Technology

Announcing GGBN/Specify Integration

Posted November 15, 2017 - 3:16pm

The Specify Software Project (www.specifysoftware.org) is pleased to announce the fruition of a joint software effort with the Global Genome Biodiversity Network (www.ggbn.org) to facilitate the communication of genetic sample data to the GGBN Portal from biological museums around the world...

Read the full post here: http://www.sustain.specifysoftware.org/2017/11/15/1913/

2017 GGBN-GGI Award Call for Proposals

Posted January 31, 2017 - 10:14am

The Awards Program sponsored by the Global Genome Initiative provides funding for projects that support the discoverability of new genetic collections through the Global Genome Biodiversity Network’s Data Portal (http://www.ggbn.org/). The submission deadline for proposals this year is 1 May 2017. The Proposal Review Committee will consider requests for up to $30,000 with clearly articulated budget justifications.

GGBN 2017 Regional North American Workshop

Posted January 30, 2017 - 4:58pm

The Global Genome Biodiversity Network Workshop on Linking DNA and Tissue Collections in North America
Smithsonian Institution National Museum of Natural History, Washington D.C.
April 11-13, 2017

The Thrill of DNA Barcoding (and Frog Eggs)

Posted December 19, 2016 - 9:49am

Inaugural Global Biodiversity Genomics Conference

Posted November 3, 2016 - 9:47am

The Smithsonian Institute for Biodiversity Genomics and BGI invite you to the Inaugural Global Biodiversity Genomics Conference in Washington, D.C. February 21-23, 2017 at the Smithsonian’s National Museum of Natural History and the JW Marriott.

Registration deadlines for talks and posters is November 15, 2016.

YES! Current Projects (2014-2016)

2015 intern prepares a Marsh Elder plant specimen for DNA extraction. Photo by Natalia Agudelo2015 intern prepares a Marsh Elder plant specimen for DNA extraction. Photo by Natalia Agudelo

Research Boot Camp - Sequencing the Marsh Elder Plant Genome

For the past two years, the interns’ Boot Camp experience has allowed them to work with an international team of scientists studying genomic changes during the process of plant domestication. Funded through a National Science Foundation research grant to decode ancient DNA of the Sunflower (Helianthus annuus), our students are working in parallel to sequence the first genome of a related plant, the Marsh Elder (Iva annua). The students receive special guest lectures and interactive discussions (some via video conferencing) on the project from anthropologists at the NMNH and Ohio State University, from plant domestication researchers at the University of California, Berkeley (UCB), and they learn about ancient DNA from the famous Gilbert Lab at the University of Copenhagen, Denmark. In 2014 the students ran genomic DNA of the Marsh Elder on an Ion Torrent Personal Genome Machine (PGM) to recover nearly 3 million reads (or fragments) of DNA sequences ranging from 200–300 base-pairs (bp) in length. Last year’s students ran genomic DNA of the same Marsh Elder plant on the Illumina MiSeq to recover nearly 20 million paired-end reads—sequenced in both directions—to re-assemble into ~600 bp in length fragments.  With these data, the scientists hope to reconstruct as much of the Marsh Elder genome as possible, to compare with the ancient DNA during domestication, and with the Sunflower genomes (both ancient and contemporary domesticated plants). 

The following YES! GGI student projects are a sample from 2013 – 2015:

Testing Field Preservation Methods for Plant DNA

Three methods of preservation are commonly used to collect plants for research, 1) drying plants in a plant press for classic museum specimens, 2) freezing tissues in liquid nitrogen, and 3) desiccating tissues with silica gel. The latter two methods are used to capture and preserve plant DNA. Using the same specimens to compare preservation methods, this project preserved plant tissue with liquid nitrogen and silica gel and then examined the quality of the DNA that was recovered. The research will continue over time to see whether DNA decomposes more rapidly with silica gel preservation versus being immediately frozen in liquid nitrogen. Silica gel is less expensive and somewhat easier to take into the field than liquid nitrogen.

Arthropod Diversity in Myanmar (Burma)

Arthropods are so diverse, it is estimated they account for 80% of the diversity of life on Earth, so it takes many experts to identify most arthropods to the genus or species and often the family level. A recent collecting expedition to Myanmar collected arthropods from two forest preserves. The specimens were brought back to the National Museum of Natural History and sampled for DNA Barcoding. The barcodes were used to find matches in GenBank, the genome sequence repository at the National Center for Biotechnology Information. When matches were found, the specimens could be more easily identified without requiring arthropod specialists for each taxonomic group.

