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We propose to create a secondary beam of neutral kaons in Hall D at Jefferson Lab to be used with the GlueX experimental setup for strange hadron spectroscopy. The superior CEBAF electron beam will enable a flux on the order of $1\times 10^4~K_L/sec$, which exceeds the flux of that previously attained at SLAC by three orders of magnitude. The use of a deuteron target will provide first measurements ever with neutral kaons on neutrons. The experiment will measure both differential cross sections and self-analyzed polarizations of the produced $\Lambda$, $\Sigma$, $\Xi$, and $\Omega$ hyperons using the GlueX detector at the Jefferson Lab Hall D. The measurements will span CM $\cos\theta$ from $-0.95$ to 0.95 in the range W = 1490 MeV to 2500 MeV. The new data will significantly constrain the partial wave analyses and reduce model-dependent uncertainties in the extraction of the properties and pole positions of the strange hyperon resonances, and establish the orbitally excited multiplets in the spectra of the $\Xi$ and $\Omega$ hyperons. Comparison with the corresponding multiplets in the spectra of the charm and bottom hyperons will provide insight into he accuracy of QCD-based calculations over a large range of masses. The proposed facility will have a defining impact in the strange meson sector through measurements of the final state $K\pi$ system up to 2 GeV invariant mass. This will allow the determination of pole positions and widths of all relevant $K^\ast(K\pi)$ $S$-,$P$-,$D$-,$F$-, and $G$-wave resonances, settle the question of the existence or nonexistence of scalar meson $\kappa/K_0^\ast(700)$ and improve the constrains on their pole parameters. Subsequently improving our knowledge of the low-lying scalar nonet in general., Comment: Final version of the KLF Proposal [C12-19-001] approved by JLab PAC48. The intermediate version of the proposal was posted in arXiv:1707.05284 [hep-ex]. 103 pages, 52 figures, 8 tables, 324 references. Several typos were fixed

The acetyltransferases CBP and p300 are multifunctional transcriptional co-activators. Here, we combined quantitative proteomics with CBP/p300-specific catalytic inhibitors, bromodomain inhibitor, and gene knockout to reveal a comprehensive map of regulated acetylation sites and their dynamic turnover rates. CBP/p300 acetylates thousands of sites, including signature histone sites and a multitude of sites on signaling effectors and enhancer-associated transcriptional regulators. Time-resolved acetylome analyses identified a subset of CBP/p300-regulated sites with very rapid (<30 min) acetylation turnover, revealing a dynamic balance between acetylation and deacetylation. Quantification of acetylation, mRNA, and protein abundance after CBP/p300 inhibition reveals a kinetically competent network of gene expression that strictly depends on CBP/p300-catalyzed rapid acetylation. Collectively, our in-depth acetylome analyses reveal systems attributes of CBP/p300 targets, and the resource dataset provides a framework for investigating CBP/p300 functions and for understanding the impact of small-molecule inhibitors targeting its catalytic and bromodomain activities.

Transcription activation involves RNA polymerase II (Pol II) recruitment and release from the promoter into productive elongation, but how specific chromatin regulators control these steps is unclear. Here, we identify a novel activity of the histone acetyltransferase p300/CREB-binding protein (CBP) in regulating promoter-proximal paused Pol II. We find that Drosophila CBP inhibition results in "dribbling" of Pol II from the pause site to positions further downstream but impedes transcription through the +1 nucleosome genome-wide. Promoters strongly occupied by CBP and GAGA factor have high levels of paused Pol II, a unique chromatin signature, and are highly expressed regardless of cell type. Interestingly, CBP activity is rate limiting for Pol II recruitment to these highly paused promoters through an interaction with TFIIB but for transit into elongation by histone acetylation at other genes. Thus, CBP directly stimulates both Pol II recruitment and the ability to traverse the first nucleosome, thereby promoting transcription of most genes.

