Diatom Menagerie

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Diatom Menagerie

Engineering microscopic algae to produce designer

materials

Alexandra Goho

Scientists have long prized diatoms, photosynthetic algae that abound in marine andfreshwater ecosystems, because they remove large amounts of a major greenhouse gas

carbon dioxidefrom the atmosphere. But another, unusual trait has recently caught theattention of materials scientists and engineers: The cell wall of this unicellular organism

is made entirely of glass. More precisely, diatom shells consist of silica, or silicon

dioxide, the primary constituent of glass. Many shells are ornately patterned with features

just tens of nanometers in size. What's more, there are thousands of different species ofdiatoms, each with a unique shell design. Some look like miniature sieves, others

resemble microscopic gears.

ORNAMENTAL ALGA. Thousands of species of freshwater and marine diatoms exist innature, each species producing a unique glass shell. This diatom resembling a sombrero

has a particularly elaborate structure, the likes of which are inspiring materials scientists.

Hildebrand


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By seeking to understand how these organisms build intricate silica structures,

researchers expect to learn valuable lessons for designing and manufacturing new kindsof nano- and micrometer-scale materials and devices. "Nature has been building things on

the nanoscale for a long time," says materials scientist Ken Sandhage of the Georgia

Institute of Technology in Atlanta. "We're just scratching the surface in terms of learning

how to take advantage of these organisms to make all sorts of devices for biomedicalapplications, telecommunications, energy storage, and sensing."

Joanna Aizenberg of Lucent Technologies' Bell Laboratories in Murray Hill, N.J., says,

"We can think of diatoms as living silicon chips." Semiconductor-chip manufacturerscarve micro- and nanoscale features out of blocks of electronic and optical materialsa

costly and time-consuming endeavor. Diatoms build structures out of silicon much more

efficiently.

Once researchers figure out how to engineer useful devices out of diatom shells, they

could enlist the reproductive capabilities of diatoms to generate trillions of silica

structures in a matter of weeks. Some species of diatoms can replicate up to eight times aday.

Sandhage says, "For a fairly small number of reproductions, you could get incredibly

large numbers of the exact-same three-dimensional structure."

Although diatoms are unlikely to put the semiconductor industry out of business in the

near future, their capacity to create complex structures on a small scale could serve as the

foundation of a powerful technology for churning out new materials.

Gene machine

Observing these glass artists under a microscope can stir the mind's eye. "Diatoms canmake just about any structure you can imagine," says Mark Hildebrand, a biologist at the

Scripps Institution of Oceanography in San Diego. He and other researchers are

investigating the molecular mechanisms that underlie shell formation.

It begins when the algal cell divides, forcing it to split its shell into two halves. The new

cells, each now bearing only half a shell, begin to reconstruct their missing halves bytaking up silicic acida simple compound of silicon, oxygen, and hydrogenfrom the

surrounding water.

Each new organism deposits the silicic acid in a compartment called the silica-depositionvesicle. There, the chemical is converted into silica particles, each measuring about 50nm in diameter. These then aggregate to form larger blocks of material. Researchers

speculate that a set of special proteins guides the formation of the silica particles and their

subsequent assembly into larger structures. Hildebrand says that other cellular proteins

outside of the vesicle stretch and mold the compartment to shape the silica inside.


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Once the half shell is complete, the vesicle merges into the cell's membrane, exposing the

newly created structure.

In the late 1990s, Hildebrand identified a gene for a protein that draws silicic acid from

the environment into the cell. This is still the only gene reported to take part in the

diatom's silicon metabolism.

That won't be the case much longer. An international team of biologists, including

Hildebrand, is preparing to publish the first genome sequence of a diatomspecifically,of the marine species Thalassiosira pseudonana. "This is really going to change

everything," says Hildebrand. "Now, we can do large-scale surveys of all the genes to

find those involved in the process."

To find those genes among the diatom's approximately 11,000 genes, Hildebrand and hiscolleagues grow the algae in the lab and then put them in a solution lacking silicon. This

stops the cells from dividing and forming new silica structures. When the researchers add

silicon back to the growth medium, the diatoms begin forming new shells. At thatmoment, the researchers analyze the organisms' genetic material to see which genes have

turned from off to on.

Resembling a small pillbox and lacking ornate features, the silica shell of T. pseudonanais "pretty dull," says Hildebrand. However, he offers it as a model organismthe fruit fly

of diatom research. Once researchers determine how shells are made in T. pseudonana, he

says, they can move on to more-complex species.

GLASSMAKERS. Many diatom shells have ordered arrays of nanometer-size pores thatmake them look like sieves. Such glass structures might serve as photonic crystals.

Hildebrand

Diatoms of the same species consistently form shells with exactly the same pattern,

suggesting that the designs are genetically programmed. By surveying a range of diatoms,

researchers may find genes that drive one species to form star-shaped shells with arrays


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of nanoscale pores and grooves, for example, while other genes create a solid structure

jutting long spikes.

