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  • 11
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    A framework for installable external tools in Skyline (2014)
    Oxford University Press
    Details
    Publication Date: 2014-08-27
    Description: : Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. The Skyline document model contains extensive mass spectrometry data from targeted proteomics experiments performed using selected reaction monitoring, parallel reaction monitoring and data-independent and data-dependent acquisition methods. Researchers have developed software tools that perform statistical analysis of the experimental data contained within Skyline documents. The new external tools framework allows researchers to integrate their tools into Skyline without modifying the Skyline codebase. Installed tools provide point-and-click access to downstream statistical analysis of data processed in Skyline. The framework also specifies a uniform interface to format tools for installation into Skyline. Tool developers can now easily share their tools with proteomics researchers using Skyline. Availability and implementation: Skyline is available as a single-click self-updating web installation at http://skyline.maccosslab.org . This Web site also provides access to installable external tools and documentation. Contact: brendanx@u.washington.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 12
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    Genome-wide CIITA-binding profile identifies sequence preferences that dictate function versus recruitment (2015)
    Oxford University Press
    Details
    Publication Date: 2015-04-02
    Description: The class II transactivator (CIITA) is essential for the expression of major histocompatibility complex class II (MHC-II) genes; however, the role of CIITA in gene regulation outside of MHC-II biology is not fully understood. To comprehensively map CIITA-bound loci, ChIP-seq was performed in the human B lymphoblastoma cell line Raji. CIITA bound 480 sites, and was significantly enriched at active promoters and enhancers. The complexity of CIITA transcriptional regulation of target genes was analyzed using a combination of CIITA -null cells, including a novel cell line created using CRISPR/Cas9 tools. MHC-II genes and a few novel genes were regulated by CIITA; however, most other genes demonstrated either diminished or no changes in the absence of CIITA. Nearly all CIITA-bound sites were within regions containing accessible chromatin, and CIITA's presence at these sites was associated with increased histone H3K27 acetylation, suggesting that CIITA's role at these non-regulated loci may be to poise the region for subsequent regulation. Computational genome-wide modeling of the CIITA bound XY box motifs provided constraints for sequences associated with CIITA-mediated gene regulation versus binding. These data therefore define the CIITA regulome in B cells and establish sequence specificities that predict activity for an essential regulator of the adaptive immune response.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 13
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    Response to comment by S. Chiswell (2013)
    Wiley
    Details
    Publication Date: 2013-11-28
    Description: [1]   Chiswell [2013] suggests that some of the conclusions drawn by Behrenfeld et al . [2013] are likely erroneous because of (1) the method used to calculate specific net biomass accumulation rates ( r ; d -1 ) over the seasonal cycle, (2) inconsistencies in the calculation of r and phytoplankton specific cell division rate, μ (d -1 ), and (3) uncertainties in the extrapolation of satellite data to the depth of the seasonal thermocline. Each of these concerns is addressed in the following subsections. We begin with a simple culture-based analogy that clarifies why switching between concentration-based and inventory-based expressions is required for calculating r when the mixed layer varies between shoaling and deepening conditions. This analogy is followed by a more specific mathematical treatment. We then explain why our previous comparisons between r and μ provide a conservative estimate of predator-prey coupling, followed by a discussion of uncertainties in satellite-based assessments of mixed layer phytoplankton biomass.
    Print ISSN: 0886-6236
    Electronic ISSN: 1944-9224
    Topics: Biology , Chemistry and Pharmacology , Geography , Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 14
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    Southern Ocean Biogeochemical Float Deployment Strategy, With Example From the Greenwich Meridian Line (GO‐SHIP A12) (2019)
    Wiley
    Details
    Publication Date: 2019
    Description: Abstract Biogeochemical Argo floats, profiling to 2,000‐m depth, are being deployed throughout the Southern Ocean by the Southern Ocean Carbon and Climate Observations and Modeling program (SOCCOM). The goal is 200 floats by 2020, to provide the first full set of annual cycles of carbon, oxygen, nitrate, and optical properties across multiple oceanographic regimes. Building from no prior coverage to a sparse array, deployments are based on prior knowledge of water mass properties, mean frontal locations, mean circulation and eddy variability, winds, air‐sea heat/freshwater/carbon exchange, prior Argo trajectories, and float simulations in the Southern Ocean State Estimate and Hybrid Coordinate Ocean Model (HYCOM). Twelve floats deployed from the 2014–2015 Polarstern cruise from South Africa to Antarctica are used as a test case to evaluate the deployment strategy adopted for SOCCOM's 20 deployment cruises and 126 floats to date. After several years, these floats continue to represent the deployment zones targeted in advance: (1) Weddell Gyre sea ice zone, observing the Antarctic Slope Front, and a decadally‐rare polynya over Maud Rise; (2) Antarctic Circumpolar Current (ACC) including the topographically steered Southern Zone chimney where upwelling carbon/nutrient‐rich deep waters produce surprisingly large carbon dioxide outgassing; (3) Subantarctic and Subtropical zones between the ACC and Africa; and (4) Cape Basin. Argo floats and eddy‐resolving HYCOM simulations were the best predictors of individual SOCCOM float pathways, with uncertainty after 2 years of order 1,000 km in the sea ice zone and more than double that in and north of the ACC.
