Current and Nascent SETI Instruments

Here we describe our ongoing efforts to develop high-performance and sensitive instrumentation for use in the search for extra-terrestrial intelligence (SETI). These efforts include our recently deployed Search for Extraterrestrial Emissions from Nearby Developed Intelligent Populations Spectrometer (SERENDIP V.v) and two instruments currently under development; the Heterogeneous Radio SETI Spectrometer (HRSS) for SETI observations in the radio spectrum and the Optical SETI Fast Photometer (OSFP) for SETI observations in the optical band. We will discuss the basic SERENDIP V.v instrument design and initial analysis methodology, along with instrument architectures and observation strategies for OSFP and HRSS. In addition, we will demonstrate how these instruments may be built using low-cost, modular components and programmed and operated by students using common languages, e.g. ANSI C.Comment: 12 pages, 5 figures, Original version appears as Chapter 2 in "The Proceedings of SETI Sessions at the 2010 Astrobiology Science Conference: Communication with Extraterrestrial Intelligence (CETI)," Douglas A. Vakoch, Edito

Selection and visualisation of outcome measures for complex post-acute acquired brain injury rehabilitation interventions.

BACKGROUND: Outcome measurement challenges rehabilitation services to select tools that promote stakeholder engagement in measuring complex interventions. OBJECTIVES: To examine the suitability of outcome measures for complex post-acute acquired brain injury (ABI) rehabilitation interventions, report outcomes of a holistic, neuropsychological ABI rehabilitation program and propose a simple way of visualizing complex outcomes. METHODS: Patient/carer reported outcome measures (PROMS), experience measures (PREMS) and staff-rated measures were collected for consecutive admissions over 1 year to an 18-week holistic, neuropsychological rehabilitation programme at baseline, 18 weeks and 3- and 6-month follow-up. RESULTS: Engagement with outcome measurement was poorest for carers and at follow-up for all stakeholders. Dependence, abilities, adjustment, unmet needs, symptomatology including executive dysfunction, and self-reassurance showed improvements at 18 weeks. Adjustment, social participation, perceived health, symptomatology including dysexecutive difficulties, and anxiety were worse at baseline for those who did not complete rehabilitation, than those who did. A radar plot facilitated outcome visualization. CONCLUSIONS: Engagement with outcome measurement was best when time and support were provided. Supplementing patient- with staff-rated and attendance measures may explain missing data and help quantify healthcare needs. The MPAI4, EBIQ and DEX-R appeared suitable measures to evaluate outcomes and distinguish those completing and not completing neuropsychological rehabilitation.National Institute for Health Researc

Neutralizing positive charges at the surface of a protein lowers its rate of amide hydrogen exchange without altering its structure or increasing its thermostability

This paper combines two techniques—mass spectrometry and protein charge ladders—to examine the relationship between the surface charge and hydrophobicity of a protein (bovine carbonic anhydrase II; BCA II) and its rate of amide hydrogen-deuterium (H/D) exchange. Mass spectrometric analysis indicated that the sequential acetylation of surface lysine-$\epsilon$-NH$_{3}$$^{+}$ groups—a type of modification that increases the net negative charge and hydrophobicity of the surface of BCA II without affecting its 2° or 3° structure—resulted in a linear increase in the total number of backbone amide hydrogen that are protected from exchange with solvent (2 h, pD 7.4, 15 ºC). Each successive acetylation produced BCA II proteins with one additional hydrogen protected after two hours in deuterated buffer (pD 7.4, 15 ºC). NMR spectroscopy demonstrated that these protected hydrogen atoms were not located on the side chain of the acetylated lysine residues (i.e., lys-$\epsilon$-NHCOCH$_{3}$). The decrease in rate of exchange associated with acetylation paralleled a decrease in thermostability: the most slowly exchanging rungs were the least thermostable (as measured by differential scanning calorimetry). The fact that the rates of H/D exchange were similar for perbutyrated BCA II (e.g., [lys-$\epsilon$-NHCO(CH$_{2}$)$_{2}$CH$_{3}$]$_{18}$) and peracetylated BCA II (e.g., [lys-$\epsilon$-NHCOCH$_{3}$]$_{18}$) suggests that the charge is more important than the hydrophobicity of surface groups in determining the rate of H/D exchange. These kinetic electrostatic effects could complicate the interpretation of experiments in which H/D exchange methods are used to probe the structural effects of non-isoelectric perturbations to proteins (i.e., phosphorylation, acetylation, or the binding of the protein to an oligonucleotide or another charged ligand or protein).Chemistry and Chemical Biolog