And that's just the beginning. "Ultimately, we'd like to genetically modify these

organisms," he says. The main thrust of his team's project, Hildebrand says, is to knock

out or modify the activity of specific genes so that researchers can engineer diatom shellsfor a wide variety of applications requiring microscopic materials with nanoscale

features.

For instance, a glassy material with well-ordered pores could serve as a photonic crystal

for optical communications (SN: 10/4/03, p. 218:http://www.sciencenews.org/articles/20031004/bob9.asp), or a microfluidic chip with

tiny channels could perform small-scale chemical reactions (SN: 9/28/02, p. 198:

Available to subscribers at http://www.sciencenews.org/articles/20020928/fob8.asp).

Silica replicator

Sandhage is leading a massive effort to exploit diatoms' manufacturing prowess, although

5 years ago, he knew next to nothing about these algae. He says that a new way of

thinking about materials design opened up when a biologist in Germany introduced him

to these unicellular organisms. Sandhage has since teamed up with Hildebrand andresearchers at Ohio State University in Columbus and the Air Force Research Laboratory

in Dayton, Ohio, to turn diatoms into mass producers of new electronic and optical

devices.

For industrial applications, one problem with diatoms is that "they have evolved to be

pretty good at making things out of silica but not of much else," says Sandhage. Many

applications require metallic or semiconductor materials, so he is working on ways toconvert diatom structures from silica to other materials.

Sandhage and his colleagues have developed a chemical process that preserves a diatom

shell's precise pattern while replacing the silicon in the shell with another element, atom

by atom. In a first experiment reported 2 years ago, the researchers converted all the

silica in a diatom shell into magnesium oxide.

They accomplished the feat by removing the organic material from the diatom shells,

placing the structures inside a metal tube, exposing them to magnesium gas, and heatingthe tube's contents. Because magnesium is more strongly attracted to oxygen than to

silicon, magnesium atoms elbow out the silicon, forming magnesium oxide. Over severalhours, the metal replaces all of the silicon atoms in the shell structure.
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EARLY CONVERTS. To make diatom structures out of materials other than silica,

researchers have developed a chemical process that replaces the silicon in the glass shell

(top) with titanium (bottom) while preserving the shell's shape and most of its features.

Sandhage

The particular structure in that experiment was derived from a diatom called Aulacoseira.

Its shell resembles a tubular capsule scored with v-shape grooves and rows of tiny pores,

measuring about 200 nm each in diameter and spaced several hundred nanometers apart.After the conversion was complete, the researchers found that the shell's features stayed

within 30 nanometers of their original size and location.

In a more recent experiment, described in the April 2004 Chemical Communications,

Sandhage's team exposed diatom shells to a titanium fluoride gas. The titanium displacedthe silicon, yielding a diatom structure made up entirely of titanium dioxide, a material

used in some commercially produced solar cells and commonly found in paints as

pigments.

The particular crystal of titanium dioxide called anatase that formed during the reaction

could be used as a catalyst to split water for making hydrogen fuel, Sandhage says. It

could also form the basis of a device that could detect specific gases. Carbon monoxide,for example, sticks to the surface of anatase and produces a detectable change in the

material's electrical resistance.

Gas sensors derived from diatom structures have great potential because "you want tohave a very high surface area with an open structure so that you get a bigger signal,"

Sandhage says. Some of the features found in diatom shellsarrays of pores or long andnarrow groovesare ideal for this kind of application, he says. What's more, diatom

shells are extremely small. "You could put lots of them in very small places," he says.

Already, the group at Ohio State University has begun testing some of the diatom-

designed titanium dioxide shells as gas sensors.


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Once Hildebrand and his team have figured out how to create organisms that make

specific structures, Sandhage plans to transform them into useful materials. The goal is to

"genetically engineer microdevices," he says.

Nature versus nurture

Rather than relying on diatoms to churn out inorganic structures, other groups areworking to isolate specific silica-forming proteins from the diatoms and use them as

templates in the assembly of the desired structures in the lab. This particular strategy is

part of a worldwide effort to harness the power of biological materials to build inorganic

structures for use in electronic and optical devices (SN: 7/5/03, p. 7:

http://www.sciencenews.org/articles/20030705/bob8.asp).

The approach may prove simpler and offer greater control over the ultimate design than

employing algae or other organisms to produce the materials. For example, by attaching

silica-binding proteins on a polymer surface in a precise arrangement, and exposing the

proteins to a solution of silicic acid, scientists at the Air Force lab in Ohio have createdrows of regularly spaced silica beads. Such an arrangement could form the basis of a

miniature lens.

