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

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

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

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

Network Hawkes Process Models for Exploring Latent Hierarchy in Social Animal Interactions

Group-based social dominance hierarchies are of essential interest in animal behavior research. Studies often record aggressive interactions observed over time, and models that can capture such dynamic hierarchy are therefore crucial. Traditional ranking methods summarize interactions across time, using only aggregate counts. Instead, we take advantage of the interaction timestamps, proposing a series of network point process models with latent ranks. We carefully design these models to incorporate important characteristics of animal interaction data, including the winner effect, bursting and pair-flip phenomena. Through iteratively constructing and evaluating these models we arrive at the final cohort Markov-Modulated Hawkes process (C-MMHP), which best characterizes all aforementioned patterns observed in interaction data. We compare all models using simulated and real data. Using statistically developed diagnostic perspectives, we demonstrate that the C-MMHP model outperforms other methods, capturing relevant latent ranking structures that lead to meaningful predictions for real data

Sequence and gene expression of chloroquine resistance transporter (pfcrt) in the association of in vitro drugs resistance of Plasmodium falciparum

<p>Abstract</p> <p>Background</p> <p><it>Plasmodium falciparum </it>chloroquine resistance (CQR) transporter protein (PfCRT) is known to be the important key of CQR. Recent studies have definitively demonstrated a link between mutations in the gene <it>pfcrt </it>and resistance to chloroquine in <it>P. falciparum</it>. Although these mutations are predictive of chloroquine resistance, they are not quantitatively predictive of the degree of resistance.</p> <p>Methods</p> <p>In this study, a total of 95 recently adapted <it>P. falciparum </it>isolates from Thailand were included in the analysis. Parasites were characterized for their drug susceptibility phenotypes and genotypes with respect to <it>pfcrt</it>. From the original 95 isolates, 20 were selected for complete <it>pfcrt </it>sequence analysis.</p> <p>Results</p> <p>Almost all of the parasites characterized carried the previously reported mutations K76T, A220S, Q271E, N326S, I356T and R371I. On complete sequencing, isolates were identified with novel mutations at K76A and E198K. There was a suggestion that parasites carrying E198K were less resistant than those that did not. In addition, <it>pfcrt </it>and <it>pfmdr1 </it>gene expression were investigated by real-time PCR. No relationship between the expression level of either of these genes and response to drug was observed.</p> <p>Conclusion</p> <p>Data from the present study suggest that other genes must contribute to the degree of resistance once the resistance phenotype is established through mutations in <it>pfcrt</it>.</p

The histone chaperones Vps75 and Nap1 form ring-like, tetrameric structures in solution

NAP-1 fold histone chaperones play an important role in escorting histones to and from sites of nucleosome assembly and disassembly. The two NAP-1 fold histone chaperones in budding yeast, Vps75 and Nap1, have previously been crystalized in a characteristic homodimeric conformation. In this study, a combination of small angle X-ray scattering, multi angle light scattering and pulsed electron–electron double resonance approaches were used to show that both Vps75 and Nap1 adopt ring-shaped tetrameric conformations in solution. This suggests that the formation of homotetramers is a common feature of NAP-1 fold histone chaperones. The tetramerisation of NAP-1 fold histone chaperones may act to shield acidic surfaces in the absence of histone cargo thus providing a ‘self-chaperoning’ type mechanism

Narratives of self and identity in women's prisons: stigma and the struggle for self-definition in penal regimes

A concern with questions of selfhood and identity has been central to penal practices in women's prisons, and to the sociology of women's imprisonment. Studies of women's prisons have remained preoccupied with women prisoners’ social identities, and their apparent tendency to adapt to imprisonment through relationships. This article explores the narratives of women in two English prisons to demonstrate the importance of the self as a site of meaning for prisoners and the central place of identity in micro-level power negotiations in prisons

Spectroscopy of the near-nuclear regions of Cygnus A: estimating the mass of the supermassive black hole

We use a combination of high spatial resolution optical and near-IR spectroscopic data to make a detailed study of the kinematics of the NLR gas in the near-nuclear regions of the powerful, FRII radio galaxy Cygnus A (z=0.0560), with the overall goal of placing limits on the mass of any supermassive black hole in the core. Our K-band infrared observations (0.75 arcsec seeing) -- taken with NIRSPEC on the Keck II telescope -- show a smooth rotation pattern across the nucleus in the Paschen alpha and H_2 emission lines along a slit position (PA180) close to perpendicular to the radio axis, however, there is no evidence for such rotation along the radio axis (PA105). Higher spatial resolution observations of the [OIII]5007 emission line -- taken with STIS on the Hubble Space Telescope (HST) -- confirm the general rotation pattern of the gas in the direction perpendicular to the radio axis, and provide evidence for steep velocity gradients within a radius of 0.1 arcsec of the core. The circular velocities measured from both the Keck and HST data lead to an estimate of the mass of the supermassive black hole of 2.5+/-0.7x10^9 solar masses. For the host galaxy properties of Cygnus A, this mass is consistent with the global correlations between black hole mass and host galaxy properties deduced for non-active galaxies. Therefore, despite the extreme power of its radio source and the quasar-like luminosity of its AGN, the black hole in Cygnus A is not unusually massive considering theluminosity of its host galaxy. Indeed, the estimated mass of the black hole in Cygnus A is similar to that inferred for the supermassive black hole in the FRI radio galaxy M87, despite the fact that the AGN and radio jets of Cygnus A are 2 -- 3 orders of magnitude more powerful.Comment: 17 pages, 12 figure