The dynamic and reversible acetylation of proteins, catalysed by histone acetyltransferases (HATs) and histone deacetylases (HDACs), is a major epigenetic regulatory mechanism of gene transcription and is associated with multiple diseases. Histone deacetylase inhibitors are currently approved to treat certain cancers, but progress on the development of drug-like histone actyltransferase inhibitors has lagged behind. The histone acetyltransferase paralogues p300 and CREB-binding protein (CBP) are key transcriptional co-activators that are essential for a multitude of cellular processes, and have also been implicated in human pathological conditions (including cancer). Current inhibitors of the p300 and CBP histone acetyltransferase domains, including natural products, bi-substrate analogues and the widely used small molecule C646, lack potency or selectivity. Here, we describe A-485, a potent, selective and drug-like catalytic inhibitor of p300 and CBP. We present a high resolution (1.95 Å) co-crystal structure of a small molecule bound to the catalytic active site of p300 and demonstrate that A-485 competes with acetyl coenzyme A (acetyl-CoA). A-485 selectively inhibited proliferation in lineage-specific tumour types, including several haematological malignancies and androgen receptor-positive prostate cancer. A-485 inhibited the androgen receptor transcriptional program in both androgen-sensitive and castration-resistant prostate cancer and inhibited tumour growth in a castration-resistant xenograft model. These results demonstrate the feasibility of using small molecule inhibitors to selectively target the catalytic activity of histone acetyltransferases, which may provide effective treatments for transcriptional activator-driven malignancies and diseases.

Expressed protein ligation is a valuable method for protein semisynthesis that involves the reaction of recombinant protein C-terminal thioesters with N-terminal cysteine (N-Cys)-containing peptides, but the requirement of a Cys residue at the ligation junction can limit the utility of this method. Here we employ subtiligase variants to efficiently ligate Cys-free peptides to protein thioesters. Using this method, we have more accurately determined the effect of C-terminal phosphorylation on the tumor suppressor protein PTEN.

Expressed protein ligation is a valuable method for protein semisynthesis that involves the reaction of recombinant protein C-terminal thioesters with N-terminal cysteine (N-Cys)-containing peptides, but the requirement of a Cys residue at the ligation junction can limit the utility of this method. Here we employ subtiligase variants to efficiently ligate Cys-free peptides to protein thioesters. Using this method, we have more accurately determined the effect of C-terminal phosphorylation on the tumor suppressor protein PTEN.

BACKGROUND: CREB-binding protein (CBP, also known as nejire) is a transcriptional co-activator that is conserved in metazoans. CBP plays an important role in embryonic development and cell differentiation and mutations in CBP can lead to various diseases in humans. In addition, CBP and the related p300 protein have successfully been used to predict enhancers in both humans and flies when they occur with monomethylation of histone H3 on lysine 4 (H3K4me1). RESULTS: Here, we compare CBP chromatin immunoprecipitation sequencing data from Drosophila S2 cells with modENCODE data and show that CBP is bound at genomic sites with a wide range of functions. As expected, we find that CBP is bound at active promoters and enhancers. In addition, we find that the strongest CBP sites in the genome are found at Polycomb response elements embedded in histone H3 lysine 27 trimethylated (H3K27me3) chromatin, where they correlate with binding of the Pho repressive complex. Interestingly, we find that CBP also binds to most insulators in the genome. At a subset of these, CBP may regulate insulating activity, measured as the ability to prevent repressive H3K27 methylation from spreading into adjacent chromatin. CONCLUSIONS: We conclude that CBP could be involved in a much wider range of functions than has previously been appreciated, including Polycomb repression and insulator activity. In addition, we discuss the possibility that a common role for CBP at all functional elements may be to regulate interactions between distant chromosomal regions and speculate that CBP is controlling higher order chromatin organization., Erratum to: CBP binding outside of promoters and enhancers in Drosophila melanogasterEpigenetics & Chromatin 2016 9:3810.1186/s13072-015-0042-4

