Science Exchange enables completion of the Kakapo 125 Project

July 5, 2017 | Posted by Team in New Innovations, Research, Science Exchange News |

Sequencing the genomes of every individual kākāpō in the entire species

Kakapo bird

The kākāpō is a species of large, flightless, nocturnal, ground-dwelling parrot of the super-family Strigopoidea endemic to New Zealand. With only 154 living individuals remaining, it’s one of the world’s rarest birds.

Genetic Rescue Foundation

Since early 2016, The Genetic Rescue Foundation, in partnership with The Department of Conservation (DOC), The University of Otago, Duke University, New Zealand Genomics Ltd (NZGL), Te Rūnanga o Ngāi Tahu, and Science Exchange, has funded and managed the effort to sequence the genomes of every individual in this quirky, critically endangered species.

DNA Portraits

The Genetic Rescue Foundation’s fundraising has come in the form of generous private donations, kākāpō DNA portrait sales and a successful crowdfunding campaign on Experiment.com.

To date, the project has successfully sequenced 80 kākāpō. Part of the work was made possible by collaborating with DNA sequencing service providers on the Science Exchange network of 2,500+ service providers. Today we’re thrilled to announce that Science Exchange will be funding the remainder of the project in order to bring it to completion!

Kinghorn Centre and Garvan Institute Logos

The remaining sequencing will be performed by The Kinghorn Centre for Clinical Genomics at The Garvan Institute of Medical Research in Sydney, Australia. The Kinghorn Centre is a frequently used provider of DNA sequencing services on the Science Exchange network.

Detailed genetic data for every individual in an entire species is a world first and represents a genomics-focused paradigm shift in modern conservation efforts. The possible discoveries that will come from this rich dataset are limitless. Scientists’ immediate efforts will be focused on finding genetic links to dwarfism, infertility and other diseases and conditions hampering kākāpō population recovery.

The dataset will be controlled by the New Zealand government but will be made available for all non-profit researchers to use. All sequencing will be completed by the end of 2017, with the full dataset available for researchers in 2018.

“Science Exchange has made completing this project possible. They’ve achieved that by providing The Genetic Rescue Foundation with unrivaled access to the world’s best scientific service providers and by stepping in to fund the remainder of the project. This data will steer kākāpō conservation decisions for years and decades to come. It may prove to be the deciding factor in saving this species.”

David Iorns

David Iorns – Founder of The Genetic Rescue Foundation

Science Exchange is proud to be involved with this pioneering conservation initiative. Join Science Exchange today and work with us to accelerate your research.

Shark Poaching Exposed by the Science Exchange Network

June 8, 2017 | Posted by Team in Research, Stories |

by Kaitlin Ziemer and JR Clark, Science Exchange | www.scienceexchange.com

Today, we celebrate World Oceans Day with a Science Exchange success story. This is a story about connecting ocean conservation advocates with the scientists whose expertise is helping to guide conservation strategy.  

World Oceans Day -- Sharks

Robust shark populations are a sign of healthy oceans. [photo credit: JR Clark]

The Project Earth team from Fusion TV approached Science Exchange with a unique sequencing project. They were working on a documentary film about the illegal poaching of sharks for use in shark cartilage capsules.

Studies have shown that shark cartilage is ineffective or even pro-inflammatory. Despite this and the importance of conserving sharks, who are the ocean’s apex predators, the cartilage capsule industry has managed to persuade retailers and consumers that shark cartilage could promote joint and bone health.

The Fusion TV Project Earth team wanted to find out if cartilage pills contained illegally obtained shark tissue. They needed a service provider who could perform DNA sequencing on 30 different supplements to see if they contained protected or endangered sharks.

Through the Science Exchange network, the Fusion TV Project Earth team obtained sequencing services from Laragen, Inc., a California-based service provider. Together, they were able to detect DNA from the endangered scalloped hammerhead sharks, whose trade is highly regulated, in the capsules sold at nationwide health food stores and pharmacies.

