Rapid creation of BAC-based human artificial chromosome vectors by transposition with synthetic alpha-satellite arrays

Efficient construction of BAC-based human artificial chromosomes (HACs) requires optimization of each key functional unit as well as development of techniques for the rapid and reliable manipulation of high-molecular weight BAC vectors. Here, we have created synthetic chromosome 17-derived alpha-satellite arrays, based on the 16-monomer repeat length typical of natural D17Z1 arrays, in which the consensus CENP-B box elements are either completely absent (0/16 monomers) or increased in density (16/16 monomers) compared to D17Z1 alpha-satellite (5/16 monomers). Using these vectors, we show that the presence of CENP-B box elements is a requirement for efficient de novo centromere formation and that increasing the density of CENP-B box elements may enhance the efficiency of de novo centromere formation. Furthermore, we have developed a novel, high-throughput methodology that permits the rapid conversion of any genomic BAC target into a HAC vector by transposon-mediated modification with synthetic alpha-satellite arrays and other key functional units. Taken together, these approaches offer the potential to significantly advance the utility of BAC-based HACs for functional annotation of the genome and for applications in gene transfer

Coal Power Development

For the past several years Alstom Power Inc. (Alstom), a leading world-wide power system manufacturer and supplier, has been in the initial stages of developing an entirely new, ultra-clean, low cost, high efficiency power plant for the global power market. This new power plant concept is based on a hybrid combustion-gasification process utilizing high temperature chemical and thermal looping technology The process consists of the oxidation, reduction, carbonation, and calcination of calcium-based compounds, which chemically react with coal, biomass, or opportunity fuels in two chemical loops and one thermal loop. The chemical and thermal looping technology can be alternatively configured as (i) a combustion-based steam power plant with CO{sub 2} capture, (ii) a hybrid combustion-gasification process producing a syngas for gas turbines or fuel cells, or (iii) an integrated hybrid combustion-gasification process producing hydrogen for gas turbines, fuel cells or other hydrogen based applications while also producing a separate stream of CO{sub 2} for use or sequestration. In its most advanced configuration, this new concept offers the promise to become the technology link from today's Rankine cycle steam power plants to tomorrow's advanced energy plants. The objective of this work is to develop and verify the high temperature chemical and thermal looping process concept at a small-scale pilot facility in order to enable AL to design, construct and demonstrate a pre-commercial, prototype version of this advanced system. In support of this objective, Alstom and DOE started a multi-year program, under this contract. Before the contract started, in a preliminary phase (Phase 0) Alstom funded and built the required small-scale pilot facility (Process Development Unit, PDU) at its Power Plant Laboratories in Windsor, Connecticut. Construction was completed in calendar year 2003. The objective for Phase I was to develop the indirect combustion loop with CO{sub 2} separation, and also syngas production from coal with the calcium sulfide (CaS)/calcium sulfate (CaSO{sub 4}) loop utilizing the PDU facility. The results of Phase I were reported in Reference 1, 'Hybrid Combustion-Gasification Chemical Looping Coal Power Development Technology Development Phase I Report' The objective for Phase II was to develop the carbonate loop--lime (CaO)/calcium carbonate (CaCO{sub 3}) loop, integrate it with the gasification loop from Phase I, and ultimately demonstrate the feasibility of hydrogen production from the combined loops. The results of this program were reported in Reference 3, 'Hybrid Combustion-Gasification Chemical Looping Coal Power Development Technology Development Phase II Report'. The objective of Phase III is to operate the pilot plant to obtain enough engineering information to design a prototype of the commercial Chemical Looping concept. The activities include modifications to the Phase II Chemical Looping PDU, solids transportation studies, control and instrumentation studies and additional cold flow modeling. The deliverable is a report making recommendations for preliminary design guidelines for the prototype plant, results from the pilot plant testing and an update of the commercial plant economic estimates

A Conceptual Model of Vegetation-hydrogeomorphology Interactions Within River Corridors

