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.

Koliber Biosciences Is Using Science Exchange To Develop Their Probiotic

January 20, 2016 | Posted by Team in Conferences, Events, Small Biotech Stories |

At the Blue Sky Bio Competition held during the SynBioBeta SF 2015 meeting, three finalists presented their ideas to the conference audience. They each hoped to win the prize resources in order to get the boost they needed to bring their ideas to fruition. Science Exchange sponsored this event, and presented the winners with $100,000 in credits to be used on the Science ExchEwa-Lisange platform. In the end, the audience decided to divide the winnings among the three finalists. Ewa Lis, founder and CEO of Koliber Biosciences and one of the winners, presented her ideas about probiotics and depression.

Ewa hopes to tackle the problem of depression. They propose to develop a probiotic strain that will produce a serotonin precursor of tryptophan directly in the gut. A probiotic supplement, especially if available over the counter, is more likely to be accepted by the large population of people that currently avoid medical treatment. It solves the problem of tryptophan degradation in the stomach and doesn’t require long treatment.

The market need for new depression treatments is clear. Depression affects 350 million people worldwide and results in $30 billion of economic loss. Two thirds of people suffering from depression do not seek medical treatment despite the existence of treatments. Moreover many failed treatments are due to patients stopping the medication themselves, often due to side effects.

Ewa and her team will use Science Exchange to develop probiotics that will ameliorate the effects of depression. To develop the strains they will use information from whole genome sequencing, RNA sequencing and analytical chemistry, services readily available via Science Exchange. Combined with their expertise in strain engineering and machine learning, they will be able to leverage the Science Exchange services to accelerate their research.

Science Exchange has many labs that can help Ewa and her team. For DNA sequencing, labs like Macrogen, Laragen, Quick Biology, Affiliated Genetics, ACGT and Applied Biological Materials can perform the work. For RNA sequencing, there are over 60 labs that can help Koliber Biosciences. In addition to these services, Science Exchange has labs that specifically focus on gut microbial community studies such as Second Genome. Lastly, Science Exchange offers many, many labs that perform standard studies such as amino acid analysis and compound synthesis. Science Exchange is the right resource to help Koliber Biosciences get started.

 

Science Exchange Supplier Spotlight: University of Wisconsin Cardiovascular Physiology Core Facility

January 15, 2016 | Posted by Team in Core facilities |

The Cardiovascular Physiology Core Facility, with over 35 years of research experience, provides researchers with a resource for creating and studying animal models of disease.

While the central focus of the facility is cardiovascular research, the techniques employed are often useful to investigators in other fields. Currently, the facility is conducting studies into diabetes, bone growth, drug toxicology, and gene therapy in liver and skeletal muscle, as well as cardiovascular disease. One of the most popular services provided by the facility is evaluation of the cardiovascular phenotype of transgenic mice.

The facilities include:

Complete animal catheterization laboratory and fluoroscopy suite
Complete animal catheterization laboratory and fluoroscopy suite


Microsurgery Stations
Microsurgery Stations

• Fully-equipped small and large animal operating theaters
• State-of the art echocardiography for large and small animal models
• ECG and blood pressure monitoring via telemetry
• Exercise training and testing
• Physiologic recording equipment
• Sonomicrometry

You can learn more about this lab’s offerings on their storefront.

Science Exchange Won Four Grants from the International Initiative for Impact Evaluation (3ie), which is funded by the Gates Foundation, to reanalyze published articles dealing with health in developing countries.

October 28, 2015 | Posted by Keith Osiewicz in Company, Reproducibility |

We won four grants to reanalyze four published journal articles in the field of public health. These grants covere four subjects: Cash transfers and sexually transmitted diseases, the necessary training of healthcare providers, circumcision and HIV and the affect of the US government’s spending in Africa on mortality. The grants come from 3ie, which is funded by the Gates Foundation. The work will be performed by a lab listed on Science Exchange: the University of Nebraska’s Center for Collaboration on Research Design and Analysis.

