Structural evidence for extracellular silica formation by diatoms.
Ontology highlight
ABSTRACT:
SUBMITTER: Mayzel B
PROVIDER: S-EPMC8324917 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Proteins associated with diatom silica are likely involved in the biogenesis of the complex, species-specific morphologies of the biomineral, but only very few such proteins have been identified. In this project we extracted and identified proteins from three related, but morphologically distinct, species of centric diatoms: Thalassiosira pseudonana, Thalassiosira oceanica and Cyclotella cryptica.
2022-05-30 | PXD026496 | Pride
Project description:Diatoms play an important role in marine biogeochemical cycle of aluminum (Al), as dissolved Al is taken up by diatoms to build their siliceous frustules and is involved in the sedimentation of diatomaceous biogenic silica (BSi). The Al incorporation in BSi facilitates decreasing the dissolution of marine BSi and thus substantially influences the biochemical processes driven by diatoms, such as CO2 sequestration. However, the role of lake BSi in the terrestrial biochemical Al cycle has not been explored, though lakes represent the second-largest sink for BSi. By identifying the previously unexplored high Al/Si atomic ratios (up to 0.052) in lake BSi, here we show lake BSi is a large terrestrial Al pool due to its high Al content, and lake sedimentary BSi constitutes a significant global sink for Al, which is on the same magnitude as the Al sink in global oceans.
| S-EPMC6811591 | biostudies-literature
Project description:BackgroundDiatoms belong to the stramenopiles, one of the largest groups of eukaryotes, which are primarily characterized by a presence of an anterior flagellum with tubular mastigonemes and usually a second, smooth flagellum. Based on cell wall morphology, diatoms have historically been divided into centrics and pennates, of which only the former have flagella and only on the sperm. Molecular phylogenies show the pennates to have evolved from among the centrics. However, the timing of flagellum loss--whether before the evolution of the pennate lineage or after--is unknown, because sexual reproduction has been so little studied in the 'araphid' basal pennate lineages, to which Pseudostaurosira belongs.Methods/principal findingSexual reproduction of an araphid pennate, Pseudostaurosira trainorii, was studied with light microscopy (including time lapse observations and immunofluorescence staining observed under confocal scanning laser microscopy) and SEM. We show that the species produces motile male gametes. Motility is mostly associated with the extrusion and retrieval of microtubule-based 'threads', which are structures hitherto unknown in stramenopiles, their number varying from one to three per cell. We also report experimental evidence for sex pheromones that reciprocally stimulate sexualization of compatible clones and orientate motility of the male gametes after an initial 'random walk'.Conclusions/significanceThe threads superficially resemble flagella, in that both are produced by male gametes and contain microtubules. However, one striking difference is that threads cannot beat or undulate and have no motility of their own, and they do not bear mastigonemes. Threads are sticky and catch and draw objects, including eggs. The motility conferred by the threads is probably crucial for sexual reproduction of P. trainorii, because this diatom is non-motile in its vegetative stage but obligately outbreeding. Our pheromone experiments are the first studies in which gametogenesis has been induced in diatoms by cell-free exudates, opening new possibilities for molecular 'dissection' of sexualization.
| S-EPMC3202595 | biostudies-literature
Project description:In the past decade, mesoporous silica nanoparticles (MSNs) with a large surface area and pore volume have attracted considerable attention for their application in drug delivery and biomedicine. Here we propose biosilica from diatoms as an alternative source of mesoporous materials in the field of multifunctional supports for cell growth: the biosilica surfaces were chemically modified by traditional silanization methods resulting in diatom silica microparticles functionalized with 3-mercaptopropyl-trimethoxysilane (MPTMS) and 3-aminopropyl-triethoxysilane (APTES). Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy analyses revealed that the -SH or -NH₂ were successfully grafted onto the biosilica surface. The relationship among the type of functional groups and the cell viability was established as well as the interaction of the cells with the nanoporosity of frustules. These results show that diatom microparticles are promising natural biomaterials suitable for cell growth, and that the surfaces, owing to the mercapto groups, exhibit good biocompatibility.
