Friday, January 29, 2016

In the News: The Blue Rose

Fig.1. The Suntry "blue" rose is at the center of a shift in plant engineering
(Credit: BlueRoseMan, 2011)

From laser technology to DNA barcoding, the modern study of plants involves increasingly unique approaches to examining preserved specimens. This week in the news, we remember the history of herbaria, grow miniature vegetables, and start a home-grown plant engineering movement that seeks to shake up genetics!

Wednesday, January 27, 2016

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.

Friday, January 22, 2016

In the News: Microbes and the Moon

Fig.1. Comet Lovejoy visible near Earth’s horizon
(Credit: NASA/Dan Burbank, 2011)

From microscopic organisms to lunar rocks, these collections offer a rare view of our solar system. In the news this week are visits with curators who collect comet dust, find new species, protect banana crops, and more!

Wednesday, January 20, 2016

Sea Turtles and Atomic Bombs

Fig.1. Hawksbill sea turtle, Eretmochelys imbricata
(Credit: Clark Anderson/Aquaimages, 2006)

At 5:30 a.m. on July 16, 1945, the first nuclear weapon was detonated under code name “Trinity.” Although disagreement still remains as to the start or nature of the Anthropocene, many scientists agree that nuclear weapons testing caused a widespread anthropogenic signal in the geologic record. In a couple short decades, these weapons tests doubled the amount of the radioactive isotope carbon-14 in our atmosphere. The isotope in the air entered plants during photosynthesis and animal tissues as animals ate the plants, leaving behind a radioactive trace in the natural world.
 

Friday, January 15, 2016

In the News: What We Leave Behind

Fig.1. Colosseum in Rome, Italy
(
Credit: David Iliff, 2007. License: CC-BY-SA 3.0)

Although Ötzi the Iceman offers scientists an unprecedented view of early European life, such direct physical evidence is not always available. This week, researchers used parasites to track Romans, mammoth bones to study Arctic dwellers, and more to overturn previously held assumptions about the ancient world.

Wednesday, January 13, 2016

The Iceman's Stomach Bug

Fig.1. Reconstruction of Ötzi
(
Credit: Thilo Parg/Wikimedia Commons, License: CC BY-SA 3.0)

In 1991, two hikers stumbled upon a mummy high in the Ötztal Alps, right on the border between Austria and Italy. This mummy - nicknamed Ötzi, or the Iceman - is Europe’s oldest natural human mummy and is arguably one of the most studied cadavers in science. From his eye color (brown) to his dental health (poor), Ötzi reveals an amazing amount about how Europeans looked and lived 5,300 years ago. An international group of scientists released a study last week in the journal Science that added yet another detail to the treasure trove of research on the corpse, which may inform our understanding of ancient human migration into Europe.

Friday, January 8, 2016

In the News: PNAS Editorial Released

Fig.1. Ebola response worker in full personal protective equipment
 (
Credit: UNMEER via Flickr, 2014

An editorial based on SciColl’s 2014 workshop on emerging infectious diseases has just been released in the Proceedings of the National Academy of Sciences. From the first case to a worldwide eradication effort, scientific collections are necessary for disease research and response. This week, public health officials join in the fight against mysterious diseases and call for increased communication and collaboration.

Tuesday, January 5, 2016

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.