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.
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.
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).
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!
Can We Defeat EBOLA with an Experimental CANCER Drug? from Experiment on Vimeo.
We are proud to share that Science Exchange user, OncoSynergy, is crowdfunding to test their experimental cancer drug, OS 2966, against ebola infection.
OS2966 is a monoclonal antibody that inhibits CD29 , a main cellular adhesion receptor that is key to cancer progression. Interestingly, CD29 is also thought to be hijacked by the ebola virus during infection. With the current ebola outbreak’s death toll exceeding 1,000 victims, it is more important than ever that promising drugs are investigated as soon as possible. As a result, OncoSynergy is using the Science Exchange network to test whether OS2966 can block ebola infection in cultured human cells.
“We have a unique opportunity to potentially effect a major impact on the current global ebola crisis,” said
Dr. W. Shawn Carbonell, MD, PhD, Founder and CEO of OncoSynergy. “However, as a seed stage
biotech startup with 6 employees, we don’t have the bandwidth to take on projects beyond our central
mission focused on cancer. We are teaming up with Science Exchange and Experiment to accomplish
the initial experiments which are an important first step towards possible clinical testing of OS2966. We
now need the public’s help to fund the work so we can start as soon as possible.”
“I am pleased to be working with Dr. Carbonell on this timely project,” said our CEO, Dr. Elizabeth Iorns. “This is a great example of how the Science Exchange platform can help facilitate science and accelerate scientific discoveries.”
If you’re interested in helping this research progress, please donate to OncoSynergy’s campaign here: https://experiment.com/projects/can-we-defeat-ebola-with-an-experimental-cancer-drug
The Science Exchange team (May 2014).
Another few months, another exciting update on our ever-expanding team. As always, I’m thrilled to introduce you to our freshest and possibly most diverse new hires at Science Exchange.
Our new hires represent something we value deeply at Science Exchange – curiosity. They come from varied backgrounds and are in varied roles, but the commonality between them all is a drive to learn.
Meet the new members of our Science Exchange team below:
- Ana Ulin’s resume would knock anyone’s socks off – she’s an electrical engineer who spent the last 8 years developing products at Google. During her time, she brought products that we all use like Google Maps and Google+ to the public, but what’s perhaps most impressive is that she learned to program by turning in handwritten coding assignments to her father starting at 7 years old! She’s truly a lifelong learner. She hit the ground running in our development team by immediately streamlining business operations with code and was awarded our FORCE award within 90 days.
- Mennah Moustafa joins our Business Development team from Sigma-Aldrich where she lead their North American strategic sales over the course of ten years. It was love at first lunch when she interviewed, and she has quickly immersed herself in all things Science Exchange since joining. She is a unique blend of smiley, inquisitive, and strategic. These traits meant that she was digesting Science Exchange materials and creating new presentations during her first week and doing headstands to boot!
- Charlotte Arthun joined us a few months ago as our Operations Manager. In addition to the game-changing efficiency she has brought to the office, Charlotte has instilled a passion for nature and zoology into our office environment. After her undergrad in biology, she spent years working as a field ecologist around the world – studying large cats like jaguars and pumas. Even now she exercises her curiosity by surveying river otters in the North Bay on weekends!
- Michael Benzinou’s background is one-of-a-kind: academic, strategic, and entrepreneurial. In addition to his PhD in Molecular Biology, he lead business development at Crown Bioscience and recently took part in Lean Launchpad where he developed a way to match CRO’s with R&D projects. He is a key member of our Business Development team who has utilized his diverse background to create an exciting bench sharing initiative (more details soon) and work on our Reproducibility Project: Cancer Biology. He is also one of the tallest and wittiest French men you will ever meet.
I hope you all have enjoyed reading about our new additions as much as I enjoy working with them. We are still hiring for more jobs, check out our open positions here.
About the author
Dan Knox is a Co-Founder of Science Exchange. Dan helped create the initial version of Science Exchange and led the company’s successful seed and Series A fundraising efforts. Now, he looks after finance, legal, HR, and operations (and even commits the occasional line of code). Dan has MSc. in Economics from City University (London) and an MBA from the Massachusetts Institute of Technology Sloan School of Management.
I’m excited to announce that top scientific suppliers BioLegend, Charles River Laboratories, Corning Incorporated, DDC Medical, EMD Millipore, Harlan Laboratories, LI-COR Biosciences, Mirus Bio, Novus Biologicals, and Sigma-Aldrich will provide more than $500,000 worth of research reagents and models to support one of our validation projects, the Reproducibility Project: Cancer Biology. The donation of reagents and models will increase the number of replication experiments that can be conducted for the Reproducibility Project: Cancer Biology, a collaboration between Science Exchange and the Center for Open Science, supported by a $1.3 million grant from the Laura and John Arnold Foundation.
