Dynamical Eigenfunction Decomposition of Turbulent Pipe Flow

The results of an analysis of turbulent pipe flow based on a Karhunen-Lo`eve decomposition are presented. The turbulent flow is generated by a direct numerical simulation of the Navier-Stokes equations using a spectral element algorithm at a Reynolds number Re_\tau=150. This simulation yields a set of basis functions that captures 90% of the energy after 2,453 modes. The eigenfunctions are categorised into two classes and six subclasses based on their wavenumber and coherent vorticity structure. Of the total energy, 81% is in the propagating class, characterised by constant phase speeds; the remaining energy is found in the non propagating subclasses, the shear and roll modes. The four subclasses of the propagating modes are the wall, lift, asymmetric, and ring modes. The wall modes display coherent vorticity structures near the wall, the lift modes display coherent vorticity structures that lift away from the wall, the asymmetric modes break the symmetry about the axis, and the ring modes display rings of coherent vorticity. Together, the propagating modes form a wave packet, as found from a circular normal speed locus. The energy transfer mechanism in the flow is a four step process. The process begins with energy being transferred from mean flow to the shear modes, then to the roll modes. Energy is then transfer ed from the roll modes to the wall modes, and then eventually to the lift modes. The ring and asymmetric modes act as catalysts that aid in this four step energy transfer. Physically, this mechanism shows how the energy in the flow starts at the wall and then propagates into the outer layer.Comment: 28 pages, 20 figures. Updated with reviewer's comments / suggestion

Crystallization of the FAD-independent acetolactate synthase of Klebsiella pneumoniae

Leucine and valine are formed in a common pathway from pyruvate in which the first intermediate is 2-acetolactate. In some bacteria, this compound also has a catabolic fate as the starting point for the butanediol fermentation. The enzyme (EC 4.1.3.18) that forms 2-acetolactate is known as either acetohydroxyacid synthase (AHAS) or acetolactate synthase (ALS), with the latter name preferred for the catabolic enzyme. A significant difference between AHAS and ALS is that the former requires FAD for catalytic activity, although the reason for this requirement is not well understood. Both enzymes require the cofactor thiamine diphosphate. Here, the crystallization and preliminary X-ray diffraction analysis of the Klebsiella pneumoniae ALS is reported. Data to 2.6 Angstrom resolution have been collected at 100 K using a rotating-anode generator and an R-AXIS IV++ detector. Crystals have unit-cell parameters a = 137.4, b = 143.9, c = 134.4 Angstrom, alpha = 90, beta = 108.4, gamma = 90degrees and belong to space group C2. Preliminary analysis indicates that there are four monomers located in each asymmetric unit

Crystallization of Arabidopsis thaliana acetohydroxyacid synthase in complex with the sulfonylurea herbicide chlorimuron ethyl

Acetohydroxyacid synthase (AHAS; EC 2.2.1.6) catalyses the formation of 2-acetolactate and 2-aceto-2-hydroxybutyrate as the first step in the biosynthesis of the branched-chain amino acids valine, leucine and isoleucine. The enzyme is inhibited by a wide range of substituted sulfonylureas and imidazolinones and many of these compounds are used as commercial herbicides. Here, the crystallization and preliminary X-ray diffraction analysis of the catalytic subunit of Arabidopsis thaliana AHAS in complex with the sulfonylurea herbicide chlorimuron ethyl are reported. This is the first report of the structure of any plant protein in complex with a commercial herbicide. Crystals diffract to 3.0 Angstrom resolution, have unit-cell parameters a = b = 179.92, c = 185.82 Angstrom and belong to space group P6(4)22. Preliminary analysis indicates that there is one monomer in the asymmetric unit and that these are arranged as pairs of dimers in the crystal. The dimers form a very open hexagonal lattice, with a high solvent content of 81%

