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.

The Reproducibility Project: Cancer Biology – Experiments have begun

July 10, 2015 | Posted by Keith Osiewicz in Uncategorized |

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:

Reproducibility project progress

Phase:

  1. Replication experiments identified for each original paper
  2. Protocols drafted
  3. Protocols transferred to Registered Report format
  4. Review and feedback from original authors (requests for necessary reagents)
  5. Expert provider identified
  6. Registered Report peer reviewed at eLife
  7. Experimental work
  8. Experiment work is finished
  9. Replication experiments analyzed and evaluated
  10. Replication Study published in eLife

Sequencing the genome of the extinct moa

June 21, 2015 | Posted by Team in Science Exchange News |

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

Learn about Next Generation Sequencing at the UCLA Clinical Microarray Core

June 12, 2015 | Posted by Keith Osiewicz in Workshops |

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.

5 Commonly Overlooked Laboratory Checks for your FDA cGMP Audits

April 1, 2015 | Posted by Team in Lab Admin Tools |

This blog post is a guest post from Edword Simpson, technical engineer at Science Exchange lab, RS Calibration.

labcheck

Ensuring that everything in your laboratory is ready for any upcoming audit is a nail-biting task. The annual FDA audit for compliance with regulatory guidelines, like the current goods manufacturing process (cGMP) is especially tedious. Manufacturing processes and equipment for pharmaceuticals are regulated very carefully by the FDA and require strict adherence to industry standards.

 

Here are five things that aren’t always given the attention they require and could easily result in regulatory action for failing to comply with cGMP: Read the rest of this entry »

Interview with Matt Owens from Harlem Biospace

March 3, 2015 | Posted by Tess Mayall in Helpful products |

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 »

Introducing lab tagging

February 26, 2015 | Posted by Becca Swett in Education, How To, Lab Admin Tools, New Feature |

Here at Science Exchange, we aim to enable efficient scientific collaboration. One of the biggest hurdles researchers face on our site is deciding where to send their requests. Conversely, it can be frustrating for lab admins to receive requests outside their capabilities. With that in mind, we are working on improving our search experience. This update will be available at the end of next month.

In preparation for our improved search experience, we’ve launched a tagging feature for labs. Labs can apply tags, such as equipment names, to their services, which will allow researchers to narrow their search to only labs that have the machine they need. Also, labs that have signed agreements with Science Exchange, like our Non-Disclosure Agreement, will receive storefront tags, allowing researchers who require that level of protection to quickly identify appropriate labs.

If you’re a lab admin on Science Exchange, we encourage you to begin tagging your services and storefront now! This will ensure that researchers will be able to find your lab more easily with our new search experience.

Read the rest of this entry »

This Week in Startups: Science Exchange

February 20, 2015 | Posted by Tess Mayall in Company |

Science Exchange CEO Elizabeth Iorns was on This Week in Startups for an hour-long deep dive into the state of science. Listen and learn about everything from cancer biology to AI to scientific publishing!

The Reproducibility Project: Cancer Biology Moves Forward

February 9, 2015 | Posted by Reproducibility Project Core Team in Reproducibility |

“Reproducibility is actually the heart of science. The fact that not everything is reproducible is not a surprise.” – Eric Lander, head of the Broad Institute at MIT in a recent Washington Post article. 

“We’re always in a gray area between perfect truth and complete falsehood,” The best researchers can do is edge closer to truth. – Giovanni Parmigiani, Dana-Farber Cancer Institute in a recent ScienceNews article

The Reproducibility Project, a collaboration between Science Exchange and the Center for Open Science, is independently replicating some of the most impactful studies in cancer biology. Along the way, not only will the collaboration shepherd 50 studies through the process of replication and meta-analysis, but it will also help to mature the discussion around reproducibility more generally. Where do the biggest challenges lie? What are some of the key predictors of whether experiments are reproducible? The answer to these questions will be critical as the reproducibility initiative gains traction.

Since December, experimental work has begun on four more replication studies, and three more Registered Reports have been published in eLife (with a fourth* accepted and on the way):

In total, eleven replications have begun or are poised to begin in the coming weeks. Read the rest of this entry »

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