    Print ISSN: 2169-9275
    Electronic ISSN: 2169-9291
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 15
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    Annual cycles of ecological disturbance and recovery underlying the subarctic Atlantic spring plankton bloom (2013)
    Wiley
    Details
    Publication Date: 2013-05-22
    Description: [1]  Satellite measurements allow global assessments of phytoplankton concentrations and, from observed temporal changes in biomass, direct access to net biomass accumulation rates ( r ). For the subarctic Atlantic basin, analysis of annual cycles in r reveal that initiation of the annual blooming-phase does not occur in spring after stratification surpasses a critical threshold, but rather in early winter when growth conditions for phytoplankton are deteriorating. This finding has been confirmed with in situ profiling float data. The objective of the current study was to test whether satellite-based annual cycles in r are reproduced by the Biogeochemical Element Cycling - Community Climate System Model and, if so, to use the additional ecosystem properties resolved by the model to better understand factors controlling phytoplankton blooms. We find that the model gives a similar early onset time for the blooming phase, that this initiation is largely due to the physical disruption of phytoplankton-grazer interactions during mixed layer deepening, and that parallel increases in phytoplankton specific division and loss rates during spring maintain the subtle disruption in food web equilibrium that ultimately yields the spring bloom climax. The link between winter mixing and bloom dynamics is illustrated by contrasting annual plankton cycles between regions with deeper and shallower mixing. We show that maximum water column inventories of phytoplankton vary in proportion to maximum winter mixing depth, implying that future reductions in winter mixing may dampen plankton cycles in the subarctic Atlantic. We propose that ecosystem disturbance-recovery sequences are a unifying property of global ocean plankton blooms.
    Print ISSN: 0886-6236
    Electronic ISSN: 1944-9224
    Topics: Biology , Chemistry and Pharmacology , Geography , Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 16
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    Student's tutorial on bloom hypotheses in the context of phytoplankton annual cycles (2017)
    Wiley
    Details
    Publication Date: 2017-08-10
    Description: Phytoplankton blooms are elements in repeating annual cycles of phytoplankton biomass and they have significant ecological and biogeochemical consequences. Temporal changes in phytoplankton biomass are governed by complex predator-prey interactions and physically-driven variations in upper water-column the growth conditions (light, nutrient, temperature). Understanding these dependencies is fundamental to assessing future change in bloom frequency, duration, and magnitude and thus represents a quintessential challenge in global change biology. A variety of contrasting hypotheses have emerged in the literature to explain phytoplankton blooms, but over time the basic tenets of these hypotheses have become unclear. Here, we provide a ‘tutorial’ on the development of these concepts and the fundamental elements distinguishing each hypothesis. The intent of this tutorial is to provide a useful background and set of tools for reading the bloom literature and to give some suggestions for future studies. Our tutorial is written for ‘students’ at all stages of their career. We hope it is equally useful and interesting to those with only a cursory interest in blooms as those deeply immersed in the challenge of understanding the temporal dynamics of phytoplankton biomass and predicting its future change. This article is protected by copyright. All rights reserved.
    Print ISSN: 1354-1013
    Electronic ISSN: 1365-2486
    Topics: Biology , Energy, Environment Protection, Nuclear Power Engineering , Geography
    Published by Wiley
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  • 17
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    Estimation of Phytoplankton Accessory Pigments From Hyperspectral Reflectance Spectra: Toward a Global Algorithm (2017)
    Wiley
    Details
    Publication Date: 2017-11-22
    Description: Phytoplankton community composition in the ocean is complex and highly variable over a wide range of space and time scales. Able to cover these scales, remote-sensing reflectance spectra can be measured both by satellite and by in situ radiometers. The spectral shape of reflectance in the open ocean is influenced by the particles in the water, mainly phytoplankton and co-varying non-algal particles. We investigate the utility of in situ hyperspectral remote-sensing reflectance measurements to detect phytoplankton pigments by using an inversion algorithm that defines phytoplankton pigment absorption as a sum of Gaussian functions. The inverted amplitudes of the Gaussian functions representing pigment absorption are compared to coincident High Performance Liquid Chromatography measurements of pigment concentration. We determined strong predictive capability for chlorophylls a, b, c 1 + c 2 , and the photoprotective carotenoids. We also tested the estimation of pigment concentrations from reflectance-derived chlorophyll a using global relationships of co-variation between chlorophyll a and the accessory pigments. We found similar errors in pigment estimation based on the relationships of co-variation versus the inversion algorithm. An investigation of spectral residuals in reflectance data after removal of chlorophyll-based average absorption spectra showed no strong relationship between spectral residuals and pigments. Ultimately, we are able to estimate concentrations of three chlorophylls and the photoprotective carotenoid pigments, noting that further work is necessary to address the challenge of extracting information from hyperspectral reflectance beyond the information that can be determined from chlorophyll a and its co-variation with other pigments.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 18
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    Kelp detritus provides high-quality food for sea urchin larvae (2017)
    Wiley
    Details
    Publication Date: 2017-10-26
    Description: Highly productive kelps release abundant particulate organic matter into the nearshore environment due to their constant fragmentation and erosion by ocean waves. The contribution of kelp detritus to coastal planktonic food webs has not previously been examined. Here, we demonstrate that detritus derived from a dominant kelp in the Northeast Pacific, Nereocystis luetkeana , provides high-quality food for planktonic sea urchin larvae. Our findings challenge the paradigm that phytoplankton are the main diet for zooplankton in nearshore regions, with implications for modeling of ocean production. Furthermore, at the benthic adult stage, sea urchins can destructively graze kelps causing the kelp ecosystem to collapse; hence, our results have implications for understanding feedback mechanisms that may determine the resilience of kelp ecosystems.
