scholarly journals Biodiversity, Community Structural Shifts, and Biogeography of Prokaryotes within Antarctic Continental Shelf Sediment

2003 ◽  
Vol 69 (5) ◽  
pp. 2463-2483 ◽  
Author(s):  
John P. Bowman ◽  
Robert D. McCuaig
Keyword(s):  
Species Richness ◽  
Continental Shelf ◽  
Structural Changes ◽  
Sediment Surface ◽  
Small Subset ◽  
Shelf Area ◽  
The Core ◽  
Shelf Sediment ◽  
Antarctic Continental Shelf ◽  
Wide Range

ABSTRACT 16S ribosomal DNA (rDNA) clone library analysis was conducted to assess prokaryotic diversity and community structural changes within a surficial sediment core obtained from an Antarctic continental shelf area (depth, 761 m) within the Mertz Glacier Polynya (MGP) region. Libraries were created from three separate horizons of the core (0- to 0.4-cm, 1.5- to 2.5-cm, and 20- to 21-cm depth positions). The results indicated that at the oxic sediment surface (depth, 0 to 0.4 cm) the microbial community appeared to be dominated by a small subset of potentially r-strategist (fast-growing, opportunistic) species, resulting in a lower-than-expected species richness of 442 operational taxonomic units (OTUs). At a depth of 1.5 to 2.5 cm, the species richness (1,128 OTUs) was much higher, with the community dominated by numerous gamma and delta proteobacterial phylotypes. At a depth of 20 to 21 cm, a clear decline in species richness (541 OTUs) occurred, accompanied by a larger number of more phylogenetically divergent phylotypes and a decline in the predominance of Proteobacteria. Based on rRNA and clonal abundance as well as sequence comparisons, syntrophic cycling of oxidized and reduced sulfur compounds appeared to be the dominant process in surficial MGP sediment, as phylotype groups putatively linked to these processes made up a large proportion of clones throughout the core. Between 18 and 65% of 16S rDNA phylotypes detected in a wide range of coastal and open ocean sediments possessed high levels of sequence similarity (>95%) with the MGP sediment phylotypes, indicating that many sediment prokaryote phylotype groups defined in this study are ubiquitous in marine sediment.

scholarly journals Comparative organic geochemistry of Indian margin (Arabian Sea) sediments: estuary to continental slope

2014 ◽  
Vol 11 (23) ◽  
pp. 6683-6696 ◽  
Author(s):  
G. Cowie ◽  
S. Mowbray ◽  
S. Kurian ◽  
A. Sarkar ◽  
C. White ◽  
...  
Keyword(s):  
Grain Size ◽  
Continental Slope ◽  
Arabian Sea ◽  
Sediment Surface ◽  
Sediment Grain Size ◽  
Organic C ◽  
Shelf Sediment ◽  
Wide Range ◽  
Hydrodynamic Processes ◽  
Upper Slope

