The Ultimate Identifier

Editor's Note: This is the first in a series of videos we will release in 2016 about the use of scientific collections and DNA technology.

When it comes to reliable plant identification in their work, Ida Lopez and Dr. Caroline Puente, of the Smithsonian’s National Museum of Natural History (NMNH) Plant DNA Barcoding Project, botany department, have a tool most associate with the retail world. But barcodes, in this case DNA barcodes, are creating many research opportunities in the scientific world in areas of ecology, evolution, conservation and more.

A DNA barcode, which is made up of approximately 600 base pairs of the species’ entire genome, can authentically identify down to the species level. A commonly used barcode marker in animals is the mitochondrial gene cytochrome oxidase 1 (CO1). This gene however does not successfully identify plant species.

“We knew that in animals the CO1 site was very indicative,” Lopez said. “Zoologists could just sequence this one site and tell exactly what type of animal it was.”

Because the CO1 gene has evolved slower in plants, it is not useful to identify plant species. So around 10 years ago, researchers, under the direction of John Kress, NMNH Department of Botany curator, began looking for candidate genes in plants. They found that they needed a combination of at least two chloroplast regions - rbcL and trnH-psbA - to create a workable plant DNA barcode. Today matK, another chloroplast gene, and a nuclear region – the Internal Transcribed Spacer (ITS) are added to insure success.

While researchers agree that fresh tissue is ideal for extracting DNA, Puente said that in cases where scientists can’t revisit a location to collect samples, museum collections, in this case botanical specimens, are invaluable.

“One of the big advantages of DNA barcoding is that we do not need a lot of tissue material” Puente said. “... You can barcode small organisms such as insects and bacteria - anything that has DNA even in limited amounts.”

A tissue sample just a little larger than a pencil eraser is enough for DNA extraction and barcoding. Lopez and Puente have specimens at their fingertips in the Department of Botany’s vast collection at NMNH. The collection holds 5 million specimens, with approximately 105,000 of those serving as type specimens.

To learn more about Lopez and Puente's work, visit The Plant DNA Barcode Project.


References
W. John Kress, Carlos García-Robledo, Maria Uriarte, and David L. Erickson (2014, November 19). DNA barcodes for ecology, evolution, and conservation. CellPress, vol 30 (1): 25-35. doi: 10.1016/j.tree.2014.10.008

What is DNA Barcoding? Barcode of Life. Retrieved from http://www.barcodeoflife.org/content/about/what-dna-barcoding 

W. John Kress, David L. Erickson. (2007, June 6) A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region. PLOSOne(6): e508. doi: 10.1371/journal.pone.0000508

Search the Department of Botany Collections. Smithsonian National Museum of Natural History. Retrieved from http://collections.nmnh.si.edu/search/botany/

Plant DNA Barcode Project. Smithsonian National Museum of Natural History. Retrieved from http://botany.si.edu/projects/DNAbarcode/

Glossary

type specimens
The representative for an animal or plant species, which acts as a reference point when a species is first named.

Our 2015 Annual Report!

During the second year of SciColl activities, we engaged the community in new and exciting ways. We launched the Global Registry of Scientific Collections and participated on five social media platforms, which helped spread the word about our Emerging Infectious Diseases Workshop report and other collections research. See our 2015 Annual Report for the full highlights!

Curious about what we are doing in 2016? Sign up for blog updates, follow us on Twitter, or contact us directly to get involved.

Teosinte Today, Maize Tomorrow

Fig.1. This photo, published in 1919, shows the stages between a simple spike of Euchlaena mexicana and an ear of maize. (Credit: Journal of Agriculture)

Jeffrey Ross-Ibarra, associate professor and section chair of the Department of Plant Sciences at the University of California at Davis, and his team study maize and teosinte evolution. Researchers and post-docs - with backgrounds in plant biology and population biology and integrated genetics and genomics - focus on various research areas, such as genetics and genomics, how human and environmental factors have affected the adaptation and domestication of crops and more.

“Domestication (of the crop) has always struck me as a really exciting story because it’s a case where the evolution of the plant was directed by, or affected by, humans,” Ross-Ibarra said about how he became interested in maize and teosinte research.

