Photochemically re-bridging disulfide bonds and the discovery of a thiomaleimide mediated photodecarboxylation of C-terminal cysteines

Described in this work is a novel method for photochemically manipulating peptides and proteins via the installation of cysteine-selective photoactive tags. Thiomaleimides, generated simply by the addition of bromomaleimides to reduced disulfide bonds, undergo [2 + 2] photocycloadditions to reconnect the crosslink between the two cysteine residues. This methodology is demonstrated to enable photoactivation of a peptide by macrocyclisation, and reconnection of the heavy and light chains in an antibody fragment to form thiol stable conjugates. Finally we report on an intriguing thiomaleimide mediated photochemical decarboxylation of C-terminal cysteines, discovered during this study

Structural requirements of membrane phospholipids for M-type potassium channel activation and binding.

M-channels are voltage-gated potassium channels that regulate cell excitability. They are heterotetrameric assemblies of Kv7.2 and Kv7.3 subunits. Their opening requires the presence of the membrane phospholipid phosphatidylinositol 4,5-bisphosphate (PI(4,5)P(2)). However, the specificity of PI(4,5)P(2) as a binding and activating ligand is unknown. Here, we tested the ability of different phosphoinositides and lipid phosphates to activate or bind to M-channel proteins. Activation of functional channels was measured in membrane patches isolated from cells coexpressing Kv7.2 and Kv7.3 subunits. Channels were activated to similar extents (maximum open probability of ∼0.8 at 0 mV) by 0.1-300 μM dioctanoyl homologs of the three endogenous phosphoinositides, PI(4)P, PI(4,5)P(2), and PI(3,4,5)P(3), with sensitivity increasing with increasing numbers of phosphates. Non-acylated inositol phosphates had no effect up to 100 μM. Channels were also activated with increasing efficacy by 1-300 μM concentrations of the monoacyl monophosphates fingolimod phosphate, sphingosine 1-phosphate, and lysophosphatidic acid but not by phosphate-free fingolimod or sphingosine or by phosphate-masked phosphatidylcholine or phosphatidylglycerol. An overlay assay confirmed that a fusion protein containing the full-length C terminus of Kv7.2 could bind to a broad range of phosphoinositides and phospholipids. A mutated Kv7.2 C-terminal construct with reduced sensitivity to PI(4,5)P showed significantly less binding to most polyphosphoinositides. We concluded that M-channels bind to, and are activated by, a wide range of lipid phosphates, with a minimum requirement for an acyl chain and a phosphate headgroup. In this, they more closely resemble inwardly rectifying Kir6.2 potassium channels than the more PI(4,5)P(2)-specific Kir2 channels. Notwithstanding, the data also support the view that the main endogenous activator of M-channels is PI(4,5)P(2)

Galaxy-Mass Correlations on 10 Mpc Scales in the Deep Lens Survey

We examine the projected correlation of galaxies with mass from small scales (<few hundred kpc) where individual dark matter halos dominate, out to 15 Mpc where correlated large-scale structure dominates. We investigate these profiles as a function of galaxy luminosity and redshift. Selecting 0.8 million galaxies in the Deep Lens Survey, we use photometric redshifts and stacked weak gravitational lensing shear tomography out to radial scales of 1 degree from the centers of foreground galaxies. We detect correlated mass density from multiple halos and large-scale structure at radii larger than the virial radius, and find the first observational evidence for growth in the galaxy-mass correlation on 10 Mpc scales with decreasing redshift and fixed range of luminosity. For a fixed range of redshift, we find a scaling of projected halo mass with rest-frame luminosity similar to previous studies at lower redshift. We control systematic errors in shape measurement and photometric redshift, enforce volume completeness through absolute magnitude cuts, and explore residual sample selection effects via simulations.Comment: 13 pages, 9 figures, re-submitted to ApJ after addressing referee comment

Convicts and coolies : rethinking indentured labour in the nineteenth century

This article seeks to shift the frame of analysis within which discussions of Indian indentured migration take place. It argues that colonial discourses and practices of indenture are best understood not with regard to the common historiographical framework of whether it was 'a new system of slavery', but in the context of colonial innovations in incarceration and confinement. The article shows how Indian experiences of and knowledge about transportation overseas to penal settlements informed in important ways both their own understandings and representations of migration and the colonial practices associated with the recruitment of indentured labour. In detailing the connections between two supposedly different labour regimes, it thus brings a further layer of complexity to debates around their supposed distinctions

Conservative Constraints on Dark Matter from the Fermi-LAT Isotropic Diffuse Gamma-Ray Background Spectrum