Abstract. Surface sediments from sites across the Indian margin of the Arabian Sea were analysed for their elemental and stable isotopic organic carbon (Corg) and total nitrogen compositions, grain size distributions and biochemical indices of organic matter (OM) source and/or degradation state. Site locations ranged from the estuaries of the Mandovi and Zuari rivers to depths of ~ 2000 m on the continental slope, thus spanning nearshore muds and sands on the shelf and both the oxygen minimum zone (OMZ) on the upper slope (~ 200–1300 m) and the seasonal hypoxic zone that appears on the shelf. Source indices showed mixed marine and terrigenous OM within the estuaries, but consistent predominance (80–100%) of marine OM on the shelf and slope. Thus, riverine terrigenous OM is diluted or replaced by autochthonous marine OM and/or is efficiently re-mineralised, within or immediately offshore of the estuaries. Organic C contents of surface shelf sediments varied from < 0.5 wt% in relict shelf sands to up to ~ 4 wt% for nearshore muds, while upper slope sites within the OMZ showed a wide range (~ 2 to 7 + wt%), progressively decreasing below the OMZ to ≤ 1 wt% at 2000 m. Thus, major variability (~ 5 wt%) was found at slope sites within the OMZ of similar depth and near-identical bottom-water O2 concentrations. A strong relationship between %Corg and sediment grain size was seen for sediments within the OMZ, but lower relative Corg contents were found for sites on the shelf and below the OMZ. Further, Corg loadings, when related to estimated sediment surface area, indicated distinct enrichment of Corg in the OMZ sediments relative to sites above and below the OMZ and to sediments from normoxic margins. Diagenetic indices confirmed that lower Corg content below the OMZ is associated with more extensive OM degradation, but that shelf sediment OM is not consistently more degraded than that found within the OMZ. Together, the results indicate that OM distribution across the margin is controlled by interplay between hydrodynamic processes and varying preservation associated with O2 availability. This inference is supported by multiple regression analysis. Hydrodynamic processes (expressed as %Silt) followed by O2 availability, can explain the large majority of %Corg variability when the shelf and slope are considered as a whole. However, while O2 becomes the primary influence on %Corg for sediments below the OMZ, %Silt is the primary influence across the OMZ and, apparently, the shelf. Thus, reduced O2 exposure is responsible for OM enrichment within the OMZ, but hydrodynamic processes are the overriding control on sediment OM distributions across both the shelf and the OMZ.

Duoethnography: A Polytheoretical Approach to (Re)Storing, (Re)Storying the Meanings That One Gives

2020 ◽  
pp. 396-423
Author(s):  
John Joseph Norris ◽  
Richard D. Sawyer
Keyword(s):  
Social Justice ◽  
Critical Theory ◽  
Third Space ◽  
The Third ◽  
The Core ◽  
Wide Range ◽  
Core Elements ◽  
Feminist Inquiry

This chapter summarizes the advancement of duoethnography throughout its fifteen-year history, employing examples from a variety of topics in education and social justice to provide a wide range of approaches that one may take when conducting a duoethnography. A checklist articulates what its cofounders consider the core elements of duoethnographies, additional features that may or may not be employed and how some studies purporting to be duoethnographies may not be so. The chapter indicates connections between duoethnography and a number of methodological concepts including the third space, the problematics of representation, feminist inquiry, and critical theory using published examples by several duoethnographers.

scholarly journals Entangling Lattice-Trapped Bosons with a Free Impurity: Impact on Stationary and Dynamical Properties

Entropy ◽  
2021 ◽  
Vol 23 (3) ◽  
pp. 290
Author(s):  
Maxim Pyzh ◽  
Kevin Keiler ◽  
Simeon I. Mistakidis ◽  
Peter Schmelcher
Keyword(s):  
Structural Changes ◽  
Many Body ◽  
Wide Range ◽  
Entropy Measures ◽  
Particle Level ◽  
The Many ◽  
The One ◽  
Tunneling Dynamics ◽  
The Individual ◽  
Trapped Bosons

We address the interplay of few lattice trapped bosons interacting with an impurity atom in a box potential. For the ground state, a classification is performed based on the fidelity allowing to quantify the susceptibility of the composite system to structural changes due to the intercomponent coupling. We analyze the overall response at the many-body level and contrast it to the single-particle level. By inspecting different entropy measures we capture the degree of entanglement and intraspecies correlations for a wide range of intra- and intercomponent interactions and lattice depths. We also spatially resolve the imprint of the entanglement on the one- and two-body density distributions showcasing that it accelerates the phase separation process or acts against spatial localization for repulsive and attractive intercomponent interactions, respectively. The many-body effects on the tunneling dynamics of the individual components, resulting from their counterflow, are also discussed. The tunneling period of the impurity is very sensitive to the value of the impurity-medium coupling due to its effective dressing by the few-body medium. Our work provides implications for engineering localized structures in correlated impurity settings using species selective optical potentials.

scholarly journals Ligand-induced structural changes analysis of ribose-binding protein as studied by molecular dynamics simulations

2021 ◽  
pp. 1-12
Author(s):  
Haiyan Li ◽  
Zanxia Cao ◽  
Guodong Hu ◽  
Liling Zhao ◽  
Chunling Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Binding Protein ◽  
Network Models ◽  
Md Simulations ◽  
Protein Domain ◽  
Opening Angle ◽  
Conformation Changes ◽  
Wide Range ◽  
Ribose Binding Protein

