Analysis of variations in channel width and sediment supply on riffle-pool dynamics, before and after dam removal

2014 Summer.Includes bibliographical references.Many gravel-bed rivers feature quasi-regular alternations of shallow and deep areas known as riffle-pool sequences, which in straight reaches are often forced by variations in channel width. The mechanisms responsible for the formation and maintenance of riffle- pool sequences are still poorly understood. There is also much uncertainty in the basic understanding of how fluvial systems respond and readjust to large sediment fluxes through time (i.e. dam removal). Here we present physical experiments, numerical modeling, and field observations aimed at improving our understanding of how downstream variations in channel width affect bed morphology and influence riffle-pool development, and how these features respond to changes in sediment supply. A two-dimensional morphodynamic model, Nays2D, has been used to explore interactions between the flow field, the sediment transport field, and the bed morphology for a channel with sinusoidal variations in width. Model predictions suggest that riffles form in wide sections of the channel while pools develop in channel constrictions, and these model results have been used to guide mobile-bed experiments we have conducted in a 21-cm wide, 9-m long flume. Artificial walls imposing a sinusoidal width variation have been installed in the flume, and during the experiments it is supplied with a constant water discharge and a sediment mixture of coarse sand and fine gravel. After riffles and pools developed under these equilibrium conditions, the sediment supply is increased during two experimental designs that simulate characteristics of a dam removal. The first experiment examined increasing sediment supply to an original equilibrium rate after a period of starvation. The second introduces a well sorted sediment pulse that was four times greater than the equilibrium feed rate. This pulse of sediment evolved primarily through dispersion, rather than translation. These physical and numerical experiments are complemented by observations from a natural experiment on the Elwha River in Washington State, where the largest dam-removal project in history is providing riffle-pool sequences with greatly increased sediment supply. Analysis of aerial imagery and repeat bathymetric measurements indicate that prior to dam removal, pools on the Elwha were co-located with local decreases in bankfull width. During dam removal, a pulse of sediment temporarily filled in the pools and increased the overall sediment transport capacity of the river, but eventually most of the pools reemerged at their prior location, suggesting that width imposes an important local control on bed morphology and riffle-pool dynamics

Thermodynamic and Mechanistic Insights into Coupled Binding and Unwinding of Collagen by Matrix Metalloproteinase 1

Local unwinding of the collagen triple helix is a necessary step for initiating the collagen degradation cascade in extracellular matrices. A few matrix metalloproteinases (MMPs) are known to support this key process, but its energetic aspects remain unknown. Here, we captured the thermodynamics of the triple helix unwinding by monitoring interactions between a collagen peptide and MMP-1(E200A) – an active-site mutant of an archetypal vertebrate collagenase – at increasing temperatures, using isothermal titration calorimetry (ITC). Coupled binding and unwinding manifests as a curved relationship between the total enthalpy change and temperature of the reaction, producing increasingly negative heat capacity change (ΔΔCp ≈ −36.3 kcal/molK2). A specially designed solid-phase binding and cleavage assay (SPBCA) reported strain in the catalytically relevant unwound state, suggesting that this state is distinct from the horizon of sampled conformations of the collagenase-susceptible site. MMP-1 appears to blend selected fit with induced fit mechanisms to catalyse collagen unwinding prior to cleavage of individual collagen chains

Reactive-site mutants of N-TIMP-3 that selectively inhibit ADAMTS-4 and ADAMTS-5: biological and structural implications.

Published versio

Enzymic characteristics of fat globule membranes from bovine colostrum and bovine milk

Fat globule membranes have been isolated from bovine colostrum and bovine milk by the dispersion of the fat in sucrose solutions at 4 degrees C and fractionation by centrifugation through discontinuous sucrose gradients. The morphology and enzymic characteristics of the separated fractions were examined. Fractions comprising a large proportion of the total extracted membrane were thus obtained having high levels of the Golgi marker enzymes UDP-galactose N-acetylglucosamine beta-4-galactosyltransferase and thiamine pyrophosphatase. A membrane-derived form of the galactosyltransferase has been solubilized from fat and purified to homogeneity. This enzyme is larger in molecular weight than previously studied soluble galactosyltransferases, but resembles in size the galactosyltransferase of lactating mammary Golgi membranes. In contrast, when fat globule membranes were prepared by traditional procedures, which involved washing the fat at higher temperatures, before extraction, galactosyltransferase was not present in the membranes, having been released into supernatant fractions, When the enzyme released by this procedure was partially purified and examined by gel filtration, it was found to be of a degraded form resembling in size the soluble galactosyltransferase of milk. The release is therefore attributed to the action of proteolytic enzymes. Our observations contrast with previous biochemical studies which suggested that Golgi membranes do not contribute to the milk fat globule membrane. They are, however, consistent with electron microscope studies of the fat secretion process, which indicate that secretory vesicle membranes, derived from the Golgi apparatus, may provide a large proportion of the fat globule membrane

