A Better Way to Share Plasmids

Today I’d like to introduce you to Addgene, a non-profit organization that helps scientists archive, store, and share their plasmids. If you are a researcher in the biomedical field you are most likely familiar with these versatile DNA-based tools used by researchers in a broad range of molecular biology-related applications. As a former molecular biology researcher, I was fascinated by the mere idea of such a repository, which led me to browse Addgene’s website and try to understand how this platform works. 

Honestly, they have an awesome website!

Melina Fan, PhD. Co-Founder at Addgene

Melina Fan, PhD. Co-Founder at Addgene

After watching their intro video, featuring Melina Fan, one of Addgene’s founders, I became even more intrigued by their vision and platform, and approached Melina, who was kind enough to give me an hour of her (very busy!) day to discuss her enterprise. We had a great chat, during which I learned that Melina, a PhD in Diabetes and obesity, fell in love with Biology when she studied DNA replication, back in high school. She then began to work in a lab at Boston University as an intern, and developed her dream of pursuing biology research.

Not all PhDs remain in Academia - a fact. But it’s always interesting to understand the motives for leaving laboratory research and moving into a new field and occupation outside of an academic institute.

Melina’s drive for leaving the lab was the same one that has brought her to found Addgene: “While I was doing my PhD in Dr. Bruce Spiegelman's lab at Harvard, I found 20 different proteins that interacted with the lab’s favorite protein (PGC-1 at the time). For testing these interactions I needed to get plasmids that encoded those proteins, and so I read papers and wrote to 20 different labs, asking them for their plasmids. Only half of them replied to me, and the quality of the plasmids I did get in the end was variable.”

Melina thought there had to be a better way of doing this, and, talking to other scientists about scientific sharing, she realized that a lot of them are interested in sharing their plasmids, but many times they simply cannot keep track of the cloning data or of where plasmids are stored after the person who cloned them has left the lab. Also, she figured: “They’re busy doing research, which is what they should be doing instead of spending time shipping out materials.”

And so, Addgene was founded in 2004, based on this experience, after Melina had graduated. Addgene’s Co-Founders, apart from Melina Fan, are Benjie Chen, a PhD in Computer Science from MIT, who wrote the tracking software and website for Addgene, and Kenneth Fan, who has a business background, and was able to handle the legal and business development part of forming a company. During the past 8 years Addgene has grown, and today has 30 employees.

Blueman_with_plasmid.jpg

Addgene’s vision is to help scientists share materials more easily and help advance science, first by archiving important materials, and secondly by making them searchable and available to the entire research community. I found it amazing that Melina and her colleagues at Addgene have really stayed close to this mission throughout all these years. 

“We were fortunate to start in Boston, which has many leading scientists. They were very supportive and open to putting their plasmids at Addgene, and they believed in us. That helped bring in other scientists and build trust in us.”

How does it actually work?

To request or deposit a plasmid at Addgene you’ll need to create an account here. Note that you need to be affiliated with an organization during your registration, in order to get a Material Transfer Agreement approval. 

The plasmid request process is easy and rather short. Once you fill out the online forms, Addgene will take care of all the rest, and get the needed approval for your plasmid to ship directly to where you need it. You can also track your order and update on your shipment’s status using the tracking number they will provide. You’ll obtain your plasmid as a bacterial stab culture.

For depositing a plasmid you may send it to Addgene either as DNA or as a bacterial streak. Addgene will either transform the DNA into bacteria or use bacterial streaks directly to generate bacterial glycerol stocks. Key regions of each plasmid are sequenced for verification before the plasmid is made available for request. Addgene’s plasmid repository contains over 20,000 plasmids from 1,300 PIs and labs so far, and this number keeps growing rapidly.

Share research materials and knowledge via Addgene

Share research materials and knowledge via Addgene

Addgene takes pride in labs who routinely use their services to store their plasmids for other labs to share: “We work with labs that send us plasmids every time they publish. We encourage labs to deposit plasmids pre-publication, so that information about deposited plasmids will appear in the Materials and Methods section. Every lab that deposits with us gets their own web page at Addgene, listing the lab’s plasmids. They can send that page’s link to anyone interested in their plasmids.”

Each depositing lab can log into their account at Addgene anytime they want to view online who has requested their plasmids. If your lab has deposited plasmids, Addgene will also update you monthly with an email summary on who has requested your materials. This type of report is very useful for grant applications, Melina explains: “The NIH has a requirement for sharing resources, and one way to fulfill that requirement is through Addgene. Some professors put in their grants the information showing they have shared plasmids via Addgene, including how many times their plasmids have been requested.”

The road to success was not short or easy, especially at the beginning. “One of the most difficult issues we encountered was the Material Transfer Agreement – MTA. Any plasmid being transferred between two academic institutes must be accompanied by this MTA, and getting those forms was difficult. We ended up building a custom system that handles all MTAs electronically, and streamlines the MTA process. Today our average MTA approval time when someone requests a plasmid is only 36 hours, which could have taken weeks to months before we developed our electronic process.”

Browsing Addgene’s website I’ve noticed it does not include any commercial ads. Not surprising, as this is a non-profit organization with a goal of serving science. I was still wondering, however, how they could keep this whole thing going. “Well, we’re a non-profit, but we must have funding to provide our services” Melina explains. “We don’t charge any money from scientists who deposit plasmids, but we charge a nominal fee to scientists who request plasmids,” says Melina. “Addgene’s shipping volume today is 6,000 plasmids per month, and the fees from those transfers cover the costs of storage, quality control, and distribution.”

When I complimented Melina on Addgene’s great platform and variety of plasmids and helpful website information, she laughed saying: “Thank you, but we still have room for improvement and for expansion. Although approximately half of our plasmids are shipped outside the US, we want to expand more internationally, and raise awareness of Addgene so that more scientists can take advantage out of this resource.”

As Addgene’s vision continues to grow and develop, additional resources are added to the website for the benefit of researchers. One example is the educational portion of the website. So, apart from the pages, where you can actually deposit plasmids or find and order them, the website holds plenty of useful resources and tools, such as the Molecular Cloning Guide, which includes many protocols, a Sequence Analyzer, a Molecular Biology Reference page that includes general information on plasmids and cloning, and a Vector Database, which holds information regarding 4,000 of the most common vector backbones, not all of which are in Addgene’s repository.

As a researcher who has left the bench to develop a tool serving the scientific community, Melina’s research background was essential, she feels: “I understand what it’s like to do research, and I use the knowledge I gained at the bench, but I’ve learned many new things. Usually, by the end of your PhD you’re a specialist on one specific topic, whereas now, I feel my knowledge is more broad. We accept plasmids and read papers from all across the various scientific fields, which is a lot of fun for us! I’ve also learned a lot from starting up a business.”

Leaving the bench for such an adventure can be an overwhelming experience for someone who was trained to do research for so many years. I asked Melina how it felt for her: “To be honest, I didn’t know if I would leave the bench forever. I still had the thought, in the back of my mind, that I might go back and do a postdoc, but I’m really enjoying this job. The impact that I, personally, have on science is probably much bigger at Addgene than it would have been if I had stayed in Academia."

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Maya Amichay, PhD

Prior to joining the BioData team in 2011, Maya performed her PhD studies in the field of plant-pathogen interactions in the Department of Molecular Biology and Ecology of Plants at Tel-Aviv University. As part of her research, Maya discovered two novel fungal genes influencing disease generation by the phytopathogenic fungus Colletotrichum. Maya's extensive lab experience with molecular biology, microbiology, and biochemistry research methods grants her a thorough understanding of day-to-day difficulties encountered by researchers, and of their needs while conducting research and managing a laboratory.