The Exocyst Complex in Health and Disease

Exocytosis involves the fusion of intracellular secretory vesicles with the plasma membrane, thereby delivering integral membrane proteins to the cell surface and releasing material into the extracellular space. Importantly, exocytosis also provides a source of lipid moieties for membrane extension. The tethering of the secretory vesicle before docking and fusion with the plasma membrane is mediated by the exocyst complex, an evolutionary conserved octameric complex of proteins. Recent findings indicate that the exocyst complex also takes part in other intra-cellular processes besides secretion. These various functions seem to converge toward defining a direction of membrane growth in a range of systems from fungi to plants and from neurons to cilia. In this review we summarize the current knowledge of exocyst function in cell polarity, signaling and cell-cell communication and discuss implications for plant and animal health and disease

Segregation of in to dislocations in InGaN

Dislocations are one-dimensional topological defects that occur frequently in functional thin film materials and that are known to degrade the performance of InxGa1-xN-based optoelectronic devices. Here, we show that large local deviations in alloy composition and atomic structure are expected to occur in and around dislocation cores in InxGa1-xN alloy thin films. We present energy-dispersive X-ray spectroscopy data supporting this result. The methods presented here are also widely applicable for predicting composition fluctuations associated with strain fields in other inorganic functional material thin films

Dislocation core structures in (0001) InGaN

Threading dislocation core structures in c-plane GaN and InxGa1−xN (0.057 ≤ x ≤ 0.20) films were investigated by aberration-corrected scanning transmission electron microscopy. a-type dislocations are unaffected by alloying with indium and have a 5/7-atom ring core structure in both GaN and InxGa1−xN. In contrast, the dissociation lengths of (a + c)-type dislocations are reduced, and new 7/4/9-atom ring and 7/4/8/5-atom ring core structures were observed for the dissociated (a + c)-type dislocations in InxGa1−xN, which is associated with the segregation of indium near (a + c)-type and c-type dislocation cores in InxGa1−xN, consistent with predictions from atomistic Monte Carlo simulations.This work was funded in part by the Cambridge Commonwealth Trust, St. John’s College and the EPSRC (grant number EP/I012591/1). MAM acknowledges support from the Royal Society through a University Research Fellowship. Additional support was provided by the EPSRC (Supplementary data for EPSRC [49] is available) through the UK National Facility for Aberration-Corrected STEM (SuperSTEM). The Titan 80-200kV ChemiSTEM™ was funded through HM Government (UK) and is associated with the capabilities of the University of Manchester Nuclear Manufacturing (NUMAN) capabilities. SJH acknowledges funding from the Defence Threat Reduction Agency (DTRA) USA (grant number HDTRA1-12-1-0013). The authors also acknowledge C. M. McGilvery and A. Kovacs for helpful discussions.This is the author accepted manuscript. It is currently under an indefinite embargo pending publication by AIP

Carrier localization in the vicinity of dislocations in InGaN

We present a multi-microscopy study of dislocations in InGaN, whereby the same threading dislocation was observed under several microscopes (atomic force microscopy, scanning electron microscopy, cathodoluminescence imaging and spectroscopy, transmission electron microscopy), and its morphological optical and structural properties directly correlated. We achieved this across an ensemble of defects large enough to be statistically significant. Our results provide evidence that carrier localization occurs in the direct vicinity of the dislocation through the enhanced formation of In-N chains and atomic condensates, thus limiting non-radiative recombination of carriers at the dislocation core. We highlight that the localization properties in the vicinity of threading dislocations arise as a consequence of the strain field of the individual dislocation and the additional strain field building between interacting neighboring dislocations. Our study therefore suggests that careful strain and dislocation distribution engineering may further improve the resilience of InGaN-based devices to threading dislocations. Besides providing a new understanding of dislocations in InGaN, this paper presents a proof-of-concept for a methodology which is relevant to many problems in materials science.This project is funded in part by the European Research Council under the European Community's Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement No. 279361 (MACONS). The research leading to these results has received funding from the European Union Seventh Framework Programme under Grant Agreement 312483-ESTEEM2 (Integrated Infrastructure InitiativeI3). F.M. would also like to acknowledge the financial support from EPSRC Doctoral Prize Awards and Cambridge Philosophical Society. M.H. would like to acknowledge support from the Lindemann Fellowship

Optical and structural properties of dislocations in InGaN

Threading dislocations in thick layers of InxGa1−xN (5% < x < 15%) have been investigated by means of cathodoluminescence, time-resolved cathodoluminescence, and molecular dynamics. We show that indium atoms segregate near dislocations in all the samples. This promotes the formation of In-N-In chains and atomic condensates, which localize carriers and hinder nonradiative recombination at dislocations. We note, however, that the dark halo surrounding the dislocations in the cathodoluminescence image becomes increasingly pronounced as the indium fraction of the sample increases. Using transmission electron microscopy, we attribute the dark halo to a region of lower indium content formed below the facet of the V-shaped pit that terminates the dislocation in low composition samples (x < 12%). For x > 12%, the facets of the V-defect featured dislocation bundles instead of the low indium fraction region. In this sample, the origin of the dark halo may relate to a compound effect of the dislocation bundles, of a variation of surface potential, and perhaps, of an increase in carrier diffusion length.ER-C Lindemann Trust Fellowshi

