Proteomic methodological recommendations for studies involving human plasma, platelets, and peripheral blood mononuclear cells

This study was designed to develop, optimize and validate protocols for blood processing prior to proteomic analysis of plasma, platelets and peripheral blood mononuclear cells (PBMC) and to determine analytical variation of a single sample of depleted plasma, platelet and PBMC proteins within and between four laboratories each using their own standard operating protocols for 2D gel electrophoresis. Plasma depleted either using the Beckman Coulter IgY-12 proteome partitioning kit or the Amersham albumin and IgG depletion columns gave good quality gels, but reproducibility appeared better with the single-use immuno-affinity column. The use of the Millipore Filter Device for protein concentration gave a 16% ( p < 0.005) higher recovery of protein in flow-through sample compared with acetone precipitation. The use of OptiPrep gave the lowest level of platelet contamination (1:0.8) during the isolation of PBMC from blood. Several proteins (among which are alpha-tropomyosin, fibrinogen and coagulation factor XIII A) were identified that may be used as biomarkers of platelet contamination in future studies. When identifying preselected spots, at least three out of the four centers found similar identities for 10 out of the 10 plasma proteins, 8 out of the 10 platelet proteins and 8 out of the 10 PBMC proteins. The discrepancy in spot identifications has been described before and may be explained by the mis-selection of spots due to laboratory-to-laboratory variation in gel formats, low scores on the peptide analysis leading to no or only tentative identifications, or incomplete resolution of different proteins in what appears as a single abundant spot. The average within-laboratory coefficient of variation (CV) for each of the matched spots after automatic matching using either PDQuest or ProteomWeaver software ranged between 18 and 69% for depleted plasma proteins, between 21 and 55% for platelet proteins, and between 22 and 38% for PBMC proteins. Subsequent manual matching improved the CV with on average between 1 and 16%. The average between laboratory CV for each of the matched spots after automatic matching ranged between 4 and 54% for depleted plasma proteins, between 5 and 60% for platelet proteins, and between 18 and 70% for PBMC proteins. This variation must be considered when designing sufficiently powered studies that use proteomics tools for biomarker discovery. The use of tricine in the running buffer for the second dimension appears to enhance the resolution of proteins especially in the high molecular weight range.     

Catalytic and electrochemical properties of new manganese(III) compounds of 2-(2′-hydroxyphenyl)-oxazoline (Hphox or HClphox). Molecular structures of [Mn(Clphox)2(MeOH)2](ClO4) and [Mn(phox)2(MeOH)2][Mn(phox)2(ClO4)2](H2O)2

New manganese(III) complexes of Hphox (2-(2′-hydroxyphenyl)-oxazoline) and HClphox (2-(5′-chloro-2′-hydroxyphenyl)-oxazoline) have been synthesised. The X-ray structures of [Mn(phox)₂(MeOH)₂][Mn(phox)₂(ClO₄)₂](H₂O)₂ and [Mn(Clphox)₂(MeOH)₂](ClO₄) show the manganese(III) ions to be octahedrally coordinated with methanol or perchlorate at the axial coordination sites. The cyclic voltammograms of the complexes, with the exception of [Mn(phox)₂(acac)] (Hacac=2,4-pentanedione), show an irreversible reduction wave of manganese(III) to manganese(II). After addition of an excess of 1-methylimidazole (1-Meim), the reduction process shifts towards lower potentials and becomes (quasi-) reversible, indicating that the presence of 1-Meim affects the catalytic efficiency of the complexes. The complexes catalyse the epoxidation of styrene by dihydrogen peroxide. The cumulative turnover numbers towards styrene oxide obtained after 15 min. vary from 16 for [Mn(Clphox)₂(MeOH)₂](ClO₄) to 26 for [Mn(phox)₂(acac)]. Ligand degradation appears to be the limiting factor for obtaining higher turnover numbers.     

The consequences of uncertainties in land use, climate and vegetation responses on the terrestrial carbon

The IPCC SRES narratives were implemented in IMAGE 2.2 to evaluate the future con-dition of the climate system (including the biosphere). A series of scenario experiments was used to assess possible ranges in emissions and concentrations of greenhouse gases, climate changeand impacts. These experiments focussed on the role of the terrestrial carbon cycle. The experi-ments show that the SRES narratives dominate human emissions and not natural processes. In contrary, atmospheric CO_2 concentration strongly differs between the experiments. Atmospheric CO_2 concentrations range for A1B from 714 to 1009 ppmv CO_2 in 2100. The spread of this range is comparable with the full SRES range as implemented in IMAGE 2.2 (515-895 μmol/mol CO_2).The most important negative and positive feedback processes in IMAGE 2.2 on the build-up ofCO_2 concentrations are CO_2 fertilisation and soil respiration respectively. Indirect effects of theseprocesses further change land-use patterns, deforestation rates and alter the natural C fluxes. Thecumulative effects of these changes have a pronounced influence on the final CO_2 concentrations. Our scenario experiments highlight the importance of a proper parameterisation of feedback proc-esses, C-cycle and land use in determining the future states of the climate system.     

