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 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.
View all of the the UCLA Microarray Core’s services.
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.
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:
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.
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.
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.
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.
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.
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.
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.
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.
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.
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 RPCB is a first of its kind attempt to directly replicate a subset of high-impact, pre-clinical cancer biology papers. Importantly, the methodology, quality control steps and replication data will be open and accessible on the Open Science Framework.
We are very excited to report that 13 Registered Reports have been accepted in eLife, and experiments from 12 of those studies are underway. These include:
- Registered Report: BET bromodomain inhibition as a therapeutic strategy to target c-Myc
- Registered Report: Interactions between cancer stem cells and their niche govern metastatic colonization
- Registered Report: Coadministration of a tumor-penetrating peptide enhances the efficacy of cancer drugs
- Registered Report: Discovery of preclinical validation of drug indications using compendia of public gene expression data
- Registered Report: Intestinal inflammation targets cancer-inducing activity of the microbiota
- Registered Report: Tumour vascularization via endothelial differentiation of glioblastoma stem-like cells
- Registered Report: The CD47-signal regulatory protein alpha (SIRPa) interaction is a therapeutic target for human solid tumors
- Registered Report: Transcriptional amplification in tumor cells with elevated c-Myc
- Registered Report: Senescence surveillance of pre-malignant hepatocytes limits liver cancer development
- Registered Report: Widespread potential for growth-factor-driven resistance to anticancer kinase inhibitors
- Registered Report: Tumour micro-environment elicits innate resistance to RAF inhibitors through HGF secretion
- Registered Report: Melanoma genome sequencing reveals frequent PREX2 mutations
Before each replicating lab begins experimental work, critical reagents (often kindly shared by authors of the original studies) are quality checked. For example, all of the cell lines are authenticated and mycoplasma tested, plasmid sequences are sequenced, and rodents are pathogen tested. These quality check steps will be included on the Open Science Framework along with the data for the replication experiments themselves.
Tracking Our Progress
Keep track here as we continue to move projects forward. Our current status as of July 2015 is described below:
- Replication experiments identified for each original paper
- Protocols drafted
- Protocols transferred to Registered Report format
- Review and feedback from original authors (requests for necessary reagents)
- Expert provider identified
- Registered Report peer reviewed at eLife
- Experimental work
- Experiment work is finished
- Replication experiments analyzed and evaluated
- Replication Study published in eLife
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!
Back by popular demand, one of our top providers is hosting a Next Generation Sequencing Workshop at UCLA. If you want to use Next Generation Sequencing in your research/clinical testing, but need help with set up, sample prep, data analysis/interpretation, the Next Generation Sequencing Workshop is the place to go.
The 4-day event is run by the UCLA Clinical Microarray Core, an expert in the clinical and research Next Generation Sequencing field. The workshop was created to give researchers/clinicians hands-on experience on all aspects of Next Generation Sequencing including wet lab experience, data analysis sessions, and discussions with experts in the field.
The event will be held from July 13 – 16, 2015 at UCLA. Registration is $1500 for non-UCLA attendees.
You can register online by visiting the UCLA Clinical Microarray Core website.