Science Exchange enables completion of the Kakapo 125 Project

July 5, 2017 | Posted by Team in Scientist Profile |

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 Scientist Profile |

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 Scientist Profile |

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.

Why requesters love Sourcing Manager & neuroscientist, Zev Wisotsky

February 27, 2017 | Posted by Keith Osiewicz in Scientist Profile |

At Science Exchange, our Masters’ and Ph.D.-level sourcing managers will help you find the right service provider for your project. Based on glowing customer testimonials, we know that our sourcing managers are one of our company’s greatest assets.

Let’s get to know them better! We’ll start with customers’ favorite, Zev Wisotsky. Trained in neuroscience, he devoted his graduate research to studying taste detection in insects.

Zev

“We love working with you, you are amazing…Thanks for everything you do.” Researcher at Gilead Sciences, to Zev

Featured Sourcing Manager: Zev Wisotsky, Ph.D.

Expertise: Neuroscience

Why requesters keep coming back to him: Zev embodies excellence in customer service. That rare combination of empathy, patience, dedication, and hyper-organization comes together in Zev, seasoned with a dash of effortless communication and a sauce of good humor.

One request he is proud of being able to source: Zev is particularly proud to have once located some difficult-to-find tuberculosis blood and peripheral blood mononuclear cell (PBMC) samples for a client that was not able to find them. This allowed our client to further their research. They were also excited to be able to start their project quickly once they joined Science Exchange.

How he solved one tough sourcing challenge: There was one overseas shipping error where Zev was able to coordinate with the client and service provider to fix and reship samples with minimal extraneous costs and time.

Experience (education and/or prior roles): Zev graduated from University of California Riverside with a degree in Neuroscience, investigating and characterizing the cellular mechanisms involved in taste detection using fruit fly and mosquito. He then completed postdoctoral research at Stanford investigating the role of brain regions involved in fear memory and addiction through silencing different brain circuits optogenetically.

Likes: Bicycling, singing and playing music

Dislikes: Traffic and stale cake

So…. do flies like beer or water? The answer is in this NPR article about Zev’s research!

Kakapo 125 – First 40 kākāpō sequenced

August 4, 2016 | Posted by Team in Scientist Profile |

Kakapo Chick

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 first 40 individual kākāpō!

Portraits

Sponsors of individual kākāpō genomes will shortly be receiving their custom DNA artwork produced by Nimble Diagnostics. 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

The data created as part of the Kakapo 125 Project will be made available to all researchers working on not-for-profit projects. To register your interest in the dataset generated to-date please send a request to The Department of Conservation (DOC).

We will soon be starting sequencing of the next 40 kākāpō genomes thanks to funding from a highly successful crowdfunding campaign on Experiment.com.

Kakapo Running

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 Scientist Profile |

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 Scientist Profile |

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.

Sequencing the genome of the extinct moa

June 21, 2015 | Posted by Team in Scientist Profile |

The moa were the tallest birds ever to walk the face of the earth. The two largest species, Dinornis robustus and Dinornis novaezelandiae, reached about 3.6 m (12 ft) in height with neck outstretched, and weighed about 230 kg (510 lb).
Moa

Ka ngaro i te ngaro a te Moa – Lost, like the Moa is lost.

Science Exchange software engineer David Iorns has been fascinated by New Zealand megafauna since childhood. In collaboration with Science Exchange, Experiment.com and the Beijing Genomics Institute he’s undertaking an attempt to sequence the moa genome.

Sequencing the moa genome is a challenging endeavor due the degraded nature of ancient DNA and the large genetic divergence of the moa. Large genetic divergence means the reference genomes required to assemble the target genome are substantially less useful than species with very similar living relatives.

Despite these technical challenges David is optimistic the sequencing attempt will result in the creation of an imperfect yet very useful moa genome. This genome will help to clarify ratite evolution and may even form the foundation of a future attempt at species revival as the science of genetic rescue and de-extinction continues to progress.

The sequencing attempt is being primarily funded via an Experiment.com crowd-sourcing campaign. Please help us to make a meaningful scientific contribution by donating to the project.

All contributions made between Monday 22nd of June 8am PST and Tuesday 23rd of June 8am PST will be matched dollar for dollar by Experiment.com!

Fund this project

Interview with Matt Owens from Harlem Biospace

March 3, 2015 | Posted by Tess Mayall in Scientist Profile |

hb_horizontal_logo

I recently talked to Matt Owens, Executive Director of Harlem Biospace. For anyone interested in biotech, startups, or the up and coming New York biotech scene, his interview below is a must-read. Check it out!

Q: Why was Harlem Biospace created?

Matt: There was so much incredible research taking place at the institutions in New York City, but there was no support system for developing that research into a company. One important first step to building those companies and commercializing that research is affordable lab space. So we built an affordable lab and working space for early-stage life science companies.

Q: What is the goal of Harlem Biospace?

Matt: The goal is to lower the barrier for commercializing a hypothesis into a technology.

Q: What kind of companies are you looking for? What’s the ideal stage and mission of the companies that apply?

Matt: The stages are very early, 1-4 people. That still covers a wide spectrum of readiness to ship a product, because the ideas are very different. It ranges from molecules for drug discovery to people with research tools that are ready to prototype and find early customers.

Most are just funding these projects themselves or have family investors, while a few have investors.

Q: What are the companies in your first batch working on?

Matt: It’s an incredibly diverse group ranging from allergy testing techniques to drug discovery to devices for preserving mouse neurons. The individuals behind them all have strong research backgrounds and a well-articulated plan for developing a company around their idea. Read the rest of this entry »

Science Exchange Stories: Ethan Perlstein, Perlstein Lab

September 25, 2014 | Posted by Tess Mayall in Scientist Profile |

Perlstein Lab Cropped

I recently spoke with our user Ethan Perlstein, whose one-of-a-kind independent lab is flipping traditional drug discovery on its head. Check out how he is changing the paradigm of traditional research, pharmacology, and more below.

Q: What is the focus of the Perlstein Lab?

Ethan: The Perlstein Lab is focused on personalized orphan drug discovery. We take a two-pronged approach. We first create a primordial disease model for a given patients’ mutation; that involves taking a change in the DNA that you see in the disease and putting it into the model organisms.

We use yeast, worms, flies, and fish that have ancestral versions of that gene. We can use those models to do drug discovery, and we can validate the hits that we get in patient derived cells of the same genotype. So it’s a closed system where everything is personalized from the outset.

Q: How did it come into existence? What was the progression from your very first crowdfunding experience to starting your own lab?

Ethan: The science behind it has been incubating a long time, since I was in grad school, so it’s been a ten-year process. Screening using a model organism is something I did in grad school, so it’s existed for awhile. As a post-doc, I took some of those scientific concepts and drilled down deeper, so that put me in a good position to have a scientific foundation.

I spent the next 18 months leaving academia and navigating the business side. Last fall, I put together a business plan, had it reviewed by business people, improved my plan, and by the end of 2014 I began fundraising.

The team started to come together in early April. The lab started to come together in terms of equipment and structure in mid-April. And now we have a fully functional lab that has yeast, worms, and flies, and it’s off to the races. Read the rest of this entry »

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