The structures of COPI-coated vesicles reveal alternate coatomer conformations and interactions

Transport between compartments of eukaryotic cells is mediated by coated vesicles. The archetypal protein coats COPI, COPII, and clathrin are conserved from yeast to human. Structural studies of COPII and clathrin coats assembled in vitro without membranes suggest that coat components assemble regular cages with the same set of interactions between components. Detailed three-dimensional structures of coated membrane vesicles have not been obtained. Here, we solved the structures of individual COPI-coated membrane vesicles by cryoelectron tomography and subtomogram averaging of in vitro reconstituted budding reactions. The coat protein complex, coatomer, was observed to adopt alternative conformations to change the number of other coatomers with which it interacts and to form vesicles with variable sizes and shapes. This represents a fundamentally different basis for vesicle coat assembly.

The construction of social identity in new nuclear operators : a longitudinal study

Countless studies have stressed the importance of social identity, particularly its role in various organizational outcomes, yet questions remain as to how identities initially develop, shift and change based on the configuration of multiple, pluralistic relationships grounded in an organizational setting. The interactive model of social identity formation has been proposed recently to explain the internalization of shared norms and values – critical in identity formation – has not received empirical examination. We analyzed multiple sources of data from nine nuclear professionals over three years to understand the construction of social identity in new entrants entering an organization. Informed by our data analyses, we found support for the interactive model and that age and level of experience influenced whether they undertook an inductive or deductive route of the group norm and value internalization. This study represents an important contribution to the study of social identity and the process by which identities are formed, particularly under conditions of duress or significant organizational disruption.

Modelling survival data to account for model uncertainty: a single model or model averaging?

This study considered the problem of predicting survival, based on three alternative models: a single Weibull, a mixture of Weibulls and a cure model. Instead of the common procedure of choosing a single “best” model, where “best” is defined in terms of goodness of fit to the data, a Bayesian model averaging (BMA) approach was adopted to account for model uncertainty. This was illustrated using a case study in which the aim was the description of lymphoma cancer survival with covariates given by phenotypes and gene expression. The results of this study indicate that if the sample size is sufficiently large, one of the three models emerge as having highest probability given the data, as indicated by the goodness of fit measure; the Bayesian information criterion (BIC). However, when the sample size was reduced, no single model was revealed as “best”, suggesting that a BMA approach would be appropriate. Although a BMA approach can compromise on goodness of fit to the data (when compared to the true model), it can provide robust predictions and facilitate more detailed investigation of the relationships between gene expression and patient survival. Keywords: Bayesian modelling; Bayesian model averaging; Cure model; Markov Chain Monte Carlo; Mixture model; Survival analysis; Weibull distribution

Spatial prediction of N2O emissions in pasture : a Bayesian model averaging analysis

Nitrous oxide (N2O) is one of the greenhouse gases that can contribute to global warming. Spatial variability of N2O can lead to large uncertainties in prediction. However, previous studies have often ignored the spatial dependency to quantify the N2O - environmental factors relationships. Few researches have examined the impacts of various spatial correlation structures (e.g. independence, distance-based and neighbourhood based) on spatial prediction of N2O emissions. This study aimed to assess the impact of three spatial correlation structures on spatial predictions and calibrate the spatial prediction using Bayesian model averaging (BMA) based on replicated, irregular point-referenced data. The data were measured in 17 chambers randomly placed across a 271 m(2) field between October 2007 and September 2008 in the southeast of Australia. We used a Bayesian geostatistical model and a Bayesian spatial conditional autoregressive (CAR) model to investigate and accommodate spatial dependency, and to estimate the effects of environmental variables on N2O emissions across the study site. We compared these with a Bayesian regression model with independent errors. The three approaches resulted in different derived maps of spatial prediction of N2O emissions. We found that incorporating spatial dependency in the model not only substantially improved predictions of N2O emission from soil, but also better quantified uncertainties of soil parameters in the study. The hybrid model structure obtained by BMA improved the accuracy of spatial prediction of N2O emissions across this study region.

Contrast transfer function correction applied to cryo-electron tomography and sub-tomogram averaging

Cryo-electron tomography together with averaging of sub-tomograms containing identical particles can reveal the structure of proteins or protein complexes in their native environment. The resolution of this technique is limited by the contrast transfer function (CTF) of the microscope. The CTF is not routinely corrected in cryo-electron tomography because of difficulties including CTF detection, due to the low signal to noise ratio, and CTF correction, since images are characterised by a spatially variant CTF. Here we simulate the effects of the CTF on the resolution of the final reconstruction, before and after CTF correction, and consider the effect of errors and approximations in defocus determination. We show that errors in defocus determination are well tolerated when correcting a series of tomograms collected at a range of defocus values. We apply methods for determining the CTF parameters in low signal to noise images of tilted specimens, for monitoring defocus changes using observed magnification changes, and for correcting the CTF prior to reconstruction. Using bacteriophage PRDI as a test sample, we demonstrate that this approach gives an improvement in the structure obtained by sub-tomogram averaging from cryo-electron tomograms.

SOTrain: A new program for training supervisors and operators in Australian sugar factories

The provision of effective training of supervisors and operators is essential if sugar factories are to operate profitably and in an environmentally sustainable and safe manner. The benefits of having supervisor and operator staff with a high level of operational skills are reduced stoppages, increased recovery, improved sugar quality, reduced damage to equipment, and reduced OH&S and environmental impacts. Training of new operators and supervisors in factories has traditionally relied on on-the-job training of the new or inexperienced staff by experienced supervisors and operators, supplemented by courses conducted by contractors such as Sugar Research Institute (SRI). However there is clearly a need for staff to be able to undertake training at any time, drawing on the content of online courses as required. An improved methodology for the training of factory supervisors and operators has been developed by QUT on behalf of a syndicate of mills. The new methodology provides ‘at factory’ learning via self-paced modules. Importantly, the training resources for each module are designed to support the training programs within sugar factories, thereby establishing a benchmark for training across the sugar industry. The modules include notes, training guides and session plans, guidelines for walkthrough tours of the stations, learning activities, resources such as videos, animations, job aids and competency assessments. The materials are available on the web for registered users in Australian Mills and many activities are best undertaken online. Apart from a few interactive online resources, the materials for each module can also be downloaded. The acronym SOTrain (Supervisor and Operator Training) has been applied to the new training program.