BACKGROUND: The ribose-binding protein (RBP) from Escherichia coli is one of the representative structures of periplasmic binding proteins. Binding of ribose at the cleft between two domains causes a conformational change corresponding to a closure of two domains around the ligand. The RBP has been crystallized in the open and closed conformations. OBJECTIVE: With the complex trajectory as a control, our goal was to study the conformation changes induced by the detachment of the ligand, and the results have been revealed from two computational tools, MD simulations and elastic network models. METHODS: Molecular dynamics (MD) simulations were performed to study the conformation changes of RBP starting from the open-apo, closed-holo and closed-apo conformations. RESULTS: The evolution of the domain opening angle θ clearly indicates large structural changes. The simulations indicate that the closed states in the absence of ribose are inclined to transition to the open states and that ribose-free RBP exists in a wide range of conformations. The first three dominant principal motions derived from the closed-apo trajectories, consisting of rotating, bending and twisting motions, account for the major rearrangement of the domains from the closed to the open conformation. CONCLUSIONS: The motions showed a strong one-to-one correspondence with the slowest modes from our previous study of RBP with the anisotropic network model (ANM). The results obtained for RBP contribute to the generalization of robustness for protein domain motion studies using either the ANM or PCA for trajectories obtained from MD.

scholarly journals Overview of Popular Techniques of Raman Spectroscopy and Their Potential in the Study of Plant Tissues

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1537
Author(s):  
Aneta Saletnik ◽  
Bogdan Saletnik ◽  
Czesław Puchalski
Keyword(s):  
Raman Spectroscopy ◽  
Cell Walls ◽  
Structural Changes ◽  
Spatial Information ◽  
Technological Development ◽  
Analytical Techniques ◽  
High Sensitivity ◽  
Plant Tissues ◽  
Wide Range ◽  
Identification Technique

Raman spectroscopy is one of the main analytical techniques used in optical metrology. It is a vibration, marker-free technique that provides insight into the structure and composition of tissues and cells at the molecular level. Raman spectroscopy is an outstanding material identification technique. It provides spatial information of vibrations from complex biological samples which renders it a very accurate tool for the analysis of highly complex plant tissues. Raman spectra can be used as a fingerprint tool for a very wide range of compounds. Raman spectroscopy enables all the polymers that build the cell walls of plants to be tracked simultaneously; it facilitates the analysis of both the molecular composition and the molecular structure of cell walls. Due to its high sensitivity to even minute structural changes, this method is used for comparative tests. The introduction of new and improved Raman techniques by scientists as well as the constant technological development of the apparatus has resulted in an increased importance of Raman spectroscopy in the discovery and defining of tissues and the processes taking place in them.

scholarly journals Insights into mammalian biology from the wild house mouse Mus musculus

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Megan Phifer-Rixey ◽  
Michael W Nachman
Keyword(s):  
House Mouse ◽  
Mus Musculus ◽  
Genetic Model ◽  
Inbred Strains ◽  
Mendelian Inheritance ◽  
Model Organisms ◽  
House Mice ◽  
Small Subset ◽  
Wild Mice ◽  
Wide Range

The house mouse, Mus musculus, was established in the early 1900s as one of the first genetic model organisms owing to its short generation time, comparatively large litters, ease of husbandry, and visible phenotypic variants. For these reasons and because they are mammals, house mice are well suited to serve as models for human phenotypes and disease. House mice in the wild consist of at least three distinct subspecies and harbor extensive genetic and phenotypic variation both within and between these subspecies. Wild mice have been used to study a wide range of biological processes, including immunity, cancer, male sterility, adaptive evolution, and non-Mendelian inheritance. Despite the extensive variation that exists among wild mice, classical laboratory strains are derived from a limited set of founders and thus contain only a small subset of this variation. Continued efforts to study wild house mice and to create new inbred strains from wild populations have the potential to strengthen house mice as a model system.

