Crystal structure of Onconase at 1.1 Å resolution--insights into substrate binding and collective motion

Onconase(?) (ONC) is an amphibian member of the pancreatic ribonuclease superfamily that is selectively toxic to tumor cells. It is a much less efficient enzyme than the archetypal ribonuclease A and, in an attempt to gain further insight, we report the first atomic resolution crystal structure of ONC, determined in complex with sulfate ions at 100 K. The electron density map is of a quality sufficient to reveal significant nonplanarity in several peptide bonds. The majority of active site residues are very well defined, with the exceptions being Lys31 from the catalytic triad and Lys33 from the B(1) subsite, which are relatively mobile but rigidify upon nucleotide binding. Cryocooling causes a compaction of the unit cell and the protein contained within. This is principally the result of an inward movement of one of the lobes of the enzyme (lobe 2), which also narrows the active site cleft. Binding a nucleotide in place of sulfate is associated with an approximately perpendicular movement of lobe 2 and has little further effect on the cleft width. Aspects of this deformation are present in the principal axes of anisotropy extracted from C(α) atomic displacement parameters, indicating its intrinsic nature. The three lowest-frequency modes of ONC motion predicted by an anisotropic network model are compaction/expansion variations in which lobe 2 is the prime mover. Two of these have high similarity to the cryocooling response and imply that the essential 'breathing' motion of ribonuclease A is conserved in ONC. Instead, shifts in conformational equilibria may contribute to the reduced ribonucleolytic activity of ONC.     

Implementing prenatal diagnosis based on cell-free fetal DNA: accurate identification of factors affecting fetal DNA yield

Objective

Cell-free fetal DNA is a source of fetal genetic material that can be used for non-invasive prenatal diagnosis. Usually constituting less than 10% of the total cell free DNA in maternal plasma, the majority is maternal in origin. Optimizing conditions for maximizing yield of cell-free fetal DNA will be crucial for effective implementation of testing. We explore factors influencing yield of fetal DNA from maternal blood samples, including assessment of collection tubes containing cell-stabilizing agents, storage temperature, interval to sample processing and DNA extraction method used.

Methods

Microfluidic digital PCR was performed to precisely quantify male (fetal) DNA, total DNA and long DNA fragments (indicative of maternal cellular DNA). Real-time qPCR was used to assay for the presence of male SRY signal in samples.

Results

Total cell-free DNA quantity increased significantly with time in samples stored in K₃EDTA tubes, but only minimally in cell stabilizing tubes. This increase was solely due to the presence of additional long fragment DNA, with no change in quantity of fetal or short DNA, resulting in a significant decrease in proportion of cell-free fetal DNA over time. Storage at 4°C did not prevent these changes.

Conclusion

When samples can be processed within eight hours of blood draw, K₃EDTA tubes can be used. Prolonged transfer times in K₃EDTA tubes should be avoided as the proportion of fetal DNA present decreases significantly; in these situations the use of cell stabilising tubes is preferable. The DNA extraction kit used may influence success rate of diagnostic tests.     

Too Few,Too Weak: Conflict of Interest Policies at Canadian Medical Schools

Introduction

The education of medical students should be based on the best clinical information available, rather than on commercial interests. Previous research looking at university-wide conflict of interest (COI) policies used in Canadian medical schools has shown very poor regulation. An analysis of COI policies was undertaken to document the current policy environment in all 17 Canadian medical schools.

Methods

A web search was used to initially locate COI policies supplemented by additional information from the deans of each medical school. Strength of policies was rated on a scale of 0 to 2 in 12 categories and also on the presence of enforcement measures. For each school, we report scores for all 12 categories, enforcement measures, and summative scores.

Results

COI policies received summative scores that ranged from 0 to 19, with 0 the lowest possible score obtainable and 24 the maximum. The highest mean scores per category were for disclosure and ghostwriting (0.9) and for gifts and scholarships (0.8).

Discussion

This study provides the first comprehensive evaluation of all 17 Canadian medical school-specific COI policies. Our results suggest that the COI policy environment at Canadian medical schools is generally permissive. Policy development is a dynamic process. We therefore encourage all Canadian medical schools to develop restrictive COI policies to ensure that their medical students are educated based on the best clinical evidence available, free of industry biases and COI relationships that may influence the future medical thinking and prescribing practices of medical students in Canada once they graduate.     

Place,scale and the racial claims made for multiracial children in the 1990 US Census

Multiracial children embody ambiguities inherent in racial categorization and expose fictions of discrete races. Nevertheless, parents of multiracial children were asked for the 1990 US Census to report a single race for their offspring. Using confidential 1990 Census micro-data, we investigate the choices parents made for the three most common racially mixed household types (Asian-white, black-white and Latino-white) in twelve large metropolitan areas. We find that context affects the reporting of children's racial identity. We examine these effects with models that incorporate three spatial scales: households, neighbourhoods and metropolitan areas. Model estimates reveal that racial claims made by parents of Latino- and Asian-white (but not black-white) children varied significantly across metropolitan area. A neighbourhood's proportion white increased the probability that parents reported their children as white, while a neighbourhood's racial diversity increased the probability that black-white parents claimed a non-white race (black or ‘other’) for their children.     

Climate Change and Heat-Related Excess Mortality in the Eastern USA

Climate change will increase extreme heat-related health risks. To quantify the health impacts of mid-century climate change, we assess heat-related excess mortality across the eastern USA. Health risks are estimated using the US Environmental Protection Agency’s Environmental Benefits Mapping and Analysis Program (BenMAP). Mid-century temperature estimates, downscaled using the Weather Research and Forecasting model, are compared to 2007 temperatures at 36 km and 12 km resolutions. Models indicate the average apparent and actual summer temperatures rise by 4.5° and 3.3° C, respectively. Warmer average apparent temperatures could cause 11,562 additional annual deaths (95% confidence interval, CI: 2641–20,095) due to cardiovascular stress in the population aged 65 years and above, while higher minimum temperatures could cause 8767 (95% CI: 5030–12,475) additional deaths each year. Modeled future climate data available at both coarse (36 km) and fine (12 km) resolutions predict significant human health impacts from warmer climates. The findings suggest that currently available information on future climates is sufficient to guide regional planning for the protection of public health. Higher resolution climate and demographic data are still needed to inform more targeted interventions.