scholarly journals Reviews and syntheses: Revisiting the boron systematics of aragonite and their application to coral calcification

2018 ◽  
Author(s):  
Thomas M. DeCarlo ◽  
Michael Holcomb ◽  
Malcolm T. McCulloch
Keyword(s):  
Partition Coefficient ◽  
Isotopic Fractionation ◽  
Computer Code ◽  
Comprehensive Analysis ◽  
Coral Skeleton ◽  
Carbonate Chemistry ◽  
Carbonate System ◽  
Coral Skeletons ◽  
User Friendly ◽  
Propagation Of Uncertainties

Abstract. The isotopic and elemental systematics of boron in aragonitic coral skeletons have recently been developed as a proxy for the carbonate chemistry of the coral extracellular calcifying fluid. With knowledge of the boron isotopic fractionation in seawater and the B / Ca partition coefficient (KD) between aragonite and seawater, measurements of coral skeleton δ11B and B / Ca can potentially constrain the full carbonate system. Two sets of abiogenic aragonite precipitation experiments designed to quantify KD have recently made possible the application of this proxy system. However, while different KD formulations have been proposed, there has not yet been a comprehensive analysis that considers both experimental datasets and explores the implications for interpreting coral skeletons. Here, we evaluate four potential KD formulations: three previously presented in the literature and one newly developed. We assess how well each formulation reconstructs the known fluid carbonate chemistry from the abiogenic experiments, and we evaluate the implications for deriving the carbonate chemistry of coral calcifying fluid. Three of the KD formulations performed similarly when applied to abiogenic aragonites precipitated from seawater and to coral skeletons. Critically, we find that some uncertainty remains in understanding the mechanism of boron elemental partitioning between aragonite and seawater, and addressing this question should be a target of additional abiogenic precipitation experiments. Despite this, boron systematics can already be applied to quantify the coral calcifying fluid carbonate system, although uncertainties associated with the proxy system should be carefully considered for each application. Finally, we present a user-friendly computer code that calculates coral calcifying fluid carbonate chemistry, including propagation of uncertainties, given inputs of boron systematics measured in coral skeleton.

scholarly journals Reviews and syntheses: Revisiting the boron systematics of aragonite and their application to coral calcification

2018 ◽  
Vol 15 (9) ◽  
pp. 2819-2834 ◽  
Author(s):  
Thomas M. DeCarlo ◽  
Michael Holcomb ◽  
Malcolm T. McCulloch
Keyword(s):  
Partition Coefficient ◽  
Isotopic Fractionation ◽  
Computer Code ◽  
Comprehensive Analysis ◽  
Coral Skeleton ◽  
Carbonate Chemistry ◽  
Carbonate System ◽  
Coral Skeletons ◽  
User Friendly ◽  
Propagation Of Uncertainties

Abstract. The isotopic and elemental systematics of boron in aragonitic coral skeletons have recently been developed as a proxy for the carbonate chemistry of the coral extracellular calcifying fluid. With knowledge of the boron isotopic fractionation in seawater and the B∕Ca partition coefficient (KD) between aragonite and seawater, measurements of coral skeleton δ11B and B∕Ca can potentially constrain the full carbonate system. Two sets of abiogenic aragonite precipitation experiments designed to quantify KD have recently made possible the application of this proxy system. However, while different KD formulations have been proposed, there has not yet been a comprehensive analysis that considers both experimental datasets and explores the implications for interpreting coral skeletons. Here, we evaluate four potential KD formulations: three previously presented in the literature and one newly developed. We assess how well each formulation reconstructs the known fluid carbonate chemistry from the abiogenic experiments, and we evaluate the implications for deriving the carbonate chemistry of coral calcifying fluid. Three of the KD formulations performed similarly when applied to abiogenic aragonites precipitated from seawater and to coral skeletons. Critically, we find that some uncertainty remains in understanding the mechanism of boron elemental partitioning between aragonite and seawater, and addressing this question should be a target of additional abiogenic precipitation experiments. Despite this, boron systematics can already be applied to quantify the coral calcifying fluid carbonate system, although uncertainties associated with the proxy system should be carefully considered for each application. Finally, we present a user-friendly computer code that calculates coral calcifying fluid carbonate chemistry, including propagation of uncertainties, given inputs of boron systematics measured in coral skeleton.

