A summary of the measured pK values of the ionizable groups in folded proteins

We tabulated 541 measured pK values reported in the literature for the Asp, Glu, His, Cys, Tyr, and Lys side chains, and the C and N termini of 78 folded proteins. The majority of these values are for the Asp, Glu, and His side chains. The average pK values are Asp 3.5 ± 1.2 (139); Glu 4.2 ± 0.9 (153); His 6.6 ± 1.0 (131); Cys 6.8 ± 2.7 (25); Tyr 10.3 ± 1.2 (20); Lys 10.5 ± 1.1 (35); C‐terminus 3.3 ± 0.8 (22) and N‐terminus 7.7 ± 0.5 (16). We compare these results with the measured pK values of these groups in alanine pentapeptides, and comment on our overall findings.     

Epigeic bryophytes do not improve bioindication by Ellenberg values in mountain forests

Based on a stratified random sample of 93 vegetation plots and coincident measurements of ecological conditions in mountain forests of the Bavarian Alps, the degree to which species composition and Ellenberg indicator values derived thereof were related to measured environmental variables was assessed for vascular understorey plants and epigeic bryophytes. According to Mantel tests vascular composition contained ca. 30% more ecological information than bryophyte composition. When expressed as average Ellenberg or Düll values, vascular plant-based values reflected 60% more of measured variables than bryophyte-based values. The differences remained after rarefaction of the vascular matrix to the gamma diversity of bryophytes, showing that indication is not a function of indicator richness. Analysing vascular plants and bryophytes combined yielded very similar, or even slightly less stringent relationships with the environment than using vascular plants only.Bivariate relationships of indicator values with corresponding ecological measurements confirmed the specific potential of the values to estimate ecological factors from both plant groups, but vascular plants performed better for all factors. Bryophyte indication was particularly poor for light, temperature and base saturation. Bryophyte-based indicator values did not significantly predict the residuals of measured ecological variables against vascular plant-based Ellenberg values.For the study region, it is concluded that indicator values of vascular forest understorey should be used without consideration of Düll's indicator values for epigeic bryopyhtes. There appears to be potential to improve bioindication by recalibrating indicator values of epigeic bryophytes based on ecological measurements and vascular plant indicator values.     

Good modeling practice for PAT applications: Propagation of input uncertainty and sensitivity analysis

The uncertainty and sensitivity analysis are evaluated for their usefulness as part of the model‐building within Process Analytical Technology applications. A mechanistic model describing a batch cultivation of Streptomyces coelicolor for antibiotic production was used as case study. The input uncertainty resulting from assumptions of the model was propagated using the Monte Carlo procedure to estimate the output uncertainty. The results showed that significant uncertainty exists in the model outputs. Moreover the uncertainty in the biomass, glucose, ammonium and base‐consumption were found low compared to the large uncertainty observed in the antibiotic and off‐gas CO₂ predictions. The output uncertainty was observed to be lower during the exponential growth phase, while higher in the stationary and death phases ‐ meaning the model describes some periods better than others. To understand which input parameters are responsible for the output uncertainty, three sensitivity methods (Standardized Regression Coefficients, Morris and differential analysis) were evaluated and compared. The results from these methods were mostly in agreement with each other and revealed that only few parameters (about 10) out of a total 56 were mainly responsible for the output uncertainty. Among these significant parameters, one finds parameters related to fermentation characteristics such as biomass metabolism, chemical equilibria and mass‐transfer. Overall the uncertainty and sensitivity analysis are found promising for helping to build reliable mechanistic models and to interpret the model outputs properly. These tools make part of good modeling practice, which can contribute to successful PAT applications for increased process understanding, operation and control purposes. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Effect of black cumin (Nigella sativa) on heart rate, some hematological values, and pancreatic β-cell damage in cadmium-treated rats

This study was designed to investigate the effect of Nigella sativa (NS) on the heart rate, some hematological values, and pancreatic β-cell damage in cadmium (Cd)-treated rats. The rats were randomly grouped into one of three experimental groups: Control, Cd treated, and Cd+NS treated. Each group contained 10 animals. The Cd-treated and Cd+NS-treated groups were injected subcutaneously daily with CdCl₂ dissolved in isotonic NaCl in the amount of 2 mL/kg for 30 d, resulting in a dosage of 0.49 mg Cd/kg/d. The control group was injected with only isotonic NaCl (2 mL/kg/d) throughout the experiment (for 30 d). Three days prior to administration of CdCl₂, the Cd+NS-treated group received the daily intraperitoneal (ip) injection of 2 mL/kg NS until the end of the study; animals in all three groups were fasted for 12 h and blood samples were taken for the determination of the glucose and insulin levels, red blood cell (RBC) and white blood cell (WBC) counts, packet cell volume (PCV), and hemoglobin (Hb) concentration. The heart rates of rats were also measured by a direct writing electrocardiograph before the blood withdrawals. It was found that NS treatment increased the lowered insulin levels, RBC and WBC counts, PCV, and neutrophil percentage in Cd-treated rats. However, the WBC count of Cd-treated rats with NS treatment was still lower than those of control values. NS treatment also decreased the elevated heart rate and glucose concentration of Cd-treated rats. Pancreatic tissues were also harvested from the sacrificed animals for morphological and immunohistochemical examinations. Cd exposure alone caused a degeneration, necrosis, and weak degranulation in the β-cells of the pancreatic islets. In Cd+NS-treated rats, increased staining of insulin and preservation of islet cells were apparent. It is concluded that NS treatment might decrease the Cd-treated disturbances on heart rate, some hematological values, and pancreatic β-cell.     

