Thursday, December 13, 2012

Diatom Essay

by AH

Figure 1 – Diversity of Diatom Shapes
Diatoms are amazing microscopic members of the algae family found everywhere throughout the world.  Anyplace that has water can be a habitat for vast quantities of different diatom species.  Their most striking feature is that each cell is enclosed by two patterned shells made out of strands of glass in an astounding variety of shapes, sizes and arrangements (see Figure 1 and Cool Diatom Video) This unique characteristic has intrigued scientists, artists and engineers alike – especially as improved microscopes and cameras have allowed us to take detailed images in order to further explore these fascinating organisms.  Diatoms are important because although they are tiny, there are huge numbers of them, and they use energy from the sun and carbon from the air to grow.  Because of this, they are essential to the food chain, estimated to account for 25% of the world’s primary productivity (Gordon 2008).  Diatoms also produce oxygen and take CO2 out of the atmosphere - as much as all the rainforests in the world (Gross 2012). Every part of the planet and everyone on the planet is affected by these microorganisms. As if that isn’t enough reason to study these photosynthetic algae, now their beautiful glass shells are providing inspiration for nanotechnology development.  Scientists are trying to understand the ability of these creatures to mold such sophisticated structures in order to exploit the process for nanoparticle creation.

Humans consider nanotechnology to be a new and exciting field that allows engineers to design the arrangement of atomic level structures to do all sorts of useful things.  Diatoms, however, seem to have perfected this technology a long time ago to build their intricately patterned shells.  We presently lack the ability to build the complicated designs on the nanometer scale that these microscopic organisms construct easily (Gordon 2008).  Many diatoms resemble the structures and devices that engineers would love to produce (see Figures 2 and 3). The potential for building these particles easily and economically based on nature’s design is incredibly enticing.  Currently, diatom shells are being used in chemical and optic applications but synthesis of artificial silica shells under biological conditions has not yet been achieved.

Figure 2Interesting Diatom
Shell Designs
Figure 3The diatom Coscinodiscus wailesii has shells that are
built out of several layers of silica

One reason that nanotechnology excites us so much is that working at this small of a scale allows manufacturing of materials one atom at a time.  This allows precise control in the building up of things rather than our current top down approach.  The implications of this are as huge as a nanometer is tiny.  A great example is to consider the difference between diamonds and graphite (see How Stuff Works Website).  Both are composed of carbon atoms (each carbon atom measures about 1/4nm across), but their three dimensional arrangement gives rise to either a beautiful, hard crystal or a slab of dark, soft rock.  Currently, we find large pieces of these materials and cut them down to fit our needs.  Nano-manufacturing promises the potential to build these and just about any conceivable material by arranging atoms.  We can build super strong and lightweight materials to improve manufacturing of cars and planes, improved fabrics and coatings, cosmetics, medical devices, and maybe someday tiny machines composed of even tinier gears and interacting parts.

Another interesting phenomenon that comes from controlling atoms is that they can be positioned to interact with each other and therefore self-assemble into the desired conformation.  For an example, think about nature’s most elegant nanotechnology that all life is based upon. A strand of DNA is approximately 2nm wide.  The chemical structure of DNA is three dimensional and the interactions between atoms shape the molecule into a two stranded helix.  The strands must be able to separate, be copied and reassemble themselves into the exact same precise arrangement that confers the stable double helix shape in order to pass on genetic information from one generation to the next. This is possible because molecules on one strand pair specifically with certain molecules on the other strand.  If the carbon, nitrogen and hydrogen atoms making up DNA were composed in a different way, this strand pairing would not occur and life as we know it could not exist.

The diatom’s mastery of building silica shells from the atomic level up could be used to produce desirable, self-assembling nanoscale devices for humans.  The potential for diatom driven design in nanotechnology is enormous.  Probably the most easily imagined is the computer chip. Incredible advances have been made to cram more and more semi-conductive parts on smaller and smaller surfaces in order to maximize speed and computing power.  The invention of microchips has moved computing from large rooms full of vacuum tubes to the portable devices of today. The desire for still smaller and more complex circuitry beyond the ability of current etching techniques is a perfect reason to explore the silica arrangement by diatoms (Bradbury 2004).  Once this process is understood, scientists could potentially manipulate diatoms to deposit nanopatterned silica with precisely the design and size necessary for function.  This silica can be converted to semi-conductive silicon by chemical processing (Bao, 2007).  This is just one of many applications being explored.  Many medical applications have been proposed, taking advantage of the porosity (and therefore a large surface are to volume ratio) of the silica shells for drug delivery or antibody display (Townley, 2008).  But before we can begin to exploit or mimic these algal cells, we must understand in detail the very complicated process by which diatoms arrange and construct their glass shells.

