Efficacy of relacin combined with sodium hypochlorite against Enterococcus faecalis biofilms

Objective: Relacin is a synthetic molecule that targets RelA, an essential protein in a conserved bacterial stress response system. It was shown to inhibit bacterial growth. The aims of this study were to evaluate the antimicrobial effect of relacin combined with sodium hypochlorite (NaOCl) on Enterococcus faecalis biofilms and to evaluate the cytotoxicity of relacin. Material and Methods: 48-h E. faecalis OG1RF biofilms were treated by various concentrations of relacin in order to determine its inhibitory concentration. Then, the 48-h biofilms were treated either with 1-min NaOCl (0.01%, 0.05%) alone, or in combination of relacin. As a means of comparison, the biofilms of ΔrelA were also treated by 1-min NaOCl (0.01%, 0.05%, 0.25%). The treatment efficacy was determined by agar plate count assays. The cytotoxicity of relacin was examined on human gingival epithelial cells Ca9-22 and murine fibroblasts NIH-3T3 by a methyl thiazolyltetrazolium (MTT) assay and a lactate dehydrogenase assay. Statistical analysis was performed by one-way or two-way analysis of variance (ANOVA) with Bonferroni’s post-hoc test and an independent Student’s t-test. A significance level of p<0.05 was used. Results: Relacin inhibited the growth of OG1RF biofilms partially at 8 mM and fully at 14 mM. The relacin (14 mM) and NaOCl combined treatment resulted in significantly higher treatment efficacy than NaOCl treatment alone. At 0.05% NaOCl, the combined treatment resulted in 5.65 (±0.19) log reduction in biofilm viability. The ΔrelA biofilms were more susceptible to NaOCl treatment than the wild type biofilms at 0.25% NaOCl. Relacin at 14 mM was not toxic to host epithelial cells and fibroblasts. Conclusions: The combination of relacin with a low concentration of NaOCl was effective and not cytotoxic

Evaluation of the Influence of Aquatic Plants and Lake Bottom on the Remote-Sensing Reflectance of Optically Shallow Waters

Aquatic plants and lake bottoms in optically shallow waters (OSWs) wield great influence on reflectance spectra, resulting in the inapplicability of most existing bio-optical models for water colour remote sensing in lakes. Based on radiative transfer theory and measured spectra from a campaign for Lake Taihu in October 2008, absorption and backscattering coefficients were used to simulate the remote-sensing reflectance, which are considered to be reliable if matched to their measured counterparts. Several cases of measured spectra at different depths, Secchi disk depth transparency, and aquatic plant height and coverage were analyzed thoroughly for spectral properties. The contribution of aquatic plants was evaluated and compared with the measured and simulated remote-sensing reflectance values. This is helpful for removing the influence of aquatic plants and lake bottoms from the spectra and for constructing an improved chlorophyll a retrieval model for OSWs, such as that for Lake Taihu, China

Phytoplankton functional types observation from space in the Fram Strait (2002-2020)

Phytoplankton in the sunlit layer of the ocean act as the base of the marine food web fueling fisheries, and also regulate key biogeochemical processes. Phytoplankton composition structure varies in ocean biomes and different phytoplankton groups drive differently the marine ecosystem and biogeochemical processes. Because of this, variations in phytoplankton composition influence the entire ocean environment, specifically the ocean energy transfer and the export of organic carbon to the deep ocean. As one of the algorithms deriving phytoplankton composition from space borne data, within the framework of the EU Copernicus Marine Service (CMEMS), EOF-PFT algorithm was developed using multi-spectral satellite data collocated to an extensive in-situ PFT data set based on HPLC pigments and sea surface temperature data (Xi et al. 2020, 2021; https://marine.copernicus.eu/). By using multi-sensor merged products and Sentinel-3 OLCI data, the algorithm provides global chlorophyll a data with per-pixel uncertainty for diatoms, haptophytes, dinoflagellates, chlorophytes and prokaryotic phytoplankton spanning the period from 2002 until today. Due to different lifespans and radiometric characteristics of the ocean color sensors, the consistency of the PFTs is evaluated to provide quality-assured data for a consistent long-term monitoring of the phytoplankton community structure. As current commonly used phytoplankton carbon estimation methods rely mostly on the backscattering property of phytoplankton, which could vary dramatically for different phytoplankton taxa, as a perspective of this study, phytoplankton carbon may be better estimated in a way that accounts for phytoplankton taxonomy

Phytoplankton Group Identification Using Simulated and In-situ Hyperspectral Remote Sensing Reflectance

