Self-interaction chromatography as a tool for optimizing conditions for membrane protein crystallization

The second virial coefficient, or B value, is a measurement of how well a protein interacts with itself in solution. These interactions can lead to protein crystallization or precipitation, depending on their strength, with a narrow range of B values (the `crystallization slot') being known to promote crystallization. A convenient method of determining the B value is by self-interaction chromatography. This paper describes how the light-harvesting complex 1-reaction centre core complex from Allochromatium vinosum yielded single straight-edged crystals after iterative cycles of self-interaction chromatography and crystallization. This process allowed the rapid screening of small molecules and detergents as crystallization additives. Here, a description is given of how self-interaction chromatography has been utilized to improve the crystallization conditions of a membrane protein

Long-Term Stability of an Area-Reversible Atom-Interferometer Sagnac Gyroscope

We report on a study of the long-term stability and absolute accuracy of an atom interferometer gyroscope. This study included the implementation of an electro-optical technique to reverse the vector area of the interferometer for reduced systematics and a careful study of systematic phase shifts. Our data strongly suggests that drifts less than 96 $\mu$deg/hr are possible after empirically removing shifts due to measured changes in temperature, laser intensity, and several other experimental parameters.Comment: 4 pages, 4 figures, submitted to PR

Investigation into TAT-related predictors of aggressive behavior in the mentally retarded.

There are nuiaerous ways of conceptualizing 9 large body of roGearch. OftBri studies differ on more than one variable* This is particularly true of investigations into the possible relationship between TAT performance and overt aggressive behavior* Little con-- distent systematic research ha.\u27j been undertaken in this area. Instead of holding a number of experimental variables or dimensions constant across studies in order to fully explore the effects of a given independ.ent variable, researchers arbitrarily select experimental dimensions. Thus there are a vast variety ox distinctly different populations examined on the basis of differing oriteiia of what con-ititutes aggressive behavior. To further complicate the matter, responses\u27 to anything from one to twenty T.AT or TAT-].lVc cards have been scored by systems often unique to a given study

mutation3D:Cancer Gene Prediction Through Atomic Clustering of Coding Variants in the Structural Proteome

A new algorithm and Web server, mutation3D (http://mutation3d.org), proposes driver genes in cancer by identifying clusters of amino acid substitutions within tertiary protein structures. We demonstrate the feasibility of using a 3D clustering approach to implicate proteins in cancer based on explorations of single proteins using the mutation3D Web interface. On a large scale, we show that clustering with mutation3D is able to separate functional from nonfunctional mutations by analyzing a combination of 8,869 known inherited disease mutations and 2,004 SNPs overlaid together upon the same sets of crystal structures and homology models. Further, we present a systematic analysis of whole-genome and whole-exome cancer datasets to demonstrate that mutation3D identifies many known cancer genes as well as previously underexplored target genes. The mutation3D Web interface allows users to analyze their own mutation data in a variety of popular formats and provides seamless access to explore mutation clusters derived from over 975,000 somatic mutations reported by 6,811 cancer sequencing studies. The mutation3D Web interface is freely available with all major browsers supported

Branes in Time-Dependent Backgrounds and AdS/CFT Correspondence

We study supergravity solutions of Dp-branes in the time-dependent orbifold background. We show that worldvolume theories decouple from the bulk gravity for p less than six. Along AdS/CFT correspondence, these solutions could provide the gravity description of noncommutative field theory with time-dependent noncommutative parameter. Type II NS5-brane (M5-brane) in the presence of RR n-form for n=0,..., 4 (C field) in this time-dependent background have also been studied.Comment: 15 pages, latex file, v2: typos corrected, ref added, v3: references added, minor change

Evidence for a nuclear compartment of transcription and splicing located at chromosome domain boundaries

The nuclear topography of splicing snRNPs, mRNA transcripts and chromosome domains in various mammalian cell types are described. The visualization of splicing snRNPs, defined by the Sm antigen, and coiled bodies, revealed distinctly different distribution patterns in these cell types. Heat shock experiments confirmed that the distribution patterns also depend on physiological parameters. Using a combination of fluorescencein situ hybridization and immunodetection protocols, individual chromosome domains were visualized simultaneously with the Sm antigen or the transcript of an integrated human papilloma virus genome. Three-dimensional analysis of fluorescence-stained target regions was performed by confocal laser scanning microscopy. RNA transcripts and components of the splicing machinery were found to be generally excluded from the interior of the territories occupied by the individual chromosomes. Based on these findings we present a model for the functional compartmentalization of the cell nucleus. According to this model the space between chromosome domains, including the surface areas of these domains, defines a three-dimensional network-like compartment, termed the interchromosome domain (ICD) compartment, in which transcription and splicing of mRNA occurs

