Estimating loop length from CryoEM images at medium resolutions

Background: De novo protein modeling approaches utilize 3-dimensional (3D) images derived from electron cryomicroscopy (CryoEM) experiments. The skeleton connecting two secondary structures such as α-helices represent the loop in the 3D image. The accuracy of the skeleton and of the detected secondary structures are critical in De novo modeling. It is important to measure the length along the skeleton accurately since the length can be used as a constraint in modeling the protein. Results: We have developed a novel computational geometric approach to derive a simplified curve in order to estimate the loop length along the skeleton. The method was tested using fifty simulated density images of helix-loop-helix segments of atomic structures and eighteen experimentally derived density data from Electron Microscopy Data Bank (EMDB). The test using simulated density maps shows that it is possible to estimate within 0.5 angstrom of the expected length for 48 of the 50 cases. The experiments, involving eighteen experimentally derived CryoEM images, show that twelve cases have error within 2 angstrom. Conclusions:The tests using both simulated and experimentally derived images show that it is possible for our proposed method to estimate the loop length along the skeleton if the secondary structure elements, such as α-helices, can be detected accurately, and there is a continuous skeleton linking the α-helices

Estimating Loop Length from CryoEM Images at Medium Resolutions

Background: De novo protein modeling approaches utilize 3-dimensional (3D) images derived from electron cryomicroscopy (CryoEM) experiments. The skeleton connecting two secondary structures such as α-helices represent the loop in the 3D image. The accuracy of the skeleton and of the detected secondary structures are critical in De novo modeling. It is important to measure the length along the skeleton accurately since the length can be used as a constraint in modeling the protein. Results: We have developed a novel computational geometric approach to derive a simplified curve in order to estimate the loop length along the skeleton. The method was tested using fifty simulated density images of helix-loop-helix segments of atomic structures and eighteen experimentally derived density data from Electron Microscopy Data Bank (EMDB). The test using simulated density maps shows that it is possible to estimate within 0.5 angstrom of the expected length for 48 of the 50 cases. The experiments, involving eighteen experimentally derived CryoEM images, show that twelve cases have error within 2 angstrom. Conclusions:The tests using both simulated and experimentally derived images show that it is possible for our proposed method to estimate the loop length along the skeleton if the secondary structure elements, such as α-helices, can be detected accurately, and there is a continuous skeleton linking the α-helices

The OSCE in a pre-registration osteopathy program: Introduction and psychometric properties

Objective To investigate the psychometric properties of the objective structured clinical examination (OSCE) conducted in the final year of a pre-professional osteopathy program. A variety of metrics are used to determine the reliability and validity of the examination. Methods Data from the OSCE conducted in 2011 was collated and analysed to establish the pass/fail rates, cost of the examination, internal consistency, and variance components. The examination was conducted over two days with students completing 5 stations on day 1 and 4 stations on day 2. Each station was of 15 min duration and there were 2 examiners per station. Results Forty-eight students and 31 examiners were involved in the examination. Twenty-six students failed at least one station with six students failing three or more stations. Cronbach's alpha was greater than 0.80 for all stations indicating that each is internally consistent and over 50% of the variance in the students' total score for a station was due to the students themselves. The total cost of conducting the examination was $AUD12,933.20. Conclusion The results of the study suggest that the OSCE format is an appropriate method for assessing clinical competency in osteopathic education. The OSCE should be used in conjunction with other forms of assessment to develop and overall picture of the students' clinical competency. Some modifications to the format of the assessment are required to improve the examination and these will be the subject of further studies

Subduction zone volcanic ash can fertilize the surface ocean and stimulate phytoplankton growth: Evidence from biogeochemical experiments and satellite data

Volcanoes confront Earth scientists with new fundamental questions: Can airborne volcanic ash release nutrients on contact with seawater, thereby excite the marine primary productivity (MPP); and, most notably, can volcanoes through oceanic fertilization affect the global climate in a way that is so far poorly understood? Here we present results from biogeochemical experiments showing that 1) volcanic ash from subduction zone volcanoes rapidly release an array of nutrients (co-)limiting algal growth in vast oceanic areas, 2) at a speed much faster (minute-scale) than hitherto known and that marine phytoplankton from low-iron oceanic areas can swiftly, within days, utilize iron from volcanic sources. We further present satellite data possibly indicating an increase of the MPP due to the seaward deposition of volcanic particulate matter. Our study supports the hypothesis that oceanic (iron) fertilization with volcanic ash may play a vital role for the development of the global climate

Rejuvenation of metallic glasses by non-affine thermal strain.

