Chlorophyll fluorescence is directly linked to the physiology of phytoplankton or plants. Here, we present a new satellite remote sensing approach to retrieve chlorophyll fluorescence at its red peak ...(~685nm) by using measurements from the hyperspectral instruments SCanning Imaging Absorption SpectroMeter for Atmospheric CHartographY (SCIAMACHY) and Global Ozone Monitoring Experiment-2 (GOME-2). This method, which is based on the Differential Optical Absorption Spectroscopy (DOAS) technique, was used to exploit narrow spectral structures resulting from the filling-in of the Fraunhofer Fe I line, which originates from fluorescence. The reference spectra for chlorophyll fluorescence were calculated by the coupled ocean–atmosphere radiative transfer model SCIATRAN. We compared our results on marine chlorophyll fluorescence observations with the MODIS Terra normalized Fluorescence Line Height (nFLH) product for the average of years 2003–2011 and year 2009. Our method also enables the retrieval of chlorophyll fluorescence above land vegetation scenes. The results for the fluorescence observed above terrestrial vegetation for July and December 2009 were compared to MODIS Enhanced Vegetation Index (EVI). The comparisons show good spatial agreement between different retrievals providing evidence for the good performance of our algorithm. The method presented is generic and can be applied to other hyperspectral instruments in the future. Having established the retrieval technique, extensive studies of chlorophyll fluorescence will improve global knowledge on physiology and photosynthetic efficiency, in both the marine and terrestrial realms, and its dependence on environmental factors.
•Detecting filling-in of Fraunhofer lines by marine chlorophyll fluorescence is shown.•Retrieval results for instruments SCIAMACHY and GOME-2 are presented.•The method is generic and can be applied to other future hyperspectral instruments.•We can also observe terrestrial vegetation fluorescence.•Our results show spatial agreement with MODIS nFLH (ocean) and EVI (land) products.
SCIATRAN is a comprehensive software package which is designed to model radiative transfer processes in the terrestrial atmosphere and ocean in the spectral range from the ultraviolet to the thermal ...infrared (0.18–40μm). It accounts for multiple scattering processes, polarization, thermal emission and ocean–atmosphere coupling. The main goal of this paper is to present a recently developed version of SCIATRAN which takes into account accurately inelastic radiative processes in both the atmosphere and the ocean. In the scalar version of the coupled ocean–atmosphere radiative transfer solver presented by Rozanov et al. 61 we have implemented the simulation of the rotational Raman scattering, vibrational Raman scattering, chlorophyll and colored dissolved organic matter fluorescence.
In this paper we discuss and explain the numerical methods used in SCIATRAN to solve the scalar radiative transfer equation including trans-spectral processes, and demonstrate how some selected radiative transfer problems are solved using the SCIATRAN package. In addition we present selected comparisons of SCIATRAN simulations with those published benchmark results, independent radiative transfer models, and various measurements from satellite, ground-based, and ship-borne instruments.
The extended SCIATRAN software package along with a detailed User's Guide is made available for scientists and students, who are undertaking their own research typically at universities, via the web page of the Institute of Environmental Physics (IUP), University of Bremen: http://www.iup.physik.uni-bremen.de.
•A new version of the software package SCIATRAN is presented.•Inelastic scattering in water and atmosphere is implemented in SCIATRAN.•Raman scattering and fluorescence can be included in radiative transfer calculations.•Comparisons to other radiative transfer models show excellent agreement.•Comparisons to observations show consistent results.
In this study the technique of Differential Optical Absorption Spectroscopy (DOAS) has been adapted for the retrieval of the absorption and biomass of two major phytoplankton groups (PhytoDOAS) from ...data of the Scanning Imaging Absorption Spectrometer for Atmospheric Chartography (SCIAMACHY) satellite sensor. SCIAMACHY measures back scattered solar radiation in the UV-Vis-NIR spectral regions with a high spectral resolution (0.2 to 1.5 nm). In order to identify phytoplankton absorption characteristics in the SCIAMACHY data in the range of 430 to 500 nm, phytoplankton absorption spectra measured in-situ during two different RV "Polarstern" expeditions were used. The two spectra have been measured in different ocean regions where different phytoplankton groups (cyanobacteria and diatoms) dominated the phytoplankton composition. Results clearly show distinct absorption characteristics of the two phytoplankton groups in the SCIAMACHY spectra. Using these results in addition to calculations of the light penetration depth derived from DOAS retrievals of the inelastic scattering (developed by Vountas et al., 2007), globally distributed pigment concentrations for these characteristic phytoplankton groups for two monthly periods (February–March 2004 and October–November 2005) were determined. This satellite information on cyanobacteria and diatoms distribution clearly matches the concentrations based on high pressure liquid chromatography (HPLC) pigment analysis of collocated water samples and concentrations derived from a global model analysis with the NASA Ocean Biogeochemical Model (Gregg et al., 2003; Gregg and Casey 2007). The quantitative assessment of the distribution of key phytoplankton groups from space enables various biogeochemical regions to be distinguished and will be of great importance for the global modeling of marine ecosystems and biogeochemical cycles which enables the impact of climate change in the oceanic biosphere to be estimated.
