Interaction of the Streptomyces Wbl protein WhiD with the principal sigma factor σHrdB depends on the WhiD [4Fe-4S] cluster

The bacterial protein WhiD belongs to the Wbl family of iron–sulfur [Fe-S] proteins present only in the actinomycetes. In Streptomyces coelicolor, it is required for the late stages of sporulation, but precisely how it functions is unknown. Here, we report results from in vitro and in vivo experiments with WhiD from Streptomyces venezuelae (SvWhiD), which differs from S. coelicolor WhiD (ScWhiD) only at the C terminus. We observed that, like ScWhiD and other Wbl proteins, SvWhiD binds a [4Fe-4S] cluster that is moderately sensitive to O2 and highly sensitive to nitric oxide (NO). However, although all previous studies have reported that Wbl proteins are monomers, we found that SvWhiD exists in a monomer–dimer equilibrium associated with its unusual C-terminal extension. Several Wbl proteins of Mycobacterium tuberculosis are known to interact with its principal sigma factor SigA. Using bacterial two-hybrid, gel filtration, and MS analyses, we demonstrate that SvWhiD interacts with domain 4 of the principal sigma factor of Streptomyces, σHrdB (σHrdB4). Using MS, we determined the dissociation constant (Kd) for the SvWhiD–σHrdB4 complex as ~0.7 μM, consistent with a relatively tight binding interaction. We found that complex formation was cluster dependent and that a reaction with NO, which was complete at 8–10 NO molecules per cluster, resulted in dissociation into the separate proteins. The SvWhiD [4Fe-4S] cluster was significantly less sensitive to reaction with O2 and NO when SvWhiD was bound to σHrdB4, consistent with protection of the cluster in the complex

Importance of charge capture in interphase regions during readout of charge-coupled devices

The current understanding of charge transfer dynamics in charge-coupled devices (CCDs) is that charge is moved so quickly from one phase to the next in a clocking sequence and with a density so low that trapping of charge in the interphase regions is negligible. However, simulation capabilities developed at the Centre for Electronic Imaging, which includes direct input of electron density simulations, have made it possible to investigate this assumption further. As part of the radiation testing campaign of the Euclid CCD273 devices, data have been obtained using the trap pumping method, a method that can be used to identify and characterize single defects within CCDs. Combining these data with simulations, we find that trapping during the transfer of charge among phases is indeed necessary to explain the results of the data analysis. This result could influence not only trap pumping theory and how trap pumping should be performed but also how a radiation-damaged CCD is readout in the most optimal way

Elastic Model Transitions: a Hybrid Approach Utilizing Quadratic Inequality Constrained Least Squares (LSQI) and Direct Shape Mapping (DSM)

A method for transitioning linear time invariant (LTI) models in time varying simulation is proposed that utilizes both quadratically constrained least squares (LSQI) and Direct Shape Mapping (DSM) algorithms to determine physical displacements. This approach is applicable to the simulation of the elastic behavior of launch vehicles and other structures that utilize multiple LTI finite element model (FEM) derived mode sets that are propagated throughout time. The time invariant nature of the elastic data for discrete segments of the launch vehicle trajectory presents a problem of how to properly transition between models while preserving motion across the transition. In addition, energy may vary between flex models when using a truncated mode set. The LSQI-DSM algorithm can accommodate significant changes in energy between FEM models and carries elastic motion across FEM model transitions. Compared with previous approaches, the LSQI-DSM algorithm shows improvements ranging from a significant reduction to a complete removal of transients across FEM model transitions as well as maintaining elastic motion from the prior state

Computed tomography measures of nutrition in patients with end-stage liver disease provide a novel approach to characterize deficits

Aim Patients with cirrhosis and end-stage liver disease (ESLD) develop severe nutrition deficits that impact on morbidity and mortality. Laboratory measures of nutrition fail to fully assess clinical deficits in muscle mass and fat stores. This study employs computed tomography imaging to assess muscle mass and subcutaneous and visceral fat stores in patients with ESLD. Methods This 1:1 case-control study design compares ESLD patients with healthy controls. Study patients were selected from a database of ESLD patients using a stratified method to assure a representative sample based on age, body mass index (BMI), gender, and model for end-stage liver disease score (MELD). Control patients were trauma patients with a low injury severity score (<10) who had a CT scan during evaluation. Cases and controls were matched for age +/- 5 years, gender, and BMI +/- 2. Results There were 90 subjects and 90 controls. ESLD patients had lower albumin levels (p<0.001), but similar total protein levels (p=0.72). ESLD patients had a deficit in muscle mass (-19%, p<0.001) and visceral fat (-13%, p<0.001), but similar subcutaneous fat (-1%, p=0.35). ESLD patients at highest risk for sarcopenia included those over age 60, BMI< 25.0, and female gender. We found degree of sarcopenia to be independent of MELD score. Conclusions These results support previous research demonstrating substantial nutrition deficits in ESLD patients that are not adequately measured by laboratory testing. Patients with ESLD have significant deficits of muscle and visceral fat stores, but a similar amount of subcutaneous fat

Architectural patterning in the Purepecha heartland: an intrasite settlement study at the urban center of Sacapu Angamuco, Michoacán, México

