Probing the (H3-H4)(2) histone tetramer structure using pulsed EPR spectroscopy combined with site-directed spin labelling

The (H3-H4)2 histone tetramer forms the central core of nucleosomes and, as such, plays a prominent role in assembly, disassembly and positioning of nucleosomes. Despite its fundamental role in chromatin, the tetramer has received little structural investigation. Here, through the use of pulsed electron-electron double resonance spectroscopy coupled with site-directed spin labelling, we survey the structure of the tetramer in solution. We find that tetramer is structurally more heterogeneous on its own than when sequestered in the octamer or nucleosome. In particular, while the central region including the H3-H3′ interface retains a structure similar to that observed in nucleosomes, other regions such as the H3 αN helix display increased structural heterogeneity. Flexibility of the H3 αN helix in the free tetramer also illustrates the potential for post-translational modifications to alter the structure of this region and mediate interactions with histone chaperones. The approach described here promises to prove a powerful system for investigating the structure of additional assemblies of histones with other important factors in chromatin assembly/fluidity

Prevalence of traumatic brain injury amongst children admitted to hospital in one health district : a population-based study

There is a dearth of information regarding the prevalence of brain injury, serious enough to require hospital admission, amongst children in the United Kingdom. In North Staffordshire a register of all children admitted with traumatic brain injury (TBI) has been maintained since 1992 presenting an opportunity to investigate the incidence of TBI within the region in terms of age, cause of injury, injury severity and social deprivation. The register contains details of 1553 children with TBI, two thirds of whom are male. This population-based study shows that TBI is most prevalent amongst children from families living in more deprived areas, however, social deprivation was not related to the cause of injury. Each year, 280 per 100,000 children are admitted for ≥24 hours with a TBI, of these 232 will have a mild brain injury, 25 moderate, 17 severe, and 2 will die. The incidence of moderate and severe injuries is higher than previous estimates. Children under 2 years old account for 18.5% of all TBIs, usually due to falls, being dropped or non-accidental injuries. Falls account for 60% of TBIs in the under 5s. In the 10-15 age group road traffic accidents were the most common cause (185, 36.7%). These findings will help to plan health services and target accident prevention initiatives more accurately

Modeling Land and Hold Short Operations: Balancing Safety and Arrival Rate

Many airports conduct simultaneous operations on intersecting runways to increase the rate of takeoffs and landings. This requires landing aircraft to hold short of the intersecting runway, which incurs a safety risk of runway incursions in the process. A Monte Carlo simulation was conducted to analyze the traffic load at maximum operational capacity at Charlotte-Douglas International Airport in order to analyze the fleet types and the rate of those landing aircraft unable to stop short of the intersecting runway. The researchers used the actual and four alternative compositions of the subject airline’s aircraft arrivals, interspersed among other airport traffic, to assess how such changes affect the rate of runway incursions, the rate of operations at the airport, and the mean number of passengers the subject airline can land per hour. The simulation revealed that runway length up to the hold short point was the biggest determinant of aircraft being unable to hold short. The total airport rate of operations decreased when heavy wake turbulence category aircraft were introduced. Despite heavy wake turbulence category aircraft carrying more passengers individually, the decreased operations rate also led to fewer passengers per hour that the subject airline could carry

Online Estimation of Network Point Processes for Event Streams

A common goal in network modeling is to uncover the latent community structure present among nodes. For many real-world networks, the true connections consist of events arriving as streams, which are then aggregated to form edges, ignoring the dynamic temporal component. A natural way to take account of these temporal dynamics of interactions is to use point processes as the foundation of network models for community detection. Computational complexity hampers the scalability of such approaches to large sparse networks. To circumvent this challenge, we propose a fast online variational inference algorithm for estimating the latent structure underlying dynamic event arrivals on a network, using continuous-time point process latent network models. We describe this procedure for networks models capturing community structure. This structure can be learned as new events are observed on the network, updating the inferred community assignments. We investigate the theoretical properties of such an inference scheme, and provide regret bounds on the loss function of this procedure. The proposed inference procedure is then thoroughly compared, using both simulation studies and real data, to non-online variants. We demonstrate that online inference can obtain comparable performance, in terms of community recovery, to non-online variants, while realising computational gains. Our proposed inference framework can also be readily modified to incorporate other popular network structures.Comment: 45 page

The histone chaperones Nap1 and Vps75 bind histones H3 and H4 in a tetrameric conformation

Histone chaperones physically interact with histones to direct proper assembly and disassembly of nucleosomes regulating diverse nuclear processes such as DNA replication, promoter remodeling, transcription elongation, DNA damage, and histone variant exchange. Currently, the best-characterized chaperone-histone interaction is that between the ubiquitous chaperone Asf1 and a dimer of H3 and H4. Nucleosome assembly proteins (Nap proteins) represent a distinct class of histone chaperone. Using pulsed electron double resonance (PELDOR) measurements and protein crosslinking, we show that two members of this class, Nap1 and Vps75, bind histones in the tetrameric conformation also observed when they are sequestered within the nucleosome. Furthermore, H3 and H4 trapped in their tetrameric state can be used as substrates in nucleosome assembly and chaperone-mediated lysine acetylation. This alternate mode of histone interaction provides a potential means of maintaining the integrity of the histone tetramer during cycles of nucleosome reassembly

The spatial effect of protein deuteration on nitroxide spin-label relaxation:implications for EPR distance measurement

This work was supported by a Wellcome Trust Senior Fellowship (095062) to T.O.-H. The Authors would also like to acknowledge funding from The MRC – United Kingdom, Grant G1100021.Pulsed electron-electron double resonance (PELDOR) coupled with site-directed spin labeling is a powerful technique for the elucidation of protein or nucleic acid, macromolecular structure and interactions. The intrinsic high sensitivity of electron paramagnetic resonance enables measurement on small quantities of bio-macromolecules, however short relaxation times impose a limit on the sensitivity and size of distances that can be measured using this technique. The persistence of the electron spin-echo, in the PELDOR experiment, is one of the most crucial limitations to distance measurement. At a temperature of around 50 K one of the predominant factors affecting persistence of an echo, and as such, the sensitivity and measurable distance between spin labels, is the electron spin echo dephasing time (Tm). It has become normal practice to use deuterated solvents to extend Tm and recently it has been demonstrated that deuteration of the underlying protein significantly extends Tm. Here we examine the spatial effect of segmental deuteration of the underlying protein, and also explore the concentration and temperature dependence of highly deuterated systems.Publisher PDFPeer reviewe

Community Detection and Classification Guarantees Using Embeddings Learned by Node2Vec

Embedding the nodes of a large network into an Euclidean space is a common objective in modern machine learning, with a variety of tools available. These embeddings can then be used as features for tasks such as community detection/node clustering or link prediction, where they achieve state of the art performance. With the exception of spectral clustering methods, there is little theoretical understanding for other commonly used approaches to learning embeddings. In this work we examine the theoretical properties of the embeddings learned by node2vec. Our main result shows that the use of k-means clustering on the embedding vectors produced by node2vec gives weakly consistent community recovery for the nodes in (degree corrected) stochastic block models. We also discuss the use of these embeddings for node and link prediction tasks. We demonstrate this result empirically, and examine how this relates to other embedding tools for network data