Protein volumes and hydration effects. The calculations of partial specific volumes, neutron scattering matchpoints and 280-nm absorption coefficients for proteins and glycoproteins from amino acid sequences

Amino acid sequences, carbohydrate compositions and residue volumes are used to compare critically calculations of partial specific volumes v, neutron scattering matchpoints and 280-nm absorption coefficients with experimental v values for proteins and glycoproteins. The v values that are obtained from amino acid densitometry underestimate experimental v values by 0.01-0.02 ml/g while the v values from crystallographic volumes overestimate the experimental v values by 0.04-0.05 ml/g. An intermediate consensus volume set of amino-acid-residue volumes is proposed in order to predict experimental v values using sequence information. The method is extended to carbohydrates and glycoproteins. Neutron scattering matchpoints can be calculated from crystallographic residue volumes on the basis of the non-exchange of 10% of the main-chain NH protons. Crystallographic results on protein-bound water are used to account for the experimental values of v and matchpoints. Finally, 280-nm absorption coefficients, A1%, 1 cm 280, of 5-27 are found to be well predicted by the Wetlaufer procedure based on the totals of Trp, Tyr and Cys residues. Average errors are +/- 0.7, and the experimental A(1%,1cm)280 values can be larger than the predicted values by 3%.     

Electrostatic interactions in ubiquitin: stabilization of carboxylates by lysine amino groups

To explore electrostatic interactions in ubiquitin, pK(a) values have been determined by NMR for all 12 carboxyl groups in wild-type ubiquitin and in variants where single lysines have been replaced by neutral residues. Aspartate pK(a) values in ubiquitin range from 3.1 to 3.8 and are generally less than model compound values. Most aspartate pK(a) values are within 0.2 pH unit of those predicted with a simple Tanford-Kirkwood model. Glutamate pK(a) values range from 3.8 to 4.5, close to model compound values and differing by 0.1-0.8 pH unit from calculated values. To determine the role of positive charges in modulating carboxyl pK(a) values, we mutated lysines at positions 11, 29, and 33 to glutamine and threonine. NMR studies with these six single-site mutants reveal significant interactions of Lys 11 and Lys 29 with Glu 34 and Asp 21, respectively: pK(a) values for Glu 34 and Asp 21 increase by approximately 0.5-0.8 pH unit, similar to predicted values, when the lysines are replaced by neutral residues. In contrast, the predicted interaction between Lys 33 and Glu 34 is not observed experimentally. In some instances, substitution of lysine by glutamine and threonine did not lead to the same changes in carboxyl pK(a) values. These may reflect new short-range interactions between the mutated residues and the carboxyl groups. Carboxyl pK(a) shifts > 0.5 pH unit result from mutations at groups that are <5 A from the carboxyl group. No interactions are observed at >10 A.     

Validation of Blood-Based Assays Using Dried Blood Spots for Use in Large Population Studies

Assessment of health in large population studies has increasingly incorporated measures of blood-based biomarkers based on the use of dried blood spots (DBS). The validity of DBS assessments made by labs used by large studies is addressed by comparing assay values from DBS collected using conditions similar to those used in the field with values from whole blood samples. The DBS approach generates values that are strongly related to whole blood levels of HbA1c, cystatin C, and C-reactive protein. Assessing lipid levels reliably with DBS appears to be a greater challenge. However, even when DBS values and values from venous blood are highly correlated, they are often on a different scale, and using conventional cutoffs may be misleading.     