This is the peer reviewed version of the following article: M. GURNELL, D. CORENBLITc, D. GARCÍA DE JALÓN, M. GONZÁLEZ DEL TÁNAGO, R. C. GRABOWSKI, M. T. O’HARE, M. SZEWCZYK (2015) A conceptual model of vegetationhydrogeomorphology interactions within river corridors. River Research and Applications (early view), which has been published in final form at 10.1002/rra.2928. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.European Union. Grant Number: no. 28265

Multitaxonomic Diversity Patterns along a Desert Riparian–Upland Gradient

Riparian areas are noted for their high biodiversity, but this has rarely been tested across a wide range of taxonomic groups. We set out to describe species richness, species abundance, and community similarity patterns for 11 taxonomic groups (forbs & grasses, shrubs, trees, solpugids, spiders, scarab beetles, butterflies, lizards, birds, rodents, and mammalian carnivores) individually and for all groups combined along a riparian–upland gradient in semiarid southeastern Arizona, USA. Additionally, we assessed whether biological characteristics could explain variation in diversity along the gradient using five traits (trophic level, body size, life span, thermoregulatory mechanism, and taxonomic affiliation). At the level of individual groups diversity patterns varied along the gradient, with some having greater richness and/or abundance in riparian zones whereas others were more diverse and/or abundant in upland zones. Across all taxa combined, riparian zones contained significantly more species than the uplands. Community similarity between riparian and upland zones was low, and beta diversity was significantly greater than expected for most taxonomic groups, though biological traits explained little variance in diversity along the gradient. These results indicate heterogeneity amongst taxa in how they respond to the factors that structure ecological communities in riparian landscapes. Nevertheless, across taxonomic groups the overall pattern is one of greater species richness and abundance in riparian zones, coupled with a distinct suite of species

Chronic Muscle Weakness and Mitochondrial Dysfunction in the Absence of Sustained Atrophy in a Preclinical Sepsis Model

Chronic critical illness is a global clinical issue affecting millions of sepsis survivors annually. Survivors report chronic skeletal muscle weakness and development of new functional limitations that persist for years. To delineate mechanisms of sepsis-induced chronic weakness, we first surpassed a critical barrier by establishing a murine model of sepsis with ICU-like interventions that allows for the study of survivors. We show that sepsis survivors have profound weakness for at least 1 month, even after recovery of muscle mass. Abnormal mitochondrial ultrastructure, impaired respiration and electron transport chain activities, and persistent protein oxidative damage were evident in the muscle of survivors. Our data suggest that sustained mitochondrial dysfunction, rather than atrophy alone, underlies chronic sepsis-induced muscle weakness. This study emphasizes that conventional efforts that aim to recover muscle quantity will likely remain ineffective for regaining strength and improving quality of life after sepsis until deficiencies in muscle quality are addressed

The role of river morphodynamic disturbance and groundwater hydrology as driving factors of riparian landscape patterns in mediterranean rivers

Original ResearchFluvial disturbances, especially floods and droughts, are the main drivers of the successional patterns of riparian vegetation. Those disturbances control the riparian landscape dynamics through the direct interaction between flow and vegetation. The main aim of this work is to investigate the specific paths by which fluvial disturbances, distributed by its components of groundwater hydrology (grndh) and morphodynamic disturbance (mrphd), drive riparian landscape patterns as characterized by the location (position in the river corridor) and shape (physical form of the patch) of vegetation patches in Mediterranean rivers. Specifically, this work assesses how the different components of fluvial disturbances affect these features in general and particularly in each succession phase of riparian vegetation. grndh and mrphd were defined by time and intensity weighted indexes calculated, respectively, from the mean annual water table elevations and the annual maximum instantaneous discharge shear stresses of the previous decade. The interactions between riparian landscape features and fluvial disturbances were assessed by confirmatory factor analysis using structural equation modeling. Two hypothetical models for patch location and shape were conceptualized and tested against empirical data collected from 220 patches at four different study sites. Both models were successfully fitted, meaning that they adequately depicted the relationships between the variables. Furthermore, the models achieved a good adjustment for the observed data, based on the evaluation of several approximate fit indexes. The patch location model explained approximately 80% of the patch location variability, demonstrating that the location of the riparian patches is primarily driven by grndh, while the mrphd had very little effect on this feature. In a multigroup analysis regarding the succession phases of riparian vegetation, the fitted model explained more than 68% of the variance of the data, confirming the results of the general model. The patch shape model explained nearly 13% of the patch shape variability, in which the disturbances came to have less influence on driving this feature. However, grndh continues to be the primary driver of riparian vegetation between the two disturbance factors, despite the proportional increase of the mrphd effect to approximately a third of the grndh effectinfo:eu-repo/semantics/publishedVersio

Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis

The morphology of roots and root systems influences the efficiency by which plants acquire nutrients and water, anchor themselves and provide stability to the surrounding soil. Plant genotype and the biotic and abiotic environment significantly influence root morphology, growth and ultimately crop yield. The challenge for researchers interested in phenotyping root systems is, therefore, not just to measure roots and link their phenotype to the plant genotype, but also to understand how the growth of roots is influenced by their environment. This review discusses progress in quantifying root system parameters (e.g. in terms of size, shape and dynamics) using imaging and image analysis technologies and also discusses their potential for providing a better understanding of root:soil interactions. Significant progress has been made in image acquisition techniques, however trade-offs exist between sample throughput, sample size, image resolution and information gained. All of these factors impact on downstream image analysis processes. While there have been significant advances in computation power, limitations still exist in statistical processes involved in image analysis. Utilizing and combining different imaging systems, integrating measurements and image analysis where possible, and amalgamating data will allow researchers to gain a better understanding of root:soil interactions

Dispersal of forest birds and trees along the Uruguay River in southern South America

The Uruguay River starts in Serra do Mar in Brazil, runs through the Paranense forest, and flows southward through grassland and savannas. It has a continuous gallery forest of 750 km from the southern border of the Paranense forest to the river mouth. The gallery forest extends for 100 km more along the Río de la Plata. 125 (68.7%) of the 182 species of forest birds recorded in the southern Paranense forest penetrate into the gallery forest of the Uruguay River and only 13 (7.1%) reach the end of the gallery forest (Punta Lara). The number of bird species is inversely correlated (r2 = 0.942) with distance and the slope of the regression is 58.10. This means a decline in diversity with 32% of species lost per unit distance. A hundred and eighty forest tree species were recorded in the southern Paranense forest, of which 113 (62.8%) penetrate into the gallery forest of the Uruguay River, and 28 (15.6%) reach Punta Lara. The number of tree species is inversely correlated (r2 = 0.976) with distance and the slope of the regression is -45.62. This means a decline in diversity with 25% of species lost per unit distance. The Uruguay River enables the dispersal of many species of forest birds and trees from the rain forest, but species richness tends to decrease with increased distance from the source area. A clear association pattern was found for birds between size, diet, habitat use and distance reached into the gallery forest. Species of smaller body size, granivores, insectivores and those that use both the interior and exterior parts of the gallery forest advanced noticeably further along the river than larger species, carnivores, nectarivores or frugivores, and those that frequent only a part of the forest. Similarly, a clear association between dispersal mechanism, water dependence and distance reached into the gallery forest was found for trees. Species with vegetative reproduction, zoochorous species and riparian species advanced markedly longer distances along the river than, anemochorous species and non-riparian species.Fil: Nores, Manuel Alberto. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Zoología Aplicada; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Cerana, María Micaela. Universidad Nacional de Córdoba; ArgentinaFil: Monserrat, Diego Andrés. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Zoología Aplicada; Argentin

Six decades of changes in the riparian corridor of a Mediterranean river: A synthetic analysis based on historical data sources