We examine the constraints on final state radiation from Weakly Interacting Massive Particle (WIMP) dark matter candidates annihilating into various standard model final states, as imposed by the measurement of the isotropic diffuse gamma-ray background by the Large Area Telescope aboard the Fermi Gamma-Ray Space Telescope. The expected isotropic diffuse signal from dark matter annihilation has contributions from the local Milky Way (MW) as well as from extragalactic dark matter. The signal from the MW is very insensitive to the adopted dark matter profile of the halos, and dominates the signal from extragalactic halos, which is sensitive to the low mass cut-off of the halo mass function. We adopt a conservative model for both the low halo mass survival cut-off and the substructure boost factor of the Galactic and extragalactic components, and only consider the primary final state radiation. This provides robust constraints which reach the thermal production cross-section for low mass WIMPs annihilating into hadronic modes. We also reanalyze limits from HESS observations of the Galactic Ridge region using a conservative model for the dark matter halo profile. When combined with the HESS constraint, the isotropic diffuse spectrum rules out all interpretations of the PAMELA positron excess based on dark matter annihilation into two lepton final states. Annihilation into four leptons through new intermediate states, although constrained by the data, is not excluded.Comment: 11 pages, 5 figures. v3: minor revisions, matches version to appear in JCA

N-body simulations with generic non-Gaussian initial conditions I: Power Spectrum and halo mass function

We address the issue of setting up generic non-Gaussian initial conditions for N-body simulations. We consider inflationary-motivated primordial non-Gaussianity where the perturbations in the Bardeen potential are given by a dominant Gaussian part plus a non-Gaussian part specified by its bispectrum. The approach we explore here is suitable for any bispectrum, i.e. it does not have to be of the so-called separable or factorizable form. The procedure of generating a non-Gaussian field with a given bispectrum (and a given power spectrum for the Gaussian component) is not univocal, and care must be taken so that higher-order corrections do not leave a too large signature on the power spectrum. This is so far a limiting factor of our approach. We then run N-body simulations for the most popular inflationary-motivated non-Gaussian shapes. The halo mass function and the non-linear power spectrum agree with theoretical analytical approximations proposed in the literature, even if they were so far developed and tested only for a particular shape (the local one). We plan to make the simulations outputs available to the community via the non-Gaussian simulations comparison project web site http://icc.ub.edu/~liciaverde/NGSCP.html.Comment: 23 pages, 10 figure

The Void Galaxy Survey

The Void Galaxy Survey (VGS) is a multi-wavelength program to study $\sim$60 void galaxies. Each has been selected from the deepest interior regions of identified voids in the SDSS redshift survey on the basis of a unique geometric technique, with no a prior selection of intrinsic properties of the void galaxies. The project intends to study in detail the gas content, star formation history and stellar content, as well as kinematics and dynamics of void galaxies and their companions in a broad sample of void environments. It involves the HI imaging of the gas distribution in each of the VGS galaxies. Amongst its most tantalizing findings is the possible evidence for cold gas accretion in some of the most interesting objects, amongst which are a polar ring galaxy and a filamentary configuration of void galaxies. Here we shortly describe the scope of the VGS and the results of the full analysis of the pilot sample of 15 void galaxies.Comment: 9 pages, 6 figures. This is an extended version of a paper to appear in "Environment and the Formation of Galaxies: 30 years later", Proceedings of Symposium 2 of JENAM 2010, eds. I. Ferreras, A. Pasquali, ASSP, Springer. Version with highres figures at http://www.astro.rug.nl/~weygaert/vgs_jenam_weygaert.col.pd

Gains in Statistical Power From Using a Dietary Biomarker in Combination With Self-reported Intake to Strengthen the Analysis of a Diet-Disease Association: An Example From CAREDS

A major problem in detecting diet-disease associations in nutritional cohort studies is measurement error in self-reported intakes, which causes loss of statistical power. The authors propose using biomarkers correlated with dietary intake to strengthen analyses of diet-disease hypotheses and to increase statistical power. They consider combining self-reported intakes and biomarker levels using principal components or a sum of ranks and relating the combined measure to disease in conventional regression analyses. They illustrate their method in a study of the inverse association of dietary lutein plus zeaxanthin with nuclear cataracts, using serum lutein plus zeaxanthin as the biomarker, with data from the Carotenoids in Age-Related Eye Disease Study (United States, 2001–2004). This example demonstrates that the combined measure provides higher statistical significance than the dietary measure or the serum measure alone, and it potentially provides sample savings of 8%–53% over analysis with dietary intake alone and of 6%–48% over analysis with serum level alone, depending on the definition of the outcome variable and the choice of confounders entered into the regression model. The authors conclude that combining appropriate biomarkers with dietary data in a cohort can strengthen the investigation of diet-disease associations by increasing the statistical power to detect them