Nils Krger, a diatom biologist at the University of Regensberg in Germany, was the firstto identify the silica-forming proteins in diatoms. The molecules of this class, which he

calls silaffins, are unusual among proteins in that many of them have long side chains of

organic molecules known as polyamines. The proteins are also decked out with an

assortment of other molecules, including sugars and phosphates.

When Krger and his colleagues added silaffins to a test tube containing silicic acid, tiny

silica spheres formed in a matter of minutes. In contrast, a solution of silicic acid withoutany proteins "can take hours or even days to form hard silica," says Krger.

The researchers also found that combining two different silaffins from the same diatom

species can yield surprising results. One of the proteins, silaffin-1, forms spheres. A

second protein, silaffin-2, doesn't by itself promote silica formation. But when theGerman team mixed the two silaffins in a solution of silicic acid, porous blocks of silica

emerged.

"It's something I didn't expect to find at all, and we don't completely understand how it

works," says Krger.

He suspects that in the diatom, different silaffins combine to form larger molecularassemblies and that interactions between the proteins and their polyamine chains hasten

the silica-formation process. Krger has found that removing the polyamine side chains

from a silaffin prevents the formation of silica. Moreover, proteins with chains of varying

lengths tend to create a different array of silica structures.
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Since his initial discovery of silaffins several years ago, Krger has identified three more

silica-forming proteins in T. pseudonanathe diatom whose genome was recentlysequenced. Each protein does something different: One produces spheres, one makes

porous shapes, and the third forms platelike structures.

Moving beyond these simple shapes will require a greater understanding of the diatom'smolecular machinery. What's more, dozens or even hundreds of proteins may govern theshell-formation process. Mapping the myriad interactions among all the components

could be a daunting task.

"It will be impossible to reproduce this process in a test tube because it's such a

complicated cellular process," says Hildebrand.

Aizenberg adds, "The question is, 'Will we be able to bridge the gap between what goes

on in nature and what we can do in the lab?'"

She recently began investigating the silica-producing properties of Euplectellaaspergillum, a deep-sea sponge that produces an intricate, cagelike glass structure (SN:9/20/03, p. 190: Available to subscribers at

http://www.sciencenews.org/articles/20030920/note13.asp). Remarkably, she says, the

material in this structure has optical properties that are very similar to those of

telecommunication fibers.

Aizenberg looks to these organisms not only for inspiration on how to improve today's

materials and devices but also for clues as to how to make processing methods less

energy-intensive and more environmentally sound. Today, commercial optical fibers aredrawn inside a furnace at 2,000C. In contrast, sponges synthesize sophisticated optical

materials in a low-temperature marine environment.

Fabrication of silicon chips and other electronic devices currently requires harsh

chemicals and generates much waste. "Diatoms and sponges know how to producematerials under ambient conditions without these harsh chemicals," says Aizenberg.

"And yet the end result is the same."

It's too early to say whether isolating silica-producing proteins to make minuscule new

widgets in the lab will prove more successful than engineering microorganisms to do thejob. Materials scientists are only beginning to uncover the secrets of this aquatic

community of glass-sculpture artists produced over millions of years of evolution.

********

Letters:

This otherwise well-written and fascinating article contains an error. You write, "Because

magnesium is more strongly attracted to oxygen than to silicon, magnesium atoms elbow

out the silicon . " The correct statement would be, "Because magnesium is more
http://www.sciencenews.org/articles/20030920/note13.asphttp://www.sciencenews.org/articles/20030920/note13.asp


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strongly attracted to oxygen than silicon is attracted to oxygen, magnesium atoms elbow

out the silicon . "

Fred Kohler

Ashland, OR

Either sentence is correct, but Mr. Kohler's is probably better. Both silicon and

magnesium are competing for oxygen, and the goal of the researchers is to produce

magnesium oxide.A. Goho

References:

Aizenberg, J., et al. 2004. Biological glass fibers: Correlation between optical and

structural properties. Proceedings of the National Academy of Sciences 101(March

9):33583363. Abstract available at http://dx.doi.org/10.1073/pnas.0307843101.

Aizenberg, J., et al. 2001. Calcitic microlenses as part of the photoreceptor system inbrittlestars. Nature 412(August 23):819822. Abstract available at

http://dx.doi.org/10.1038/35090573.

Brott, L.L., et al. 2001. Ultrafast holographic nanopatterning of biocatalytically formedsilica. Nature 413(Sept. 20):291293. Abstract available at

http://dx.doi.org/10.1038/35095031.

Drum, R.W., and Richard Gordon. 2003. Star Trek replicators and diatomnanotechnology. Trends in Biotechnology 21(August):325328. Abstract available at

http://dx.doi.org/10.1016/S0167-7799(03)00169-0.

Krger, N., R. Deutzmann, and M. Sumper. 1999. Polycationic peptides from diatom

biosilica that direct silica nanosphere formation. Science 286(Nov. 5):11291132.