scholarly journals A genomic view of coral-associated Prosthecochloris and a companion sulfate-reducing bacterium

2019 ◽  
Author(s):  
Yu-Hsiang Chen ◽  
Shan-Hua Yang ◽  
Kshitij Tandon ◽  
Chih-Ying Lu ◽  
Hsing-Ju Chen ◽  
...  
Keyword(s):  
Environmental Changes ◽  
Sulfur Metabolism ◽  
Genomic Analysis ◽  
Coral Skeleton ◽  
Pigment Synthesis ◽  
Sulfate Reducing ◽  
Coral Skeletons ◽  
Functional Genomic Analysis ◽  
Ecological Roles ◽  
Isopora Palifera

AbstractEndolithic microbial symbionts in the coral skeleton may play a pivotal role in maintaining coral health. However, compared to aerobic microorganisms, research on the roles of endolithic anaerobic microorganisms and microbe-microbe interactions in the coral skeleton are still in their infancy. In our previous study, we showed that a group of coral-associated Prosthecochloris (CAP), a genus of anaerobic green sulfur bacteria, was dominant in the skeleton of the coral Isopora palifera. Though CAP is diverse, the 16S rRNA phylogeny presents it as a distinct clade separate from other free-living Prosthecochloris. In this study, we build on previous research and further characterize the genomic and metabolic traits of CAP by recovering two new near-complete CAP genomes—Candidatus Prosthecochloris isoporaea and Candidatus Prosthecochloris sp. N1—from coral Isopora palifera endolithic cultures. Genomic analysis revealed that these two CAP genomes have high genomic similarities compared with other Prosthecochloris and harbor several CAP-unique genes. Interestingly, different CAP species harbor various pigment synthesis and sulfur metabolism genes, indicating that individual CAPs can adapt to a diversity of coral microenvironments. A novel near-complete SRB genome—Candidatus Halodesulfovibrio lyudaonia—was also recovered from the same culture. The fact that CAP and various sulfate-reducing bacteria (SRB) co-exist in coral endolithic cultures and coral skeleton highlights the importance of SRB in the coral endolithic community. Based on functional genomic analysis of Ca. P. sp. N1 and Ca. H. lyudaonia, we also propose a syntrophic relationship between the SRB and CAP in the coral skeleton.ImportanceLittle is known about the ecological roles of endolithic microbes in the coral skeleton; one potential role is as a nutrient source for their coral hosts. Here, we identified a close ecological relationship between CAP and SRB. Recovering novel near-complete CAP and SRB genomes from endolithic cultures in this study enabled us to understand the genomic and metabolic features of anaerobic endolithic bacteria in coral skeletons. These results demonstrate that CAP members with similar functions in carbon, sulfur, and nitrogen metabolisms harbor different light-harvesting components, suggesting that CAP in the skeleton adapts to niches with different light intensities. Our study highlights the potential ecological roles of CAP and SRB in coral skeletons and paves the way for future investigations into how coral endolithic communities will respond to environmental changes.

Comparative Evaluation of Combustion Codes for Low-Btu Gas Applications

1991 ◽  
Author(s):  
Tah-Teh Yang ◽  
Ajay K. Agrawal
Keyword(s):  
Structural Integrity ◽  
Combustion Process ◽  
Computer Code ◽  
Physical Models ◽  
Gas Combustion ◽  
Combustion Modeling ◽  
Coal Gas ◽  
Combustion Models ◽  
Efficient Combustion ◽  
User Friendly

Four computer codes (PHOENICS, PCGC, FLUENT and INTERN) representing a spectrum of existing combustion modeling capabilities were evaluated for low-Btu gas applications. In particular, the objective was to identify computer code(s) that can be used effectively for predictions of (a) the flow field to yield efficient combustion, (b) the temperature field to ensure structural integrity and (c) species concentrations to meet environmental emission standards in a gas turbine combustor operating on low-Btu coal gas. Detailed information on physical models, assumptions, limitations and operational features of various codes was obtained through a series of computational runs of increasing complexity and grouped as (a) experimental validation, (b) code comparison and (c) application to coal gas combustion. INTERN is not suitable for the present application since it has been tailored to model combustion process of premixed hydrocarbon fuels. FLUENT is easy to use and has detailed combustion models (in Version 3), however, it is not favored here because the user is unable to alter, modify or change the existing model(s). While PCGC-2 has the most comprehensive models for combustion, it is not user friendly and is inherently limited to axisymmetric geometry. PCGC-3 is expected to overcome these drawbacks. Built in combustion models in PHOENICS are similar to those in FLUENT. However, the user can implement advanced models on PHOENICS leading to a flexible and powerful combustion code.