桂西北典型喀斯特区生态服务价值的环境响应及其空间尺度特征

Study on ecosystem service values (ESVs) is the bridge of understanding ecosystem and economic decision-making. To investigate the response of ESVs to ambient environment and their spatial scales is an urgent work in the process of ecological restoration and sustainable development in southwest China. Based on the previous research results, the remote images, and weather data of 31 years (1975-2005), the response of ESVs to ambient environment and their spatial scales in a typical karst area of northwest Guangxi, China were evaluated with the method of empirical mode decomposition (EMD) in this paper. The results showed that ESVs had obvious variations with changes in elevation, rocky types and soil types, and had corresponding characteristics of spatial scales. The ESVs in middle and low elevation areas were higher, but they decreased due to human activities such as deforestation. The ESVs in peak-cluster depression areas were lower, and they would increase as influenced by policies such as returning farmland to forestland. The ESVs were influenced by rocky types, showing lower values but an increasing trend in the typical karst regions while higher values but a decreasing trend in non-karst regions. The average ESVs in the west part of the study region, which is not only the main nature reserve for rare wildlife species in Guangxi, but also one of the best preserved natural vegetation regions in China, were more than 15,000 RMB Yuan ha-1,. Comparatively, the ESVs were less than 10,000 Yuan ha-1 in the middle part of the region attributed to low vegetation coverage, serious peak-cluster depression and karst rocky desertification. After about 20 years, that is from 1985 to 2005, the ecosystem conditions had been improved and the ESVs had increased in the middle and eastern part of this study region. On the contrary, in most western part, which was dominated by subtropical evergreen broad-leaved forest, they had been worsened, and the balance values of ESVs were negative. As for the relationships of ESVs with rocky types and soil types, lime soil and red soil were the two main soil types that contributed to ESVs (The total contribution was above 60%, and it is 63.77%,64.37%,64.56%,64.91% respectively in the four years of 1985, 1990, 2000 and 2005.). The variance contribution of intrinsic mode function (IMF) and trend (R) showed that there were obvious special sales for ESVs in this study area, and the main spatial scales were about 2.7 km, 5.5 km, and 11.6 km. The variance contribution ratio was 12.29%, 11.26%, 11.49% respectively, and the trend (R) was high (17.74%). In conclusion, this study indicated that ecosystem conditions in the typical karst area were improved owing to the application of rocky desertification control policies, such as ecological migration and returning farmland to forestland. Besides, the main spatial scales of ESVs in the study area were the interactions of terrain, physiognomy, land use / land cover and human activities.     

HPLC-based Measurement of Glycated Hemoglobin using Dried Blood Spots Collected under Adverse Field Conditions

Glycated hemoglobin (HbA1c) measured using high-performance liquid chromatography (HPLC) assays with venous blood and dried blood spots (DBS) are compared for 143 paired samples collected in Aceh, Indonesia. Relative to gold-standard venous-blood values, DBS-based values reported by the HPLC are systematically upward biased for HbA1c<8% and the fraction diabetic (HbA1c ≥ 6.5%) is overstated almost five-fold. Inspection of chromatograms from DBS assays indicates the % glycosylated calculated by the HPLC excludes part of the hemoglobin A which is misidentified as a hemoglobin variant. Taking this into account, unbiased DBS-based values are computed using data from the machine-generated chromatograms. When the DBS are collected in a clinic-like setting, under controlled humidity/temperature conditions, the recalculated values are almost identical to venous-based values. When DBS are collected under field conditions, the recalculated values are unbiased, but only about half the HbA1c values are measured reliably, calling into question the validity of the other half. The results suggest that collection conditions, particularly humidity, affect the quality of the DBS-based measures. Cross-validating DBS-based HbA1c values with venous samples collected under exactly the same environmental conditions is a prudent investment in population-based studies.     

Very fast empirical prediction and rationalization of protein pKa values

A very fast empirical method is presented for structure-based protein pKa prediction and rationalization. The desolvation effects and intra-protein interactions, which cause variations in pKa values of protein ionizable groups, are empirically related to the positions and chemical nature of the groups proximate to the pKa sites. A computer program is written to automatically predict pKa values based on these empirical relationships within a couple of seconds. Unusual pKa values at buried active sites, which are among the most interesting protein pKa values, are predicted very well with the empirical method. A test on 233 carboxyl, 12 cysteine, 45 histidine, and 24 lysine pKa values in various proteins shows a root-mean-square deviation (RMSD) of 0.89 from experimental values. Removal of the 29 pKa values that are upper or lower limits results in an RMSD = 0.79 for the remaining 285 pKa values.     

Physiological pH values in the digestive tract of perch <Emphasis Type="Italic">Perca fluviatilis</Emphasis> from different habitats

Physiological pH values are determined in the gastrointestinal tract of the perch Perca fluviatilis from lakes Chany and Baikal. Values of pH are detected to vary significantly along the digestive tract. Such factors as a segment of the digestive tract, presence/absence of food, season of the year, and habitat affect pH values. Environmental temperature is the main factor affecting pH values that is confirmed by the decrease in pH values upon water temperature rise in spring, lower pH values in summer compared to other seasons, and lower pH in fish from the waterbody (Lake Chany) with higher temperature of water.     