Measurements and Modeling of Ingress in a New 1.5-Stage Turbine Research Facility

2016 ◽  
Vol 139 (1) ◽  
Author(s):  
Marios Patinios ◽  
James A. Scobie ◽  
Carl M. Sangan ◽  
J. Michael Owen ◽  
Gary D. Lock
Keyword(s):  
Theoretical Model ◽  
Gas Turbines ◽  
Test Facility ◽  
Radial Clearance ◽  
Operating Life ◽  
The Core ◽  
Wide Range ◽  
Purge Flow ◽  
Rotor Disk ◽  
Engine Components

In gas turbines, hot mainstream flow can be ingested into the wheel-space formed between stator and rotor disks as a result of the circumferential pressure asymmetry in the annulus; this ingress can significantly affect the operating life, performance, and integrity of highly stressed, vulnerable engine components. Rim seals, fitted at the periphery of the disks, are used to minimize ingress and therefore reduce the amount of purge flow required to seal the wheel-space and cool the disks. This paper presents experimental results from a new 1.5-stage test facility designed to investigate ingress into the wheel-spaces upstream and downstream of a rotor disk. The fluid-dynamically scaled rig operates at incompressible flow conditions, far removed from the harsh environment of the engine which is not conducive to experimental measurements. The test facility features interchangeable rim-seal components, offering significant flexibility and expediency in terms of data collection over a wide range of sealing flow rates. The rig was specifically designed to enable an efficient method of ranking and quantifying the performance of generic and engine-specific seal geometries. The radial variation of CO2 gas concentration, pressure, and swirl is measured to explore, for the first time, the flow structure in both the upstream and downstream wheel-spaces. The measurements show that the concentration in the core is equal to that on the stator walls and that both distributions are virtually invariant with radius. These measurements confirm that mixing between ingress and egress is essentially complete immediately after the ingested fluid enters the wheel-space and that the fluid from the boundary layer on the stator is the source of that in the core. The swirl in the core is shown to determine the radial distribution of pressure in the wheel-space. The performance of a double radial-clearance seal is evaluated in terms of the variation of effectiveness with sealing flow rate for both the upstream and the downstream wheel-spaces and is found to be independent of rotational Reynolds number. A simple theoretical orifice model was fitted to the experimental data showing good agreement between theory and experiment for all cases. This observation is of great significance as it demonstrates that the theoretical model can accurately predict ingress even when it is driven by the complex unsteady pressure field in the annulus upstream and downstream of the rotor. The combination of the theoretical model and the new test rig with its flexibility and capability for detailed measurements provides a powerful tool for the engine rim-seal designer.

The vulnerability of Arctic shelf sediments to climate change

2015 ◽  
Vol 23 (4) ◽  
pp. 461-479 ◽  
Author(s):  
Robie W. Macdonald ◽  
Zou Zou A. Kuzyk ◽  
Sophia C. Johannessen
Keyword(s):  
Organic Carbon ◽  
Carbon Sources ◽  
The Arctic ◽  
Sedimentary Environments ◽  
Carbon Supply ◽  
Shelf Sediment ◽  
Wide Range ◽  
Metabolic Conditions ◽  
Shelf Sediments ◽  
Ocean Ecosystem

The sediments of the pan-Arctic shelves contribute an important component to the Arctic Ocean ecosystem by providing a habitat for biota (benthos), a repository for organic and inorganic non-conservative substances entering or produced within the ocean, a reactor and source of transformed substances back to the water column, and a mechanism of burial. Sediments interact with ice, ocean, and the surrounding land over a wide range of space and time scales. We discuss the vulnerability of shelf sediment to changes in (i) organic carbon sources, (ii) pathways of sediment and organic carbon supply, and (iii) physical and biogeochemical alteration (diagenesis). Sedimentary environments of the shelves and basins are likely to exhibit a wide variance in their response to global change because of their wide variation in sediment sources, processes, and metabolic conditions. In particular, the Chukchi and Barents shelves are dominated by inflowing waters from oceans to the south, whereas the interior shelves are more closely tied to terrigenous sources due to river inflow and coastal erosion.

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