Riparian corridors in semi-arid Mediterranean environments are ecosystems of high biodiversity and complexity. However, they are threatened because of high levels of human intervention. River damming and related flow manipulation is considered as one of the most prominent human impacts on riparian corridors. This study combines historical time series information on river flows and their human manipulation, historical aerial images depicting changes in riparian land cover and ground observations of the species - age composition and morphology of the riparian corridor of a Mediterranean river (the Mijares River, Eastern Spain) over the last 60years. In this sense, we explored how to integrate information from a wide variety of data sources, and we extracted a variety of indices and undertook analyses that identified and summarized spatio-temporal changes in riparian structure and in the driving flow processes. Results revealed an increase in the cover and density of woody vegetation and a decrease in bare sediment areas (essential for recruitment of riparian pioneer species), with a synchronous reduction in the complexity of the riparian corridor of the middle reaches of the Mijares River. These vegetation changes have accompanied a decrease in the magnitude and variability of river flows over the last six decades, with higher severity since dam closure. This study illustrates the effectiveness of combining disparate historical data sources and the effectiveness of processing these sources to extract informative metrics that can improve the understanding and management of riparian systems. © 2012 John Wiley & Sons, Ltd.The authors are grateful to Paula De Lamo (who worked in an early version of this study), Carlos Gonzalez-Hidalgo (who gave us access to the MOPREDAS database) and Alicia Garcia-Arias and Oscar Belmar (for their support in the calculation of confusion matrices and in the flow regime analysis, respectively). We also thank Confederacion Hidrografica del Jucar (Spanish Ministry of Agriculture, Food and Environment) and the professors Juan Marco Segura and Javier Paredes for the hydrological data provided to develop this study. TECNOMA S. A. provided logistic support. Finally, we acknowledge the Universitat Politecnica de Valencia for the two grants of the Support Programme for Research and Development 'Programa de Apoyo a la Investigacion y Desarrollo' (PAID 00-10 and 00-11). This study was partially funded by the Spanish Ministry of Economy and Competitiveness with the projects 'Recent environmental changes in fluvial systems: morphological and sedimentological consequences' (CGL2009-14220-C02-02-BTE) and SCARCE (Consolider-Ingenio 2010 CSD2009-00065). The feedback of two anonymous reviewers has been very helpful and is greatly appreciated.Garófano-Gómez, V.; Martinez-Capel, F.; Bertoldi, W.; Gurnell, Á.; Estornell Cremades, J.; Segura-Beltrán, F. (2012). Six decades of changes in the riparian corridor of a Mediterranean river: A synthetic analysis based on historical data sources. Ecohydrology. 0:0-0. https://doi.org/10.1002/eco.1330S00

Association between anemia and quality of life in a population sample of individuals with chronic obstructive pulmonary disease

BACKGROUND: Several studies investigated the association of anemia with health related quality of life (HRQL) in patients with chronic disease. However, there is little evidence regarding the association of anemia with HRQL in patients with chronic obstructive pulmonary disease (COPD). METHODS: This is a post-hoc analysis of a study which enrolled a population of adults aged 35–79 randomly selected from residents of Erie and Niagara Counties, NY, between 1996 and 2000. In addition to demographic information and physical measurements, we obtained spirometry data and hemoglobin levels. We used modified Global Initiative for Chronic Obstructive Lung Disease (GOLD) criteria to define COPD, and World Health Organization (WHO) criteria to define anemia. To assess HRQL we used the Short Form-36 (SF-36) to assess physical functioning (PF), physical component summary (PCS) measures and mental component summary (MCS) measures. RESULTS: In the entire study population (n = 2704), respondents with anemia had lower scores on the physical functioning domain [45.4 (SD10.9) vs. 49.2 (SD 9.1); p < 0.0001]. Among patients with COPD (n = 495) the PF scores (39.9 vs. 45.4) and the PCS (41.9 vs. 45.9) were significantly lower in individuals with anemia compared to those without. In multiple regression analysis, the association between hemoglobin and PCS was positive (regression coefficient 0.02, p = 0.003). There was no significant association of hemoglobin with PF scores or the mental component summary measure after adjusting for covariates in patients with COPD. CONCLUSION: In patients with moderate to very severe COPD anemia may be associated with worse HRQL. However, co-morbidities may explain part or all of this association in these patients