Diatoms take up silica dissolved in the oceans, rivers, lakes and even soil bound water. They lace that silica together in huge vesicles inside their bodies and then move it outside the cell making a protective glass house composed of two shells called frustules (Zurzolo, 2001).  The pores in the frustule can be on the nanometer or micrometer scale and the patterning is typically repetitive but results in complex three dimensional structures.  Figures 4 and 5 demonstrate this by showing scanning electron microscope images of a diatom frustule at different magnifications. Diatoms are symmetrical, with the symmetry being radial (circular diatoms – Figure 4) or bilateral (pennate diatoms – Figure 5) and patterns forming that are presumably genetically distinct and determine species differentiation. The construction of the frustule has been studied but the details are still being worked out in research labs across the world. Understanding each step of this process is important so that we can eventually control it to produce custom made structures. Current research has identified new cellular components that help explain the process of frustule formation.
Figure 4 – SEM Images of Coscinodiscus wailesii showing (from left to right) the two
valves (500X magnification), pores in the frustule surface (5000X), and detail at 20,000X
Figure 5 - SEM Image of Nanostructured Biosilica from the Pennate Diatom Pinnularia.  
Recently, researchers at the University of Bristol investigated how diatoms floating around in the ocean get silica into their bodies.  They took genetic material coding for the silica transport proteins from the diatom Thalassiosira pseudonana (see Figure 6) and transformed it into the yeast Saccharomyces cerevisea.  Yeast is a model lab organism and has the ability to produce large amounts of proteins from other organisms to make studying those proteins easier. Researchers were then able to observe these proteins binding to the water soluble form of silica (silicic acid) and bringing it across the cell membrane in a salt dependent transport reaction (Curnow, 2012).  They also found that differing types of silica transport proteins were produced at different rates suggesting a mechanism to choose high affinity or low affinity silicic acid binding depending on the environment encountered by the diatom.

Figure 6 Diatom species
Thalassiosira pseudonana
Once the silicic acid is inside the cell, the diatom must be able to convert it into silica in a very specific pattern. Although several research groups have identified many biomolecules (>75 genes) that are somehow involved in silica processing, it is only recently that some more detailed understanding has been achieved. Research at the Georgia Institute of Technology has uncovered proteins in Thalassiosira pseudonana that not only mineralize silicic acid to silica but also form a scaffold for the organization of the developing silica frustule (Scheffel 2011).  These molecules are part of an organic matrix located in the center girdle region of the diatom and vary by species, presumably giving rise to the diverse shape and pattern of diatom frustules.

Studies have also revealed the role of the cytoskeleton in frustule formation.  The cytoskeleton is a mixture of actin filaments and microtubules that fill each cell and help it keep its shape and structural organization.  Researchers at the University of California San Diego used microscopy to generate images showing the impact of the cytoskeleton on the developing frustules in silica deposition vesicles in five diatom species. Although the cytoskeleton is not involved with the mineralization of silica, it impacts the size and pattern of the frustules (Tesson 2010).  They saw that the microtubule arrangement resulted in positioning of vesicles that led to indentations in the silica patterns correlating with microtubule interaction. They also found actin rings around the silica deposition vesicles membranes suggesting that actin filaments are involved in expanding the vesicles and positioning them in certain areas of the cell, thereby influencing frustule size pattern formation.

As illuminating as these recent findings are, they also illustrate the fact that silica frustule formation is complicated and involves specific components as well as overall cellular organization.  Much more time and energy must be spent before we truly understand biology enough to mimic it.  Since diatoms have been on the scene for about 200 million years (Gross 2012), it seems logical to learn from these biological processes in order steer production of shapes that will fit our needs. Several complete genomes are available for diatoms and this has led to the recent flurry of frustule related discoveries.  Nanotechnology based on diatom machinery could allow us to build custom devices for use in health care, industrial chemistry, material science, computer based technology and in other ways unimaginable today.  Perhaps one day we can thank diatoms for showing us how to create nanostructures that greatly improve our daily lives.

Bao, Z., Weatherspoon, M. R., Shian, S., Cai, Y., Graham, P. D., Allan, S. M., Ahmad, G., et al. (2007). Chemical reduction of three-dimensional silica micro-assemblies into microporous silicon replicas. Nature, 446(7132), 172–5. doi:10.1038/nature05570
Bradbury, J. (2004). Nature’s nanotechnologists: unveiling the secrets of diatoms. PLoS biology, 2(10), e306. doi:10.1371/journal.pbio.0020306
Curnow, P., Senior, L., Knight, M. J., Thamatrakoln, K., Hildebrand, M., & Booth, P. J. (2012). Expression, purification, and reconstitution of a diatom silicon transporter. Biochemistry, 51(18), 3776–85. doi:10.1021/bi3000484
Gordon, R., Losic, D., Tiffany, M. A., Nagy, S. S., & Sterrenburg, F. a S. (2009). The Glass Menagerie: diatoms for novel applications in nanotechnology. Trends in biotechnology, 27(2), 116–27. doi:10.1016/j.tibtech.2008.11.003
Gross, M. (2012). The mysteries of the diatoms. Current biology : CB, 22(15), R581–5. doi:10.1016/j.cub.2012.07.041
Scheffel, A., Poulsen, N., Shian, S., & Kröger, N. (2011). Nanopatterned protein microrings from a diatom that direct silica morphogenesis. Proceedings of the National Academy of Sciences of the United States of America, 108(8), 3175–80. doi:10.1073/pnas.1012842108
Tesson, B., & Hildebrand, M. (2010). Extensive and intimate association of the cytoskeleton with forming silica in diatoms: control over patterning on the meso- and micro-scale. PloS one, 5(12), e14300. doi:10.1371/journal.pone.0014300
Townley, H. E., Parker, a. R., & White-Cooper, H. (2008). Exploitation of Diatom Frustules for Nanotechnology: Tethering Active Biomolecules. Advanced Functional Materials, 18(2), 369–374. doi:10.1002/adfm.200700609
Zurzolo, C., & Bowler, C. (2001). Exploring Bioinorganic Pattern Formation in Diatoms . A Story of Polarized Trafficking, 127(December), 1339–1345. doi:10.1104/pp.010709.lineages

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