The grants cover various aspects of healthcare in developing countries. The first grant will analyze a paper published in Lancet in 2012 by Sarah Baird, Richard Garfein, Craig McIntosh and Berk Ozler. This paper, Effect of a Cash Transfer Programme for Schooling on Prevalence of HIV and Herpes Simplex Type 2 in Malawi: A Cluster Randomized Trial, showed that direct cash transfers decreased the prevalence of HIV and herpes simplex virus 2 (HSV-2) as well as the sexual behavior of the young women receiving transfers for 18 months. The second grant will reanalyze the 2012 paper published in Lancet, Task shifting of antiretroviral treatment from doctors to primary-care nurses in South Africa (STRETCH): a pragmatic, parallel, cluster-randomised trial. This paper examined the affect of using nurses, instead of scarce doctors to administer anti-retroviral treatment to patients with HIV. They found that STRETCH was not inferior to standard care and supports expanding the pool of ART prescribers beyond doctors to nurses. The third grant seeks to replicate the paper from 2011, Effect of circumcision of HIV-negative men on transmission of human papillomavirus to HIV-negative. This paper addresses an important question about HPV prevention and it evaluates male circumcision as a HPV prevention strategy among rural African HIV-negative women who lack both resources and vaccines that cover the existing high-risk HPV genotypes. The results from Wawer et al. (2011) provide strong support for use of male circumcision for HPV prevention and cervical neoplasia in HIV negative female partners. The fourth grant will examine a study published in JAMA in 2012 titled, HIV Development Assistance and Adult Mortality in Africa. This study investigates the relationship between increased funding to countries receiving aid through the President’s Emergency Plan for AIDS relief (PEPFAR) and adult mortality more generally. PEPFAR is the initiative developed by President George W Bush which increased funding to select countries from 2004 to 2010. The main finding of the paper is that PEPFAR countries had dramatically lower mortality than non-PEPFAR countries.

Dr. Nicole Perfito, Science Exchange lead for these projects says, “Using Science Exchange to gather the resources to reanalyze these experiments means it can be done faster and cheaper than would normally occur.

The analysis of these papers will bring extra scientific rigor to the study of health in developing countries. The University of Nebraska’s Center for Collaboration on Research Design and Analysis will do the analysis of these journal articles under the direction of Dr. Nicole Perfito at Science Exchange. Once the results are complete, these replicated studies will be published in peer-reviewed journals.

The UCLA Microarray Core just received new HiSeq 3000 and HiSeq 4000 instruments

September 28, 2015 | Posted by Keith Osiewicz in Uncategorized |

The UCLA Clinical Microarray Core/JCCC Genomics Shared Resource (CMC/GSR), directed by Dr. Xinmin Li, just received new Illumina HiSeq 3000 and HiSeq 4000 instruments. These instruments greatly expand the lab’s ability to sequence nucleic acids and perform many next generation sequencing applications including whole genome and whole exome sequencing. Here is a table from the Illumina website describing the capabilities of these new instruments.

illumina-3-4-use

View all of the the UCLA Microarray Core’s services.

 

How does Science Exchange rank service providers?

September 28, 2015 | Posted by Keith Osiewicz in How To |

At Science Exchange, we want to make it easier to find the best service providers to help you with your project. Our product development team has built features such as a search box that displays results as you type, and search results that are filterable to help you quickly find what you are seeking. These features are powered by a core search algorithm that references important service provider-specific information to rank the search results.

Blog-search-1

Once you enter a search, the algorithm determines the relevancy of search results based on the keyword you entered. The algorithm then looks at the service provider storefronts that pass through this filter and ranks them based on a service provider score. This score is calculated by looking at the following features:

 

Responsiveness

Because we want requesters to hear back as soon as possible, service providers that respond to requests for quotes in a timely fashion have higher scores. We value providers who have consistently responded to their requests quickly. Plus, it is the polite thing to do. You are never penalized for declining requests. Declining a request is considered responsive behavior.

Productivity

The service provider that regularly and consistently completes orders has a higher score and will rank higher in the search results. Requesters are more comfortable working with proven providers. If you are a provider, learn more about sending your own quotes to help boost your productivity quotient.

