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opencc-by-4.0Apr 2021View details →

Metadata of "Light-Emitting Biosilica by In Vivo Functionalization of Phaeodactylum tricornutum Diatom Microalgae with Organometallic Complexes"

Metadata of "Light-Emitting Biosilica by In Vivo Functionalization of Phaeodactylum tricornutum Diatom Microalgae with Organometallic Complexes"

opencc-by-4.0Jul 2022View details →

Scanning electron microscope images of Dunaliela tertiolecta and Phaeodactylum tricornutum cultures and scanning electron microscope images and cryogenic electron microscope images of isolated small cellular particles from respective conditioned media

Scanning electron microscope images of cultures of microalgae Dunaliela tertiolecta and Phaeodactylum tricornutum and scanning electron microscope images and cryogenic electron microscope images of isolated small cellular particles from respective conditioned media are presented. Each image is supplemented by description of the preparation of the sample and the data on the imaging technique and equipment. The data are curated by Veronika Kralj-Iglic and Anna Romolo, University of Ljubljana, Faculty of Health Sciences, Laboratory of Clinical Biophysics.

dryad40/100

Dataset for: Temperature sensitivity of carbon concentrating mechanisms in the diatom Phaeodactylum tricornutum

Marine diatoms are key primary producers across diverse habitats in the global ocean. Diatoms rely on a biophysical carbon concentrating mechanism (CCM) to supply high concentrations of CO2 around their carboxylating enzyme, RuBisCO. The necessity and energetic cost of the CCM are likely to be highly sensitive to temperature, as temperature impacts CO2 concentration, diffusivity, and the kinetics of CCM components. Here, we used membrane inlet mass spectrometry (MIMS) and modeling to capture temperature regulation of the CCM in the diatom Phaeodactylum tricornutum (Pt). We found that enhanced carbon fixation rates by Pt at elevated temperatures were accompanied by increased CCM activity capable of maintaining RuBisCO close to CO2 saturation but that the mechanism varied. At 10 and 18 °C, diffusion of CO2 into the cell, driven by Pt's 'chloroplast pump' was the major inorganic carbon source. However, at 18 °C, upregulation of the chloroplast pump enhanced (while retaining the proportion of) both diffusive CO2 and active HCO3- uptake into the cytosol, and significantly increased chloroplast HCO3- concentrations. In contrast, at 25 °C, compared to 18 °C, the chloroplast pump had only a slight increase in activity. While diffusive uptake of CO2 into the cell remained constant, active HCO3- uptake across the cell membrane increased resulting in Pt depending equally on both CO2 and HCO3- as inorganic carbon sources. Despite changes in the CCM, the overall rate of active carbon transport remained double that of carbon fixation across all temperatures tested. The implication of the energetic cost of the Pt CCM in response to increasing temperatures was discussed.

opencc-zeroMar 2023View details →

Figure 5 in Response of marine microalgae Phaeodactylum tricornutum, Prorocentrum cordatum and Gyrodinium fissum to complex pollution of Sevastopol bays (Black Sea)

Figure 5. Influence of the polluted waters of the Sevastopol area to P. tricornutum (I), P. cordatum (II) and G. fissum (III): a) – inhibition effect, b) stimulated effect and c) absence of effect.

Figure 4 in Response of marine microalgae Phaeodactylum tricornutum, Prorocentrum cordatum and Gyrodinium fissum to complex pollution of Sevastopol bays (Black Sea)

Figure 4. Dynamics of the cells abundance in the cultures of P. tricornutum (a), P. cordatum (b) and G. fissum (c) in control (1), on the water of the mussel farm area (2), Artillery Bay (3) and Sevastopol Bay (4) in October 2020.

Figure 1 in Response of marine microalgae Phaeodactylum tricornutum, Prorocentrum cordatum and Gyrodinium fissum to complex pollution of Sevastopol bays (Black Sea)

Figure 1. Map of the seawater sampling stations location: 1 – mussel farm area, 2 – Artillery Bay, 3 – Sevastopol Bay.

Figure 3 in Response of marine microalgae Phaeodactylum tricornutum, Prorocentrum cordatum and Gyrodinium fissum to complex pollution of Sevastopol bays (Black Sea)

Figure 3. Dynamics of the cells abundance in the cultures of P. tricornutum (a), P. cordatum (b) and G. fissum (c) in control (1), on the water from the mussel farm area (2), Artillery Bay (3) and Sevastopol Bay (4) in September 2020.

publicMar 2023View details →

dryad40/100

Dataset for: Temperature sensitivity of carbon concentrating mechanisms in the diatom Phaeodactylum tricornutum

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zenodo32/100

Raw data on dynamic light scattering assessment of small cellular particles isolated from conditioned culture media of Dunaliella tertiolecta and Phaeodactylum tricornutum. Effect of Triton X-100 and temperature

