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.
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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 |

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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.

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