Positive Recommendations

At Science Exchange, we offer people the chance to review service providers, and those that have many good reviews are ranked higher in the search results. However, we also take into account how long a service provider has been on Science Exchange. If you request a service from a lab, please write a review after the project is finished. If you are a service provider, please solicit recommendations from the requesters with which you work. You can also ask previous collaborators for endorsement; learn more.

New Lab Boost

We value our long-time Science Exchange service providers, but we also want to introduce new providers to the community effectively. Therefore, new providers receive a rankings boost during the first month after they join Science Exchange. If you are a service provider, take advantage of this boost by responding quickly to any requests and ideally completing projects so that when the boost goes away at the end of the first month, you will still appear high in the search results.

We will continue to optimize the search experience on Science Exchange. Check this blog regularly to stay informed of any changes.

 

Have an idea for a product or company? Enter your idea in the Blue Sky Bio Competition for a chance to win over $500K in prizes.

September 25, 2015 | Posted by Keith Osiewicz in Company, Events |

We at Science Exchange love new ideas, and so we are partnering with SynBioBeta to sponsor the SynBioBeta SF 2015-Blue Sky Bio Competition. If you have an idea for a product, project or new company, please enter the competition by submitting an application. You have a chance of winning $500K in prizes that will help you bring your idea to fruition. Please enter by 12:00 pm PST on October 2nd.Blue-Sky-Bio-Competition

This competition consists of two stages. In the first stage, the judges will review all of the entrants and winnow away the group to 3 finalists. These three finalists will then compete in the second stage of the competition which will take place live and on-stage during the SynBioBeta 2015 conference. You will have 6 minutes to present a PowerPoint presentation describing your idea. The audience will be the judges for this stage of the competition, and they will have 4 minutes to vote for the best idea. Results will be shown live on the stage screen and the 1st, 2nd & 3rd place winners will be displayed.

We are donating $100K in credits to be used on Science Exchange. With these credits the winner can choose from over 4,000 services from over 900 service providers. Our online marketplace enables you to choose your own service providers, or you can use our Concierge service where our friendly team helps you find the right service providers for your project.

The SynBioBeta SF 2015-Blue Sky Bio competition takes place in the in the Robertson Auditorium in the Mission Bay Conference Center on Wednesday, Nov. 4th, from 4:35 to 5:35. Learn more.

Two Papers Published in the Online Journal PeerJ; First Step to Reproducing Critical Prostate Cancer Findings.

September 22, 2015 | Posted by Keith Osiewicz in Research, Science Exchange News |

Science Exchange published two papers in PeerJ, the online journal, that are being funded by the Prostate Cancer Foundation-Movember Foundation Reproducibility Initiative. This initiative seeks to address growing concerns about reproducibility in scientific research by conducting replications of recent papers in the field of prostate cancer.  It is a collaboration between the Prostate Cancer Foundation, the Movember Initiative, and Science Exchange.  These two papers represent the first step to reproducing the original experiments. Today’s papers are meant to report what the collaborators will do so the scientific community has a full understanding of the process. PeerJ will publish the final results of the replications.

The first paper, The Androgen Receptor Induces a Distinct Transcriptional Program in Castration-Resistant Prostate Cancer in Man by Sharma and colleagues, was originally published in Cancer Cell in 2013. Of thousands of targets for the androgen receptor (AR), the authors elucidated a subset of 16 core genes that were consistently down-regulated with castration and re-emerged with castration resistance. These 16 AR binding sites were distinct from those observed in cells in culture. The authors suggested that cellular context can have dramatic effects on downstream transcriptional regulation of AR binding sites. The present study will attempt to replicate Fig. 7C by comparing gene expression of the 16 core genes identified by Sharma and colleagues in xenograft tumor tissue compared to androgen treated LNCaP cells in vitro.