The infinitesimal, the deterministic, and the probabilistic: Alternate container inspection policies in invasive species management

Recently, Batabyal and Nijkamp (2005, Stochastic Environmental Research and Risk Assessment 19: 340–347) have shown that in an inspection cycle, regardless of whether the inspection policy choice is made on the basis of an optimization exercise or on the basis of a rule of thumb, the “container policy” dominates the “temporal policy” because the former results in lower long run expected net cost (LRENC) from inspections. In this paper, we continue this line of inquiry and analyze container policies in three scenarios. In the first scenario the time taken to conduct inspections is negligible. In the second scenario, this inspection time is deterministic and in the third scenario this inspection time is stochastic. Specifically, we compare and contrast the LRENC and the optimal container policy in each of these three scenarios.      

Points, patches, and regions: scaling soil biogeochemical patterns in an urbanized arid ecosystem

Cities are rapidly growing throughout the world and are altering biologic processes in many regions, with global consequences. Urbanization in the Phoenix, USA metropolitan region has dramatically altered regional ecosystem patterns, but little is known about how these changes have influenced soil organic matter, total nitrogen, and the distribution of nitrogen stable isotopes. Because urban development is a phenomenon occurring at multiple scales, ecological consequences of urbanization will likely differ between individual patches and the entire metropolitan region. To investigate such changes we conducted spatially explicit surveys including three dominant land‐use types in this region: native desert, agriculture, and mesic residential. These data were combined for analysis with previously collected samples from a synoptic regional survey. A landscape scaling approach was implemented to compare the dependence of soil variability on the sampled extent and the uncertainty associated with scaling from points to patches, land‐use types, and the Phoenix metropolitan region. The multiple‐scale analysis of soil properties showed that variation in total soil nitrogen, soil organic matter, and δ⁵N content of soils differed between patch and regional scales. The majority of variation in the urbanized patch types was exhibited between patches while for the native desert the majority of variation was observed within individual patches. These differences show the impact of urbanization on the scaling relations of ecosystem components. Overall, urbanization in this region appears to have increased soil organic matter by 44%, total nitrogen by 48%, and has elevated δ¹⁵N by 21%.     

Hematocrit and blood chemistry values in three genera of captive hornbills

This study reports hematocrit and blood chemistry values for captive adult individuals belonging to three genera of hornbills (Bucerotidae), Aceros, Anthracoceros, and Ceratogymna, and evaluates genera and gender specific differences in these values. Ceratogymna differs significantly from the other two genera in the concentration of total proteins, cholesterol, triglycerides, phosphorus, potassium, and sodium. Blood glucose concentrations in Aceros were lower than those in the other two genera. Plasma levels of enzymes differed between Aceros and Ceratogymna. With respect to gender differences, Aceros males had greater plasma levels of alanine aminotransferase (ALT), calcium and phosphorus than did the females, and the Ceratogymna males had higher concentrations of triglycerides. Body mass was correlated with hematocrit, cholesterol, total proteins, and urea in Aceros and with calcium concentration in Ceratogymna. These results are the first data available on reference ranges of blood values in individuals of this family of birds and may therefore be very useful as a complementary diagnostic tool in the veterinary care of individuals of these species in captivity. Zoo Biol 0:1–9, 2005. © 2005 Wiley‐Liss, Inc.     

Problem of distinguishing false-positive tests from acute or transient Helicobacter pylori infections