Two-color,rolling-circle amplification on antibody microarrays for sensitive,multiplexed serum-protein measurements

The ability to conveniently and rapidly profile a diverse set of proteins has valuable applications. In a step toward further enabling such a capability, we developed the use of rolling-circle amplification (RCA) to measure the relative levels of proteins from two serum samples, labeled with biotin and digoxigenin, respectively, that have been captured on antibody microarrays. Two-color RCA produced fluorescence up to 30-fold higher than direct-labeling and indirect-detection methods using antibody microarrays prepared on both polyacrylamide-based hydrogels and nitrocellulose. Replicate RCA measurements of multiple proteins from sets of 24 serum samples were highly reproducible and accurate. In addition, RCA enabled reproducible measurements of distinct expression profiles from lower-abundance proteins that were not measurable using the other detection methods. Two-color RCA on antibody microarrays should allow the convenient acquisition of expression profiles from a great diversity of proteins for a variety of applications.     

Effect of superovulation induction on embryonic development on day 5 and subsequent development and survival after nonsurgical embryo transfer in pigs

To evaluate the effects of eCG dosage on recovery and quality of Day 5 embryos and on subsequent development and survival after embryo transfer, batches of 5 to 10 donor sows were treated with 1000 or 1500 IU eCG. Recipients from the same batch were synchronously treated with 800 IU eCG. Ovulation was induced with 750 IU hCG (72 h after eCG) in donors and recipients. Donors were inseminated and embryos were collected at 162 h after hCG (120 h after ovulation). Ovulation rate was lower using 1000 IU eCG (28.5+/-11.7; n=48) than 1500 IU eCG (45.7+/-20.3; n=32; P<0.0001). Embryo recovery rate (82.9+/-16.9%) and percentage expanded blastocysts (56.2+/-31.4%) were similar (P>0.05). Expanded blastocysts from each group of sows were pooled into 2 groups within eCG treatment, containing embryos from normally ovulating sows (< or = 25 corpora lutea [CL]) or from superovulated sows (> 25 CL). Average diameter and number of cells of a random sample of the expanded blastocysts per pool were recorded. The average diameter of blastocysts (160.5+/-11.5 microm) was not affected by eCG dosage or ovulation rate (P>0.10). The average number of cells per embryo was higher in the 1000 IU eCG group (84.3+/-15.3) than in the 1500 IU eCG group (70.2+/-1.9; P<0.05) but was similar for normal and superovulated donors within each eCG group (P>0.10). Of the 4 groups, litters of 28 to 30 blastocysts were nonsurgically transferred to 27 synchronous recipients. Pregnant recipients were slaughtered on Day 37 after hCG treatment to evaluate embryonic development and survival. Pregnancy rate for the 1000 and 1500 IU eCG donor groups was 71% (10/14) and 46% (6/13; P>0.10), respectively. The number of implantations and fetuses for the 1000 IU eCG groups was 12.9+/-3.0 and 11.1+/-2.7, and 14.2+/-7.0 and 10.5+/-4.6, respectively, for the 1500 IU eCG groups (P>0.10). After post-priory categorizing the litters of blastocysts to below or above the average diameter (158 microm) of the transferred embryos, irrespective of eCG dosage or ovulation rate, the pregnancy rate was 43% (6/14) and 77% (10/13; P<0.10), respectively. Post-priory categorizing the transferred litters to below or above the average number of cells per embryo litter, irrespective of eCG dosage or ovulation rate, showed no differences in pregnancy rates or number of implantations and fetuses (P>0.10). It was concluded that eCG dosage affects embryonic development at Day 7 after hCG, and this effect was not due to ovulation rate. Embryonic survival after nonsurgical transfer was not related to eCG dosage but tended to be related to the diameter of the blastocysts.     