The second paper Androgen Receptor Splice Variants Determine Taxane Sensitivity in Prostate Cancer by Thadani-Mulero and colleagues was published in Cancer Research in 2014. The experiment that will be replicated is reported in Fig. 6A. Thadani-Mulero and colleagues generated xenografts from two prostate cancer cell lines; LuCaP 86.2, which expresses predominantly the ARv567 splice variant of the androgen receptor (AR), and LuCaP 23.1, which expresses the full length AR as well as the ARv7 variant. Treatment of the tumors with the taxane docetaxel showed that the drug inhibited tumor growth of the LuCaP 86.2 cells but not of the LuCaP 23.1 cells, indicating that expression of splice variants of the AR can affect sensitivity to docetaxel.

Labs listed on Science Exchange will perform the lab work. These labs include Nobel Life Sciences, ProNovus Bioscience LLC, and the Stem Cell and Xenograft Core at the University of Pennsylvania.

Technology Spotlight: A new frontier (and a new family) in biomarker discovery

August 14, 2015 | Posted by Keith Osiewicz in Lab Profiles |

Biomarker research is one of the hottest areas of science right now, and it’s easy to see why: finding quicker and easier ways to diagnose and treat human disease is the ambition of researchers, physicians and patients alike. Tissue and blood samples are now frequently collected during clinical trials for downstream analysis of proteins, nucleic acids, and other molecules that can indicate the presence and/or progression of disease. However, researchers everywhere are starting to look at a less popular biofluid as the next horizon in biomarker discovery: urine. For the Pendergrast brothers of Ymir Genomics, urine biomarker research is a family affair.

While proteins have classically been considered the ideal biomarker, microRNAs (miRNAs) are gaining traction as robust indicators of pathology. These small, non-coding RNAs are often misregulated in disease, and changes in their expression patterns can be discerned through microarray or next-generation sequencing techniques. In various biofluids, both proteins and miRNAs are often found complexed with lipids in small, extracellular vesicles knowns as exosomes. These exosomes are shed from cells all over the body, and may be a critical for cell–cell communication.
barchart

Many studies are now finding that the same exosomes and biomarkers present in blood are also found in urine (J. Mol. Cell Card. 2012 53:668; reviewed in Front. Gen. 2013 4:1). Urine has several advantages over plasma: It can be collected noninvasively (no needles! pain free!) and in large quantities. Urine samples are neither infectious nor considered biohazardous, making disposal much easier. While plasma is generally obtained from a single time point, multiple urine samples can be collected over a period of time, allowing for easier monitoring of time-dependent changes in biomarker levels. Also important, proteins and miRNAs are highly stable in urine for long periods of time (Biomark Med. 2013 7:4).

Yet, the issue remains: How do you isolate biomarker-containing exosomes from urine? Many researchers have struggled to answer this question. Enter Ymir Genomics.

Ymir Genomics: Brothers united for biomarkers

Just over two years ago, Ymir Genomics was founded in Cambridge, MA as a partnership between three brothers with distinct skillsets: Dr. Shannon Pendergrast (Chief Scientific Officer), an accomplished molecular biologist; Scott Pendergrast (Chief Executive Officer), a seasoned business leader; and Stephen Pendergrast (Chief Technology Officer), a software development guru. The company has two goals: 1) provide new tools to facilitate the discovery of biomarkers from biofluids such as blood and urine and 2) use these tools to discover novel urine biomarkers to fight human disease.image2

One of their signature discoveries has been a novel method to isolate intact exosomes from human or animal urine, obtaining both high quality proteins and RNAs for use in biomarker analysis. Their method is significantly cheaper, faster and more robust than existing techniques. Pure, high-quality proteins and nucleic acids can be isolated, even from very dilute samples. These samples can then be used for various proteomic and genomic analyses.

Since their start two years ago, Ymir has already been featured in Science, Newsweek, and The Boston Globe. Beyond developing new tools to advance biomarker discovery, Ymir also offers experimental services to researchers, including exosome, miRNA and protein isolation from urine and other biofluids. Additionally, they routinely collaborate with other nearby companies to offer downstream services, such as qPCR or miRNA arrays.

To learn more about the services offered by Ymir, contact them directly through their Science Exchange storefront.

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.

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