Screening of DUB activity and specificity by MALDI-TOF mass spectrometry

Deubiquitylases (DUBs) are key regulators of the ubiquitin system which cleave ubiquitin moieties from proteins and polyubiquitin chains. Several DUBs have been implicated in various diseases and are attractive drug targets. We have developed a sensitive and fast assay to quantify in vitro DUB enzyme activity using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Unlike other current assays, this method uses unmodified substrates, such as diubiquitin topoisomers. By analyzing 42 human DUBs against all diubiquitin topoisomers we provide an extensive characterization of DUB activity and specificity. Our results confirm the high specificity of many members of the OTU and JAMM DUB families and highlight that all USPs tested display low linkage selectivity. We also demonstrate that this assay can be deployed to assess the potency and specificity of DUB inhibitors by profiling 11 compounds against a panel of 32 DUBs

Maximising the value of transmitted data from PSATs tracking marine fish: a case study on Atlantic bluefin tuna

This is the final version. Available from BMC via the DOI in this record. Availability of data and materials: The data sets generated and analysed during the current study are not publicly available due to funder restrictions but may be available from the corresponding author on reasonable request.Background: The use of biologging tags to answer questions in animal movement ecology has increased in recent decades. Pop-up satellite archival tags (PSATs) are often used for migratory studies on large fish taxa. For PSATs, movements are normally reconstructed from variable amounts of transmitted data (unless tags are recovered, and full data archives accessed) by coupling geolocation methods with a state-space modelling (SSM) approach. Between 2018 and 2019, we deployed Wildlife Computers PSATs (MiniPATs) from which data recovery varied considerably. This led us to examine the effect of PSAT data volume on SSM performance (i.e., variation in reconstructed locations and their uncertainty). We did this by comparing movements reconstructed using partial ( 1000 km); (ii) for fish that travelled long distances, mean distance of locations from corresponding complete data set locations were inversely correlated with the volume of data received; (iii) if only 5% of data was used for geolocation, reconstructed locations for long-distance fish differed by 2213 ± 647 km from the locations derived from complete data sets; and, (iv) track reconstructions omitted migrations into the Mediterranean Sea if less than 30% of data was used for geolocation. Conclusions: For Wildlife Computers MiniPATs in our specific application, movements reconstructed with as little as 30% of the total geolocation data results in plausible outputs from the GPE3. Below this data volume, however, significant differences of more than 2000 km can occur. Whilst for a single species and manufacturer, this highlights the importance of careful study planning and the value of conducting study-specific sensitivity analysis prior to inclusion of modelled locations in research outputs. Based on our findings, we suggest general steps and refinements to maximise the value of light geolocation data from PSATs deployed on aquatic animals and highlight the importance of conducting data sensitivity analyses.European Maritime and Fisheries FundDepartment for Environment, Food and Rural Affairs (UK

Cooperation and Contagion in Web-Based, Networked Public Goods Experiments

A longstanding idea in the literature on human cooperation is that cooperation should be reinforced when conditional cooperators are more likely to interact. In the context of social networks, this idea implies that cooperation should fare better in highly clustered networks such as cliques than in networks with low clustering such as random networks. To test this hypothesis, we conducted a series of web-based experiments, in which 24 individuals played a local public goods game arranged on one of five network topologies that varied between disconnected cliques and a random regular graph. In contrast with previous theoretical work, we found that network topology had no significant effect on average contributions. This result implies either that individuals are not conditional cooperators, or else that cooperation does not benefit from positive reinforcement between connected neighbors. We then tested both of these possibilities in two subsequent series of experiments in which artificial seed players were introduced, making either full or zero contributions. First, we found that although players did generally behave like conditional cooperators, they were as likely to decrease their contributions in response to low contributing neighbors as they were to increase their contributions in response to high contributing neighbors. Second, we found that positive effects of cooperation were contagious only to direct neighbors in the network. In total we report on 113 human subjects experiments, highlighting the speed, flexibility, and cost-effectiveness of web-based experiments over those conducted in physical labs

From Nonspecific DNA–Protein Encounter Complexes to the Prediction of DNA–Protein Interactions

©2009 Gao, Skolnick. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.doi:10.1371/journal.pcbi.1000341DNA–protein interactions are involved in many essential biological activities. Because there is no simple mapping code between DNA base pairs and protein amino acids, the prediction of DNA–protein interactions is a challenging problem. Here, we present a novel computational approach for predicting DNA-binding protein residues and DNA–protein interaction modes without knowing its specific DNA target sequence. Given the structure of a DNA-binding protein, the method first generates an ensemble of complex structures obtained by rigid-body docking with a nonspecific canonical B-DNA. Representative models are subsequently selected through clustering and ranking by their DNA–protein interfacial energy. Analysis of these encounter complex models suggests that the recognition sites for specific DNA binding are usually favorable interaction sites for the nonspecific DNA probe and that nonspecific DNA–protein interaction modes exhibit some similarity to specific DNA–protein binding modes. Although the method requires as input the knowledge that the protein binds DNA, in benchmark tests, it achieves better performance in identifying DNA-binding sites than three previously established methods, which are based on sophisticated machine-learning techniques. We further apply our method to protein structures predicted through modeling and demonstrate that our method performs satisfactorily on protein models whose root-mean-square Ca deviation from native is up to 5 Å from their native structures. This study provides valuable structural insights into how a specific DNA-binding protein interacts with a nonspecific DNA sequence. The similarity between the specific DNA–protein interaction mode and nonspecific interaction modes may reflect an important sampling step in search of its specific DNA targets by a DNA-binding protein