The Fusion TV Project Earth team urged both the cartilage pill manufacturers and retailers to share more precise information about the origins of the shark material found in the pills. In response, two major retailers removed shark cartilage pills from their stores and website.

These results showed that scientific evidence can influence positive change and help to protect our natural environment. And by providing the Fusion TV Project Earth team with easy access to the world’s best scientific service providers, Science Exchange helped put the data directly into the hands of the agents of change.

About the authors:

 

Kaitlin Ziemer, B.S., is a Senior Sourcing Manager and Account Lead at Science Exchange. With her extensive prior experience in managing toxicology and regulated studies for large biopharma and contract research organizations, Kaitlin now specializes in human and animal tissue procurement.

JR Clark, M.S., is Science Exchange’s expert in shark biology, given his extensive research experience in evolutionary development and reproductive behavior of vertebrates. As a Sourcing Manager, he manages a wide variety of projects from basic research through drug discovery.

Kakapo 125 – Second 40 kākāpō sequenced

April 11, 2017 | Posted by Team in Science Exchange News |

Kakapo - Trevor

Science Exchange is a collaborator in the Kakapo 125 Project. The objective of this project is to sequence the genomes of all known living kākāpō. We’re pleased to share an update on the project’s progress. NZGL has completed sequencing the second 40 individual kākāpō!

The project is now past the halfway point with approximately 70 individuals remaining before we’ve successfully sequenced every individual in the entire species.

In the News

Scientific American Kakapo

The Kakapo 125 Project has been receiving worldwide media coverage. Here’s a selection of articles published about this groundbreaking work.

Sponsorship

Portraits

Sponsors of individual kākāpō genomes will shortly be receiving their custom DNA artwork. Each DNA portrait is constructed from the genetic data of the individual kākāpō and is guaranteed to be unique. Genome sponsorship forms a key component of ongoing fundraising for the project as we strive to sequence every genome in an entire species.

sponsor a genome button


Science Exchange is proud to be involved with this pioneering conservation initiative. Join Science Exchange today and work with us to accelerate your research.

A Voyage Through the PacBio Genome Galaxy

March 16, 2016 | Posted by Team in Science Exchange News |

We are pleased to support the Genome Galaxy Initiative from PacBio. SMRT Sequencing Technology manufacturer PacBio recently unveiled the Genome Galaxy Initiative. The Genome Galaxy Initiative, based on the Experiment platform, supports expedited, open-access genomic projects. It’s a central location for SMRT Sequencing-based projects seeking crowdfunding, and fosters a community of scientists and patrons interested in asking research questions that can only be answered with long-read sequencing. As high-quality genome assemblies from the PacBio RS II and the Sequel System have become even more affordable and accessible, partnering with Experiment is a great fit. Through this program, even more scientists will have access to the most comprehensive view of genomes, transcriptomes, and epigenomes from SMRT Sequencing.

The Genome Galaxy Initiative

One of the initiatives flagship participants is the Kakapo 125 Project. An effort to sequence the genomes of every individual in the entire kākāpō species. This project was made possible thanks to the high quality reference genome generated by Dr. Jason Howard at Duke’s Jarvis Lab using SMRT Sequencing technology.

Kakapo Jasira

Other projects in the Genome Galaxy include efforts to find bacteria within ticks to stop diseases, as well as an investigation into the incredible nitrogen capturing properties of the fern Azolla. In addition to fostering a growing community of SMRT Sequencing related projects PacBio is also offering a grant program exploring the “most interesting genome” as voted for by the public. 2016 applications for this grant are now closed with a winner to be announced in April.

Science Exchange is also assisting in the Genome Galaxy Initiative with a number of its projects including the Kakapo 125 being managed on its platform. As well as hosting many of the projects Science Exchange is also the easiest and most comprehensive place to find SMRT Sequencing service providers.

science-exchange-smrt-sequencing

The Genome Galaxy Initiative is another great example of the industry coming together to support open access science and to help out with funding at the grassroots level. Science Exchange is excited to be affiliated with this initiative and looks forward to seeing many new and exciting stars being discovered there.