Inhibition of histone demethylases has within recent years advanced into a new strategy for treating cancer and other diseases. Targeting specific histone demethylases can be challenging as the active sites of KDM1A-B and KDM-4A-D histone demethylases, respectively, are highly conserved. Most inhibitors developed up-to-date target either the cofactor- or substrate-binding sites of these enzymes, resulting in a lack of selectivity and off-target effects. This study describes the discovery of the first peptide-based inhibitors of KDM4 histone demethylases that do not share the histone peptide sequence, or inhibit through substrate competition. Through screening of DNA-encoded peptide libraries against KDM1 and -4 histone demethylases by phage display, two cyclic peptides targeting the histone demethylase KDM4C were identified and developed as inhibitors by amino acid replacement, truncation and chemical modifications. Hydrogen/deuterium exchange mass spectrometry revealed that the peptide-based inhibitors target KDM4C through substrate-independent interactions located on the surface remote from the active site within less conserved regions of KDM4C. The sites discovered in this study provide a new approach of targeting KDM4C through substrate- and cofactor-independent interactions, and may be further explored to develop potent selective inhibitors and biological probes for the KDM4 family.

Phage display (PD) is frequently used to discover peptides capable of binding to biological protein targets. The structural characterization of peptide-protein complexes is often challenging due to their low binding affinities and high structural flexibility. Here, we investigate the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) to characterize interactions of low affinity peptides with their cognate protein targets. The HDX-MS workflow was optimized to accurately detect low-affinity peptide-protein interactions by use of ion mobility, electron transfer dissociation, non-binding control peptides and statistical analysis of replicate data. We show that HDX-MS can identify regions in the two epigenetic regulator proteins KDM4C and KDM1A that are perturbed through weak interactions with PD-identified peptides. Two peptides cause reduced HDX on opposite sides of the active site of KDM4C, indicating distinct binding modes. In contrast, the perturbation site of another PD-selected peptide inhibiting the function of KDM1A maps to a GST-tag. Our results demonstrate that HDX-MS can validate and map weak peptide-protein interactions, and pave the way for understanding and optimizing the binding of peptide scaffolds identified through PD and similar ligand discovery approaches.

Lysine acetylation regulates transcription by targeting histones and nonhistone proteins. Here we report that the central regulator of transcription, RNA polymerase II, is subject to acetylation in mammalian cells. Acetylation occurs at eight lysines within the C-terminal domain (CTD) of the largest polymerase subunit and is mediated by p300/KAT3B. CTD acetylation is specifically enriched downstream of the transcription start sites of polymerase-occupied genes genome-wide, indicating a role in early stages of transcription initiation or elongation. Mutation of lysines or p300 inhibitor treatment causes the loss of epidermal growth-factor-induced expression of c-Fos and Egr2, immediate-early genes with promoter-proximally paused polymerases, but does not affect expression or polymerase occupancy at housekeeping genes. Our studies identify acetylation as a new modification of the mammalian RNA polymerase II required for the induction of growth factor response genes.

Free to read It is well established that the coordinated regulation of activity-dependent gene expression by the histone acetyltransferase (HAT) family of transcriptional coactivators is crucial for the formation of contextual fear and spatial memory, and for hippocampal synaptic plasticity. However, no studies have examined the role of this epigenetic mechanism within the infralimbic prefrontal cortex (ILPFC), an area of the brain that is essential for the formation and consolidation of fear extinction memory. Here we report that a postextinction training infusion of a combined p300/CBP inhibitor (Lys-CoA-Tat), directly into the ILPFC, enhances fear extinction memory in mice. Our results also demonstrate that the HAT p300 is highly expressed within pyramidal neurons of the ILPFC and that the small-molecule p300-specific inhibitor (C646) infused into the ILPFC immediately after weak extinction training enhances the consolidation of fear extinction memory. C646 infused 6 h after extinction had no effect on fear extinction memory, nor did an immediate postextinction training infusion into the prelimbic prefrontal cortex. Consistent with the behavioral findings, inhibition of p300 activity within the ILPFC facilitated long-term potentiation (LTP) under stimulation conditions that do not evoke long-lasting LTP. These data suggest that one function of p300 activity within the ILPFC is to constrain synaptic plasticity, and that a reduction in the function of this HAT is required for the formation of fear extinction memory.