Calibration of Ellenberg indicator values for the Faroe Islands

Abstract. Elenberg's bio‐indication system for soil moisture (F), soil nitrogen (N) and soil reaction (R) was examined, based on 559 vegetation samples and environmental characteristics (vegetation cover, soil depth, soil moisture, chemical soil properties) from four Faroe islands. The original indicator values from central Europe were used for the calculation of weighted community indicator values of F, N and R. These were regressed with respect to environmental data, applying standard curvilinear regression and generalized linear modelling (GLM) and new predicted values of community indicator values were obtained from the best model. Faroe species optima values of 162 taxa for one or more of the three EUenberg scales were derived from fitting Huisman‐Olff‐Fresco (HOF) models of species abundance with respect to predicted community indicator values and are proposed as new EUenberg species indicator values to be used in the Faroe Islands. F was best correlated with a GLM model containing soil moisture, organic soil fraction, soil depth and total vegetation cover, R with a GLM model containing pH and calcium in % organic soil fraction, N with total phosphorus in % organic soil fraction. The calibrated species indicator scales are much truncated, as compared with the original values, resulting in significantly different overall distributions of the original and new species indicator values. The recalculated community indicator values are much better correlated to environmental measurements. Several species do not have clear optima, but linear or monotone relationships to the examined indicator scales. This probably indicates that the occurrence of some species in the Faroe Islands are either determined by factors other than moisture, pH or soil nutrient status or, given the young age and environmental instability of the islands, are governed by stochastic mechanisms. Extension of Ellenberg indicator values outside central Europe should always be carefully calibrated by means of adequate environmental data and adequate statistical models, such as HOF models, should be applied.     

Relations between the dissociation constants of dibasic acids.

The relationships between the molecular pK values of a dibasic acid, its titration pK values and the pH values at which the concentration of monohydronated species is half-maximal are presented. These enable any pair of the values to be found from any other pair.     

Distribution functions of variables characterizing the mycelial morphology of Streptomyces hygroscopicus grown in glucose-limited chemostat cultures

The distribution of variables characterizing the morphology of the mycelium of Streptomyces hygroscopicus grown in glucose-limited chemostat cultures at different specific growth rates were investigated statistically. The values of the hyphal growth unit (L/N) and the values of the distance from the apex to the first branch (Lp) are normally distributed, but the values of the distance between neighbouring branches are logarithmically normal distributed. The distribution functions are discussed from the biological point of view.     

Pollen influx values measured in different sedimentary environments and their palaeoecological implications

Aspects which need to be considered when calculating pollen influx values in three sedimentary environments (pollen traps, peats and lake sediments) are reviewed. Examples of influx values (grains cm^-2 year^-1) in northern Fennoscandia for two arboreal taxa Betula and Pinus, calculated from these three different environments are presented. Such long term average pollen influx values can be used to indicate the presence/absence and density of the species within the vicinity of the sampling site. Contrary to expectations, conditions do exist in which numerically comparable values are obtained from all three environments. Using these pollen influx values to interpret forest and woodland history in tree-line situations, from both peats and lake sediments, a higher degree of precision can be obtained than through the more classical pollen percentage method alone.     

Charge-charge interactions are key determinants of the pK values of ionizable groups in ribonuclease Sa (pI=3.5) and a basic variant (pI=10.2)

The pK values of the titratable groups in ribonuclease Sa (RNase Sa) (pI=3.5), and a charge-reversed variant with five carboxyl to lysine substitutions, 5K RNase Sa (pI=10.2), have been determined by NMR at 20 degrees C in 0.1M NaCl. In RNase Sa, 18 pK values and in 5K, 11 pK values were measured. The carboxyl group of Asp33, which is buried and forms three intramolecular hydrogen bonds in RNase Sa, has the lowest pK (2.4), whereas Asp79, which is also buried but does not form hydrogen bonds, has the most elevated pK (7.4). These results highlight the importance of desolvation and charge-dipole interactions in perturbing pK values of buried groups. Alkaline titration revealed that the terminal amine of RNase Sa and all eight tyrosine residues have significantly increased pK values relative to model compounds.A primary objective in this study was to investigate the influence of charge-charge interactions on the pK values by comparing results from RNase Sa with those from the 5K variant. The solution structures of the two proteins are very similar as revealed by NMR and other spectroscopic data, with only small changes at the N terminus and in the alpha-helix. Consequently, the ionizable groups will have similar environments in the two variants and desolvation and charge-dipole interactions will have comparable effects on the pK values of both. Their pK differences, therefore, are expected to be chiefly due to the different charge-charge interactions. As anticipated from its higher net charge, all measured pK values in 5K RNase are lowered relative to wild-type RNase Sa, with the largest decrease being 2.2 pH units for Glu14. The pK differences (pK(Sa)-pK(5K)) calculated using a simple model based on Coulomb's Law and a dielectric constant of 45 agree well with the experimental values. This demonstrates that the pK differences between wild-type and 5K RNase Sa are mainly due to changes in the electrostatic interactions between the ionizable groups. pK values calculated using Coulomb's Law also showed a good correlation (R=0.83) with experimental values. The more complex model based on a finite-difference solution to the Poisson-Boltzmann equation, which considers desolvation and charge-dipole interactions in addition to charge-charge interactions, was also used to calculate pK values. Surprisingly, these values are more poorly correlated (R=0.65) with the values from experiment. Taken together, the results are evidence that charge-charge interactions are the chief perturbant of the pK values of ionizable groups on the protein surface, which is where the majority of the ionizable groups are positioned in proteins.     