Kakapo 125 – Sequencing the genomes of all known kākāpō

February 1, 2016 | Posted by Team in Science Exchange News |

Kakapo-2

Science Exchange is pleased to announce it will be collaborating in the Kakapo 125 Project. The objective of this project is to sequence the genomes of all 125 known living kākāpō.

The kākāpō is a species of large, flightless, nocturnal, ground-dwelling parrot of the super-family Strigopoidea endemic to New Zealand. It is critically endangered; as of February 2016, the total known population is only 125 living individuals.

The Kākāpō Recovery Team relies on genetic information to manage kākāpō matings in order to ensure maximum genetic diversity. Having the whole genome of all remaining individuals would allow the team to better understand the relatedness of individuals to optimize breeding.

New Zealand Genomics LtdSequencing of the first 40 kākāpō genomes is already underway at Science Exchange’s newest New Zealand based service provider New Zealand Genomics Ltd (NZGL).

The Kakapo 125 Project is the latest project organized by The Genetic Rescue Foundation. The Genetic Rescue Foundation is a not-for-profit organization dedicated to advancing scientific techniques that enable us to preserve global biodiversity. It was founded by Science Exchange software engineer and citizen/wannabe scientist David Iorns.

The Genetic Rescue Foundation has successfully raised funding for the first 40 genomes but is actively fundraising to complete the remaining 85. A core component of this fundraising will be the Experiment.com crowdfunding campaign that will run from February 1st – April 30th 2016. If you would like to help save one of the world’s most unique and charismatic birds as well as playing a part in sequencing the genomes of every individual in an entire species please contribute to the project.

Fund this project

The Kakapo 125 Project is a collaboration between a number of government, nonprofit, iwi and commercial entities.

Kakapo 125 collaborators

All of the collaborators have played an important role in the project to-date. The following individuals have been particularly critical to the projects progression.

  • Andrew Digby, Science Advisor Kakapo/Takahe DOC – Andrew works for the Department of Conservation (DOC) in New Zealand. He is leading the Kakapo 125 Project and conceived the idea of sequencing the genomes of the entire kākāpō species.
  • Bruce Robertson, Molecular Ecologist, Otago University – Bruce’s research focuses on conservation genetics and molecular ecology. He has been working on kākāpō genetics since 1996.
  • Jason Howard, Neuroscientist, Duke University – Jason (in Erich Jarvis’s lab) and his team at Duke were the first to sequence the kākāpō genome.

Sequencing the genomes of all 125 known living kākāpō is an ambitious and exciting endeavor that will help save one of the world’s most endangered species. It will also create a rich, open access genetic dataset that will be the foundation of some compelling research in years to come. Science Exchange is proud to add the Kakapo 125 Project to its long list of impactful scientific projects facilitated and managed via its platform.

Download information about the project in a distributable, media friendly format.
Download press kit


Learn more about how Science Exchange can accelerate your research.

UCSC Paleogenomics Lab joins quest for moa genome

August 11, 2015 | Posted by Team in Science Exchange News |

UCSC Logo

Science Exchange is excited to welcome the UCSC Paleogenomics Lab to our platform!

The Paleogenomics Lab is a joint venture between renowned scientists Beth Shapiro, and Richard (Ed) Green. Their research focuses on a wide range of evolutionary and ecological questions, mostly involving the application of genomics techniques to better understand how species and populations evolve through time.

The first Science Exchange project directed to the UCSC Paleogenomics Lab comes from citizen/wannabe scientist and Science Exchange software engineer David Iorns. After a successful Experiment.com crowdfunding campaign David is collaborating with Beth and her team to help perform preliminary sample preparation and analysis. Assuming the samples contain high enough levels of endogenous DNA the prepared libraries will then be sent to collaborator Dr. Guojie Zhang at The Beijing Genomics Institute where the libraries will undergo more rigorous sequencing.

