Tag Archives: biomineralization

Growing shells atom-by-atom

The University of California at Davis (UC Davis) and the University of Washington (state) collaborated in research into fundamental questions on how aquatic animals grow. From an Oct. 24, 2016 news item on ScienceDaily,

For the first time scientists can see how the shells of tiny marine organisms grow atom-by-atom, a new study reports. The advance provides new insights into the mechanisms of biomineralization and will improve our understanding of environmental change in Earth’s past.

An Oct. 24, 2016 UC Davis news release by Becky Oskin, which originated the news item, provides more detail,

Led by researchers from the University of California, Davis and the University of Washington, with key support from the U.S. Department of Energy’s Pacific Northwest National Laboratory, the team examined an organic-mineral interface where the first calcium carbonate crystals start to appear in the shells of foraminifera, a type of plankton.

“We’ve gotten the first glimpse of the biological event horizon,” said Howard Spero, a study co-author and UC Davis geochemistry professor. …

Foraminifera’s Final Frontier

The researchers zoomed into shells at the atomic level to better understand how growth processes may influence the levels of trace impurities in shells. The team looked at a key stage — the interaction between the biological ‘template’ and the initiation of shell growth. The scientists produced an atom-scale map of the chemistry at this crucial interface in the foraminifera Orbulina universa. This is the first-ever measurement of the chemistry of a calcium carbonate biomineralization template, Spero said.

Among the new findings are elevated levels of sodium and magnesium in the organic layer. This is surprising because the two elements are not considered important architects in building shells, said lead study author Oscar Branson, a former postdoctoral researcher at UC Davis who is now at the Australian National University in Canberra. Also, the greater concentrations of magnesium and sodium in the organic template may need to be considered when investigating past climate with foraminifera shells.

Calibrating Earth’s Climate

Most of what we know about past climate (beyond ice core records) comes from chemical analyses of shells made by the tiny, one-celled creatures called foraminifera, or “forams.” When forams die, their shells sink and are preserved in seafloor mud. The chemistry preserved in ancient shells chronicles climate change on Earth, an archive that stretches back nearly 200 million years.

The calcium carbonate shells incorporate elements from seawater — such as calcium, magnesium and sodium — as the shells grow. The amount of trace impurities in a shell depends on both the surrounding environmental conditions and how the shells are made. For example, the more magnesium a shell has, the warmer the ocean was where that shell grew.

“Finding out how much magnesium there is in a shell can allow us to find out the temperature of seawater going back up to 150 million years,” Branson said.

But magnesium levels also vary within a shell, because of nanometer-scale growth bands. Each band is one day’s growth (similar to the seasonal variations in tree rings). Branson said considerable gaps persist in understanding what exactly causes the daily bands in the shells.

“We know that shell formation processes are important for shell chemistry, but we don’t know much about these processes or how they might have changed through time,” he said. “This adds considerable uncertainty to climate reconstructions.”

Atomic Maps

The researchers used two cutting-edge techniques: Time-of-Flight Secondary Ionization Mass Spectrometry (ToF-SIMS) and Laser-Assisted Atom Probe Tomography (APT). ToF-SIMS is a two-dimensional chemical mapping technique which shows the elemental composition of the surface of a polished sample. The technique was developed for the elemental analysis of complex polymer materials, and is just starting to be applied to natural samples like shells.

APT is an atomic-scale three-dimensional mapping technique, developed for looking at internal structures in advanced alloys, silicon chips and superconductors. The APT imaging was performed at the Environmental Molecular Sciences Laboratory, a U.S. Department of Energy Office of Science User Facility at the Pacific Northwest National Laboratory.

This foraminifera is just starting to form its adult spherical shell. The calcium carbonate spherical shell first forms on a thin organic template, shown here in white, around the dark juvenile skeleton. Calcium carbonate spines then extend from the juvenile skeleton through the new sphere and outward. The bright flecks are algae that the foraminifera “farm” for sustenance.Howard Spero/University of California, Davis

This foraminifera is just starting to form its adult spherical shell. The calcium carbonate spherical shell first forms on a thin organic template, shown here in white, around the dark juvenile skeleton. Calcium carbonate spines then extend from the juvenile skeleton through the new sphere and outward. The bright flecks are algae that the foraminifera “farm” for sustenance.Howard Spero/University of California, Davis

An Oct. 24, 2016 University of Washington (state) news release (also on EurekAlert) adds more information (there is a little repetition),

Unseen out in the ocean, countless single-celled organisms grow protective shells to keep them safe as they drift along, living off other tiny marine plants and animals. Taken together, the shells are so plentiful that when they sink they provide one of the best records for the history of ocean chemistry.

Oceanographers at the University of Washington and the University of California, Davis, have used modern tools to provide an atomic-scale look at how that shell first forms. Results could help answer fundamental questions about how these creatures grow under different ocean conditions, in the past and in the future. …

“There’s this debate among scientists about whether shelled organisms are slaves to the chemistry of the ocean, or whether they have the physiological capacity to adapt to changing environmental conditions,” said senior author Alex Gagnon, a UW assistant professor of oceanography.

