SciCombinator

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Concept: Diatom

171

Diatoms, the major contributors of the global biogenic silica cycle in modern oceans, account for about 40% of global marine primary productivity. They are an important component of the biological pump in the ocean, and their assemblage can be used as useful climate proxies; it is therefore critical to better understand the changes induced by environmental pH on their physiology, silicification capability and morphology. Here, we show that external pH influences cell growth of the ubiquitous diatom Thalassiosira weissflogii, and modifies intracellular silicic acid and biogenic silica contents per cell. Measurements at the single-cell level reveal that extracellular pH modifications lead to intracellular acidosis. To further understand how variations of the acid-base balance affect silicon metabolism and theca formation, we developed novel imaging techniques to measure the dynamics of valve formation. We demonstrate that the kinetics of valve morphogenesis, at least in the early stages, depends on pH. Analytical modeling results suggest that acidic conditions alter the dynamics of the expansion of the vesicles within which silica polymerization occurs, and probably its internal pH. Morphological analysis of valve patterns reveals that acidification also reduces the dimension of the nanometric pores present on the valves, and concurrently overall valve porosity. Variations in the valve silica network seem to be more correlated to the dynamics and the regulation of the morphogenesis process than the silicon incorporation rate. These multiparametric analyses from single-cell to cell-population levels demonstrate that several higher-level processes are sensitive to the acid-base balance in diatoms, and its regulation is a key factor for the control of pattern formation and silicon metabolism.

Concepts: Developmental biology, Cell wall, PH, Silicon, Acid-base homeostasis, Bicarbonate, Diatom, Silicic acid

170

DNA barcoding is a molecular tool that exploits a unique DNA sequence of a standardized gene or non-coding region for the species identification of unknown individuals. The investigation into a suitable barcode for diatoms is ongoing and there are several promising candidates including mitochondrial, plastidial and nuclear markers. We analyzed 272 sequences from 76 diatoms species in the orders Thalassiosirales, Lithodesmiales and Cymatosirales, using distance and character based approaches, to assess the applicability of a DNA barcode based on the hypervariable V4 region of the nuclear 18S rRNA gene. We show that the proposed V4 barcode separated ca. 97% of all centric diatom taxa tested using a threshold p-distance of 0.02 and that many problem pairs were further separated using a character based approach. The reliability of amplification, extensive reference library and variability seen in the V4 region make it the most promising candidate to date for a barcode marker for diatoms particularly when combined with DNA character analysis.

Concepts: DNA, Gene, Molecular biology, Species, Ribosomal RNA, DNA barcoding, Identification, Diatom

158

In diatoms, the main photosynthetic pigments are chlorophylls a and c, fucoxanthin, diadinoxanthin and diatoxanthin. The marine pennate diatom Haslea ostrearia has long been known for producing, in addition to these generic pigments, a water-soluble blue pigment, marennine. This pigment, responsible for the greening of oysters in western France, presents different biological activities: allelopathic, antioxidant, antibacterial, antiviral, and growth-inhibiting. A method to extract and purify marennine has been developed, but its chemical structure could hitherto not be resolved. For decades, H. ostrearia was the only organism known to produce marennine, and can be found worldwide. Our knowledge about H. ostrearia-like diatom biodiversity has recently been extended with the discovery of several new species of blue diatoms, the recently described H. karadagensis, H. silbo sp. inedit. and H. provincialis sp. inedit. These blue diatoms produce different marennine-like pigments, which belong to the same chemical family and present similar biological activities. Aside from being a potential source of natural blue pigments, H. ostrearia-like diatoms thus present a commercial potential for aquaculture, cosmetics, food and health industries.