| S-EPMC5597278 | biostudies-literature
Project description:Algal viruses are important contributors to carbon cycling, recycling nutrients and organic material through host lysis. Although viral infection has been described as a primary mechanism of phytoplankton mortality, little is known about host defense responses. We show that viral infection of the bloom-forming, planktonic diatom Chaetoceros socialis induces the mass formation of resting spores, a heavily silicified life cycle stage associated with carbon export due to rapid sinking. Although viral RNA was detected within spores, mature virions were not observed. 'Infected' spores were capable of germinating, but did not propagate or transmit infectious viruses. These results demonstrate that diatom spore formation is an effective defense strategy against viral-mediated mortality. They provide a possible mechanistic link between viral infection, bloom termination, and mass carbon export events and highlight an unappreciated role of viruses in regulating diatom life cycle transitions and ecological success.
| S-EPMC7894508 | biostudies-literature
Project description:Core-shell structures containing active materials can be fabricated using almost infinite reactant combinations. A mechanism to describe their formation is therefore useful. In this work, nanoscale all-silica shell capsules with an aqueous core were fabricated by the HCl-catalyzed condensation of tetraethyl orthosilicate (TEOS), using Pickering emulsion templates. Pickering emulsions were fabricated using modified commercial silica (LUDOX TMA) nanoparticles as stabilizers. By following the reaction over a 24 h period, a general mechanism for their formation is suggested. The interfacial activity of the Pickering emulsifiers heavily influenced the final capsule products. Fully stable Pickering emulsion templates with interfacially active particles allowed a highly stable sub-micrometer (500-600 nm) core-shell structure to form. Unstable Pickering emulsions, i.e., where interfacially inactive silica nanoparticles do not adsorb effectively to the interface and produce only partially stable emulsion droplets, resulted in capsule diameter increasing markedly (1+ μm). Scanning electron microscope (SEM) and transmission electron microscope (TEM) measurements revealed the layered silica "colloidosome" structure: a thin yet robust inner silica shell with modified silica nanoparticles anchored to the outer interface. Varying the composition of emulsion phases also affected the size of capsule products, allowing size tuning of the capsules. Silica capsules are promising protective nanocarriers for hydrophilic active materials in applications such as heat storage, sensors, and drug delivery.
| S-EPMC8057668 | biostudies-literature
Project description:Biological production and decay of the reactive oxygen species (ROS) hydrogen peroxide (H2O2) and superoxide (O[Formula: see text]) likely have significant effects on the cycling of trace metals and carbon in marine systems. In this study, extracellular production rates of H2O2 and O[Formula: see text] were determined for five species of marine diatoms in the presence and absence of light. Production of both ROS was measured in parallel by suspending cells on filters and measuring the ROS downstream using chemiluminescence probes. In addition, the ability of these organisms to break down O[Formula: see text] and H2O2 was examined by measuring recovery of O[Formula: see text] and H2O2 added to the influent medium. O[Formula: see text] production rates ranged from undetectable to 7.3 × 10(-16) mol cell(-1) h(-1), while H2O2 production rates ranged from undetectable to 3.4 × 10(-16) mol cell(-1) h(-1). Results suggest that extracellular ROS production occurs through a variety of pathways even amongst organisms of the same genus. Thalassiosira spp. produced more O[Formula: see text] in light than dark, even when the organisms were killed, indicating that O[Formula: see text] is produced via a passive photochemical process on the cell surface. The ratio of H2O2 to O[Formula: see text] production rates was consistent with production of H2O2 solely through dismutation of O[Formula: see text] for T. oceanica, while T. pseudonana made much more H2O2 than O[Formula: see text]. T. weissflogii only produced H2O2 when stressed or killed. P. tricornutum cells did not make cell-associated ROS, but did secrete H2O2-producing substances into the growth medium. In all organisms, recovery rates for killed cultures (94-100% H2O2; 10-80% O[Formula: see text]) were consistently higher than those for live cultures (65-95% H2O2; 10-50% O[Formula: see text]). While recovery rates for killed cultures in H2O2 indicate that nearly all H2O2 was degraded by active cell processes, O[Formula: see text] decay appeared to occur via a combination of active and passive processes. Overall, this study shows that the rates and pathways for ROS production and decay vary greatly among diatom species, even between those that are closely related, and as a function of light conditions.