These companies chose to donate to the project, because they are committed to improving the quality of research and we are thrilled to have their support!
The Reproducibility Project: Cancer Biology is independently replicating 50 recent, high-impact cancer biology studies using the Science Exchange network of expert labs. The aim of the project is to use independent replication studies to identify best practices that maximize reproducibility and facilitate an accurate accumulation of knowledge, enabling potentially impactful novel findings to be built upon by the scientific community.
Studies from Amgen and Bayer report that the majority of published results cannot be independently reproduced, but there has been no open systematic review of replication in cancer biology. The Reproducibility Project: Cancer Biology will generate an open replication dataset made available on the Open Science Framework that can be used to examine the rate of reproducibility in this field and to study factors associated with the reproducibility of experimental results.
We continue to be amazed by the wide-ranging support for this project from the scientific community – thank you so much!
Of course, the more scientific supplies that are donated the more we can get done, so if you are involved with a company that is interested in donating please email me here.
About the author
Elizabeth Iorns is the CEO of Science Exchange and Director of the Reproducibility Initiative. Elizabeth conceived the idea for Science Exchange while an Assistant Professor at the University of Miami and as CEO she drives the company’s vision, strategy and growth. She is passionate about creating a new way to foster scientific collaboration that will break down existing silos, democratize access to scientific expertise and accelerate the speed of scientific discovery. Elizabeth has a Ph.D. in Cancer Biology from the Institute of Cancer Research in London, and conducted postdoctoral research in Cancer Biology from the University of Miami’s Miller School of Medicine where her research focused on identifying mechanisms of breast cancer development and progression.
We are proud to announce that we have just launched our largest product update ever – our newly designed Laboratory Storefront platform which consolidates lab management tools in order to optimize project management and internal workflow for Science Exchange laboratories.
Our vision for Science Exchange has always been to improve the efficiency of scientific research through tools that promote collaboration. We’ve spent the past three years towards this goal, building a marketplace for researchers to search and order over 2000 experiments, and helping labs to promote and manage these services online. The Laboratory Storefront is a critical step towards streamlining and improving our laboratories’ internal processes.
Read the rest of this entry »
The Science Exchange team’s vision is the democratization of science where any researcher can access the expertise and equipment they need to perform their research in a quick and efficient way.
In January, WIRED wrote an article about the new Illumina HiSeq X Ten, the first system capable of sequencing the human genome for $1,000. The machine consists of ten concurrent sequencers capable of producing 1.8 terabases of data every 3 days. This means it can sequence up to 18,000 genomes per year.
WIRED cautioned that the system designed for population-scale research with a $10 million price tag would be affordable for only a few.
The post also listed the only 3 institutes who already have the system in place including the Broad Institute of MIT (Boston, MA), the Garvan Institute of Medical Research (Sydney, Australia), and Macrogen (South Korea).
Last week, the Garvan Institute’s Kinghorn Centre for Clinical Genomics listed their Illumina HiSeq X Ten on Science Exchange.
Our vision is coming true. This amazing technology that was previously ‘affordable for only a few’ is now available to all researchers.
You can visit the Kinghorn Centre’s Science Exchange storefront to access the Illumina HiSeq X Ten. It’s an exciting time to be a scientist!
The Science Exchange team (December 2013)
When I did my last team related post, we had just finished a whirlwind of hiring that expanded the Science Exchange team to nine stellar and diverse “athletes” (in the Jason Freedman sense of the word). Well, I’m proud to share that the team has continued to grow. Over the last six months, we’ve been fortunate enough to find one perfect candidate after another.
So, without further ado, meet the newest additions to the team:
- Conria D’Souza is the first Canadian to join the Science Exchange team. She is a perfect combination of social and scientific… making her an amazing fit for our Customer Development Manager position. Before she joined Science Exchange, she devoured everything that was ever written about us and maybe knew us better than we knew ourselves. After joining the team we discovered that Conria is also an amazing graphic artist… bonus! Read the rest of this entry »
Over a year ago, I began my mission to improve scientific reproducibility. I created the Reproducibility Initiative with PLOS, figshare, and Mendeley to provide a mechanism for scientists to independently replicate findings and be rewarded for doing so. We have made great strides in our effort such as the validation of more than 1000 antibodies for antibodies-online. However, today is the day that I have made progress very near and dear to my heart. The Reproducibility Initiative has received a $1.3 million grant from the Laura and John Arnold Foundation to validate 50 landmark cancer biology studies.
Read the rest of this entry »