Raw data on dynamic light scattering assessment of small cellular particles isolated from conditioned culture media of microalgae Dunaliella tertiolecta (D. tertiolecta) and Phaeodactylum tricurnutum (P. tricornutum) by dynamic light scattering are presented. The project contains spreadsheet files with the measured dependencies of g2 function on time. We collected several g2 functions for each setting (3 for D. tertiolecta samples, 5 for D. tertiolecta with added TX100, 3 for P. tricornutum samples, 3 for P. tricornutum with added TX100). Curves were analyzed independently and compared with the respective averaged curve fitted by the inverse Laplace transform program CONTIN (freely available at: <a href="http://s-provencher.com/index.shtml">http://s-provencher.com/index.shtml</a>, the code was accessed 25. 1. 2011). The correlation curves were fitted with up to 50 exponents. For analysis of stability of small cellular particles with respect to temperature change, we have overall reports for each microalgae type and reports on the size distribution function, data for the g2 function and dependence of scattered light intensity on time for each temperature measured. There were 14 temperatures chosen for each type of microalgae. The files are marked with respective temperatures. The samples were prepared as described below: Cultivation of the algae: Cultures of D. tertiolecta CCAP 19/22 and P. tricornutum CCAP 1052/1A from the Culture Collection of Algae and Protozoa (CCAP) of SAMS (Oban, Scotland) were grown in artificial seawater (Reef Crystals, Aquarium Systems, France). 22 g of salt was dissolved in one litre of distilled water, sterile filtered (0.2-micron cellulose filters, ref. 11107-47-CAN, Sartorius Stedim Biotech GmbH, Germany), autoclaved, and supplemented with Guillard’s (F/2) Marine Water Enrichment Solution (ref. G0154, Sigma Aldrich, USA). Cultures were grown in a respirometer (Echo, Slovenia) in 0.5-L borosilicate bottles, at 20 °C and 20 % illumination (approximately 250 μmol/m2s) with a 14-hour light / 10-hour dark cycle, with aeration of 0.2 L/min. Isolation of small cellular nanoparticles: Small cellular particles were isolated by differential centrifugation, using a protocol widely used for the isolation of extracellular vesicles (Théry C, Amigorena S, Raposo G, Clayton A. Isolation and Characterization of Exosomes from Cell Culture Supernatants and Biological Fluids. Current Protocols in Cell Biology. 2006;30(1). doi:10.1002/0471143030.cb0322s30). Microalgal cells were removed by low-speed centrifugation (300 g, 10 min, 4°C, centrifuge Centric 260R with rotor RA 6/50 (Domel, Slovenia)), using 50 mL conical centrifuge tubes (ref. S.078.02.008.050, Isolab Laborgeräte GmbH, Germany); and 2000 g, 10 min, 4°C (Centric 400R centrifuge with rotor RS4/100 (Domel, Slovenia)), using 15 mL conical centrifuge tubes (ref. S.078.02.001.050, Isolab Laborgeräte GmbH, Germany). Each step was repeated twice. Then, the cell-depleted medium was centrifuged twice at 10 000g and 4°C for 30 min (Beckman L8-70M ultracentrifuge, rotor SW55Ti (Beckman Coulter, USA)), using thin-wall polypropylene centrifuge tubes (ref. 326819, Beckman Coulter, USA) to remove larger cell debris. Finally, small cellular particles were pelleted by centrifugation at 118 000 g and 4°C, for 70 min in the same type of ultracentrifuge and ultracentrifuge tubes. The isolate obtained from about 30 mL of conditioned media was not visible to the eye. For treatment with Triton X-100, the sample was incubated with Triton X-100 at concentration of 0.1%. Dynamic light scattering (DLS): The average hydrodynamic radius (Rh) of NPs and the average intensity of scattered light (I) were assessed for characterization of small cellular particles by DLS. The value of I was interpreted as a measure of small cellular particles concentration (in the case of preserved particle size distribution) or as a topological change (in the case of altered particle size distribution)(Paterna A, Rao E, Adamo G, et al. Isolation of Extracellular Vesicles From Microalgae: A Renewable and Scalable Bioprocess. Front Bioeng Biotechnol. 2022;10:836747. doi:10.3389/fbioe.2022.836747; Brown W, ed. Dynamic Light Scattering: The Method and Some Applications. Clarendon Press ; Oxford University Press; 1993). For analysis of the samples we used Instrument 3D-DLS-SLS cross-correlation spectrometer from LS Instruments GmbH (Fribourg, Switzerla nd) with a 100 mW DPSS laser (Cobolt Flamenco, Cobolt AB, Sweden) having a wavelength λ0 = 660 nm. Before measurements, samples were equilibrated in a decalin bath at 25 °C for 15 min. The scattered light was measured at an angle θ = 90° for 120 s. The correlation functions and integral time-averaged intensities I(θ)&equiv; I(q) (where q is the scattering vector, defined as q =(4πn0/λ0)sin(θ/2), with n0  the refractive index of the medium, in our case estimated by the corresponding value for water, i.e. n0 = 1.33 at 25°C), were recorded simultaneously. The Rh values of small cellular particles were obtained from the diffusion coefficients (D) that were assessed from the correlation function of the scattered electric field (g1(t)). The g1(t) function was calculated from the measured correlation function of the scattered light intensity g2(t) by applying Siegert’s relation (Schärtl W. Light Scattering from Polymer Solutions and Nanoparticle Dispersions. Springer; 2007; Shurer CR, Kuo JCH, Roberts LM, et al. Physical Principles of Membrane Shape Regulation by the Glycocalyx. Cell. 2019;177(7):1757-1770.e21. doi:10.1016/j.cell.2019.04.017). To convert D to Rh, the Stokes-Einstein equation was used (Rh = kT6πηD, where k is the Boltzmann constant, T is the absolute temperature, and η is the viscosity of the medium in which the particles diffuse). It was assumed that particles have a spherical shape. The viscosity of the medium was not known. We approximated the viscosity value to that of of water at 25°C.To test the effect of Triton X-100 on the samples, 0.1% (V/V) of Triton X-100 was added to the sample before the measurement. The change in Rh distribution and the change of scattered light intensity (ΔI = Isample - Isample+0.1%.TX100) was determined. The analysis was made with an in-house created software based on the inverse Laplace transform program CONTIN (freely available at: <a href="http://s-provencher.com/index.shtml">http://s-provencher.com/index.shtml</a>, the code was accessed 25. 1. 2011). We collected several intensity correlation functions for each setting. Curves were analyzed independently and compared with the averaged curve. The correlation curves were fitted with up to 50 exponents. To test the effect of Triton X-100 on NPs, 0.1% (V/V) of Triton X-100 was added to the sample before the measurement. The change in Rh distribution and the change of scattered light intensity (ΔI = Isample - Isample+0.1%.TritonX-100) was determined. Thermal stability analysis was performed using the LitesizerTM 500 instrument (Anton Paar GmbH). Samples were heated from 15 °C to 80 °C in 5 °C steps. When the target temperature was reached, the samples were equilibrated for another 5 minutes before 10 measurements of 20 s duration were performed. The size distributions were determined from the mean correlation function using the Anton Paar Kalliope Professional; Version 2.16.0. (Anton Paar GmbH), <a href="https://www.anton-paar.com/corp-en/products/details/software-for-particle-analysis-kalliopetm/">https://www.anton-paar.com/corp-en/products/details/software-for-particle-analysis-kalliopetm/</a>,  applying the CONTIN approach. A new version of KalliopeTM 4.12.0 <a href="https://www.kalliope.com/2021/05/03/versione-firmware-4-12-0/?lang=en">https://www.kalliope.com/2021/05/03/versione-firmware-4-12-0/?lang=en</a> is freely available online.

