Influence of Combinatorial Histone Modifications on Antibody and Effector Protein Recognition

SummaryIncreasing evidence suggests that histone posttranslational modifications (PTMs) function in a combinatorial fashion to regulate the diverse activities associated with chromatin. Yet how these patterns of histone PTMs influence the adapter proteins known to bind them is poorly understood. In addition, how histone-specific antibodies are influenced by these same patterns of PTMs is largely unknown. Here we examine the binding properties of histone-specific antibodies and histone-interacting proteins using peptide arrays containing a library of combinatorially modified histone peptides. We find that modification-specific antibodies are more promiscuous in their PTM recognition than expected and are highly influenced by neighboring PTMs. Furthermore, we find that the binding of histone-interaction domains from BPTF, CHD1, and RAG2 to H3 lysine 4 trimethylation is also influenced by combinatorial PTMs. These results provide further support for the histone code hypothesis and raise specific concerns with the quality of the currently available modification-specific histone antibodies

Quantum Control of a Single Qubit

Measurements in quantum mechanics cannot perfectly distinguish all states and necessarily disturb the measured system. We present and analyse a proposal to demonstrate fundamental limits on quantum control of a single qubit arising from these properties of quantum measurements. We consider a qubit prepared in one of two non-orthogonal states and subsequently subjected to dephasing noise. The task is to use measurement and feedback control to attempt to correct the state of the qubit. We demonstrate that projective measurements are not optimal for this task, and that there exists a non-projective measurement with an optimum measurement strength which achieves the best trade-off between gaining information about the system and disturbing it through measurement back-action. We study the performance of a quantum control scheme that makes use of this weak measurement followed by feedback control, and demonstrate that it realises the optimal recovery from noise for this system. We contrast this approach with various classically inspired control schemes.Comment: 12 pages, 7 figures, v2 includes new references and minor change

Fidelity and the communication of quantum information

We compare and contrast the error probability and fidelity as measures of the quality of the receiver's measurement strategy for a quantum communications system. The error probability is a measure of the ability to retrieve classical information and the fidelity measures the retrieval of quantum information. We present the optimal measurement strategies for maximizing the fidelity given a source that encodes information on the symmetric qubit-states

Protein modifications in transcription elongation

Posttranslational modifications (PTMs) of proteins play essential roles in regulating signaling, protein-protein modifications and subcellular localization. In this review, we focus on posttranslational modification of histones and RNA polymerase II (RNAPII) and their roles in gene transcription. A survey of the basic features of PTMs is provided followed by a more detailed account of how PTMs on histones and RNAPII regulate transcription in the model organism Saccharomyces cerevisiae. We emphasize the interconnections between histone and RNAPII PTMs and speculate upon the larger role PTMs have in regulating protein function in the cell

Accessible information and optimal strategies for real symmetrical quantum sources

We study the problem of optimizing the Shannon mutual information for sources of real quantum states i.e. sources for which there is a basis in which all the states have only real components. We consider in detail the sources ${\cal E}_M$ of $M$ equiprobable qubit states lying symmetrically around the great circle of real states on the Bloch sphere and give a variety of explicit optimal strategies. We also consider general real group-covariant sources for which the group acts irreducibly on the subset of all real states and prove the existence of a real group-covariant optimal strategy, extending a theorem of Davies (E. B. Davies, IEEE. Inf. Theory {\bf IT-24}, 596 (1978)). Finally we propose an optical scheme to implement our optimal strategies, enough simple to be realized with present technology.Comment: RevTeX, 16 pages, 4 eps figures with psfig, submitted to Phys. Rev. A, corrected output error of Fig. 1 in the previous versio

Peptide Microarrays to Interrogate the “Histone Code”

