Scientific Collections vs. Pandemics: an unfair match?

Fig. 1. Ebola Signs and Symptoms.

Editor’s Note: SciColl held our first community workshop on Emerging Infectious Diseases in October 2014. This October we're posting several pieces that highlight the important work where collections continue to play an integral role.

Editor’s Note: SciColl intern, Ebubechi Okpalugo from Pembroke College, contributed this article as part of her time in the SciColl office during Summer 2017.

Sweeping across three countries and claiming over 11,000 lives, the 2014 West African Ebola outbreak is almost impossible to forget. First identified in 1976, in a remote village named Zaire in what is now the Democratic Republic of Congo, there have been multiple outbreaks of the virus since. But the 2014 pandemic, caused by the Zaire strain, has been the most deadly. Striking on the border of three of the poorest African nations, Sierra Leone, Guinea and Liberia, the virus spread to an unprecedented scale. Liberia, the worst hit, was not officially declared Ebola-free until the 13^th of January 2016.

Could it have been stopped quicker? That’s where scientific collections come in.

The Archaeogenomics Equation

What do you get when you mix archaeology, ecology, wildlife management, and conservation genomics? No, this isn’t a tagline similar to a duck-in-a-bar joke. What you have is an emerging field of studying called conservation archaeogenomics.

At the forefront of this work are Robert Fleischer and Jesús Maldonado, both of the Center for Conservation Genomics (CCG) at the Smithsonian Conservation Biology Institute and National Zoo. The purpose of archaeogenomics is to use genomic methods to learn how humans impacted the environment over time, and Fleischer and Maldonado use this information to make recommendations for conservation.

Brave New World

Fig.1. Cannabis sativa. (Credit: Biodiversity Heritage Library)

In a laboratory, just outside downtown Portland, Mowgli Holmes and his team at Phylos Bioscience are embarking on a brave new world.

“We’re creating the first genetically defined collection that has ever been,” he said. “... We know less about it than any other crop.”

That crop Holmes is referring to is cannabis, and that collection he and his team of genetic researchers have been working on the past couple of years is an extensive genomic dataset. Holmes and his group will expand upon the "draft" genomics work previously done.

Monday Morning Coffee Break: April 4

(Credit: Lynn Johnson/National Geographic Creative) 

#collections #cannabis #genomics #genome #DNA #ancientDNA

A Year in the Life of Scientific Collections

Fig.1. Scenes from the Svalbard Global Seed Vault (Credit left to right: Neil Palmer/CIAT, 2011; Mari Tefre/Global Crop Diversity Trust, 2008; Dag Terje Filip Endresen/Svalbard Global Seed Vault, 2008)

Earlier this year, the International Center for Agricultural Research in the Dry Areas (ICARDA) made a request to withdraw seeds from the Svalbard Global Seed Vault, which holds more than 850,000 samples from every country in the world. This request is the first of its kind for the “Doomsday Vault” that holds duplicate seed samples for national and international gene banks. The Syrian civil war forced ICARDA to move its headquarters from Aleppo, Syria, to Beirut, Lebanon, in 2012, and researchers managed to save 80 percent of the seed samples by sending them into storage at Svalbard.

Although such a withdrawal will allow ICARDA to regenerate these precious samples, it reveals the vulnerability of collections to war or even natural disasters. The year of 2015 marked a specific effort by individuals and organizations around the world to protect and sustain scientific collections, from those housed in natural history museums to frozen specimens in gene banks. We identified major trends that have affected both how collections are viewed in science and policy, as well as how they can be protected for generations to come. Read to learn more about what happened in the collections world this year, and what you should watch out for in 2016.

Ancient DNA and a History of Human Migration

Fig.1. Members of the Ari tribe in modern southwest Ethiopia are probably direct
 descendants of the Mota man (Credit: Carsten ten Brink via Flickr)

Around 60,000 to 100,000 years ago, modern humans migrated out of Africa and proceeded to populate every corner of the world. Although ancient DNA analyses have added complexity to the routes of human migration, from Neolithic farmers to early hunter-gatherers in Europe, the birthplace of humanity has remained elusive. Among other challenges, regional hot temperatures that quickly degrade genetic material barred ancient African remains from such studies. However, in research published last week in the journal Science, a skeleton found in a remote cave in Ethiopia produced Africa’s first ancient human genome.

Monday Morning Coffee Break: Oct. 12

(Credit: Graphic by Nature World Report ) 

#humangenome #DNA #humanmigration #Africa

In the News: Filter-Feeders and Whale Drones

Fig.1. This basking shark is one of several species that independently evolved the ability to filter feed (Credit: Greg Skormal/NOAA Fisheries Service, 2011)

Breathalyzer tests for whales and climate change-fighting sea creatures are part of ongoing research in marine animal science. Read to learn more about checking the health of whales, the unusual octopus genome, plankton-feeding sharks, and more!

Monday Morning Coffee Break: Aug. 3

(Credit: UC Davis) 

#genome #plantgenome #plantbreeding #foodsecurity

In the News: Tracing History, from Roman Times to Chernobyl

Fig.1. A radiation warning sign hangs on barbed wire outside a cafe in Pripyat, a city forced to evacuate after the Chernobyl disaster (Credit: D. Markosian, 2011)

Repositories can hold an amazing wealth of information, from genomic data on human evolution to environmental records of political change. Learn about these unique collections and the institutions that hold them in this Follow Friday post:

Monday Morning Coffee Break: June 22

(Credit: Sergio Bertazzo) 

#dinosaurs #fossils #bones #proteins #collections #scientificcollections

Smallpox, now online!

Fig.1. Transmission electron micrograph depicts smallpox virus virions (Mag. 370,000x). Credit: Dr. F. Murphy and S. Whitfield, CDC-PHIL #1849.

In 1979, the World Health Assembly declared the world free from smallpox. This virulent disease killed about 300 million people in the 20th century alone and reached all corners of the Earth. Decisive multilateral and bilateral efforts to eradicate the disease officially began in 1966 and ended with the last naturally occurring case in Somalia in 1977. A recent New York Times opinion piece, however, argued that the smallpox could return with a vengeance.