When a spatially uniform temperature change is imposed on a solid with more than one phase, or on a polycrystal of a single, non-cubic phase (showing anisotropic expansion-contraction), the resulting thermal strain is inhomogeneous (non-affine). Thermal cycling induces internal stresses, leading to structural and property changes that are usually deleterious. Glasses are the solids that form on cooling a liquid if crystallization is avoided--they might be considered the ultimate, uniform solids, without the microstructural features and defects associated with polycrystals. Here we explore the effects of cryogenic thermal cycling on glasses, specifically metallic glasses. We show that, contrary to the null effect expected from uniformity, thermal cycling induces rejuvenation, reaching less relaxed states of higher energy. We interpret these findings in the context that the dynamics in liquids become heterogeneous on cooling towards the glass transition, and that there may be consequent heterogeneities in the resulting glasses. For example, the vibrational dynamics of glassy silica at long wavelengths are those of an elastic continuum, but at wavelengths less than approximately three nanometres the vibrational dynamics are similar to those of a polycrystal with anisotropic grains. Thermal cycling of metallic glasses is easily applied, and gives improvements in compressive plasticity. The fact that such effects can be achieved is attributed to intrinsic non-uniformity of the glass structure, giving a non-uniform coefficient of thermal expansion. While metallic glasses may be particularly suitable for thermal cycling, the non-affine nature of strains in glasses in general deserves further study, whether they are induced by applied stresses or by temperature change.This research was supported by the World Premier International Research Center Initiative (WPI), MEXT, Japan, by NSF China and MOST 973 China, and by the Engineering and the Engineering and Physical Sciences Research Council, UK (Materials World Network project). Y.H.S. acknowledges support from a China Scholarship Council (CSC) scholarship.This is the author accepted manuscript. The final version is available from Nature Publishing Group via http://dx.doi.org/10.1038/nature1467

Rs1888747 polymorphism in the FRMD3 gene, gene and protein expression: Role in diabetic kidney disease

© 2016 Buffon et al. Background: We carried out a case-control study in patients with type 2 diabetes mellitus (T2DM) to evaluate the association between seven single nucleotide polymorphisms (SNPs) previously described to be linked to diabetic kidney disease (DKD) in type 1 diabetes mellitus (T1DM). Additionally, we evaluated gene and protein expression related to the polymorphism associated with DKD. Methods: The association study included 1098 T2DM patients (718 with DKD and 380 without DKD). Out of the 13 polymorphisms associated with DKD in a previous study with T1DM, seven were chosen for evaluation in this sample: rs1888747, rs9521445, rs39075, rs451041, rs1041466, rs1411766 and rs6492208. The expression study included 91 patients who underwent nephrectomy. Gene expression was assessed by RT-qPCR and protein expression in kidney samples was quantified by western blot and it localization by immunohistochemistry. Results: The C/C genotype of rs1888747 SNP was associated with protection for DKD (OR = 0.6, 95 % CI 0.3-0.9; P = 0.022). None of the other SNPs were associated with DKD. rs1888747 is located near FRMD3 gene. Therefore, FRMD3 gene and protein expression were evaluated in human kidney tissue according to rs1888747 genotypes. Gene and protein expression were similar in subjects homozygous for the C allele and in those carrying the G allele. Conclusions: Replication of the association between rs1888747 SNP and DKD in a different population suggests that this link is not the result of chance. rs1888747 SNP is located at the FRMD3 gene, which is expressed in human kidney. Therefore, this gene is a candidate gene for DKD. However, in this study, no rs1888747 genotype or specific allele effect on gene and/or protein expression of the FRMD3 gene was demonstrated