The new work shows, he said, that they do exert some biologically-based control over shell formation.

“I think it’s just incredible that we were able to peer into the intricate details of those first moments that set how a seashell forms,” Gagnon said. “And that’s what sets how much of the rest of the skeleton will grow.”

The results could eventually help understand how organisms at the base of the marine food chain will respond to more acidic waters. And while the study looked at one organism, Orbulina universa, which is important for understanding past climate, the same method could be used for other plankton, corals and shellfish.

The study used tools developed for materials science and semiconductor research to view the shell formation in the most detail yet to see how the organisms turn seawater into solid mineral.

“We’re interested more broadly in the question ‘How do organisms make shells?'” said first author Oscar Branson, a former postdoctoral researcher at the University of California, Davis who is now at Australian National University in Canberra. “We’ve focused on a key stage in mineral formation — the interaction between biological template materials and the initiation of shell growth by an organism.”

These tiny single-celled animals, called foraminifera, can’t reproduce anywhere but in their natural surroundings, which prevents breeding them in captivity. The researchers caught juvenile foraminifera by diving in deep water off Southern California. Then they then raised them in the lab, using tiny pipettes to feed them brine shrimp during their weeklong lives.

Marine shells are made from calcium carbonate, drawing the calcium and carbon from surrounding seawater. But the animal first grows a soft template for the mineral to grow over. Because this template is trapped within the growing skeleton, it acts as a snapshot of the chemical conditions during the first part of skeletal growth.

To see this chemical picture, the authors analyzed tiny sections of foraminifera template with a technique called atom probe tomography at the Pacific Northwest National Laboratory. This tool creates an atom-by-atom picture of the organic template, which was located using a chemical tag.

Results show that the template contains more magnesium and sodium atoms than expected, and that this could influence how the mineral in the shell begins to grow around it.

“One of the key stages in growing a skeleton is when you make that first bit, when you build that first bit of structure. Anything that changes that process is a key control point,” Gagnon said.

The clumping suggests that magnesium and sodium play a role in the first stages of shell growth. If their availability changes for any reason, that could influence how the shell grows beyond what simple chemistry would predict.

“We can say who the players are — further experiments will have to tell us exactly how important each of them is,” Gagnon said.

Follow-up work will try to grow the shells and create models of their formation to see how the template affects growth under different conditions, such as more acidic water.

“Translating that into, ‘Can these forams survive ocean acidification?’ is still many steps down the line,” Gagnon cautioned. “But you can’t do that until you have a picture of what that surface actually looks like.”

The researchers also hope that by better understanding the exact mechanism of shell growth they could tease apart different aspects of seafloor remains so the shells can be used to reconstruct more than just the ocean’s past temperature. In the study, they showed that the template was responsible for causing fine lines in the shells — one example of the rich chemical information encoded in fossil shells.

“There are ways that you could separate the effects of temperature from other things and learn much more about the past ocean,” Gagnon said.

Here’s a link to and a citation for the paper,

Nanometer-Scale Chemistry of a Calcite Biomineralization Template: Implications for Skeletal Composition and Nucleation, Proceedings of the National Academy of Sciences, www.pnas.org/cgi/doi/10.1073/pnas.1522864113

This paper is behind a paywall.

Dem bones at McGill; innovation from the Canadian business community?; the archiving frontier; linking and copyright

I have a number of bits today amongst them, Canadian nanotechnology, Canadian business innovation, digital archiving, and copyrights and linking.

A Quebec biotech company, Enobia Pharma is working with Dr. Marc McKee on treatments for genetic bone diseases. From the news item on Nanowerk,

The field is known as biomineralization and it involves cutting-edge, nanotech investigation into the proteins, enzymes and other molecules that control the coupling of mineral ions (calcium and phosphate) to form nano-crystals within the bone structure. The treatment, enzyme replacement therapy to treat hypophosphatasia, is currently undergoing clinical testing in several countries including Canada. Hypophosphatasia is a rare and severe disorder resulting in poor bone mineralization. In infants, symptoms include respiratory insufficiency, failure to thrive and rickets.

This research in biomineralization (coupling of mineral ions to form nano-crystals) could lead to better treatments for other conditions such as cardiovascular diseases, arthritis, and kidney stones.

McKee’s research is being funded in part by the Canadian Institutes of Health Research  From the Nanowerk news item,

McKee’s research program is a concrete example of how university researchers are working with private sector partners as an integral part of Canada’s innovative knowledge economy, and the positive outcomes their collaborations can offer.

I don’t think that businesses partnering with academic institutions in research collaborations is precisely what they mean when they talk about business innovation (research and development). From a March 2, 2010 article about innovation by Preston Manning in the Globe & Mail,

Government competition policy and support for science, technology, and innovation (STI) can complement business leadership on the innovation front, but it is not a substitute for such leadership. Action to increase innovation in the economy is first and foremost a business responsibility.

