A Rapid Cloning Method Employing Orthogonal End Protection

We describe a novel in vitro cloning strategy that combines standard tools in molecular biology with a basic protecting group concept to create a versatile framework for the rapid and seamless assembly of modular DNA building blocks into functional open reading frames. Analogous to chemical synthesis strategies, our assembly design yields idempotent composite synthons amenable to iterative and recursive split-and-pool reaction cycles. As an example, we illustrate the simplicity, versatility and efficiency of the approach by constructing an open reading frame composed of tandem arrays of a human fibronectin type III (FNIII) domain and the von Willebrand Factor A2 domain (VWFA2), as well as chimeric (FNIII)n-VWFA2-(FNIII)n constructs. Although we primarily designed this strategy to accelerate assembly of repetitive constructs for single-molecule force spectroscopy, we anticipate that this approach is equally applicable to the reconstitution and modification of complex modular sequences including structural and functional analysis of multi-domain proteins, synthetic biology or the modular construction of episomal vectors

Between self, family and society:Syrian male perspectives on intimate partner relationship negotiation in The Netherlands

This paper seeks to disentangle gendered perspectives on intimate partner relationships after forced migration. It targets lived experiences of young Syrian men in the Netherlands (18-35 years old) and explores the extent to which attitudes, traditions and behaviours in relation to gender- and partner roles are contested, re-produced or transformed in the context of societal change. The study employs a qualitative life course perspective, using interdisciplinary social theory to flesh out the interplay of relevant micro- and macro processes in which intimate partner relationship attitudes, traditions and behaviours are defined. We draw from narrative interviews, themed around core life course principles such as agency, linked lives, and time and place, and use narrative analyses. The paper offers two main contributions. First, we demonstrate that intimate partner relationship negotiation after forced migration is a nuanced, complex and ambiguous process, conditioned by intersections of self, family and society, personal biographies and culturally defined agentic behavior. Hence, the paper stimulates incorporating interdisciplinary social theory in migration research to more adequately capture intercultural experiences of migrants. Second, by scrutinising divergent experiences and strategies, we challenge one-sided, static accounts of immigrant men, and emphasise respondents are active agents that negotiate their contextual positions in the Netherlands as intimate partners, husband and fathers

Crystal structure of quinohemoprotein alcohol dehydrogenase from Comamonas testosteroni - Structural basis for substrate oxidation and electron transfer

Quinoprotein alcohol dehydrogenases are redox enzymes that participate in distinctive catabolic pathways that enable bacteria to grow on various alcohols as the sole source of carbon and energy. The x-ray structure of the quinohemoprotein alcohol dehydrogenase from Comamonas testosteroni has been determined at 1.44 Angstrom resolution. It comprises two domains. The N-terminal domain has a beta-propeller fold and binds one pyrrolo-quinoliue quinone cofactor and one calcium ion in the active site. A tetrahydrofuran-2-carboxylic acid molecule is present in the substrate-binding cleft. The position of this oxidation product provides valuable information on the amino acid residues involved in the reaction mechanism and their function. The C-terminal domain is an a-helical type I cytochrome c with His(608) and Met(647) as heme-iron ligands. This is the first reported structure of an electron transfer system between a quinoprotein alcohol dehydrogenase and cytochrome c. The shortest distance between pyrroloquinoline quinone and heme c is 12.9 Angstrom, one of the longest physiological edge-to-edge distances yet determined between two redox centers. A highly unusual disulfide bond between two adjacent cysteines bridges the redox centers. It appears essential for electron transfer. A water channel delineates a possible pathway for proton transfer from the active site to the solvent.</p

The Dependence of Galaxy Shape on Luminosity and Surface Brightness Profile

For a sample of 96,951 galaxies from the Sloan Digital Sky Survey Data Release 3, we study the distribution of apparent axis ratios as a function of r-band absolute magnitude and surface brightness profile type. We use the parameter fracDeV to quantify the profile type (fracDeV = 1 for a de Vaucouleurs profile; fracDeV = 0 for an exponential profile). When the apparent axis ratio q_{am} is estimated from the moments of the light distribution, the roundest galaxies are very bright (M_r \sim -23) de Vaucouleurs galaxies and the flattest are modestly bright (M_r \sim -18) exponential galaxies. When the apparent axis ratio q_{25} is estimated from the axis ratio of the 25 mag/arcsec^2 isophote, we find that de Vaucouleurs galaxies are flatter than exponential galaxies of the same absolute magnitude. For a given surface brightness profile type, very bright galaxies are rounder, on average, than fainter galaxies. We deconvolve the distributions of apparent axis ratios to find the distribution of the intrinsic short-to-long axis ratio gamma, assuming constant triaxiality T. For all profile types and luminosities, the distribution of apparent axis ratios is inconsistent with a population of oblate spheroids, but is usually consistent with a population of prolate spheroids. Bright galaxies with a de Vaucouleurs profile (M_r < -21.84, fracDeV > 0.9) have a distribution of q_{am} that is consistent with triaxiality in the range 0.4 < T < 0.8, with mean intrinsic axis ratio 0.66 < gamma < 0.69. The fainter de Vaucouleurs galaxies are best fit with prolate spheroids (T = 1) with mean axis ratio gamma = 0.51.Comment: 32 pages, 12 figures, to appear in Ap

The Ellipticity of the Disks of Spiral Galaxies

The disks of spiral galaxies are generally elliptical rather than circular. The distribution of ellipticities can be fit with a log-normal distribution. For a sample of 12,764 galaxies from the Sloan Digital Sky Survey Data Release 1 (SDSS DR1), the distribution of apparent axis ratios in the i band is best fit by a log-normal distribution of intrinsic ellipticities with ln epsilon = -1.85 +/- 0.89. For a sample of nearly face-on spiral galaxies, analyzed by Andersen and Bershady using both photometric and spectroscopic data, the best fitting distribution of ellipticities has ln epsilon = -2.29 +/- 1.04. Given the small size of the Andersen-Bershady sample, the two distribution are not necessarily inconsistent. If the ellipticity of the potential were equal to that of the light distribution of the SDSS DR1 galaxies, it would produce 1.0 magnitudes of scatter in the Tully-Fisher relation, greater than is observed. The Andersen-Bershady results, however, are consistent with a scatter as small as 0.25 magnitudes in the Tully-Fisher relation.Comment: 19 pages, 5 figures; ApJ, accepte