| S-EPMC4812844 | biostudies-literature
Project description:Purpose: The Goal of this study is to look at 1) Differences in genome wide localization of Scc2 between wild type and scc4-m35 cells in S-phase 2) Differences in genome wide localisation of Scc1 cohesin between wild type and scc4-m35 in metaphase arrested cells. Method: 1) Wild-type (AM15307) and scc4-m35 (AM15311) cells carrying SCC2-3FLAG were fixed for 2 hr, 15 min following an a-factor arrest. Samples were harvested, anti-HA ChIP was performed and both input and IP samples were sequenced for both strains. 2) Wild-type (AM1145), wild type constructed in the same way as the mutant strain (carrying a HIS3 marker) (AM15540) and scc4-m35 mutant (AM15537) cells carrying SCC1-6HA were synchronised with a-factor and arrested in mitosis by treatment with nocodazole/benomyl for 2 hr. Samples were harvested, anti-HA ChIP was performed and input and IP samples were sequenced for the three strains. Results: 1) This experiment did not yield meaningful data. 2) All 16 centromeres were specifically depleted of Scc1 in the scc4-m35 background. Scc1 depletion extended roughly 10 kilobases to either side of the core centromere but not to chromosome arms 1) ChIP-seq for S. cerevisiae Scc2-3FLAG in S-phase cells in Wild type and in scc4-m35 mutant (samples VM1-VM4). 2) ChIP-seq for Scc1-6HA in metaphase-arrested cells in Wild type and in scc4-m35 mutant (samples VM5-VM10) Vasso Makrantoni: experiments and Alastair Kerr: ChIP Seq Data analysis https://github.com/AlastairKerr/Hinshaw2015
2015-06-05 | E-GEOD-68573 | biostudies-arrayexpress
Project description:The rapid growth of diatoms makes them one of the most pervasive and productive types of plankton in the world's ocean, but the physiological basis for their high growth rates remains poorly understood. Here, we evaluate the factors that elevate diatom growth rates, relative to other plankton, using a steady-state metabolic flux model that computes the photosynthetic C source from intracellular light attenuation and the carbon cost of growth from empirical cell C quotas, across a wide range of cell sizes. For both diatoms and other phytoplankton, growth rates decline with increased cell volume, consistent with observations, because the C cost of division increases with size faster than photosynthesis. However, the model predicts overall higher growth rates for diatoms due to reduced C requirements and the low energetic cost of Si deposition. The C savings from the silica frustule are supported by metatranscriptomic data from Tara Oceans, which show that the abundance of transcripts for cytoskeleton components in diatoms is lower than in other phytoplankton. Our results highlight the importance of understanding the origins of phylogenetic differences in cellular C quotas, and suggest that the evolution of silica frustules may play a critical role in the global dominance of marine diatoms. IMPORTANCE This study addresses a longstanding issue regarding diatoms, namely, their fast growth. Diatoms, which broadly are phytoplankton with silica frustules, are the world's most productive microorganisms and dominate in polar and upwelling regions. Their dominance is largely supported by their high growth rate, but the physiological reasoning behind that characteristic has been obscure. In this study, we combine a quantitative model and metatranscriptomic approaches and show that diatoms' low carbon requirements and low energy costs for silica frustule production are the key factors supporting their fast growth. Our study suggests that the effective use of energy-efficient silica as a cellular structure, instead of carbon, enables diatoms to be the most productive organisms in the global ocean.
| S-EPMC10269801 | biostudies-literature
Project description:Purpose: The goal of this study is to look at differences in genome wide localisation of Scc1 cohesin between wild type and scc4-m35 in metaphase arrested cells. Method: Wild-type (AM1145), wild type constructed in the same way as the mutant strain (carrying a HIS3 marker) (AM15540) and scc4-m35 mutant (AM15537) cells carrying SCC1-6HA were synchronised with a-factor and arrested in mitosis by treatment with nocodazole/benomyl for 2 hr. Samples were harvested, anti-HA ChIP was performed and input and IP samples were sequenced for the three strains. Results: All 16 centromeres were specifically depleted of Scc1 in the scc4-m35 background. Scc1 depletion extended roughly 10 kilobases to either side of the core centromere but not to chromosome arms
2015-06-05 | GSE68573 | GEO