI include potential negative impacts on indigenous microbes whose biodegradative functions could contribute to contaminant remediation. With respect to a two-step polychlorinated biphenyl remediation scenario comprising nZVI dechlorination followed by aerobic biodegradation, we examined the effect of polyacrylic acid (PAA)-coated nZVI (mean diameter = 12.5 nm) applied at 10 g nZVI kg−1 to Aroclor-1242 contaminated and uncontaminated soil over 28 days. nZVI had a limited effect on Aroclor congener profiles, but, either directly or indirectly via changes to soil physico-chemical conditions (pH, Eh), nZVI addition caused perturbation to soil bacterial community composition, and reduced the activity of chloroaromatic mineralizing microorganisms. We conclude that nZVI addition has the potential to inhibit microbial functions that could be important for PCB remediation strategies combining nZVI treatment and biodegradation.

Synthesis, characterization, crystal structure, and DNA-binding of ruthenium(II) complexes of heterocyclic nitrogen ligands resulting from a benzimidazole-based quinazoline derivative

The reaction of cis-[RuCl2(dmso)(4)] with [6-(2-pyridinyl)-5,6-dihydrobenzimidazo[1,2-c] quinazoline] (L) afforded in pure form a blue ruthenium(II) complex, [Ru(L-1)(2)] (1), where the original L changed to [2-(1H-benzoimidazol-2-yl)-phenyl]-pyridin-2-ylmethylene-amine (HL1). Treatment of RuCl3 center dot 3H(2)O with L in dry tetrahydrofuran in inert atmosphere led to a green ruthenium(II) complex, trans-[RuCl2(L-2)(2)] (2), where L was oxidized in situ to the neutral species 6-pyridin-yl-benzo[4,5]imidazo[1,2-c] quinazoline (L-2). Complex 2 was also obtained from the reaction of RuCl3 center dot 3H(2)O with L-2 in dry ethanol. Complexes 1 and 2 have been characterized by physico-chemical and spectroscopic tools, and 1 has been structurally characterized by single-crystal X-ray crystallography. The electrochemical behavior of the complexes shows the Ru(III)/Ru(II) couple at different potentials with quasi-reversible voltammograms. The interaction of these complexes with calf thymus DNA by using absorption and emission spectral studies allowed determination of the binding constant K-b and the linear Stern-Volmer quenching constant K-SV

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.

Atmospheric chemistry and physics in the atmosphere of a developed megacity (London): an overview of the REPARTEE experiment and its conclusions

The REgents PARk and Tower Environmental Experiment (REPARTEE) comprised two campaigns in London in October 2006 and October/November 2007. The experiment design involved measurements at a heavily trafficked roadside site, two urban background sites and an elevated site at 160–190 m above ground on the BT Tower, supplemented in the second campaign by Doppler lidar measurements of atmospheric vertical structure. A wide range of measurements of airborne particle physical metrics and chemical composition were made as well as measurements of a considerable range of gas phase species and the fluxes of both particulate and gas phase substances. Significant findings include (a) demonstration of the evaporation of traffic-generated nanoparticles during both horizontal and vertical atmospheric transport; (b) generation of a large base of information on the fluxes of nanoparticles, accumulation mode particles and specific chemical components of the aerosol and a range of gas phase species, as well as the elucidation of key processes and comparison with emissions inventories; (c) quantification of vertical gradients in selected aerosol and trace gas species which has demonstrated the important role of regional transport in influencing concentrations of sulphate, nitrate and secondary organic compounds within the atmosphere of London; (d) generation of new data on the atmospheric structure and turbulence above London, including the estimation of mixed layer depths; (e) provision of new data on trace gas dispersion in the urban atmosphere through the release of purposeful tracers; (f) the determination of spatial differences in aerosol particle size distributions and their interpretation in terms of sources and physico-chemical transformations; (g) studies of the nocturnal oxidation of nitrogen oxides and of the diurnal behaviour of nitrate aerosol in the urban atmosphere, and (h) new information on the chemical composition and source apportionment of particulate matter size fractions in the atmosphere of London derived both from bulk chemical analysis and aerosol mass spectrometry with two instrument types.

Towards a unified approach for the determination of the bioaccessibility of organic pollutants

Bioaccessibility studies have been widely used as a research tool to determine the potential human exposure to ingested contaminants. More recently they have been practically applied for soil borne toxic elements. This paper reviews the application of bioaccessibility tests across a range of organic pollutants and contaminated matrices. Important factors are reported to be: the physiological relevance of the test, the components in the gut media, the size fraction chosen for the test and whether it contains a sorptive sink. The bioaccessibility is also a function of the composition of the matrix (e.g. organic carbon content of soils) and the physico-chemical characteristics of the pollutant under test. Despite the widespread use of these tests, there are a large number of formats used and very few validation studies with animal models. We propose a unified format for a bioaccessibility test for organic pollutants. The robustness of this test should first be confirmed through inter laboratory comparison, then tested in-vivo.