Cord blood Lin(-)CD45(-) embryonic-like stem cells are a heterogeneous population that lack self-renewal capacity.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Human umbilical cord blood (hUCB) has been proposed to contain not only haematopoietic stem cells, but also a rare pluripotent embryonic-like stem cell (ELSc) population that is negative for hematopoietic markers (Lin(-)CD45(-)) and expresses markers typical of pluripotent cells. The aim of this work was to isolate, characterise and expand this ELSc fraction from hUCB, as it may provide a valuable cell source for regenerative medicine applications. We found that we could indeed isolate a Lin(-)CD45(-) population of small cells (3-10 µm diameter) with a high nucleus to cytoplasm ratio that expressed the stem cell markers CD34 and CXCR4. However, in contrast to some previous reports, this fraction was not positive for CD133. Furthermore, although these cells expressed transcripts typical of pluripotent cells, such as SOX2, OCT3/4, and NANOG, they were not able to proliferate in any of the culture media known to support stem cell growth that we tested. Further analysis of the Lin(-)CD45(-) population by flow cytometry showed the presence of a Lin(-)CD45(-)Nestin(+) population that were also positive for CD34 (20%) but negative for CXCR4. These data suggest that the Lin(-)CD45(-) stem cell fraction present in the cord blood represents a small heterogeneous population with phenotypic characteristics of stem cells, including a Lin(-)CD45(-)Nestin(+) population not previously described. This study also suggests that heterogeneity within the Lin(-)CD45(-) cell fraction is the likely explanation for differences in the hUCB cell populations described by different groups that were isolated using different methods. These populations have been widely called "embryonic-like stem cell" on the basis of their phenotypical similarity to embryonic stem cells. However, the fact they do not seem to be able to self-renew casts some doubt on their identity, and warns against defining them as "embryonic-like stem cell" at this stage.Anthony Nolan and the Great Ormond Street Hospital Charity for financial support. Cesar Alvarez-Gonzalez is a fellowship from Consejo Nacional de Ciencia y Tecnologia (CONACyT) and Instituto Jaliscience de la Juventud (IJJ); Mexico

Facile crystallization of Escherichia coli ketol-acid reductoisomerase

Ketol-acid reductoisomerase (EC 1.1.1.86) catalyses the second reaction in the biosynthesis of branched-chain amino acids. The reaction involves an Mg2+-dependent alkyl migration followed by an NADPH-dependent reduction of the 2-keto group. Here, the crystallization of the Escherichia coli enzyme is reported. A form with a C-terminal hexahistidine tag could be crystallized under 18 different conditions in the absence of NADPH or Mg2+ and a further six crystallization conditions were identified with one or both ligands. With the hexahistidine tag on the N-terminus, 20 crystallization conditions were found, some of which required the presence of NADPH, NADP(+), Mg2+ or a combination of ligands. Finally, the selenomethionine-substituted enzyme with the N-terminal tag crystallized under 15 conditions. Thus, the enzyme is remarkably easy to crystallize. Most of the crystals diffract poorly but several data sets were collected at better than 3.2 Angstrom resolution; attempts to phase them are currently in progress

How to Build a World: Stereoscopes, Tourism, and Land in Zion National Park

This thesis fundamentally questions how representations of the environment and land impact how we relate to and live in it. By examining a set of 1925 stereoscope images of Zion National Park, it considers how use-based perceptions of place – structured by the entertainment of tourism and mass media – become part of the mundane practices of consumption. By revealing how these capitalist-colonial relationships to the land have been built through time, an analysis of these stereoscope slides reveals that these stories are anything but natural in hopes of making room for other stories to be built instead. The second part is an installation project extrapolating this research into a multimedia virtual reality and illustration piece that takes on the viewpoint of a fictional Martian travel agency. This section ultimately looks to reveal how use-based relationships to our environments have been packaged and sold throughout time, embodied by a comparison between the stereoscope and 21st Century Virtual Reality. Overall, by looking at how these capital-colonial narratives around land have been built, this thesis looks to propose one method of many through which to re-frame environmental issues as able to be addressed

Expression levels of MHC class I molecules are inversely correlated with promiscuity of peptide binding.

Highly polymorphic major histocompatibility complex (MHC) molecules are at the heart of adaptive immune responses, playing crucial roles in many kinds of disease and in vaccination. We report that breadth of peptide presentation and level of cell surface expression of class I molecules are inversely correlated in both chickens and humans. This relationship correlates with protective responses against infectious pathogens including Marek's disease virus leading to lethal tumours in chickens and human immunodeficiency virus infection progressing to AIDS in humans. We propose that differences in peptide binding repertoire define two groups of MHC class I molecules strategically evolved as generalists and specialists for different modes of pathogen resistance. We suggest that differences in cell surface expression level ensure the development of optimal peripheral T cell responses. The inverse relationship of peptide repertoire and expression is evidently a fundamental property of MHC molecules, with ramifications extending beyond immunology and medicine to evolutionary biology and conservation

Energetic Modes in Turbulent Pipe Flow From Resolvent Analysis

We describe a method to investigate the mode shapes in turbulent pipe flow at a given wavenumber pair that are most responsive to harmonic forcing in the sense that the they correspond to the largest singular value in a Schmidt decomposition of the linear Navier-Stokes operator using the turbulent mean profile as the base flow. The ideas follow logically from the work of Sharma & McKeon (2009), who considered a similar approach for laminar pipe flow