Glycosylation sites and site-specific glycosylation in human Tamm- Horsfall glycoprotein

The N-glycosylation sites of human Tamm-Horsfall glycoprotein from one healthy male donor have been characterized, based on an approach using endoproteinase Glu-C (V-8 protease, Staphylococcus aureus ) digestion and a combination of chromatographic techniques, automated Edman sequencing, and fast atom bombardment mass spectrometry. Seven out of the eight potential N-glycosylation sites, namely, Asn52, Asn56, Asn208, Asn251, Asn298, Asn372, and Asn489, turned out to be glycosylated, and the potential glycosylation site at Asn14, being close to the N-terminus, is not used. The carbohydrate microheterogeneity on three of the glycosylation sites was studied in more detail by high-pH anion-exchange chromatographic profiling and 500 MHz1H-NMR spectroscopy. Glycosylation site Asn489 contains mainly di- and tri-charged oligosaccharides which comprise, among others, the GalNAc4 S (beta1-4)GlcNAc terminal sequence. Only glycosylation site Asn251 bears oligomannose-type carbohydrate chains ranging from Man5GlcNAc2to Man8GlcNAc2, in addition to a small amount of complex- type structures. Profiling of the carbohydrate moieties of Asn208 indicates a large heterogeneity, similar to that established for native human Tamm-Horsfall glycoprotein, namely, multiply charged complex-type carbohydrate structures, terminated by sulfate groups, sialic acid residues, and/or the Sda-determinant.      

Protection against cartilage and bone destruction by systemic interleukin-4 treatment in established murine type II collagen-induced arthritis

Destruction of cartilage and bone are hallmarks of human rheumatoid arthritis (RA), and controlling these erosive processes is the most challenging objective in the treatment of RA. Systemic interleukin-4 treatment of established murine collagen-induced arthritis suppressed disease activity and protected against cartilage and bone destruction. Reduced cartilage pathology was confirmed by both decreased serum cartilage oligomeric matrix protein (COMP) and histological examination. In addition, radiological analysis revealed that bone destruction was also partially prevented. Improved suppression of joint swelling was achieved when interleukin-4 treatment was combined with low-dose prednisolone treatment. Interestingly, synergistic reduction of both serum COMP and inflammatory parameters was noted when low-dose interleukin-4 was combined with prednisolone. Systemic treatment with interleukin-4 appeared to be a protective therapy for cartilage and bone in arthritis, and in combination with prednisolone at low dosages may offer an alternative therapy in RA.     

Surface N balances and reactive N loss to the environment from global intensive agricultural production systems for the period 1970–2030

Data for the historical years 1970 and 1995 and the FAO-Agriculture Towards 2030 projection are used to calculate N inputs (N fertilizer, animal manure, biological N fixation and atmospheric deposition) and the N export from the field in harvested crops and grass and grass consumption by grazing animals. In most industrialized countries we see a gradual increase of the overall N recovery of the intensive agricultural production systems over the whole 1970–2030 period. In contrast, low N input systems in many developing countries sustained low crop yields for many years but at the cost of soil fertility by depleting soil nutrient pools. In most developing countries the N recovery will increase in the coming decades by increasing efficiencies of N use in both crop and livestock production systems. The surface balance surplus of N is lost from the agricultural system via different pathways, including NH3 volatilization, denitrification, N₂O and NO emissions, and nitrate leaching from the root zone. Global NH₃-N emissions from fertilizer and animal manure application and stored manure increased from 18 to 34 Tg·yr^?1 between 1970 and 1995, and will further increase to 44 Tg·yr^?1 in 2030. Similar developments are seen for N₂O-N (2.0 Tg·yr^?1 in 1970, 2.7 Tg·yr^?1 in 1995 and 3.5 Tg·yr^?1 in 2030) and NO-N emissions (1.1 Tg·yr^?1 in 1970,1.5 Tg·yr^?1 in 1995 and 2.0 Tg·yr^?1 in 2030).     

The UDP-glucose Dehydrogenase of Escherichia coli K-12 Displays Substrate Inhibition by NAD That Is Relieved by Nucleotide Triphosphates

UDP-glucose dehydrogenase (Ugd) generates UDP-glucuronic acid, an important precursor for the production of many hexuronic acid-containing bacterial surface glycostructures. In Escherichia coli K-12, Ugd is important for biosynthesis of the environmentally regulated exopolysaccharide known as colanic acid, whereas in other E. coli isolates, the same enzyme is required for production of the constitutive group 1 capsular polysaccharides, which act as virulence determinants. Recent studies have implicated tyrosine phosphorylation in the activation of Ugd from E. coli K-12, although it is not known if this is a feature shared by bacterial Ugd proteins. The activities of Ugd from E. coli K-12 and from the group 1 capsule prototype (serotype K30) were compared. Surprisingly, for both enzymes, site-directed Tyr → Phe mutants affecting the previously proposed phosphorylation site retained similar kinetic properties to the wild-type protein. Purified Ugd from E. coli K-12 had significant levels of NAD substrate inhibition, which could be alleviated by the addition of ATP and several other nucleotide triphosphates. Mutations in a previously identified UDP-glucuronic acid allosteric binding site decreased the binding affinity of the nucleotide triphosphate. Ugd from E. coli serotype K30 was not inhibited by NAD, but its activity still increased in the presence of ATP.