Given that the commonly used parameter obtained directly from hyperspectral earth observation sensors is the remote sensing reflectance (Rrs), we focused on identification of dominant phytoplankton groups by using Rrs spectra directly. Based on five standard absorption spectra representing five different phytoplankton spectral groups, a simulated database of Rrs (C2X database, compiled within the ESA SEOM C2X Project) that includes 105 different water optical conditions was built with HydroLight. In our previous study we have proposed an identification approach to determine phytoplankton groups with the use of simulated C2X data, and the skill of the identification were also tested by investigating how and to what extend water optical constituents (Chl, NAP, and CDOM) impact the accuracy of this identification (Xi et al. 2017). To furthermore test whether the approach is applicable in various natural waters, we have collected a large set of in situ data from waters with different optical types, including coastal waters such as the German Bight and British coastal waters, and inland waters such as Elbe River and several lakes in Germany. Both in situ Rrs and absorption spectra (ap) are used to identify the dominating phytoplankton group in these waters. Identification results from both approaches are compared, and the identification performance of the Rrs-based approach can therefore be evaluated for natural water applications

High resolution water column phytoplankton composition across the Atlantic Ocean from ship-towed vertical undulating radiometry.

Different phytoplankton groups dominate ocean biomes and they drive differently the marine food web and the biogeochemical cycles. However, their distribution over most parts of the global ocean remains uncertain due to limitations in the sampling resolution of currently available in situ and satellite data. Information below surface waters are especially limited because satellite sensors only provide information on the first optical depth. We present measurements obtained during Polarstern cruise PS113 (May–June 2018) across the Atlantic Ocean from South America to Europe along numerous transects. We measured the hyperspectral underwater radiation field continuously over several hours from a vertical undulating platform towed behind the ship. Equivalent measurements were also taken at specific stations. The concentrations of phytoplankton pigments were determined on discrete water samples. Via diagnostic pigment analysis we derived the phytoplankton group chlorophyll a concentration (Chla) from this pigment data set. We obtained high resolution phytoplankton group Chla data from depth resolved apparent optical properties derived from the underwater radiation data by applying an empirical orthogonal function (EOF) analysis to the spectral data set and subsequently developing regression models using the pigment based phytoplankton group Chla and selected EOF modes. To our knowledge, this is the first data set with high horizontal coverage (50–150 km) and resolution (∼1 km) that is also resolved vertically for the Chla of major taxonomic phytoplankton groups. Subsampling with 500 permutations for cross validation verified the high robustness of our estimates to enable predictions of seven different phytoplankton groups’ Chla and of total Chla (R2 and median percent differences of the cross validation are within 0.45–0.68 and 29–53%, respectively). Our depth resolved phytoplankton groups’ Chla data reflect well the different biogeochemical provinces within the Atlantic Ocean transect and follow the distributions encountered by previous point observations. This verifies the high quality of our retrievals and provides the prospect to put similar radiometers on profiling floats or gliders which would enable the large-scale collection of vertically resolved phytoplankton data at much improved horizontal coverage relative to discrete sampling

Robust prognostic model based on immune infiltration-related genes and clinical information in ovarian cancer

Immune infiltration of ovarian cancer (OV) is a critical factor in determining patient's prognosis. Using data from TCGA and GTEx database combined with WGCNA and ESTIMATE methods, 46 genes related to OV occurrence and immune infiltration were identified. Lasso and multivariate Cox regression were applied to define a prognostic score (IGCI score) based on 3 immune genes and 3 types of clinical information. The IGCI score has been verified by K-M curves, ROC curves and C-index on test set. In test set, IGCI score (C-index = 0.630) is significantly better than AJCC stage (C-index = 0.541, p < 0.05) and CIN25 (C-index = 0.571, p < 0.05). In addition, we identified key mutations to analyse prognosis of patients and the process related to immunity. Chi-squared tests revealed that 6 mutations are significantly (p < 0.05) related to immune infiltration: BRCA1, ZNF462, VWF, RBAK, RB1 and ADGRV1. According to mutation survival analysis, we found 5 key mutations significantly related to patient prognosis (p < 0.05): CSMD3, FLG2, HMCN1, TOP2A and TRRAP. RB1 and CSMD3 mutations had small p-value (p < 0.1) in both chi-squared tests and survival analysis. The drug sensitivity analysis of key mutation showed when RB1 mutation occurs, the efficacy of six anti-tumour drugs has changed significantly (p < 0.05).Peer reviewe

20-year satellite observations of phytoplankton functional types (PFTs) in the Atlantic Ocean