Concepts: Algae, Life, Species, Pigment, Kingdom, Diatom, Diatoms, Pennales

35

Silicon is produced in a variety of ways as an ultra-high capacity lithium-ion battery (LIB) anode material. The traditional carbothermic reduction process required is expensive and energy-intensive; in this work, we use an efficient magnesiothermic reduction to convert the silica-based frustules within diatomaceous earth (diatomite, DE) to nanosilicon (nanoSi) for use as LIB anodes. Polyacrylic acid (PAA) was used as a binder for the DE-based nanoSi anodes for the first time, being attributed for the high silicon utilization under high current densities (up to 4C). The resulting nanoSi exhibited a high BET specific surface area of 162.6 cm(2) g(-1), compared to a value of 7.3 cm(2) g(-1) for the original DE. DE contains SiO2 architectures that make ideal bio-derived templates for nanoscaled silicon. The DE-based nanoSi anodes exhibit good cyclability, with a specific discharge capacity of 1102.1 mAh g(-1) after 50 cycles at a C-rate of C/5 (0.7 A gSi(-1)) and high areal loading (2 mg cm(-2)). This work also demonstrates the fist rate capability testing for a DE-based Si anode; C-rates of C/30 - 4C were tested. At 4C (14.3 A gSi(-1)), the anode maintained a specific capacity of 654.3 mAh g(-1) - nearly 2x higher than graphite’s theoretical value (372 mAh g(-1)).

Concepts: Silicon, Battery, Rechargeable battery, Lithium-ion battery, Lithium, Lithium battery, Diatom, Electric car

32

The 2010 Deepwater Horizon oil spill resulted in 1.6-2.6 × 10(10) grams of petrocarbon accumulation on the seafloor. Data from a deep sediment trap, deployed 7.4 km SW of the well between August 2010 and October 2011, disclose that the sinking of spill-associated substances, mediated by marine particles, especially phytoplankton, continued at least 5 mo following the capping of the well. In August/September 2010, an exceptionally large diatom bloom sedimentation event coincided with elevated sinking rates of oil-derived hydrocarbons, black carbon, and two key components of drilling mud, barium and olefins. Barium remained in the water column for months and even entered pelagic food webs. Both saturated and polycyclic aromatic hydrocarbon source indicators corroborate a predominant contribution of crude oil to the sinking hydrocarbons. Cosedimentation with diatoms accumulated contaminants that were dispersed in the water column and transported them downward, where they were concentrated into the upper centimeters of the seafloor, potentially leading to sustained impact on benthic ecosystems.

Concepts: Petroleum, Carbon, Polycyclic aromatic hydrocarbon, Benzene, Hydrocarbon, Aromatic hydrocarbon, Phytoplankton, Diatom

28

Diatoms are major contributors to the photosynthetic productivity of marine phytoplankton. In these organisms, fucoxanthin-chlorophyll proteins (FCPs) serve as light-harvesting proteins. We have explored the FCP complexes in Phaeodactylum tricornutum under low light (LL) and high light (HL) conditions. Sub-fractionating the pool of major FCPs yielded different populations of trimeric complexes. Only Lhcf and Lhc-like proteins were found in the trimers. Under LL, the first polypeptide fraction contained six different Lhcfs and was mainly composed of Lhcf10. It was characterised by the highest amount of fucoxanthin (Fx). The second was dominated by Lhcf10, Lhcf5 and Lhcf2, and had a lower Fx/Chl c ratio. Little Fx/Chl c also characterised the most abundant FCP complexes, found in fraction 3, composed mainly of Lhcf5. These FCPs bound Fx molecules with the strongest bathochromic shift. The last two fractions contained FCP complexes that were built mainly of Lhcf4, harbouring more Fx molecules that absorbed at shorter wavelengths. Under HL, the same main polypeptides were retrieved in the different fractions and spectroscopic features were almost identical except for a higher diadinoxanthin content. The total amount of Lhcf5 was reduced under HL, whereas the amount of the last two fractions and thereby Lhcf4 was increased. Lhcf11 was identified in different LL fractions, but not detected in any HL fraction, while two new Lhc-like proteins were only found under HL. This is the first report on different trimeric FCP complexes in pennate diatoms, which differ in polypeptide composition and pigmentation, and are differentially expressed by light.

Concepts: Algae, Spectroscopy, Peptide, Wavelength, Diatom, Phaeodactylum tricornutum, Diatoms, Planktology

28

Frustules, the silica shells of diatoms, have unique porous architectures with good mechanical strength. In recent years, biologists have learned more about the mechanism of biosilica shells formation; meanwhile, physicists have revealed their optical and microfluidic properties, and chemists have identified ways to modify them into various materials while maintaining their hierarchical structures. These efforts have provided more opportunities to use biosilica structures in microsystems and other commercial products. This review focuses on the preparation of biosilica structures and their applications, especially in the development of microdevices. We discuss existing methods of extracting biosilica from diatomite and diatoms, introduce methods of separating biosilica structures by shape and sizes, and summarize recent studies on diatom-based devices used for biosensing, drug delivery, and energy applications. In addition, we introduce some new findings on diatoms, such as the elastic deformable characteristics of biosilica structures, and offer perspectives on planting diatom biosilica in microsystems.