scholarly journals The rise of big data and supporting technologies in keeping watch on the world's forests

2020 ◽  
Vol 22 (1) ◽  
pp. 129-141
Author(s):  
R. Taylor ◽  
C. Davis ◽  
J. Brandt ◽  
M. Parker ◽  
T. Stäuble ◽  
...  
Keyword(s):  
Remote Sensing ◽  
Big Data ◽  
Language Processing ◽  
Lower Cost ◽  
Forest Policy ◽  
Forest Products ◽  
Comprehensive Analysis ◽  
Geospatial Data ◽  
User Friendly ◽  
Analysis Of Social Networks

Technology-driven advances in the gathering, processing and delivery of big data are making it easier to monitor forests and make informed decisions over their use and management. This paper first describes how innovations in remote sensing and cloud computing are enabling generation of geospatial data more often, at lower cost and in more user-friendly formats. Second, it describes the evolution of systems and technologies to trace forest products, and agricultural commodities linked to deforestation, from source to final use. Third, it reviews the potential for emerging data mining technologies such as natural language processing, web scraping and computer vision to support forest policy analysis and augment geospatial data gathered through remote sensing. The paper gives examples of how these technologies are being used and may be used in the future to monitor and respond to deforestation, fire and natural disasters, improve governance by enabling faster and more comprehensive analysis of social networks, policies and regulations, and increase traceability and transparency within supply chains.

scholarly journals Ferromagnetic Resonance Spectroscopy and Rock Magnetic Characterization of Fossil Coral Skeletons in Ishigaki Islands, Japan

Geosciences ◽  
2018 ◽  
Vol 8 (11) ◽  
pp. 400
Author(s):  
Yuho Kumagai ◽  
Norihiro Nakamura ◽  
Tetsuro Sato ◽  
Toshitaka Oka ◽  
Hirokuni Oda
Keyword(s):  
Ferromagnetic Resonance ◽  
Single Domain ◽  
Coral Skeleton ◽  
Resonance Spectroscopy ◽  
Continuous Growth ◽  
Coral Skeletons ◽  
Ishigaki Island ◽  
Biogenic Magnetite ◽  
A Chain ◽  
Fossil Coral

Skeletons of hermatypic corals (e.g., Porites) might have enormous potential as a high-resolution paleomagnetic recorder owing to their rapid and continuous growth over hundreds of years at a rate of up to 2 cm/year, although typical corals show an extremely weak intensity of remanence and low stability. We found that coral tsunami boulders with negligible amounts of calcite on Ishigaki Island show a measurable intensity of remanence; thus, we attempted to characterize the magnetic assemblages in this coral skeleton to determine whether it is of biogenic or detrital magnetite using first-order reversal curve (FORC) measurements, ferromagnetic resonance (FMR) spectroscopy, and petrological observations through field-emission type scanning electron microscope (FE-SEM) with an acid treatment. The FMR derivative spectra of coral skeleton samples represent multiple derivative maxima and extended low-field absorption, indicating the presence of intact biogenic magnetite chains. FORC diagrams represent a “central ridge” signature with a vertical spread. These FMR and FORC features indicate the magnetization of these coral skeletons that are mainly created using intact biogenic magnetites and mixtures of grains from collapsed biogenic magnetites, pseudo-single domain grains, and multi-domain grains such as detrital magnetite. FE-SEM observations confirm the presence of a chain-like structure of iron oxides corresponding to the features of biogenic magnetite. Therefore, the magnetic mineral assemblage in coralline boulders from Ishigaki Island consists of dominant biogenic-origin single-domain magnetite and a trace amount of detrital component, indicating that fossil coral skeletons in Ishigaki Island have potential for utilization in paleomagnetic studies.