Lifetime-based pH sensors: indicators for acidic environments

We characterized the pH-dependent intensity decays of three fluorophores, Oregon green 514 carboxylic acid, Cl-NERF, and DM-NERF, using frequency-domain fluorometry, with the objective of identifying lifetime-based sensors for low pH values. These three probes were originally designed as dual excitation wavelength-ratiometric probes, with high photostability and high quantum yields in aqueous solutions. We found that their fluorescence intensity decays were strongly dependent on pH. Moreover, global intensity decays analysis reveals that these probes have double exponential intensity decays at intermediate pH values and that the decay time amplitudes are greatly dependent on pH. The longer lifetime components originated from the unprotonated forms and the shorter components from the protonated forms. Both forms can emit fluorescence at intermediate pH values. The apparent pKa values were also determined from the titration curves of phase angles and modulations versus pH for the purpose of pH sensing. The apparent pKa values range from pH 3 to 5, a range where lifetime-based sensors are not presently reported. Since these probes show low pKa values and display substantial phase and modulation changes with pH, they are suitable as lifetime-based pH sensors to monitor the pH changes in acidic environments. One potential application of these probes is to trace the pH in different cellular compartments.     

pKa values and the pH dependent stability of the N-terminal domain of L9 as probes of electrostatic interactions in the denatured state. Differentiation between local and nonlocal interactions

pKa values were measured for the 6 carboxylates in the N-terminal domain of L9 (NTL9) by following NMR chemical shifts as a function of pH. The contribution of each carboxylate to the pH dependent stability of NTL9 was estimated by comparing the pKa values for the native and denatured state of the protein. A set of peptides with sequences derived from NTL9 were used to model the denatured state. In the protein fragments, the pKa values measured for the aspartates varied between 3.8 and 4.1 and the pKa values measured for the glutamates varied between 4.1 and 4.6. These results indicate that the local sequence can significantly influence pKa values in the denatured state and highlight the difficulties in using standard pKa values derived from small compounds. Calculations based on the measured pKa values suggest that the free energy of unfolding of NTL9 should decrease by 4.4 kcal mol-1 when the pH is lowered from 6 to 2. In contrast, urea and thermal denaturation experiments indicate that the stability of the protein decreases by only 2.6 kcal mol-1 when the carboxylates are protonated. This discrepancy indicates that the protein fragments are not a complete representation of the denatured state and that nonlocal sequence effects perturb the pKa's in the denatured state. Increasing the salt concentration from 100 to 750 mM NaCl removes the discrepancy between the stabilities derived from denaturation experiments and the stability changes calculated from the pKa values. At high concentrations of salt there is also less variation of the pKa values measured in the protein fragments. Our results argue that in the denatured state of NTL9 there are electrostatic interactions between groups both local and nonlocal in primary sequence.     

Basic haematological values in the African buffalo (Syncerus caffer caffer) and in the red buffalo (Syncerus caffer nanus)

Basic haematological values in 13 African buffaloes (Syncerus caffer caffer), 11 cows and 2 bulls, and in 2 red buffaloes (Syncerus caffer nanus), 1 bull and 1 cow, are reported. In the African buffalo, the erythrocyte count--mean 9.76 X 10(12) 1(-1)--ranged from 6.72 to 12.42 X 10(12) 1(-1), the haematocrit values--mean 0.391--varied from 0.32 to 0.47 and the haemoglobin content--mean 148.17--was in the range from 122.1 to 172.5 g 1(-1). For the red buffalo only individual values are given. In the African buffaloes, the leukocyte counts--mean 7.39 X 10(9) 1(-1)--ranging from 5.1 to 12.4 X 10(9) 1(-1) were slightly increased compared with man. For the red buffalo only individual values are reported. These values are compared with data abstracted from the literature for related buffalo species. The age-dependent decrease of erythrocyte counts and the age-dependent rise of the eosinophile proportion in the differential count are discussed.     