BACKGROUND: Reliable detection of acute Helicobacter pylori infections remains problematic. The high prevalence of false-positive non-invasive tests in low H. pylori prevalence populations makes identification of acute and transient infections difficult. METHODS: We explored the use of serum pepsinogens (PG) for diagnosis of acute infection in patients following H. pylori challenge such that the onset of the infection was known. We then compared those findings to a group of children with presumed acute infections defined as a positive urea breath test (UBT) and negative IgG serology. RESULTS: We examined the pattern and calculated cut-off values of PG levels in 18 adult volunteers with known acute H. pylori infection. We then compared the results with sera from nine symptomatic children with presumed acute H. pylori infection and a matched control group of nine children who did not meet criteria for acute H. pylori infection. In acute infection, both PGI and II levels increased following H. pylori infection reaching a peak by 2 weeks post-infection. The frequency of a positive test defined as a value > mean +2 SD was 17, 71, and 94% at week 1, 2, and 4 post-infection, respectively. Only one child with presumed acute H. pylori infection had an elevated serum PGI and one had an elevated PGII. Five of the children had follow-up UBTs and four were negative consistent with the diagnosis of false-positive UBT. H. pylori infection was confirmed in the child with an elevated PGI level. CONCLUSIONS: These data suggest that a single positive noninvasive test in populations of low prevalence is most likely a false-positive result. This suggests that a single positive test requires confirmation preferably using a test that measures a different parameter (e.g., UBT confirmed by stool antigen test). It appears that most "transient"H. pylori infections are diagnosed on the basis of false-positive tests. PG levels are possible candidates as the confirmatory test.     

Data depth, data completeness, and their influence on quantitative genetic estimation in two contrasting bird populations

Evolutionary biologists increasingly use pedigree‐based quantitative genetic methods to address questions about the evolutionary dynamics of traits in wild populations. In many cases, phenotypic data may have been collected only for recent parts of the study. How does this influence the performance of the models used to analyse these data? Here we explore how data depth (number of years) and completeness (number of observations) influence estimates of genetic variance and covariance within the context of an existing pedigree. Using long‐term data from the great tit Parus major and the mute swan Cygnus olor, species with different life‐histories, we examined the effect of manipulating the amount of data included on quantitative genetic parameter estimates. Manipulating data depth and completeness had little influence on estimated genetic variances, heritabilities, or genetic correlations, but (as expected) did influence confidence in these estimates. Estimated breeding values in the great tit were not influenced by data depth but were in the mute swan, probably because of differences in pedigree structure. Our analyses suggest the ‘rule of thumb’ that data from 3 years and a minimum of 100 individuals per year are needed to estimate genetic parameters with acceptable confidence, and that using pedigree data is worthwhile, even if phenotypes are only available toward the tips of the pedigree.     

Seasonal variations in bulk tissue, fatty acid and monosaccharide δC values of leaves from mesotrophic grassland plant communities under different grazing managements

Leaves of 26 grass, herb, shrub and tree species were collected from mesotrophic grasslands to assess natural variability in bulk, fatty acid and monosaccharide δ¹³C values under different grazing management (cattle- or deer-grazed) on three sample dates (May, July and October) such that interspecific and spatiotemporal variations in whole leaf tissues and compound-specific δ¹³C values could be determined. The total mean leaf bulk δ¹³C value for plants was −28.9‰ with a range of values spanning 7.5‰. Significant interspecific variation between bulk leaf δ¹³C values was only determined in October (P = <0.001) when δ¹³C values of the leaf tissues from both sites was on average 1.5‰ depleted compared to during July and May. Samples from May were significantly different between fields (P = 0.03) indicating an effect from deer- or cattle-grazing in young leaves. The average individual monosaccharide δ¹³C value was 0.8‰ higher compared with whole leaf tissues. Monosaccharides were the most abundant components of leaf biomass, i.e. arabinose, xylose, mannose, galactose and glucose, and therefore, fluctuations in their individual δ¹³C values had a major influence on bulk δ¹³C values. An average depletion of ca. 1‰ in the bulk δ¹³C values of leaves from the deer-grazed field compared to the cattle-grazed field could be explained by a general depletion of 1.1‰ in glucose δ¹³C values, as glucose constituted >50% total leaf monosaccharides. In October, δ¹³C values of all monosaccharides varied between species, with significant variation in δ¹³C values of mannose and glucose in July, and mannose in May. This provided an explanation for the noted variability in the tissue bulk δ¹³C values observed in October 1999. The fatty acids C_16:0, C_18:2 and C_18:3 were highly abundant in all plant species. Fatty acid δ¹³C values were lower than those of bulk leaf tissues; average values of −37.4‰ (C_16:0), −37.0‰ (C_18:2) and −36.5‰ (C_18:3) were determined. There was significant interspecific variation in the δ¹³C values of all individual fatty acids during October and July, but only for C_18:2 in May (P = <0.05). This indicated that seasonal trends observed in the δ¹³C values of individual fatty acids were inherited from the isotopic composition of primary photosynthate. However, although wide diversity in δ¹³C values of grassland plants ascribed to grazing management, interspecific and spatiotemporal influences was revealed, significant trends (P = <0.0001) for fatty acid and monosaccharide δ¹³C values: δ¹³C_16:0 < δ¹³C_18:2 < δ¹³C_18:3 and δ¹³C_arabinose > δ¹³C_xylose > δ¹³C_glucose > δ¹³C_galactose, respectively, previously described, appear consistent across a wide range of species at different times of the year in fields under different grazing regimes.