Learning effective amino acid interactions through iterative stochastic techniques

The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within coarse-grained models is the task of deducing effective interaction potentials between the amino acids. Over the years several techniques have been developed to extract potentials that are able to discriminate satisfactorily between the native and non-native folds of a pre-assigned protein sequence. In general, when these potentials are used in actual dynamical folding simulations, they lead to a drift of the native structure outside the quasi-native basin. In this study, we present and validate an approach to overcome this difficulty. By exploiting several numerical and analytical tools we set up a rigorous iterative scheme to extract potentials satisfying a pre-requisite of any viable potential: the stabilization of proteins within their native basin (less than 3-4 \AA$$ cRMS). The scheme is flexible and is demonstrated to be applicable to a variety of parametrizations of the energy function and provides, in each case, the optimal potentials.Comment: Revtex 17 pages, 10 eps figures. Proteins: Structure, Function and Genetics (in press

GEMINI 3D spectroscopy of BAL+IR+Fe II QSOs: II. IRAS 04505-2958 an explosive QSO with hypershell and a new scenario for galaxy formation and galaxy end

From a study of BAL + IR + Fe II QSOs (using deep Gemini GMOS-IFU spectroscopy) new results are presented: for IRAS 04505-2958. Specifically, we have studied in detail the out flow (OF) process and their associated structures, mainly at two large galactic scales: (i) two blobs/shells (S1, S2) at radius r = 1.1 and 2.2 kpc; and (ii) an external hypergiant shell (S3) at r = 11 kpc. In addition, the presence of two very extended hypergiant shells (S4, S5) at r = 80 kpc is discussed. From this GMOS study the following main results were obtained: (i) For the external hypergiant shell S3 the kinematics GMOS maps of the ionized gas show very similar features to those observed for the prototype of exploding external supergiant shell: in NGC 5514. (ii) The main knots K1, K2 and K3 -of this hypergiant shell S3- show a stellar population and emission line ratios associated with the presence of a starburst + OF/shocks. (iii) The internal shells S1 and S2 show structures, OF components and properties very similar to those detected in the nuclear shells of Mrk 231. (iv) The shells S1+S2 and S3 are aligned at PA = 131: i.e. suggesting that the OF process is in the blow-out phase with bipolar structure. In addition, the shells S4 and S5 (at 80-100 kpc scale) are aligned at PA = 40, i.e.: a bipolar OF perpendicular to the internal OF. Finally, the generation of UHE cosmic rays and neutrino/ dark-matter -associated with HyNe in BAL + IR + Fe II QSOs- is discussed.Comment: Submitted MNRAS, 81 pages, 25 Figure

Photoproduction of phi(1020) mesons on the proton at large momentum transfer

The cross section for $\phi$ meson photoproduction on the proton has been measured for the first time up to a four-momentum transfer -t = 4 GeV^2, using the CLAS detector at the Thomas Jefferson National Accelerator Facility. At low four-momentum transfer, the differential cross section is well described by Pomeron exchange. At large four-momentum transfer, above -t = 1.8 GeV^2, the data support a model where the Pomeron is resolved into its simplest component, two gluons, which may couple to any quark in the proton and in the $\phi$.Comment: 5 pages; 7 figure

eta-prime photoproduction on the proton for photon energies from 1.527 to 2.227 GeV

Differential cross sections for the reaction gamma p -> eta-prime p have been measured with the CLAS spectrometer and a tagged photon beam with energies from 1.527 to 2.227 GeV. The results reported here possess much greater accuracy than previous measurements. Analyses of these data indicate for the first time the coupling of the etaprime N channel to both the S_11(1535) and P_11(1710) resonances, known to couple strongly to the eta N channel in photoproduction on the proton, and the importance of j=3/2 resonances in the process.Comment: 6 pages, 3 figure