Boron isotope analysis of coral skeletons by laser ablation MC-ICP-MS: new insights into calcification and environmental reconstruction at high temporal resolution

2020 ◽  
Author(s):  
Gavin L. Foster ◽  
Thomas B. Chalk ◽  
Christopher D. Standish
Keyword(s):  
Laser Ablation ◽  
Trace Element ◽  
Temporal Resolution ◽  
Isotope Analysis ◽  
Coral Skeleton ◽  
Boron Isotope ◽  
High Temporal Resolution ◽  
Carbonate System ◽  
Seawater Ph ◽  
Icp Ms

<p>Despite being some of the largest bio-constructions on the planet, coral reefs are made by many millions of cm- to mm-sized polyps of Scleractinian corals. Calcification occurs in a micron sized space sandwiched between the coral animal and the existing skeleton, known as the extra cellular medium (ECM). The coral animal has a tight control on the carbonate system in this space through deploying enzymatic pumps (e.g. Ca-ATPase) and secreting acidic-rich proteins. Tracking the state of the carbonate system in the ECM is therefore key to forming a mechanistic understanding of how environmental change, such as ocean acidification, influences skeletal formation and ultimately the growth and resilience of these important ecosystems.</p><p>Traditional means to examine ECM composition is through the use of micro-electrodes. While these approaches have revealed many key insights they are, by their nature, invasive.  They also only provide snap shots of information for corals grown in the laboratory. The boron isotopic composition of the coral skeleton and its boron content (expressed as B/Ca ratio) have recently emerged as a viable alternative approach to fully characterise the carbonate system in the ECM.  However, most studies employ bulk sampling techniques which require averaging across both structural elements of the coral skeleton and many months to years of growth. Laser ablation MC-ICP-MS approaches are now available as an alternative sampling protocol (e.g. Standish et al. 2019), and along with B/Ca (and other trace element) measurements this not only allows a reconstruction of the full carbonate system of the ECM from an analysis of the skeleton of any coral (cultured or wild) at unprecedented spatial and temporal resolution, but it also allows an examination of the influence of the carbonate system in the ECM on trace element incorporation. </p><p>Here we present boron isotope and trace element analyses of several tropical, reef-building, corals to examine the nature and magnitude of fine scale variation in ECM composition.  By studying corals from locations where external seawater is well known we also gain insights into trace element incorporation and whether external seawater pH can be accurately reconstructed from the boron-based proxies at weekly (or better) resolution. </p><p> </p><p>Standish, C.D., Chalk, T.B., Babila, T.L., Milton, J.A., Palmer, M.R., Foster, G.L. (2019) The effect of matrix interferences in situ boron isotope analysis by laser ablation MC-ICP-MS, Rapid Communications in Mass Spectrometry 33: 959–968 https://doi.org/10.1002/rcm.8432</p>

scholarly journals SUSD3D Computer Code as Part of the XSUN-2017 Windows Interface Environment for Deterministic Radiation Transport and Cross-Section Sensitivity-Uncertainty Analysis

2017 ◽  
Vol 2017 ◽  
pp. 1-16 ◽  
Author(s):  
Ivan A. Kodeli ◽  
Slavko Slavič
Keyword(s):  
Cross Section ◽  
Radiation Transport ◽  
Computer Code ◽  
Data Bank ◽  
Code System ◽  
Input And Output ◽  
Complete Chain ◽  
Driven System ◽  
Accelerator Driven System ◽  
User Friendly

A Windows interface XSUN-2017 facilitating the deterministic radiation transport and cross-section sensitivity-uncertainty (S/U) calculation is presented. The package was developed to assist the users in the preparation of input cards, rapid modification, and execution of the complete chain of codes including TRANSX, PARTISN, and SUSD3D, all available from the OECD/NEA Data Bank and RSICC. The objective of this work was to make the input and output handling for these codes as user-friendly as possible, passing information among codes internally. XSUN-2017 allows a user-friendly viewing of results obtained from the PARTISN and SUSD3D programs. The first version of the Windows interface XSUN-2013 was developed in 2013 and submitted to OECD/NEA Data Bank Computer Code Collection and RSICC in early 2014. An updated version, XSUN-2017, will be released in 2017. The package includes also the new version of the SUSD3D code. The XSUN-2017 and SUSD3D code systems and recent improvements and updates are described. Examples of the use and validation are presented, including the S/U intercomparison exercise using the SNEAK-7 benchmarks involving the XSUN-2017 code system comparison with the codes such as TSUNAMI, SERPENT, and MCNP6, and the S/U analysis of the keff and βeff parameters for the MYRRHA accelerator driven system (ADS).