Using DNA Barcoding for Conservation of Amphibians and Reptiles in Myanmar (Burma)

Frogs, lizards and snakes were collected in remote protected areas of Myanmar, shipped to the National Museum of Natural History and tissues were processed for DNA Barcoding. DNA analysis through barcoding, or sequencing areas of mitochondrial DNA, revealed cryptic species that look alike physically, but are genetically distinct, and helped researchers understand the geographic distribution of species. The amphibian and reptile biodiversity is rich in this poorly known area of southeast Asia; several new species were discovered during this expedition.

Genomic Era: Systematics of Demosponges

Sponges are important organisms in reef systems and on the ocean floor. The goal of this project was to add to our knowledge of the evolutionary history of sponges by adding genomic support to the sponge phylogenetic tree and to place new species onto the tree. Next Generation Sequencing was used to sequence complete mitochondrial genes to identify genes that, in combination, can discriminate closely related species and reveal evolutionary relationships among sponges.

YES! Youth Engagement through Science

YES! Youth Engagement through Science

2015 intern prepares DNA samples for sequencing. Photo by Adrian Van Allen2015 intern prepares DNA samples for sequencing. Photo by Adrian Van Allen

Program Description:

The Smithsonian Institution’s National Museum of Natural History and Global Genome Initiative are committed to increasing opportunities in biodiversity research for interested students in under-represented communities. The Youth Engagement through Science (YES!) program is a multi-year trajectory designed to help participants build their science and communication skills, explore careers in science by working side by side with scientists, and prepare for the next step in their education through a college preparation course. The YES! 2.0- Global Genome Initiative experience builds on the knowledge and skills acquired through the first year of the YES! 1.0 Program by adding hands-on experiences working with DNA in the Museum’s genomics laboratory and doing independent research projects using the technology of genomic science.

Program Components:

Summer Session: 7 weeks, June – August

During the first two weeks, interns participate in a Genomics Boot Camp learning skills such as pipetting, running gels, DNA extraction, amplification, DNA sequencing reactions, library preparation for genomic analyses, and other lab protocols to pursue a team-based research project with Smithsonian Global Genome Initiative scientists and collaborators. They participate in multi-institutional, collaborative research projects, and receive in-depth lectures and live chat discussions from local, remote, and even international scholars. The students also participate in discussions about the methods they are using and other genomic applications in evolutionary biology. Following Boot Camp, interns transition to independent, mentored research projects in biodiversity genetics and genomics. Throughout the summer interns also visit other local research institutions such as the National Zoo's Center for Conservation and Evolutionary Genetics, the National Institutes of Health (NIH), and the Systematic Entomology Laboratory at the United States Department of Agriculture (USDA).  In addition to research experience, the interns receive training and mentoring in scientific writing and presentations skills and in communicating their research to public audiences.  The summer culminates in a Community Day experience in which interns share their research from Boot Camp and their mentored research experiences to their families, friends, and museum visitors.

Fall Session: 6 weeks, September - October (Saturdays only)

Interns will engage in college preparation activities (optional) and will work on developing a TED-like presentation about their science experience in the YES! 2.0 program. Between October – December interns will give their presentations to their school community and peers.

Yes! Projects

Yes! Internship Opportunities

In face of mass extinctions, Smithsonian’s Global Genome Initiative quietly saves world’s DNA

Posted April 6, 2016 - 1:52pm

It is rare but not entirely uncommon to see a manatee swimming in the Atlantic waters of Maryland and Virginia. This one was dead, however, bobbing in the surf off Assateague Island near the Maryland-Virginia border in late October...

http://insider.si.edu/2016/04/face-mass-extinctions-smithsonians-global-genome-initiative-quietly-saving-dna/

Smithsonian Targeted Enrichment Workshop - In Review

Posted March 31, 2016 - 1:58pm

On March 15th, the Smithsonian Institute for Biodiversity Genomics (SIBG) Bioinformatics Group hosted an all-day target enrichment/bait capture workshop. This workshop was geared toward researchers who currently use or would like to use target capture techniques and data in their research.

Paul Frandsen (ORIS/OCIO) offered a short Hydra training workshop on Monday March 14th. This two-hour training provided a short introduction to Hydra, which helped prepare participants for the exercises given during the targeted enrichment workshop.

Smithsonian Targeted Enrichment Workshop: 15 March 2016

Posted February 12, 2016 - 2:59pm

On March 15th, the Smithsonian Institute for Biodiversity Genomics (SIBG) Bioinformatics Group will be hosting an all day target enrichment/bait capture workshop. This workshop is geared toward researchers who currently use or would like to use target capture techniques and data in their research.

The workshop will start with an introductory lecture at 9:30am on March 15th, 2016: Planning a Successful Target Enrichment Project with MYbaits.

Presented by: Alison M. Devault, Ph.D.

Product Manager, MYbaits & NGS

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