opencc-by-4.0Aug 2022View details →

dryad32/100

Data from: Phylogenetic analysis and a review of the history of the accidental phytoplankter, Phaeodactylum tricornutum Bohlin (Bacillariophyta)

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publicApr 2019View details →

zenodo28/100

Figure 2 in Response of marine microalgae Phaeodactylum tricornutum, Prorocentrum cordatum and Gyrodinium fissum to complex pollution of Sevastopol bays (Black Sea)

Figure 2. Dynamics of the cells abundance in the cultures of P. tricornutum (a), P. cordatum (b) and G. fissum (c) in control (1), on the water from the mussel farm area (2), Artillery Bay (3) and Sevastopol Bay (4) in June 2020.

openGEO-OpenDec 2019View details →

Early dynamics of photosynthetic Lhcf2 and Lhcf15 transcription and mRNA stabilities in response to herbivory-related decadienal in Phaeodactylum tricornutum

GEO Series GSE142157. Phaeodactylum tricornutum. 8 samples. Type: Expression profiling by high throughput sequencing.

openGEO-OpenJan 2015View details →

Next generation sequencing of Phaeodactylum tricornutum grown with and without nitrogen

GEO Series GSE56346. Phaeodactylum tricornutum. 6 samples. Type: Expression profiling by high throughput sequencing.

openGEO-OpenDec 2014View details →

System responses to equal doses of photosynthetically usable radiation of blue, green, and red light in the marine diatom Phaeodactylum tricornutum.

GEO Series GSE55959. Phaeodactylum tricornutum. 27 samples. Type: Expression profiling by array.

openGEO-OpenJun 2015View details →

Whole cell response to nitrogen deprivation in the diatom Phaeodactylum tricornutum

GEO Series GSE58946. Phaeodactylum tricornutum. 12 samples. Type: Expression profiling by array.

openGEO-OpenMar 2023View details →

Evolutionary and functional analysis of DNA methyltransferases in micro-eukaryotes: Insights from the model diatom Phaeodactylum tricornutum [RNA-seq]

GEO Series GSE186856. Phaeodactylum tricornutum. 6 samples. Type: Expression profiling by high throughput sequencing.

openGEO-OpenMar 2013View details →

Gene regulation of carbon fixation, storage and utilization in the diatom Phaeodactylum tricornutum acclimated to light/dark cycles

GEO Series GSE42514. Phaeodactylum tricornutum. 16 samples. Type: Expression profiling by array.

openGEO-OpenJun 2013View details →

Whole genome McrBC-chip on DNA methylation of diatom Phaeodactylum tricornutum

GEO Series GSE47947. Phaeodactylum tricornutum. 3 samples. Type: Methylation profiling by genome tiling array.