2012 Spring.Includes bibliographical references.The overall goal of this thesis is to examine the architectural patterns of Sacapu Angamuco (Angamuco), a recently discovered Early-Middle Postclassic (A.D. 900-1350) urban settlement in the Lake Pátzcuaro Basin (LPB), Michoacán, Mexico that is located on an ancient lava flow, or malpais, and was extensively modified by prehispanic inhabitants to construct thousands of structures such as platforms, mounds, plazas, passages, stairs, and temples. Central to this thesis is how prehispanic residents of Angamuco organized their buildings and social space. The study of architectural remains is one critical component of ancient urbanism which is fundamental to Mesoamerican societies. Angamuco provides a rich opportunity to understand urbanism in the LPB. Understanding the spatial context of buildings and how they are grouped in functionally discernable ways is crucial to interpreting the internal function(s) of the settlement, as well as contributing to regional settlement pattern analyses. This thesis incorporates intensive survey using GPS, GIS, and remote sensing to document architecture and analyze the spatial patterns of architecture at Angamuco using data from the 2010 field season. An overview of relevant definitions and approaches to Mesoamerican urban settlement studies and the study of spatial patterning and classification of architecture is presented. A description of the physical setting of the LPB and Angamuco, the cultural-historical background of the region, and background information on previous archaeological work addressing urbanism, settlement patterns, and architecture in the LPB region is discussed. The research methodology used to collect data on Angamuco's architecture and settlement patterns is reviewed. The core of this work concerns an analysis of Angamuco architecture, beginning with description of the form and function of individual architectural features and analysis of architectural group form and patterning in the study area. Finally, the analysis is synthesized with the questions guiding this research, as well as current knowledge about Postclassic urbanism in the LPB and beyond. Ultimately, it is hoped that work at Angamuco will improve understanding of Postclassic LPB architecture, settlement patterns, and the role of cities before and during the development of the Tarascan Empire

Parametric Correlations for Generic Scramjet Combustors with Ramp-Type Injectors

Development of an efficient scramjet combustor requires the use of computational models due to the cost of full-scale physical testing in the speed regime of Mach 10 through Mach 18. This study focuses upon the database generated by one such computational model, SHIP3D, which describes a generic scramjet combustor using ramp-type file! injectors. Three generalized parametric equations have been developed from this database, which describe the fuel-air mixing efficiency within the scramjet combustor as a function of normalized-axial combustor distance, ramp injector-region lift coefficient, and stoichiometry. It is shown that one of the three equations nearly models the trends as accurate as a first­ order least-squares regression of the computational data

Playing games to improve conceptual understanding and cooperation in social dilemmas.

People make decisions every day that have significant impact on others. The current experiment investigates the learning and decision-making processes involved when small groups confront a complex social dilemma under different learning conditions designed to imitate common educational interventions used in classrooms and non-laboratory settings. Participants (N=96) were randomly assigned to one of three conditions. In the Explore-First condition (n=32), participants played one round of a simulated social dilemma board game before receiving a lesson on social dilemmas, then played a second round. In the Lesson-First condition (n=32), participants received the lesson before playing the game. In the Contrast condition (n=32), participants received the lesson without playing the board game. Participants in the Explore-First condition performed significantly better on a quiz assessing their conceptual understanding of social dilemmas and transfer to new dilemmas. Individuals in the Explore-First condition also found the lesson more interesting, and generally showed greater acceptance of public policies intended to improve ecological sustainability. Educational interventions to improve cooperation in social dilemmas may benefit from an initial exploratory phase, where individuals experience critical features of the problem before being taught about them

Chapter 11: Genome-Wide Association Studies

Genome-wide association studies (GWAS) have evolved over the last ten years into a powerful tool for investigating the genetic architecture of human disease. In this work, we review the key concepts underlying GWAS, including the architecture of common diseases, the structure of common human genetic variation, technologies for capturing genetic information, study designs, and the statistical methods used for data analysis. We also look forward to the future beyond GWAS

Comparison of angiogenesis-related factor expression in primary tumor cultures under normal and hypoxic growth conditions

<p>Abstract</p> <p>Background</p> <p>A localized hypoxic environment occurs during tumor growth necessitating an angiogenic response or tumor necrosis results. Novel cancer treatment strategies take advantage of tumor-induced vascularisation by combining standard chemotherapeutic agents with angiogenesis-inhibiting agents. This has extended the progression-free interval and prolonged survival in patients with various types of cancer. We postulated that the expression levels of angiogenesis-related proteins from various primary tumor cultures would be greater under hypoxic conditions than under normoxia.</p> <p>Methods</p> <p>Fifty cell sources, including both immortalized cell lines and primary carcinoma cells, were incubated under normoxic conditions for 48 hours. Then, cells were either transferred to a hypoxic environment (1% O₂) or maintained at normoxic conditions for an additional 48 hours. Cell culture media from both conditions was collected and analyzed via an ELISA-based assay to determine expression levels of 11 angiogenesis-related factors: VEGF, PDGF-AA, PDGF-AA/BB, IL-8, bFGF/FGF-2, EGF, IP-10/CXCL10, Flt-3 ligand, TGF-β1, TGF-β2, and TGF-β3.</p> <p>Results</p> <p>A linear correlation between normoxic and hypoxic growth conditions exists for expression levels of eight of eleven angiogenesis-related proteins tested including: VEGF, IL-8, PDGF-AA, PDGF-AA/BB, TGF-β1, TGF-β2, EGF, and IP-10. For VEGF, the target of current therapies, this correlation between hypoxia and higher cytokine levels was greater in primary breast and lung carcinoma cells than in ovarian carcinoma cells or tumor cell lines. Of interest, patient cell isolates differed in the precise pattern of elevated cytokines.</p> <p>Conclusion</p> <p>As linear correlations exist between expression levels of angiogenic factors under normoxic and hypoxic conditions <it>in vitro</it>, we propose that explanted primary cells may be used to probe the <it>in vivo </it>hypoxic environment. Furthermore, differential expression levels for each sample across all proteins examined suggests it may be possible to build a predictor for angiogenesis-related anticancer agents, as each sample has a unique expression profile. Further studies should be performed to correlate <it>in vitro </it>protein expression levels of angiogenesis-related factors with <it>in vivo </it>patient response.</p