Available at http://dx.doi.org/10.1126/science.286.5442.1129.

Poulsen, N., M. Sumper, and N. Krger. 2003. Biosilica formation in diatoms:

Characterization of native silaffin-2 and its role in silica morphogenesis. Proceedings of

the National Academy of Sciences 100(Oct. 14):1207512080. Available at

http://dx.doi.org/10.1073/pnas.2035131100.

Sandhage, K.H., et al. 2002. Novel, bioclastic route to self-assembled, 3D, chemically

tailored meso/nanostructures: Shape-preserving reactive conversion of biosilica (Diatom)microshells. Advanced Materials 14(March 18):429433. Abstract available at

http://dx.doi.org/10.1002/1521-4095(20020318)14:63.0.CO;2-C.

Sundar, V.C. and J. Aizenberg. 2003. Fibre-optical features of a glass sponge. Nature

424(August 21):899900. Abstract available at http://dx.doi.org/10.1038/424899a.
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Unocic, R.R., et al. 2004. Anatase assemblies from algae: Coupling biological self-

assembly of 3-D nanoparticle structures with synthetic reaction chemistry. Chemical

Communications 7(April):796797. Available at http://dx.doi.org/10.1039/b400599f.

Further Readings:

Gorman, J. 2003. Microbial materials. Science News 164(July 5):79. Available at

http://www.sciencenews.org/articles/20030705/bob8.asp.

Hildebrand, M., and R. Wetherbee. 2003. Components and control of silification indiatoms. In Progress in Molecular and Subcellular Biology, Vol. 33: Silicon

Biomineralization, W.E.G. Mller, ed. Berlin: Springer-Verlag.

Naik, R.R., et al. 2004. Peptide templates for nanoparticle synthesis derived frompolymerase chain reaction-driven phage display. Advanced Functional Materials

14(January):2530. Abstract available at http://dx.doi.org/10.1002/adfm.200304501.

Naik, R.R., et al. 2002. Silica-precipitating peptides isolated from a combinatorial phage

display peptide library. Journal of Nanoscience and Nanotechnology 2(February):95100.

Abstract available at http://dx.doi.org/10.1166/jnn.2002.074.

Naik, R.R., et al. 2002. Biomimetic synthesis and patterning of silver nanoparticles.

Nature Materials 1(November):169172. Abstract available at

http://dx.doi.org/10.1038/nmat758.

Round, F.E., R.M. Crawford, and D.G. Mann. 1990. The Diatoms: Biology and

Morphology of the Genera. Cambridge, England: Cambridge University Press.

Weiss, P. 2003. Hot crystal. Science News 164(Oct. 4):218220. Available at

http://www.sciencenews.org/articles/20031004/bob9.asp.

______. 2003. Channeling light in the deep sea. Science News 164(Sept. 20):190.

Available to subscribers at http://www.sciencenews.org/articles/20030920/note13.asp).

______. 2002. Liquid logic: Tiny plumbing networks concoct and compute. Science

News 162(Sept. 28):198. Available to subscribers at

http://www.sciencenews.org/articles/20020928/fob8.asp.

Sources:

Joanna Aizenberg

Bell Laboratories/Lucent Technologies700 Mountain Avenue

Room 1C-365

Murray Hill, NJ 07974-2008
http://dx.doi.org/10.1039/b400599fhttp://www.sciencenews.org/articles/20030705/bob8.asphttp://dx.doi.org/10.1002/adfm.200304501http://dx.doi.org/10.1166/jnn.2002.074http://dx.doi.org/10.1038/nmat758http://www.sciencenews.org/articles/20031004/bob9.asphttp://www.sciencenews.org/articles/20030920/note13.asphttp://www.sciencenews.org/articles/20020928/fob8.asphttp://www.sciencenews.org/articles/20020928/fob8.asphttp://www.sciencenews.org/articles/20030920/note13.asphttp://www.sciencenews.org/articles/20031004/bob9.asphttp://dx.doi.org/10.1038/nmat758http://dx.doi.org/10.1166/jnn.2002.074http://dx.doi.org/10.1002/adfm.200304501http://www.sciencenews.org/articles/20030705/bob8.asphttp://dx.doi.org/10.1039/b400599f


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Mark Hildebrand

Marine Biology Research DivisionScripps Institution of Oceanography

University of California, San Diego

9500 Gilman Drive

San Diego, CA 92093-0202

Nils Krger

Lehrstuhl Biochemie I

Universittsstrasse 31Universitt Regensburg

93053 Regensburg

Germany

Kenneth Sandhage

Department of Materials Science and Engineering

Georgia Institute of Technology771 Ferst Drive, N.W.Love Building, Room 258

Atlanta, GA 30332-0245

From Science News, Volume 166, No. 3, July 17, 2004, p. 42.

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