Incineration of Nanoclay Composites Leads to Byproducts with Reduced Cellular Reactivity

Addition of nanoclays into a polymer matrix leads to nanocomposites with enhanced properties to be used in plastics for food packaging applications. Because of the plastics’ high stored energy value, such nanocomposites make good candidates for disposal via municipal solid waste plants. However, upon disposal, increased concerns related to nanocomposites’ byproducts potential toxicity arise, especially considering that such byproducts could escape disposal filters to cause inhalation hazards. Herein, we investigated the effects that byproducts of a polymer polylactic acid-based nanocomposite containing a functionalized montmorillonite nanoclay (Cloisite 30B) could pose to human lung epithelial cells, used as a model for inhalation exposure. Analysis showed that the byproducts induced toxic responses, including reductions in cellular viability, changes in cellular morphology, and cytoskeletal alterations, however only at high doses of exposure. The degree of dispersion of nanoclays in the polymer matrixappeared to influence the material characteristics, degradation, and ultimately toxicity. With toxicity of the byproduct occurring at high doses, safety protocols should be considered, along with deleterious effects investigations to thus help aid in safer, yet still effective products and disposal strategies

Activation of gene expression by detergent-like protein domains

The mechanisms by which transcriptional activation domains (tADs) initiate eukaryotic gene expression have been an enigma for decades because most tADs lack specificity in sequence, structure, and interactions with targets. Machine learning analysis of data sets of tAD sequences generated in vivo elucidated several functionality rules: the functional tAD sequences should (i) be devoid of or depleted with basic amino acid residues, (ii) be enriched with aromatic and acidic residues, (iii) be with aromatic residues localized mostly near the terminus of the sequence, and acidic residues localized more internally within a span of 20–30 amino acids, (iv) be with both aromatic and acidic residues preferably spread out in the sequence and not clustered, and (v) not be separated by occasional basic residues. These and other more subtle rules are not absolute, reflecting absence of a tAD consensus sequence, enormous variability, and consistent with surfactant-like tAD biochemical properties. The findings are compatible with the paradigm-shifting nucleosome detergent mechanism of gene expression activation, contributing to the development of the liquid-liquid phase separation model and the biochemistry of near-stochastic functional allosteric interactions

The ansamycin antibiotic, rifamycin SV, inhibits BCL6 transcriptional repression and forms a complex with the BCL6-BTB/POZ domain

BCL6 is a transcriptional repressor that is over-expressed due to chromosomal translocations, or other abnormalities, in ~40% of diffuse large B-cell lymphoma. BCL6 interacts with co-repressor, SMRT, and this is essential for its role in lymphomas. Peptide or small molecule inhibitors, which prevent the association of SMRT with BCL6, inhibit transcriptional repression and cause apoptosis of lymphoma cells in vitro and in vivo. In order to discover compounds, which have the potential to be developed into BCL6 inhibitors, we screened a natural product library. The ansamycin antibiotic, rifamycin SV, inhibited BCL6 transcriptional repression and NMR spectroscopy confirmed a direct interaction between rifamycin SV and BCL6. To further determine the characteristics of compounds binding to BCL6-POZ we analyzed four other members of this family and showed that rifabutin, bound most strongly. An X-ray crystal structure of the rifabutin-BCL6 complex revealed that rifabutin occupies a partly non-polar pocket making interactions with tyrosine58, asparagine21 and arginine24 of the BCL6-POZ domain. Importantly these residues are also important for the interaction of BLC6 with SMRT. This work demonstrates a unique approach to developing a structure activity relationship for a compound that will form the basis of a therapeutically useful BCL6 inhibitor