C. Miguel Pinto, the Disease Detective

Fig.1. Red Queen lecturing Alice (Credit: John Tenniel, 1871)

“Now, here, you see, it takes all the running you can do to keep in the same place,”

- Lewis Carroll’s Through the Looking Glass

In Lewis Carroll’s Through the Looking Glass, Alice once again finds herself in a fantastical world. A chess piece called the Red Queen describes the rules of the Looking-Glass land, claiming that no matter how far Alice runs, the girl will stay in the same place. Evolutionary biologist Leigh Van Valen adopted this story in 1973 to illustrate the concept of an evolutionary arms race in which species must constantly evolve to remain extant. In symbiotic relationships, like that of parasites and hosts, an adaptation in one will affect the other. Therefore these organisms continually evolve, or “run,” to counter pressures posed by the opposite in order to survive.

This type of relationship fascinates C. Miguel Pinto, a George E. Burch and Peter Buck Postdoctoral Fellow at Smithsonian’s National Museum of Natural History (NMNH). He explores the evolutionary underpinnings of mammals and the parasites they hold. In particular, Pinto studies Trypanosoma parasites in bats.

The woman with the (specimen) solution

Gunter

After nearly three decades with the Centers for Disease Control & Prevention, Elaine Gunter was looking for a change. Since 1978, her role in the central laboratory for the National Health and Nutrition Examination Survey included designing specimen collections for various field studies, managing personnel, and developing assays.

In 2001, she was promoted to a the deputy director position of the Division of Laboratory Sciences at CDC. While working in the management and operations realm, she found she was dealing with the “suits” of Washington, D.C., who were trying to run science agencies as a business.

That’s when she took the leap.

Happy Birthday, Collections in the News!

One year ago today, Collections in the News published its first article about ongoing research regarding collections and how they can tell us more about the world. To celebrate, here are our top five most viewed and shared articles from the past year:  

Collection Spotlight: NMNH Vertebrate Paleontology 

We learned about preserving fossils for future researchers and museum visitors, thanks to Dr. Hans-Dieter Sues, curator of Vertebrate Paleontology at the Smithsonian’s National Museum of Natural History.

Microbes and Middle Schools 

Dr. Julia Stevens at the North Carolina Museum of Natural Sciences told us why teaching middle school students about soil microbiology is important for the future of science. 

Tracing the History of Disease

New technologies were applied to old history in Dr. Loren Sackett’s work with wildlife diseases that cross over into humans.

“Evil Twin” of Climate Change

Ocean acidification is an ongoing threat to sea life and is only part of how climate change will affect our world, but information from sediment cores may help us to mitigate the problem.

Smallpox, Now Online! 

In an age where digitizing collections are the norm, we talked about how the question of open-access data is at the forefront of biosecurity.

Change in the Delta

Fig.1: An aerial view of the Copper River Delta in Alaska. (Credit: Andrew Morin)

After years of working at the Northwest Fishery Science Center as a project manager, focusing her work on salmon, Carmella Vizza felt she needed a change.

“I decided it was time for me to go back to grad school to be more involved in conducting my own research,” Vizza said.

Microbes and Middle Schools

Fig.1. Students at Mills Park Middle School studying how dandelions recruit different microbial communities in various soil types (Credit: Laura Cochrane, Mills Park Middle School).

Editor’s Note: For our third installment in the International Year of Soils series, we spoke with Dr. Julia Stevens about her work with soil microbiology and connecting students to science. To learn more about her work with middle school students, click here.

For Julia Stevens, a challenging aspect of teaching microbiology to middle schoolers is the sheer scope of something so small.

Drug Discovery in your Backyard

Fig.1. Example plates of fungi being isolated from soil samples in the Natural Products Discovery Group citizen science project at the University of Oklahoma (Credit: Candace Coker, University of Oklahoma).

Editor’s Note: For the second article in our International Year of Soils series, learn about how to find the next generation of medicine in your own backyard!

In 1928, Alexander Fleming returned from holiday to find something amazing growing on his Petri dishes. Once full of Staphylococcus bacteria, it was now growing mold. Secretions from this mold, later identified as Penicillium notatum, proved to kill a host of harmful bacteria and became the first true antibiotic. Robert Cichewicz, a professor of chemistry and biochemistry at the University of Oklahoma, would classify Fleming’s bacteria-killing compounds as natural products, a term applied to many types of compounds made by cells, but are not necessary for their survival like essential proteins or lipids.

Teaching old data new tricks

Fig.1. Rock core samples, pictured, stored at the U.S. Geological Survey's Core Research Center. Data derived from core samples, among other types of samples, are useful in testing climate models. (Credit: USGS, 2012)

There’s an old saying that history repeats itself. But in the case of Carrie Morrill’s research, she’s looking to history to prepare for the future.