Histone posttranslational modifications (PTMs) play a pivotal role in regulating the dynamics and function of chromatin. Supported by an increasing body of literature, histone PTMs such as methylation and acetylation function together in the context of a “histone code,” which is read, or interpreted, by effector proteins that then drive a functional output in chromatin (e.g., gene transcription). A growing number of domains that interact with histones and/or their PTMs have been identified. While significant advances have been made in our understanding of how these domains interact with histones, a wide number of putative histone-binding motifs have yet to be characterized, and undoubtedly, novel domains will continue to be discovered. In this chapter, we provide a detailed method for the construction of combinatorially modified histone peptides, microarray fabrication using these peptides, and methods to characterize the interaction of effector proteins, antibodies, and the substrate specificity of histone-modifying enzymes. We discuss these methods in the context of other available technologies and provide a user-friendly approach to enable the exploration of histone–protein–enzyme interactions and function

Mesoscopic mechanism of exchange interaction in magnetic multilayers

We discuss a mesoscopic mechanism of exchange interaction in ferromagnet-normal metal-ferromagnet multilayers. We show that in the case when the metal's thickness is larger than the electron mean free path, the relative orientation of magnetizations in the ferromagnets is perpendicular. The exchange energy between ferromagnets decays with the metal thickness as a power law

A Neutron Star with a Massive Progenitor in Westerlund 1

We report the discovery of an X-ray pulsar in the young, massive Galactic star cluster Westerlund 1. We detected a coherent signal from the brightest X-ray source in the cluster, CXO J164710.2-455216, during two Chandra observations on 2005 May 22 and June 18. The period of the pulsar is 10.6107(1) s. We place an upper limit to the period derivative of Pdot<2e-10 s/s, which implies that the spin-down luminosity is Edot<3e33 erg/s. The X-ray luminosity of the pulsar is L_X = 3(+10,-2)e33 (D/5 kpc)^2 erg/s, and the spectrum can be described by a kT = 0.61+/-0.02 keV blackbody with a radius of R_bb = 0.27+/-0.03 (D/5 kpc}) km. Deep infrared observations reveal no counterpart with K1 Msun. Taken together, the properties of the pulsar indicate that it is a magnetar. The rarity of slow X-ray pulsars and the position of CXO J164710.2-455216 only 1.6' from the core of Westerlund 1 indicates that it is a member of the cluster with >99.97% confidence. Westerlund 1 contains 07V stars with initial masses M_i=35 Msun and >50 post-main-sequence stars that indicate the cluster is 4+/-1 Myr old. Therefore, the progenitor to this pulsar had an initial mass M_i>40 Msun. This is the most secure result among a handful of observational limits to the masses of the progenitors to neutron stars.Comment: 4 pages, 5 figures. Final version to match ApJL (added one figure since v2

Exploring VIIRS Continuity with MODIS in an Expedited Capability for Monitoring Drought-Related Vegetation Conditions

Vegetation has been effectively monitored using remote sensing time-series vegetation index (VI) data for several decades. Drought monitoring has been a common application with algorithms tuned to capturing anomalous temporal and spatial vegetation patterns. Drought stress models, such as the Vegetation Drought Response Index (VegDRI), often use VIs like the Normalized Difference Vegetation Index (NDVI). The EROS expedited Moderate Resolution Imaging Spectrora-diometer (eMODIS)-based, 7-day NDVI composites are integral to the VegDRI. As MODIS satellite platforms (Terra and Aqua) approach mission end, the Visible Infrared Imaging Radiometer Suite (VIIRS) presents an alternate NDVI source, with daily collection, similar band passes, and moderate spatial resolution. This study provides a statistical comparison between EROS expedited VIIRS (eVIIRS) 375-m and eMODIS 250-m and tests the suitability of replacing MODIS NDVI with VIIRS NDVI for drought monitoring and vegetation anomaly detection. For continuity with MODIS NDVI, we calculated a geometric mean regression adjustment algorithm using 375-m resolution for an eMODIS-like NDVI (eVIIRS’) eVIIRS’ = 0.9887 × eVIIRS − 0.0398. The resulting statistical comparisons (eVIIRS’ vs. eMODIS NDVI) showed correlations consistently greater than 0.84 throughout the three years studied. The eVIIRS’ VegDRI results characterized similar drought patterns and hotspots to the eMODIS-based VegDRI, with near zero bias