Concepts: Structure, Silicon, Strength of materials, Diatom, Diatoms, Silicic acid, Frustule, Diatomaceous earth

28

Dispersants are commonly used to mitigate the impact of oil spills, however, the ecological cost associated with their use is uncertain. The toxicity of weathered oil, dispersed weathered oil, and the hydrocarbon-based dispersant Slickgone NS(®), to the diatom Phaeodactylum tricornutum has been examined using standardized toxicity tests. The assumption that most toxicity occurs via narcosis was tested by measuring membrane damage in diatoms after exposure to one of the petroleum products. The mode of toxic action was determined using microarray-based gene expression profiling in diatoms after exposure to one of the petroleum products. The diatoms were found to be much more sensitive to dispersants than to the water accommodated fraction (WAF), and more sensitive to the chemically enhanced WAF (CEWAF) than to either the WAF itself or the dispersants. Exposure to dispersants and CEWAF caused membrane damage, while exposure to WAF did not. The gene expression profiles resulting from exposure to all three petroleum mixtures were highly similar, suggesting a similar mode of action for these compounds. The observed toxicity bore no relationship to PAH concentrations in the water column or to total petroleum hydrocarbon (TPH), suggesting that an undescribed component of the oil was causing toxicity. Taken together, these results suggest that the use of dispersants to clean up oil spills will dramatically increase the oil toxicity to diatoms, and may have implications for ecological processes such as the timing of blooms necessary for recruitment.

Concepts: Gene expression, Petroleum, Toxicity, DNA microarray, Diatom, Phaeodactylum tricornutum, Diatoms, Exxon Valdez oil spill

28

We present a novel manufacture route for silica-titania photocatalysts using the diatom microalga Pinnularia sp. Diatoms self-assemble into porous silica cell walls, called frustules, with periodic micro-, meso- and macroscale features. This unique hierarchical porous structure of the diatom frustule is used as a biotemplate to incorporate titania by a sol-gel methodology. Important material characteristics of the modified diatom frustules under study are morphology, crystallinity, surface area, pore size and optical properties. The produced biosilica-titania material is evaluated towards photocatalytic activity for NO(x) abatement under UV radiation. This research is the first step to obtain sustainable, well-immobilised silica-titania photocatalysts using diatoms.

Concepts: Algae, Cancer, Optical fiber, Cell wall, Photocatalysis, Diatom, Silicic acid, Frustule

27

Diatomaceous earth (DE), or diatomite silica microparticles originated from fossilized diatoms are a potential substitute for its silica-based synthetic counterparts to address limitations in conventional drug delivery. This study presents the impact of engineered surface chemistry of DE microparticles on their drug loading and release properties. Surface modifications with four silanes, including 3-aminopropyltriethoxy silane (APTES), methoxy-poly-(ethylene-glycol)-silane (mPEG-silane), 7-octadecyltrichlorosilane (OTS), 3-(glycidyloxypropyl)trimethoxysilane (GPTMS) and two phosphonic acids, such as 2-carboxyethyl-phosphonic acid (2 CEPA) and 16-phosphono-hexadecanoic acid (16 PHA) were explored in order to tune drug loading and release characteristics of water insoluble (indomethacin) and water soluble drugs (gentamicin). Successful grafting of these functional groups with different interfacial properties was confirmed using X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared spectroscopy (FTIR) spectroscopy. Thermogravimetric analysis (TGA) was applied to determine the amount of loaded drugs and UV-spectrophotometry to analyse in-vitro drug release from modified DE substrates. Differences in drug release time (13-26 days) and loading capacity (14-24%) were observed depending on functional groups on the surface of DE microparticles. It was found that hydrophilic surfaces, due to the presence of polar carboxyl, amine or hydrolysed epoxy group, favor extended release of indomethacin, while the hydrophobic DE surface modified by organic hydrocarbons gives a better sustained release profile for gentamicin. This work demonstrates that by changing surface functionalities on DE microparticles, it is possible to tune their drug loading and release characteristics for both hydrophobic and hydrophilic drugs and therefore achieve optimal drug delivery performance.

Concepts: Spectroscopy, Amine, Functional group, Solubility, Amide, X-ray photoelectron spectroscopy, Fourier transform spectroscopy, Diatom