Saving the Avocado Tree, One Beetle at a Time

Fig.1. The redbay ambrosia beetle (Xyleborus glabratus) is currently wreaking havoc among avocado crops in Florida. (Credit: USDA, 2012)

Little do guacamole lovers know that two different types of ambrosia beetles -- Xyleborus glabratus and Euwallacea sp. -- and the fungi they carry are terrorizing avocado groves in Florida and California, respectively, where more than 99% of the U.S.’s avocado crop is grown. But fear not, the USDA Agricultural Research Service’s Crop Bioprotection Research Unit is on the case.

Q&A with the Scientists: Luca Bartolozzi

Fig.1.: Luca Bartolozzi working in the field. (Submitted by Luca Bartolozzi).

Editor’s Note: The first in our series of Q&As with researchers and curators globally is with Luca Bartolozzi, curator of the entomology department at the University of Florence’s Natural History Museum.

Collection Spotlight: Schistosomiasis Collection at the Natural History Museum (SCAN)

Fig.1. Adult male and female Schistosoma parasite worms. The female is thinner and fits within the male (Photo courtesy of David Rollinson, NHM)

For our second article in the Collection Spotlight series, we spoke with Dr. David Rollinson and Dr. Aidan Emery. They are researchers at the Natural History Museum, London who work with the Schistosomiasis Collection at the Natural History Museum (SCAN). Here is what they had to say about this collection.

Collection Spotlight: NMNH Vertebrate Paleontology

Fig.1. Hatcher the Triceratops and Stan the T. rex are center stage in “The Last American Dinosaurs” at the National Museum of Natural History (Credit: Donald E. Hurlbert, Smithsonian Institution).

In this new article series, we will highlight interesting collections and the people involved with them. Last week we spoke with Dr. Hans-Dieter Sues, curator of Vertebrate Paleontology at the Smithsonian’s National Museum of Natural History (NMNH). Here is what he had to say about this intriguing (and old) collection.

If you wanted to know Dr. Sues’ favorite collection specimen, he would probably stop you from finishing the question.

CDC for Wildlife Diseases

Fig.1. Little brown bats (Myotis lucifugus) are especially vulnerable to White Nose Syndrome, with 90%-100% mortality during an outbreak (Photographer: Merlin Tuttle)

Last week, the U.S. Fish & Wildlife Service awarded more than $1.2 million to 30 states in an effort to combat White Nose Syndrome, a deadly disease affecting many bat species. Since its appearance in 2006, this disease has spread fast with greater than 90 percent mortality in some bat species. A 2009 study done by researchers at the National Wildlife Health Center in Madison, WI, determined that the fatal epizootic was caused by the fungus Pseudogymonoascus destructans. Although the White Nose Syndrome is only known to infect bats, declines in bat populations affect ecosystems and agriculture.

No Man is an Island

Fig.1. Salmonella bacteria can cause food poisoning and typhoid fever

One mild September day around 4 p.m. nearly two years ago, members of FDA’s Coordinated Outbreak Response and Evaluation (CORE) Network sat down with their state and federal partners to talk about a Salmonella outbreak. They quickly traced the outbreak’s source to a brand of peanut butter sold in Trader Joe’s. By 8 p.m. EDT that evening, they had a call with Trader Joe’s corporate offices, and by 9:40 p.m., Trader Joe’s issued a nationwide advisory to remove the product from their shelves.

Tracing the History of Disease

In 1894, two research physicians independently identified the bacterium that causes bubonic plague. The bacillus, now known as Yersinia pestis, had finally been found as the pathogen to a disease that killed millions. This discovery was timely because just six years later the plague arrived to the United States on a ship carrying passengers from Hong Kong to San Francisco. Over the next nine years, the bubonic plague swept through the city.

A Modern Solution to an Ancient Problem

Eight centuries before the Black Death, a plague swept through the Byzantine Empire and then Europe with devastating consequences. More than 100 million people were killed from the 6th to 8th centuries in a pandemic known as the Plague of Justinian, or the first pandemic. Until last year, the cause of the disease was disputed, with arguments ranging from influenza to smallpox. Dave Wagner, an associate professor at Northern Arizona University, worked with scientists from around the world to confidently identify the bacterium Yersinia pestis as the cause of the pandemic.