Navigating the demands of academic work to shape an academic job

Findings from interviews with mid-career academics in English and Australian universities elucidate how academics interpret and navigate complex institutional contexts in shaping academic jobs. The paper argues that how they do this is a function of what they notice and respond to as well as the mode of reflexivity they employ. Three core areas are seen to affect academics sense of agency as they shape their own jobs: how they orient themselves to the world around them including the academic institution and department; their underlying goals and purposes as they seek to have a fulfilling role; and how they relate to structural conditions of the workplace. The paper argues that understanding academics’ differing foci of awareness in these areas is helpful to institutional policies and strategies

Responding to university policies and initiatives: the role of reflexivity in the mid-career academic

How do academics make sense of university policies and strategic initiatives and act on them? Interviews were conducted with 27 mid-career academics in different disciplines, different research-intensive university environments and two countries (England and Australia). Data were analysed iteratively utilising a critical realist perspective, specifically, Archer’s modes of reflexivity. The paper argues that individuals’ responses to university policies and initiatives, to changes in policy and policy conflicts can at least partially be understood through interrogating the modes of reflexivity they employ

The hydrology of prehistoric farming systems in a central Arizona ecotone

The prehistoric land use and water management in the semi-arid Southwest was examined. Remote sensing data, geology, hydrology and biology are discussed along with an evaluation of remote sensing contributions, recommendations for applications, and proposed future remote sensing studies

Academic artisans in the research university

In the changing context of universities, organisational structures for teaching and research problematize academic roles. This paper draws on a critical realist analysis of surveys and interviews with academics from universities in England and Australia. It identifies important academic work, not captured simply in descriptions of teaching or research. It shows that many academics, who are not research high flyers nor award-winning teachers, carry out this essential work which contributes to the effective functioning of their universities. That work is referred to as academic artisanal work and the people who do it as academic artisans. Characteristics and examples of academic artisans are presented and the nature of artisanal work is explored. Implications for higher education management and for future studies are discussed. The paper points to an urgent need to better understand the complex nature of academic work

Determinants of Chronic Illness Among Aged Population in Ghana: A Multinomial Logit Approach

Generally, the constant change in demographic trends among the aged depict gradual increase in the size of the aged population globally. The aged population is often capitalised with degenerative conditions such as chronic illness which affect their ability to function effectively and often require special support. Despite the increase in the size of the aged population and their associated degenerative conditions, very few descriptive studies on the determinants of chronic illness among the aged has been researched especially in developing countries such as Ghana and there is no compelling evidence on the association of chronic illness and its determinants. Thus, this study seeks to analyse and predict the impact of age, gender, education, marital status, Quality of Life (QoL), social cohesion, settlement and depression on chronic illness among the aged population in Ghana. From the studies a Multinomial Logit Regression (MLR) was employed to analyse the data obtained from the Ghana Statistical Service (GSS) under, Ageing and Adult Health (SAGE), 2012. It was revealed that out of the 1384 sampled, 71% had no chronic illness whilst 22% and 7% had one and two or more chronic illness respectively. Again, it was observed that, Depression State, Gender, Marital Status and Settlement Type (rural or urban) play significant roles in determining the likelihood of the aged getting chronic illness while Physical Function, Social Cohesion, QoL, Age and Education Level were not statistically significant determinants of chronic illness. Our findings demonstrate that chronic illness among the aged is constantly increasing in Ghana especially in the urban communities and need to be addressed urgently through governmental policies and programs in the quest to help salvage the deteriorating conditions of the aged.   Keywords: Aged Population, Multinomial Logit Model, Chronic Illnes

Research productivity and academics' conceptions of research

This paper asks the question: do people with different levels of research productivity and identification as a researcher think of research differently? It discusses a study that differentiated levels of research productivity among English and Australian academics working in research-intensive environments in three broad discipline areas: science, engineering and technology; social science and humanities; and medicine and health sciences. The paper explores the different conceptions of research held by these academics in terms of their levels of research productivity, their levels of research training, whether they considered themselves an active researcher and a member of a research team, and their disciplinary differences