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Topic Name: UW Researchers Say Diatoms Could be Harboring the Next Big Breakthrough in Computer Chips

Category: Biodesign

Research persons: Michael Sussman, Virginia Armbrust

Location: University of Wisconsin-Madison, United States

Details

Denizens of oceans, lakes and even wet soil, diatoms are unicellular algae that encase themselves in intricately patterned, glass-like shells. Curiously, these tiny phytoplankton could be harboring the next big breakthrough in computer chips.

Diatoms build their hard cell walls by laying down submicron-sized lines of silica, a compound related to the key material of the semiconductor industry—silicon. “If we can genetically control that process, we would have a whole new way of performing the nanofabrication used to make computer chips,” says Michael Sussman, a University of Wisconsin-Madison biochemistry professor and director of the UW-Madison’s Biotechnology Center.

To that end, a team led by Sussman and diatom expert Virginia Armbrust of the University of Washington has reported finding a set of 75 genes specifically involved in silica bioprocessing in the diatom Thalassiosira pseudonana, as published today in the online Early Edition of the Proceedings of the National Academy of Sciences. Armbrust, an oceanography professor who studies the ecological role of diatoms, headed up the effort to sequence the genome of T. pseudonana, which was completed in 2004.

The new data will enable Sussman to start manipulating the genes responsible for silica production and potentially harness them to produce lines on computer chips. This could vastly increase chip speed, Sussman says, because diatoms are capable of producing lines much smaller than current technology allows.

“The semiconductor industry has been able to double the density of transistors on computer chips every few years. They’ve been doing that using photolithographic techniques for the past 30 years,” explains Sussman. “But they are actually hitting a wall now because they’re getting down to the resolution of visible light.”

Before diatoms were appreciated for their engineering prowess, they interested ecologists for their role in the planet’s carbon cycle. These photosynthetic cells soak up carbon dioxide and then fall to the ocean floor. They account for upwards of 20 percent of the carbon dioxide that is removed from the atmosphere each year, an amount comparable to that removed by all of the planet’s rainforests combined.

“We want to see which genes express under different environmental conditions because these organisms are so important in global carbon cycling,” explains Thomas Mock, a postdoctoral researcher in Armbrust’s lab and the paper’s first author.

But research on these algae has uncovered other enticing possibilities. As he learned about diatoms, Sussman became intrigued by the fact that each species of diatom—there may be around 100,000 of them—is believed to sport a uniquely designed cell wall.

To determine which genes are involved in creating those distinctive patterns, the research team used a DNA chip developed by Sussman, UW-Madison electrical engineer Franco Cerrina and UW-Madison geneticist Fred Blattner, the three founders of the biotechnology company NimbleGen. Put simply, the chip allows scientists to see which genes are involved in a given cellular process. In this case, the chip identified genes that responded when diatoms were grown in low levels of silicic acid, the raw material they use to make silica.

Of the 30 genes that increased their expression the most during silicic acid starvation, 25 are completely new, displaying no similarities to known genes.

“Now we know which of the organism’s 13,000 genes are most likely to be involved in silica bioprocessing. Now we can zero in on those top 30 genes and start genetically manipulating them and see what happens,” says Sussman.

For his part, Sussman is optimistic that in the long run these findings will help him improve the DNA chip he helped develop — the very one used to gather data for this research project. “It’s like the Lion King song,” he says. “You know, ‘the circle of life.’”

Note for Diatoms
Diatoms are a major group of eukaryotic algae, and are one of the most common types of phytoplankton. Most diatoms are unicellular, although some form chains or simple colonies. A characteristic feature of diatom cells is that they are encased within a unique cell wall made of silica (hydrated silicon dioxide) called a frustule. These frustules show a wide diversity in form, some quite beautiful and ornate, but usually consist of two asymmetrical sides with a split between them, hence the group name. Fossil evidence suggests that they originated during, or before, the early Jurassic Period.
Diatom communities are becoming an increasingly popular tool for monitoring environmental conditions past and present. This can be useful in studies on water quality and climate change.
Diatoms are traditionally divided into two orders: centric diatoms (Centrales), which are radially symmetric, and pennate diatoms (Pennales), which are bilaterally symmetric. The former are paraphyletic to the latter. A more recent classification divides the diatoms into three classes: centric diatoms (Coscinodiscophyceae), pennate diatoms without a raphe (Fragilariophyceae), and pennate diatoms with a raphe (Bacillariophyceae). It is probable there will be further revisions as understanding of their relationships increases.

Note for Phytoplankton
Phytoplankton are the autotrophic component of plankton. The name comes from the Greek terms, phyton or "plant" and πλαγκτος ("planktos"), meaning "wanderer" or "drifter". Most phytoplankton are too small to be individually seen with the unaided eye. However, when present in high enough numbers, they may appear as a green discoloration of the water due to the presence of chlorophyll within their cells (although the actual color may vary with the species of phytoplankton present due to varying levels of chlorophyll or the presence of accessory pigments such as phycobiliproteins).
Phytoplankton obtain energy through a process called photosynthesis and must therefore live in the well-lit surface layer (termed the euphotic zone) of an ocean, sea, lake, or other body of water. Through photosynthesis, phytoplankton are responsible for much of the oxygen present in the Earth's atmosphere – half of the total amount produced by all plant life. Their cumulative energy fixation in carbon compounds (primary production) is the basis for the vast majority of oceanic and also many freshwater food webs (chemosynthesis is a notable exception). As a side note, one of the more remarkable food chains in the ocean – remarkable because of the small number of links – is that of phytoplankton fed on by krill (a type of shrimp) fed on by baleen whales.

Note for Thalassiosira pseudonana
Thalassiosira pseudonana is a species of marine centric diatom. It was chosen as the first eukaryotic marine phytoplankton for whole genome sequencing because T. pseudonana is a model for diatom physiology studies, belongs to a genus widely distributed throughout the world's oceans, and has a relatively small genome at 34 mega base pairs.
The clone of T. pseudonana that was sequenced is CCMP 1335 and is available from the Center for Culture of Marine Phytoplankton. This clone was originally collected in 1958 from Moriches Bay (Long Island, New York) and has been maintained continuously in culture.

Contributions to this paper were also made by Vaughn Iverson, Chris Berthiaume, Karie Holtermann and Colleen Durkin of the University of Washington; Manoj Pratim Samanta of Systemix Institute; Matthew Robison, Sandra Splinter BonDurant, Kathryn Richmond, Matthew Rodesch, Toivo Kallas, Edward L. Huttlin and Francesco Cerrina of the University of Wisconsin-Madison.

Funding came from the Gordon and Betty Moore Foundation, the National Science Foundation, the UW National Institutes of Health Genomic Sciences Training Grant and the postdoctoral program of the German Academic Exchange Service.