DNA values in somatic tissues of Dermestes (Dermestidae: Coleoptera)

The distribution of DNA values in some somatic tissues of seven Dermestes species has been investigated. In all cases the DNA values are distributed as members of a doubling series. Distributions are found to be similar between species and sexes for the same tissue but different between tissues in the same species. Species DNA values derived from somatic tissues agree with DNA values previously determined for spermatids. These data are discussed in relation to the range of species DNA values (2.7 x) and the process of differentiation.     

The electron affinities of deprotonated adenine, guanine, cytosine, uracil, and thymine

Electron attachment rates and gas phase acidities for the canonical tautomers of the nucleobases and electron affinities for thymine, deprotonated thymine, and cytosine are reported The latter are from a new analysis of published photoelectron spectra. The values for deprotonated thymine are (all in eV) keto-N1-H, 3.327(5); enol-N3-H, 3.250(5), enol-C2OH, 3.120(5) enol-N1-H, 3.013(5), and enol-C4OH,3.123(5). The values for deprotonated cytosine, keto-N1-H, 3.184(5); trans-NH-H, 3.008(5); cis-NH-H, 3.039(5); and enol-N1-H, 2.750(5) and enol-O-H, 2.950(5). The gas phase acidities from these values are obtained from these values using experimental or theoretical calculations of bond dissociation energies. Kinetic and thermodynamic properties for thermal electron attachment to thymine are obtained from mass spectrometric data. We report an activation energy of 0.60 eV and electron affinity of thymine, 1.0(1) eV.     

The Electron Affinities of Deprotonated Adenine,Guanine, Cytosine,Uracil, and Thymine

Electron attachment rates and gas phase acidities for the canonical tautomers of the nucleobases and electron affinities for thymine, deprotonated thymine, and cytosine are reported The latter are from a new analysis of published photoelectron spectra. The values for deprotonated thymine are (all in eV) keto-N1-H, 3.327(5); enol-N3-H, 3.250(5), enol-C2OH, 3.120(5) enol-N1-H, 3.013(5), and enol-C4OH,3.123(5). The values for deprotonated cytosine, keto-N1-H, 3.184(5); trans-NH-H, 3.008(5); cis-NH-H, 3.039(5); and enol-N1-H, 2.750(5) and enol-O-H, 2.950(5). The gas phase acidities from these values are obtained from these values using experimental or theoretical calculations of bond dissociation energies. Kinetic and thermodynamic properties for thermal electron attachment to thymine are obtained from mass spectrometric data. We report an activation energy of 0.60 eV and electron affinity of thymine, 1.0(1) eV.     

Clinical blood values of the northern fur seal, Callorhinus ursinus

Clinical blood values are reported for 14 blood components in the northern fur seal (Callorhinus ursinus) and compared with human clinical ranges. Certain values such as cholesterol, globulins and blood urea nitrogen deviate markedly from published human values. The distribution of serum proteins in fur seals, man and northern elephant seals also are given and compared.     

Reliability of Ellenberg indicator values for moisture,nitrogen and soil reaction: a comparison with field measurements

Abstract. Ellenberg indicator values for moisture, nitrogen and soil reaction were correlated with measured soil and vegetation parameters. Relationships were studied through between‐species and between‐site comparisons, using data from 74 roadside plots in 14 different plant communities in The Netherlands forming a wide range. Ellenberg moisture values correlated best with the average lowest moisture contents in summer. Correlations with the annual average groundwater level and the average spring level were also good. Ellenberg N‐values appeared to be only weakly correlated with soil parameters, including N‐mineralization and available mineral N. Instead, there was a strong relation with biomass production. We therefore endorse Hill & Carey's (1997) suggestion that the term N‐values be replaced by ‘productivity values'. For soil reaction, many species values appeared to need regional adjustment. The relationship with soil pH was unsatisfactory; mean indicator values were similar for all sites at pH > 4.75 because of wide species tolerances for intermediate pH levels. Site mean reaction values correlated best (r up to 0.92) with the total amount of calcium (exchangeable Ca²⁺ plus Ca from carbonates). It is therefore suggested that reaction values are better referred to as ‘calcium values'. Using abundance values as weights when calculating mean indicator values generally improved the results, but, over the wide range of conditions studied, differences were small. Indicator values for bryophytes appeared well in line with those for vascular plants. It was noted that the frequency distributions of indicator values are quite uneven. This creates a tendency for site mean values to converge to the value most common in the regional species pool. Although the effect on overall correlations is small, relationships tended to be less linear. Uneven distributions also cause the site mean indicator values at which species have their optimum to deviate from the actual Ellenberg values of these species. Suggestions for improvements are made. It is concluded that the Ellenberg indicator system provides a very valuable tool for habitat calibration, provided the appropriate parameters are considered.