A competitive labelling method for determining the ionization constants and reactivity of individual histidine residues in proteins. The histidines of α-chymotrypsin

A competitive labelling method (Kaplan et al., 1971), using tritiated 1-fluoro-2,4-dinitrobenzene as the labelling reagent, is described for determining the ionization constants and reactivities of individual histidine residues in proteins. When this method was applied to the two histidines of alpha-chymotrypsin, histidine-57 was found to have pK(a) 6.8 and a reactivity ten times that of alpha-N-acetyl-l-histidine. Histidine-40 had pK(a) 6.7 and a reactivity approximately six times that of alpha-N-acetyl-l-histidine. Between pH7.5 and 8 the reactivities of both histidines decrease simultaneously to approximately that of alpha-N-acetyl-l-histidine. The high reactivities of the histidines are attributed to hydrogen bonding, which increases the nucleophilicity of the imidazole ring. The sharp decrease in reactivity between pH7.5 and 8 is attributed to a conformational change that disrupts the hydrogen bonding by these residues. The reactivity data support the proposal of a charge-relay mechanism involving histidine-57 (Blow et al., 1969), which makes serine-195 more nucleophilic but indicates that this system is fully operative only in the enzyme-substate complex.     

Mitochondrial DNA structure and colony expansion dynamics of New Zealand fur seals (Arctocephalus forsteri) around Banks Peninsula

New Zealand fur seals are one of many pinniped species that survived the commercial sealing of the eighteenth and nineteenth centuries in dangerously low numbers. After the enforcement of a series of protection measures in the early twentieth century, New Zealand fur seals began to recover from the brink of extinction. We examined the New Zealand fur seal populations of Banks Peninsula, South Island, New Zealand using the mitochondrial DNA control region. We identified a panmictic population structure around Banks Peninsula. The most abundant haplotype in the area showed a slight significant aggregated structure. The Horseshoe Bay colony showed the least number of shared haplotypes with other colonies, suggesting a different origin of re-colonisation of this specific colony. The effective population size of the New Zealand fur seal population at Banks Peninsula was estimated at approximately 2500 individuals. The exponential population growth rate parameter for the area was 35, which corresponds to an expanding population. In general, samples from adjacent colonies shared 4.4 haplotypes while samples collected from colonies separated by between five and eight bays shared 1.9 haplotypes. The genetic data support the spill-over dynamics of colony expansion already suggested for this species. Approximate Bayesian computations analysis suggests re-colonisation of the area from two main clades identified across New Zealand with a most likely admixture coefficient of 0.41 to form the Banks Peninsula population. Approximate Bayesian computations analysis estimated a founder population size of approximately 372 breeding individuals for the area, which then rapidly increased in size with successive waves of external recruitment. The population of fur seals in the area is probably in the late phase of maturity in the colony expansion dynamic.     

Effect of hydrocarbon concentration of pasture production (<i>Brachiaria humidicola</i>) in Texistepec,Veracruz

In this study, the relationship between the concentration of extra-heavy crude petroleum in a clayey material and the toxicity, field capacity, temperature, and growth of a tropical forage grass (Brachiara humidicola) was determined empirically. For this type of petroleum the acute toxicity (Microtox^®) was slight (CE₅₀ = 63200 - 76400 mg/kg) even at high hydrocarbon concentrations (29279 mg/kg). Nonetheless, serious impacts were encountered in terms of an increase in soil temperature (+ 1.3 °C), reduction in field capacity (-10.7%) and reduction in aerial biomass (-97%). The relationship between hydrocarbon concentration and biomass resulted in a typical dose-response curve (r = 0.99), where a concentration of 2626 mg/kg of hydrocarbons corresponds to a maintenance of 90% biomass. Furthermore, during the duration of this study (one year) the biodegradation was proportional to the pasture biomass production (r = 0.997) indicating a synergistic relationship between the petroleum biodegrading microorganisms in the rhizosphere and the pasture.     