TP53 nonsense mutations in cancer produce truncated inactive p53 protein. We show that 5-FU metabolite 5-Fluorouridine (FUr) induces full-length p53 in human tumor cells carrying R213X nonsense ...mutant TP53. Ribosome profiling visualized translational readthrough at the R213X premature stop codon and demonstrated that FUr-induced readthrough is less permissive for canonical stop codon readthrough compared to aminoglycoside G418. FUr is incorporated into mRNA and can potentially base-pair with guanine, allowing insertion of Arg tRNA at the TP53 R213X UGA premature stop codon and translation of full-length wild-type p53. We confirmed that full-length p53 rescued by FUr triggers tumor cell death by apoptosis. FUr also restored full-length p53 in TP53 R213X mutant human tumor xenografts in vivo. Thus, we demonstrate a novel strategy for therapeutic rescue of nonsense mutant TP53 and suggest that FUr should be explored for treatment of patients with TP53 nonsense mutant tumors.
In this study temporal variations of coccolithophore blooms are investigated using satellite data. Eight years (from 2003 to 2010) of data of SCIAMACHY, a hyper-spectral satellite sensor on-board ...ENVISAT, were processed by the PhytoDOAS method to monitor the biomass of coccolithophores in three selected regions. These regions are characterized by frequent occurrence of large coccolithophore blooms. The retrieval results, shown as monthly mean time series, were compared to related satellite products, including the total surface phytoplankton, i.e. total chlorophyll a (from GlobColour merged data) and the particulate inorganic carbon (from MODIS-Aqua). The inter-annual variations of the phytoplankton bloom cycles and their maximum monthly mean values have been compared in the three selected regions to the variations of the geophysical parameters: sea-surface temperature (SST), mixed-layer depth (MLD) and surface wind-speed, which are known to affect phytoplankton dynamics. For each region, the anomalies and linear trends of the monitored parameters over the period of this study have been computed. The patterns of total phytoplankton biomass and specific dynamics of coccolithophore chlorophyll a in the selected regions are discussed in relation to other studies. The PhytoDOAS results are consistent with the two other ocean color products and support the reported dependencies of coccolithophore biomass dynamics on the compared geophysical variables. This suggests that PhytoDOAS is a valid method for retrieving coccolithophore biomass and for monitoring its bloom developments in the global oceans. Future applications of time series studies using the PhytoDOAS data set are proposed, also using the new upcoming generations of hyper-spectral satellite sensors with improved spatial resolution.
Frequent environmental changes and abiotic gradients of the Wadden Sea require appropriate adaptations of the local organisms and make it suitable for investigations on functional structure of ...macrozoobenthic communities from marine to terrestrial boundaries. To investigate community patterns and food use of the macrozoobenthos, a transect of 11 stations was sampled for species number, abundance and stable isotope values (δ13C and δ15N) of macrozoobenthos and for stable isotope values of potential food resources. The transect was located in the back-barrier system of the island of Spiekeroog (southern North Sea, Germany). Our results show that surface and subsurface deposit feeders, such as Peringia ulvae and different oligochaete species, dominated the community, which was poor in species, while species present at the transect stations reached high abundance. The only exception was the upper salt marsh with low abundances but higher species richness because of the presence of specialized semi-terrestrial and terrestrial taxa. The macrozoobenthos relied predominantly on marine resources irrespective of the locality in the intertidal zone, although δ13C values of the consumers decreased from −14.1±1.6‰ (tidal flats) to −21.5±2.4‰ (salt marsh). However, the ubiquitous polychaete Hediste diversicolor showed a δ15N enrichment of 2.8‰ (an increase of about one trophic level) from bare sediments to the first vegetated transect station, presumably due to switching from suspension or deposit feeding to predation on smaller invertebrates. Hence, we conclude that changes in feeding mode represent an important mechanism of adaptation to different Wadden Sea habitats.