Phytoplankton composition structure varies in ocean biomes. Different phytoplankton groups drive differently the marine ecosystem and biogeochemical processes. Therefore, variations in phytoplankton composition influence the entire ocean environment, specifically the ocean energy transfer, the deep ocean carbon export, water quality etc. As one of the algorithms deriving phytoplankton composition from space borne data, the EOF-PFT algorithm was developed using multi-spectral satellite data collocated to an extensive global in-situ PFT data set based on HPLC pigments and sea surface temperature data (Xi et al. 2020, 2021). By using multi-sensor merged products and Sentinel-3 OLCI data, the algorithm provides global chlorophyll a (Chla) data with per-pixel uncertainty for diatoms, haptophytes, dinoflagellates, chlorophytes and prokaryotic phytoplankton spanning the period from 2002 until today, with products available on the EU Copernicus Marine Service (CMEMS). The objectives of this study are to 1) evaluate CMEMS PFT products and improve their continuity along the products derived from different satellite sensors, and 2) 20-year satellite PFT products for time series analysis of climatology, trends, anomaly and phenology of multiple PFTs in the whole Atlantic and its different biogeochemical provinces (Longhurst, 2006)

High-resolution physical--biogeochemical structure of a filament and an eddy of upwelled water off northwest Africa

Nutrient rich water upwells offshore of Northwest Africa and is subsequently advected westwards. There it forms eddies and filaments with a rich spatial structure of physical and biological/biogeochemical properties. Here we present a high resolution (2.5 km) section through upwelling filaments and an eddy obtained in May 2018 with a Triaxus towed vehicle equipped with various oceanographic sensors. Physical processes at the mesoscale and submesoscale such as symmetric instability, trapping of fluid in eddies, and subduction of low potential vorticity (which we use as a water mass tracer) water can explain the observed distribution of biological production and export. We found a nitrate excess (higher nitrate concentrations than would be expected from oxygen values if only influenced by production and remineralization processes) core of an anti-cyclonic mode water eddy. We also found a high nitrate concentration region of ~5 km width in the mixed layer where symmetric instability appears to have injected nutrients from below into the euphotic zone. A similar region a little further south had high chlorophyll-a concentrations suggesting that nutrients had been injected there a few days earlier. Considering that such interactions of physics and biology are ubiquitous in the world's upwelling regions, we assume that they have strong influences on the productivity of such systems and their role in CO2 uptake. The intricate interplay of different parameters at kilometer scale needs to be taken into account when interpreting single profile and/or bottle data in dynamically active regions of the ocean

Satellite monitoring of surface phytoplankton functional types in the Atlantic Ocean over 20 years (2002–2021)

An analysis of multi-satellite-derived products of four major phytoplankton functional types (PFTs – diatoms, haptophytes, prokaryotes and dinoflagellates) was carried out to investigate the PFT time series in the Atlantic Ocean between 2002 and 2021. The investigation includes the 2-decade trends, climatology, phenology and anomaly of PFTs for the whole Atlantic Ocean and its different biogeochemical provinces in the surface layer that optical satellite signals can reach. The PFT time series over the whole Atlantic region showed mostly no clear trend over the last 2 decades, except for a small decline in prokaryotes and an abrupt increase in diatoms during 2018–2019, which is mainly observed in the northern Longhurst provinces. The phenology of diatoms, haptophytes and dinoflagellates is very similar: at higher latitudes bloom maxima are reached in spring (April in the Northern Hemisphere and October in the Southern Hemisphere), in the oligotrophic regions in winter time and in the tropical regions during May to September. In general, prokaryotes show opposite annual cycles to the other three PFTs and present more spatial complexity. The PFT anomaly (in percent) of 2021 compared to the 20-year mean reveals mostly a slight decrease in diatoms and a prominent increase in haptophytes in most areas of the high latitudes. Both diatoms and prokaryotes show a mild decrease along coastlines and an increase in the gyres, while prokaryotes show a clear decrease at mid-latitudes to low latitudes and an increase on the western African coast (Canary Current Coastal Province, CNRY and Guinea Current Coastal Province, GUIN) and southwestern corner of North Atlantic Tropical Gyral Province (NATR). Dinoflagellates, as a minor contributor to the total biomass, are relatively stable in the whole Atlantic region. This study illustrated the past and current PFT state in the Atlantic Ocean and acted as the first step to promote long-term consistent PFT observations that enable time series analyses of PFT trends and interannual variability to reveal potential climate-induced changes in phytoplankton composition on multiple temporal and spatial scales