Members of the epidermal growth factor receptor family (EGFR/ERBB1, ERBB2/HER2, ERBB3/HER3 and ERBB4/HER4) are key targets for inhibition in cancer therapy. Critical for activation is the formation of an asymmetric dimer by the intracellular kinase domains, in which the carboxy-terminal lobe (C lobe) of one kinase domain induces an active conformation in the other. The cytoplasmic protein MIG6 (mitogen-induced gene 6; also known as ERRFI1) interacts with and inhibits the kinase domains of EGFR and ERBB2 (refs 3-5). Crystal structures of complexes between the EGFR kinase domain and a fragment of MIG6 show that a approximately 25-residue epitope (segment 1) from MIG6 binds to the distal surface of the C lobe of the kinase domain. Biochemical and cell-based analyses confirm that this interaction contributes to EGFR inhibition by blocking the formation of the activating dimer interface. A longer MIG6 peptide that is extended C terminal to segment 1 has increased potency as an inhibitor of the activated EGFR kinase domain, while retaining a critical dependence on segment 1. We show that signalling by EGFR molecules that contain constitutively active kinase domains still requires formation of the asymmetric dimer, underscoring the importance of dimer interface blockage in MIG6-mediated inhibition.

Since the first direct observations of antineutrino events by Reines and Cowan in the 1950's [1], nuclear reactors have been an important tool in the study of neutrino properties. More recently, the study of neutrino oscillations has been a very active area of research. The pioneering observation of oscillations by the KamLAND experiment has provided crucial information on the neutrino mixing matrix. New experiments to study the remaining unknown mixing angle are currently under development. These recent studies and potential future developments will be discussed.

The improper activation of the Abl tyrosine kinase results in chronic myeloid leukemia (CML). The recognition of an inactive conformation of Abl, in which a catalytically important Asp-Phe-Gly (DFG) motif is flipped by approximately 180 degrees with respect to the active conformation, underlies the specificity of the cancer drug imatinib, which is used to treat CML. The DFG motif is not flipped in crystal structures of inactive forms of the closely related Src kinases, and imatinib does not inhibit c-Src. We present a structure of the kinase domain of Abl, determined in complex with an ATP-peptide conjugate, in which the protein adopts an inactive conformation that resembles closely that of the Src kinases. An interesting aspect of the Src-like inactive structure, suggested by molecular dynamics simulations and additional crystal structures, is the presence of features that might facilitate the flip of the DFG motif by providing room for the phenylalanine to move and by coordinating the aspartate side chain as it leaves the active site. One class of mutations in BCR-Abl that confers resistance to imatinib appears more likely to destabilize the inactive Src-like conformation than the active or imatinib-bound conformations. Our results suggest that interconversion between distinctly different inactive conformations is a characteristic feature of the Abl kinase domain.

Wide-angle seismic data recorded on 13 ocean bottom instruments in the Southern Iberia Abyssal Plain have been analysed for the presence of P-wave azimuthal anisotropy. Small anisotropy (< 7 %) was identifed at depths of 3-7 km below the top of the basement, with a fast velocity direction oriented at N142°E. Similar studies over oceanic crust have found that the fast velocity direction corresponds with the plate spreading direction. It is difficult to reconcile the direction found here with other observations, and rotation of the upper mantle by motion along low-angle normal faults is proposed to account for the discrepancy. Margin parallel extension is identified in MCS profiles collected over crust formed within 20 m.y. of the onset of seafloor spreading and is related to the uphft of the region west of Gahcia Bank. Small amounts of extension are identified in margin normal profiles. Sub-horizontal reflections identified in all the profiles result from out-of-plane energy, compositional and hydrothermal layering and previous shot multiples. Modelling of the satellite free-air gravity anomalies along the I AM-10 profile revealed crust of 5 - 6 ±l km thickness with up to 10% variations of the lower crustal density. These variations are consistent with the presence of a previously unmapped fracture zone which affects 125±5-110±5 Ma crust. The density models and crustal reflectivity of the profiles collected over the early-formed oceanic crust are similar to those of profiles collected away from margins. Regions of enhanced reflectivity of the basement surface are attributed to the emplacement of lava flows as a result of additional magma supply during the propagation of the paleo-ridge. The conformable sediment sequence, consistent with the seismic stratigraphy identi- fled in the Southern Iberia Abyssal Plain, indicates changes in the sedimentation pattern during the Eocene as a result of the subduction of the southern margin of the Bay of Bis- cay. Anomalous