•The macrozoobenthos from marine-terrestrial boundaries relied predominantly on marine resources.•The polychaete Hediste diversicolor suspension/deposit feeding to predation switched from higher, vegetated habitats.•The habitat-related diet shift of H. diversicolor represents a unique adaptation to the changing environmental conditions.•Diet switching and marine resources resulted in similar macrozoobenthos communities along the marine-terrestrial gradient.
The euphotic depth (Zeu) is a key parameter in modelling primary production (PP) using satellite ocean colour. However, evaluations of satellite Zeu products are scarce. The objective of this paper ...is to investigate existing approaches and sensors to estimate Zeu from satellite and to evaluate how different Zeu products might affect the estimation of PP in the Southern Ocean (SO). Euphotic depth was derived from MODIS and SeaWiFS products of (i) surface chlorophyll-a (Zeu-Chla) and (ii) inherent optical properties (Zeu-IOP). They were compared with in situ measurements of Zeu from different regions of the SO. Both approaches and sensors are robust to retrieve Zeu, although the best results were obtained using the IOP approach and SeaWiFS data, with an average percentage of error (E) of 25.43% and mean absolute error (MAE) of 0.10m (log scale). Nevertheless, differences in the spatial distribution of Zeu-Chla and Zeu-IOP for both sensors were found as large as 30% over specific regions. These differences were also observed in PP. On average, PP based on Zeu-Chla was 8% higher than PP based on Zeu-IOP, but it was up to 30% higher south of 60°S. Satellite phytoplankton absorption coefficients (aph) derived by the Quasi-Analytical Algorithm at different wavelengths were also validated and the results showed that MODIS aph are generally more robust than SeaWiFS. Thus, MODIS aph should be preferred in PP models based on aph in the SO. Further, we reinforce the importance of investigating the spatial differences between satellite products, which might not be detected by the validation with in situ measurements due to the insufficient amount and uneven distribution of the data.
•Analysis of euphotic depth and phytoplankton absorption from SeaWiFS and MODIS•Two approaches (empirical and semi-analytical) for estimating euphotic depth•Validation and comparison using in situ measurements•Large differences in the spatial distribution of euphotic depth between approaches•Quantitative analysis of the influence on primary production estimates.
Human leukocyte antigen (HLA) restriction of conventional T-cell targeting introduces complexity in generating T-cell therapy strategies for patients with cancer with diverse HLA-backgrounds. A ...subpopulation of atypical, major histocompatibility complex-I related protein 1 (MR1)-restricted T-cells, distinctive from mucosal-associated invariant T-cells (MAITs), was recently identified recognizing currently unidentified MR1-presented cancer-specific metabolites. It is hypothesized that the MC.7.G5 MR1T-clone has potential as a pan-cancer, pan-population T-cell immunotherapy approach. These cells are irresponsive to healthy tissue while conferring T-cell receptor(TCR) dependent, HLA-independent cytotoxicity to a wide range of adult cancers. Studies so far are limited to adult malignancies. Here, we investigated the potential of MR1-targeting cellular therapy strategies in pediatric cancer. Bulk RNA sequencing data of primary pediatric tumors were analyzed to assess MR1 expression. In vitro pediatric tumor models were subsequently screened to evaluate their susceptibility to engineered MC.7.G5 TCR-expressing T-cells. Targeting capacity was correlated with qPCR-based MR1 mRNA and protein overexpression. RNA expression of MR1 in primary pediatric tumors varied widely within and between tumor entities. Notably, embryonal tumors exhibited significantly lower MR1 expression than other pediatric tumors. In line with this, most screened embryonal tumors displayed resistance to MR1T-targeting in vitro. MR1T susceptibility was observed particularly in pediatric leukemia and diffuse midline glioma models. This study demonstrates potential of MC.7.G5 MR1T-cell immunotherapy in pediatric leukemias and diffuse midline glioma, while activity against embryonal tumors was limited. The dismal prognosis associated with relapsed/refractory leukemias and high-grade brain tumors highlights the promise to improve survival rates of children with these cancers.
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