scholarly journals Implications of observed inconsistencies in carbonate chemistry measurements for ocean acidification studies

2012 ◽  
Vol 9 (2) ◽  
pp. 1781-1792 ◽  
Author(s):  
C. J. M. Hoppe ◽  
G. Langer ◽  
S. D. Rokitta ◽  
D. A. Wolf-Gladrow ◽  
B. Rost
Keyword(s):  
Ocean Acidification ◽  
High Pco2 ◽  
Small Scale ◽  
Ecological Data ◽  
Carbonate Chemistry ◽  
Carbonate System ◽  
Saturation State ◽  
Severe Problem ◽  
Important Approach ◽  
Calcite Saturation

Abstract. The growing field of ocean acidification research is concerned with the investigation of organisms' responses to increasing pCO2 values. One important approach in this context is culture work using seawater with adjusted CO2 levels. As aqueous pCO2 is difficult to measure directly in small scale experiments, it is generally calculated from two other measured parameters of the carbonate system (often AT, CT or pH). Unfortunately, the overall uncertainties of measured and subsequently calculated values are often unknown. Especially under high pCO2, this can become a severe problem with respect to the interpretation of physiological and ecological data. In the few datasets from ocean acidification research where all three of these parameters were measured, pCO2 values calculated from AT and CT are typically about 30 % lower (i.e. ~300 μatm at a target pCO2 of 1000 μatm) than those calculated from AT and pH or CT and pH. This study presents and discusses these discrepancies as well as likely consequences for the ocean acidification community. Until this problem is solved, one has to consider that calculated parameters of the carbonate system (e.g. pCO2, calcite saturation state) may not be comparable between studies, and that this may have important implications for the interpretation of CO2 perturbation experiments.

scholarly journals miRGalaxy: Galaxy-Based Framework for Interactive Analysis of microRNA and isomiR Sequencing Data

Cancers ◽  
2021 ◽  
Vol 13 (22) ◽  
pp. 5663
Author(s):  
Ilias Glogovitis ◽  
Galina Yahubyan ◽  
Thomas Würdinger ◽  
Danijela Koppers-Lalic ◽  
Vesselin Baev
Keyword(s):  
Small Rna ◽  
Data Analytics ◽  
Comprehensive Analysis ◽  
Sequencing Data ◽  
Detailed Structure ◽  
Diagnostic Biomarkers ◽  
Interactive Analysis ◽  
Depth Analysis ◽  
Structure Complexity ◽  
User Friendly

Tools for microRNA (miR) sequencing data analyses are broadly used in biomedical research. However, the complexity of computational approaches still remains a challenge for biologists with scarce experience in data analytics and bioinformatics. Here, we present miRGalaxy, a Galaxy-based framework for comprehensive analysis of miRs and their sequence variants—miR isoforms (isomiRs). Though isomiRs are commonly reported in deep-sequencing experiments, their detailed structure complexity and specific differential expression (DE) remain not fully examined by the majority of the available analysis tools. miRGalaxy encompasses biologist-user-friendly tools and workflows dedicated to the analysis of the isomiR-ome and its complex behavior in various biological samples. miRGalaxy is developed as a modular, accessible, redistributable, shareable, and user-friendly framework for scientists working with small RNA (sRNA)-seq data. Due to its modular workflow, advanced users can customize the steps and tools for their needs. In addition, the framework provides an analysis report where the significant output results are summarized in charts and visualizations. miRGalaxy can be accessed via preconfigured Docker image flavor and a Toolshed installation if the user already has a running Galaxy instance. Over the last decade, studies on the expression of miRs and isomiRs in normal and deregulated tissues have led to the discovery of their potential as diagnostic biomarkers. The detection of miRs in biofluids further expanded the exploration of the miR repertoire as a source of liquid biopsy biomarkers. Here we show the miRGalaxy framework application for in-depth analysis of the sRNA-seq data from two different biofluids, milk and plasma, to identify, annotate, and discover specific differentially expressed miRs and isomiRs.

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