This NebGuide provides cleaning, sanitizing, mechanical, environmental and other procedures to follow to assure a low bacterial count in milk. Bacteria are tiny, rapidly reproducing microorganisms that are too small to be seen without a high power microscope. Their very tiny size makes it very difficult to eliminate them from dairy equipment. Because bacterial growth in milk may cause spoilage and possibly human illnesses, a low bacterial count is one of the best indicators of top quality milk. Milk will almost always be of top quality if properly harvested from healthy, clean cows with clean equipment, cooled quickly and kept cold.

The purpose of this evaluation was to assess the suitability of the AN/PRC-64 radio set for use in the high atmospheric noise level existing in the Republic of Vietnam (RVN) and for use by US Special Forces patrols in the counterinsurgency environment of the RVN. Two geographically different areas were chosen for the evaluation. Phase I was conducted in the Mekong Delta and phase II in the Central Highlands. The radios were used by US Special Forces 'A' detachments during patrol operations and at forward operational base stations in lieu of radio set AN/GRC109. Data were collected from personal observations, discussions with Special Forces advisors and signal officers, and operators' logs. The principal result of this evaluation was the determination that the AN/ PRC-64 radio set provides reliable continuous wave (CW) communication at distances between 60 and 500 kilometers. It provides reliable voice communication only at distances between 0 and 20 kilometers and then only in the Mekong Delta. The whisper capability of the radio set is reliable and just as effective as a normal voice transmission. User reaction to the AN/PRC-64 was excellent and they recommend its adoption for counterinsurgency operations.

This report is a continuation of the final report for contract AF19 (628)-5193. The assumptions and assertions of that report are examined, and estimates made of how these may affect the worth and accuracy of numerical predications of contrail properties. A special type of analytic-experimental analysis is proposed to ferret out nonthermodynamic variables, and is applied to flight test data. Following the analysis, further computer simulation is explored. Additional data lead to bounds on the values of heretofore unspecifiable parameters. Further experimental study is indicated. The data is presented in terms of the dependence of contrail formation on ambient temperature and relative humidity. (Author)

Proteomic technologies, such as yeast two-hybrid, mass spectrometry (MS), protein/peptide arrays and fluorescence microscopy, yield multi-dimensional data sets, which are often quite large and either not published or published as supplementary information that is not easily searchable. Without a system in place for standardizing and sharing data, it is not fruitful for the biomedical community to contribute these types of data to centralized repositories.

Acoustic Emission (AE) sensors were used to detect signals arising from a cylindrical roller bearing with artificial defects seeded onto the outer raceway. High frequency analysis indicated the condition of the bearings through the determination of an increase in the structural resonances of the system as the size of an artificial defect was increased. As higher loads were applied, frequencies around 100kHz were excited, indicating the release of AE possibly attributed to friction and the plastic deformation as peaks, induced through engraving of the raceway, were over-rolled and worn down. Sensitivity of AE to this level in bearings indicates that detection of subsurface cracking may be possible in future work, providing early indication of incipient failure.

This is a study of Japanese government organization for waging war, particularly to consider the degree of cooperation that existed between components of the Japanese armed forces, and between them and other governmental agencies. Also discussed are the solutions reached on various command, control, and logistical problems, and the effects of those solutions employed upon preparation for war and the course of military and naval operations. The contents contain plans for conquest, the Japanese people, war organization of the government and the national economy, interservice relationships (relationships between the services and other departments of government), and war planning in the Army and Navy general staffs.