Compiling the genome of an extinct species is an immense challenge. We touched on many of the complexities involved in our original announcement. However the experts participating in the project are world leaders in their field and we are confident significant progress can be made leading to exciting new discoveries about the genetic makeup of this iconic species.

Would you like to collaborate with the UCSC Paleogenomics Lab or any of our other world class laboratories? Learn more about how Science Exchange can accelerate your research.

Guest post: The rise of contractual conservatism – will it subvert sharing of scientific resources?

March 7, 2012 | Posted by Guest in Core facilities |

This is a guest post by Stephen Byers, Director of the Lombardi Shared Resources at the Lombardi Comprehensive Cancer Center, Georgetown University (full bio below). 

As director of shared resources at Georgetown University’s Lombardi Comprehensive Cancer Center and as Director of the Translation Technologies component of the Georgetown/Howard Univerity CTSA, my goal is to provide our researchers with the highest quality experimental resources, at the best possible price.  Sometimes that means adding in a new technology to our core facilities, sometimes it means reaching out to our CTSA network partners, sometimes it means negotiating with another institution altogether.   One reason I attend the Association of Biomolecular Resource Facilities (ABRF) annual conference is to keep up with cutting edge resources and explore what it makes sense for us expand or introduce as part of our core services and when it makes sense for us to find partners.

Different core facilities develop specializations, driven both by foresight as well as serendipity.   Georgetown, for example, has invested in an outstanding Metabolomics Shared Resource Program.  We’re finding that, in many cases, high throughput analysis of metabolites in blood or urine with LC-Mass Spectrometry is as good as genomic profiling at segregating outcomes in diseases… and a whole lot cheaper.  We can generate as many as 20-30,000 metabolite data points in an hour at $60/hr for 6 samples.  The real challenge for this field, as for much of post-genomic science, is the informatics that goes into analyzing all this data.  Under the guidance of our metabolomics gurus, Al Fornace and Amrita Cheema, and Medical Informatics Director Subha Madhavan, we are improving our informatics services and finding no shortage of investigators eager to take advantage of this technology.

Read the rest of this entry »

Guest post: The things you can learn from sequencing: Microbes, Primates, and Climate Change

March 6, 2012 | Posted by Guest in Research |

This is a guest post by Carl Yeoman, a postdoctoral research fellow at the Institute for Genomic Biology at the University of Illinois Urbana-Champaign who will start as Assistant Professor in the Animal and Range Sciences Dept. at Montana State University in August (full bio below). 

At this year’s Association of Biomolecular Resource Facilities (ABRF) 2012 conference, I will present the work that my colleagues and I have been doing at University of Illinois Urbana-Champaign using both 454 Life Sciences pyrosequencing and Illumina technologies to study the gastrointestinal and vaginal microbial ecosystems of humans and non-human wild primates.

Historically, microbiologists would interrogate these microbial ecosystems under a microscope or by trying to culture them in agar or broth containing nutrients. Microbes, however are extremely heterogeneous in their requirements for optimal growth. In fact, only ~1% of all microbes have been successfully grown in culture. Microbes grow at different rates (slower growing microbes will be outcompeted in non-replenishing culture), have different nutritional requirements and are often dependent upon other co-resident microbes for growth. These factors mean that culture-based analyses are inadequate for surveying microbial ecosystems, while the diversity of microbes in most ecosystems makes microscope-based analyses impossible.

Read the rest of this entry »

About Science Exchange

We are transforming scientific collaboration by creating a marketplace where scientists can order experiments from the world's top labs.

Check the Science Exchange blog for updates, opinions, guest posts and the latest happenings at Science Exchange HQ!

Visit Science Exchange →

Subscribe to the blog
Never miss a post! Science Exchange blog posts delivered right to your inbox.
Thank you for joining the SciEx revolution!
Powered By WPFruits.com