    Print ISSN: 0024-3590
    Electronic ISSN: 1939-5590
    Topics: Biology , Geosciences , Physics
    Published by Wiley on behalf of The Association for the Sciences of Limnology and Oceanography (ASLO).
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  • 19
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    Correction of profiles of in-situ chlorophyll fluorometry for the contribution of fluorescence originating from non-algal matter (2016)
    Wiley
    Details
    Publication Date: 2016-10-16
    Description: In situ chlorophyll fluorometers have been widely employed for more than half a century, and to date, it still remains the most used instrument to estimate chlorophyll-a concentration in the field, especially for measurements onboard autonomous observation platforms, e.g., Bio-Argo floats and gliders. However, in deep waters (〉 300 m) of some specific regions, e.g., subtropical gyres and the Black Sea, the chlorophyll fluorescence profiles frequently reveal “deep sea red fluorescence” features. In line with previous studies and through the analysis of a large data set (cruise transect in the South East Pacific and data acquired by 82 Bio-Argo floats), we show that the fluorescence signal measured by a humic-like DOM fluorometer is highly correlated to the “deep sea red fluorescence.” Both fluorescence signals are indeed linearly related in deep waters. To remove the contribution of non-algal organic matter from chlorophyll fluorescence profiles, we introduce a new correction. Rather that removing a constant value (generally the deepest chlorophyll a fluorescence value from the profile, i.e., so-called “deep-offset correction”), we propose a correction method which relies on DOM fluorometry and on its variation with depth. This new method is validated with chlorophyll concentration extracted from water samples and further applied on the Bio-Argo float data set. More generally, we discuss the potential of the proposed method to become a standard and routine procedure in quality-control and correction of chlorophyll a fluorescence originating from Bio-Argo network.
    Electronic ISSN: 1541-5856
    Topics: Biology , Geosciences
    Published by Wiley on behalf of The Association for the Sciences of Limnology and Oceanography (ASLO).
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  • 20
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    Recommendations for obtaining unbiased chlorophyll estimates from in situ chlorophyll fluorometers: A global analysis of WET Labs ECO sensors (2017)
    Wiley
    Details
    Publication Date: 2017-05-05
    Description: Chlorophyll fluorometers provide the largest in situ global data set for estimating phytoplankton biomass because of their ease of use, size, power consumption, and relatively low price. While in situ chlorophyll a (Chl) fluorescence is proxy for Chl a concentration, and hence phytoplankton biomass, there exist large natural variations in the relationship between in situ fluorescence and extracted Chl a concentration. Despite this large natural variability, we present here a global validation data set for the WET Labs Environmental Characterization Optics (ECO) series chlorophyll fluorometers that suggests a factor of 2 overestimation in the factory calibrated Chl a estimates for this specific manufacturer and series of sensors. We base these results on paired High Pressure Liquid Chromatography (HPLC) and in situ fluorescence match ups for which non-photochemically quenched fluorescence observations were removed. Additionally, we examined matchups between the factory-calibrated in situ fluorescence and estimates of chlorophyll concentration determined from in situ radiometry, absorption line height, NASA's standard ocean color algorithm as well as laboratory calibrations with phytoplankton monocultures spanning diverse species that support the factor of 2 bias. We therefore recommend the factor of 2 global bias correction be applied for the WET Labs ECO sensors, at the user level, to improve the global accuracy of chlorophyll concentration estimates and products derived from them. We recommend that other fluorometer makes and models should likewise undergo global analyses to identify potential bias in factory calibration.
    Electronic ISSN: 1541-5856
    Topics: Biology , Geosciences
    Published by Wiley on behalf of The Association for the Sciences of Limnology and Oceanography (ASLO).
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