Manning goes on to describe what he’s done on this matter and asks for suggestions on how to encourage Canadian business to be more innovative. (Thanks to Pasco Phronesis for pointing me to Manning’s article.) I guess the problem is that what we’ve been doing has worked well enough and so there’s no great incentive to change.

I’ve been on an archiving kick lately and so here’s some more. The British Library recently (Feb.25.10) announced public access to their UK Web Archive, a project where they have been saving online materials. From the news release,

British Library Chief Executive, Dame Lynne Brindley said:

“Since 2004 the British Library has led the UK Web Archive in its mission to archive a record of the major cultural and social issues being discussed online. Throughout the project the Library has worked directly with copyright holders to capture and preserve over 6,000 carefully selected websites, helping to avoid the creation of a ‘digital black hole’ in the nation’s memory.

“Limited by the existing legal position, at the current rate it will be feasible to collect just 1% of all free UK websites by 2011. We hope the current DCMS consultation will enact the 2003 Legal Deposit Libraries Act and extend the provision of legal deposit through regulationto cover freely available UK websites, providingregular snapshots ofthe free UK web domain for the benefit of future research.”

Mike Masnick at Techdirt notes (here) that the British Library has to get permission (the legal position Dame Brindley refers to) to archive these materials and this would seem to be an instance where ‘fair use’ should be made to apply.

On the subject of losing data, I read an article by Mike Roberts for the Vancouver Province, January 22, 2006, p. B5 (digital copy here) that posed this question, What if the world lost its memory? It was essentially an interview with Luciana Duranti (chair of the Master of Archival Studies programme and professor at the School of Library, Archival and Information Studies at the University of British Columbia, Canada) where she commented about the memories we had already lost. From the article,

Alas, she says, every day something else is irretrievably lost.

The research records of the U.S. Marines for the past 25 years? Gone.

East German land-survey records vital to the reunification of Germany? Toast.

A piece of digital interactive music recorded by Canadian composer Keith Hamel just eight years ago?

“Inaccessible, over, finito,” says Duranti, educated in her native Italy and a UBC prof since 1987.

Duranti, director of InterPARES (International Research on Permanent Authentic Records in Electronic Systems), an international cyber-preservation project comprising 20 countries and 60 global archivists, says original documentation is a thing of the past.

I was shocked by how much ‘important’ information had been lost and I assume still is. (Getting back to the UK Web Archives, if they can only save 1% of the UK’s online material then a lot has got to be missing.)

For anyone curious about InterPARES, I got my link for the Roberts article from this page on the InterPARES 1 website.

Back to Techdirt and Mike Masnick who has educated me as to a practice I had noted but not realized is ‘the way things are done amongst journalists’. If you spend enough time on the web, you’ll notice stories that make their way to newspapers without any acknowledgment of  their web or writerly origins and I’m not talking about news releases which are designed for immediate placement in the media or rewritten/reworked before placement. From the post on Techdirt,

We recently wrote about how the NY Post was caught taking a blogger’s story and rewriting it for itself — noting the hypocrisy of a News Corp. newspaper copying from someone else, after Rupert Murdoch and his top execs have been going around decrying various news aggregators (and Google especially) for “stealing” from News Corp. newspapers. It’s even more ridiculous when you think about it — because the “stealing” that Rupert is upset about is Google linking to the original story — a step that his NY Post writer couldn’t even be bothered to do.

Of course, as a few people pointed out in the comments, this sort of “re-reporting” is quite common in the traditional news business. You see it all the time in newspapers, magazines and broadcast TV. They take a story that was found somewhere else and just “re-report” it, so that they have their own version of it.

That’s right, it’s ‘re-reporting’ without attributions or links. Masnick’s post (he’s bringing in Felix Salmon’s comments) attributes this to a ‘print’ mentality where reporters are accustomed to claiming first place and see acknowledgments and links as failure while ‘digital natives’ acknowledge and link regularly since they view these as signs of respect. I’m not going to disagree but I would like to point out that citing sources is pretty standard for academics or anyone trained in that field. I imagine most reporters have one university or college degree, surely they learned the importance of citing one’s sources. So does training as a journalist erode that understanding?

And, getting back to this morning’s archival subtheme, at the end of Clark Hoyt’s (blogger for NY Times) commentary about the plagiarism he had this to say,

Finally, The Times owes readers a full accounting. I asked [Philip] Corbett [standards editor] for the examples of Kouwe’s plagiarism and suggested that editors’ notes be appended to those articles on the Web site and in The Times’s electronic archives. Corbett would not provide the examples and said the paper was not inclined to flag them, partly because there were some clear-cut cases and others that were less clear. “Where do you draw the line?” he asked.

I’d draw it at those he regards as clear. To do otherwise is to leave a corrupted record within the archives of The Times. It is not the way to close the case.

One last thing, Heather Haley is one of the guests appearing tonight in Rock Against Prisons.

Tuesday, March 9, 2010

7:00pm – 11:55pm

Little Mountain Gallery

195 east 26th Ave [Vancouver, Canada]

More details from my previous announcement about this event here.