Big and aerial invaders: dominance of exotic spiders in burned New Zealand tussock grasslands

As post-disturbance community response depends on the characteristics of the ecosystem and the species composition, so does the invasion of exotic species rely on their suitability to the new environment. Here, we test two hypotheses: exotic spider species dominate the community after burning; and two traits are prevalent for their colonisation ability: ballooning and body size, the latter being correlated with their dispersal ability. We established spring burn, summer burn and unburned experimental plots in a New Zealand tussock grassland area and collected annual samples 3 and 4 years before and after the burning, respectively. Exotic spider abundance increased in the two burn treatments, driven by an increase in Linyphiidae. Indicator analysis showed that exotic and native species characterised burned and unburned plots, respectively. Generalised linear mixed-effects models indicated that ballooning had a positive effect on the post-burning establishment (density) of spiders in summer burn plots but not in spring plots. Body size had a positive effect on colonisation and establishment. The ability to balloon may partly explain the dominance of exotic Linyphiidae species. Larger spiders are better at moving into and colonising burned sites probably because of their ability to travel longer distances over land. Native species showed a low resilience to burning, and although confirmation requires longer-term data, our findings suggest that frequent fires could cause long lasting damage to the native spider fauna of tussock grasslands, and we propose limiting the use of fire to essential situations.     

The Quality of Methods Reporting in Parasitology Experiments

There is a growing concern both inside and outside the scientific community over the lack of reproducibility of experiments. The depth and detail of reported methods are critical to the reproducibility of findings, but also for making it possible to compare and integrate data from different studies. In this study, we evaluated in detail the methods reporting in a comprehensive set of trypanosomiasis experiments that should enable valid reproduction, integration and comparison of research findings. We evaluated a subset of other parasitic (Leishmania, Toxoplasma, Plasmodium, Trichuris and Schistosoma) and non-parasitic (Mycobacterium) experimental infections in order to compare the quality of method reporting more generally. A systematic review using PubMed (2000–2012) of all publications describing gene expression in cells and animals infected with Trypanosoma spp was undertaken based on PRISMA guidelines; 23 papers were identified and included. We defined a checklist of essential parameters that should be reported and have scored the number of those parameters that are reported for each publication. Bibliometric parameters (impact factor, citations and h-index) were used to look for association between Journal and Author status and the quality of method reporting. Trichuriasis experiments achieved the highest scores and included the only paper to score 100% in all criteria. The mean of scores achieved by Trypanosoma articles through the checklist was 65.5% (range 32–90%). Bibliometric parameters were not correlated with the quality of method reporting (Spearman''s rank correlation coefficient <−0.5; p>0.05). Our results indicate that the quality of methods reporting in experimental parasitology is a cause for concern and it has not improved over time, despite there being evidence that most of the assessed parameters do influence the results. We propose that our set of parameters be used as guidelines to improve the quality of the reporting of experimental infection models as a pre-requisite for integrating and comparing sets of data.     

Evidence That Multiple Defects in Lipid Regulation Occur before Hyperglycemia during the Prodrome of Type-2 Diabetes

Background

Blood-vessel dysfunction arises before overt hyperglycemia in type-2 diabetes (T2DM). We hypothesised that a metabolomic approach might identify metabolites/pathways perturbed in this pre-hyperglycemic phase. To test this hypothesis and for specific metabolite hypothesis generation, serum metabolic profiling was performed in young women at increased, intermediate and low risk of subsequent T2DM.

Methods

Participants were stratified by glucose tolerance during a previous index pregnancy into three risk-groups: overt gestational diabetes (GDM; n = 18); those with glucose values in the upper quartile but below GDM levels (UQ group; n = 45); and controls (n = 43, below the median glucose values). Follow-up serum samples were collected at a mean 22 months postnatally. Samples were analysed in a random order using Ultra Performance Liquid Chromatography coupled to an electrospray hybrid LTQ-Orbitrap mass spectrometer. Statistical analysis included principal component (PCA) and multivariate methods.

Findings

Significant between-group differences were observed at follow-up in waist circumference (86, 95%CI (79–91) vs 80 (76–84) cm for GDM vs controls, p<0.05), adiponectin (about 33% lower in GDM group, p = 0.004), fasting glucose, post-prandial glucose and HbA_1c, but the latter 3 all remained within the ‘normal’ range. Substantial differences in metabolite profiles were apparent between the 2 ‘at-risk’ groups and controls, particularly in concentrations of phospholipids (4 metabolites with p≤0.01), acylcarnitines (3 with p≤0.02), short- and long-chain fatty acids (3 with p< = 0.03), and diglycerides (4 with p≤0.05).

Interpretation

Defects in adipocyte function from excess energy storage as relatively hypoxic visceral and hepatic fat, and impaired mitochondrial fatty acid oxidation may initiate the observed perturbations in lipid metabolism. Together with evidence from the failure of glucose-directed treatments to improve cardiovascular outcomes, these data and those of others indicate that a new, quite different definition of type-2 diabetes is required. This definition would incorporate disturbed lipid metabolism prior to hyperglycemia.