Notes from the North – Collaboration and Communication

March is just around the corner, so there are just a couple of weeks before the CMDB and Genetics program students and faculty will be joining me for a weekend in Portland! As much as I want to advertise for the retreat and mention that it is student driven in that talks will be on topics selected by students, the day is structured based on student feedback, and the Saturday night social trivia session was voted in by students, I don’t want readers from other programs to feel left out of my article’s audience. Note on image: lobster coloration really can display Tufts support, the pattern occurs in bilateral gynandromorphs (half male, half female) where one side has normal black/brown color and the other side has a rare color mutation causing a blue carapace. The chance of a half blue/half brown lobster may be as little as 1 in 100 million.

Now, the real reason I mention the retreat is that over the last three months I have been collaborating with student and faculty colleagues at three separate campuses along the New England coast to help bring this retreat together. It has required learning and practicing organizational skills, shared decision-making skills, delegation, and diplomacy. These are all skills worth cultivating for anyone who may participate in scientific collaboration, so it is helpful to seek out collaborative experiences early in a scientific career. Here is how helping to plan a retreat becomes practice for collaboration and communication:

Integration of multiple viewpoints. One of the great advantages of working as a group toward a common goal is that collectively the group has abundant experience to draw from in order to propose ideas and predict where problems may arise. While planning the CMDB/Genetics retreat we felt it was important to be respectful of all organizer opinions and concerns and at the same time try to incorporate as many ideas from the retreat participants as possible. This of course meant instances when compromise and diplomacy were necessary. Delegation of point people for specific tasks also helped mitigate conflict because one person has had primary responsibility while others advise.

Faculty as peers as well as advisors. Speaking of advising, I have found that a benefit of helping to organize such a large event for the CMDB and Genetics programs has been the need to interact with many faculty and staff in a capacity slightly different from that of my usual student role. Over the course of our academic careers our view of academic mentors shifts from their being “sages on the stage” in high school, undergrad, and early graduate school, to being approachable human beings with advice that ranges far beyond the scholarly later in graduate school, post-doctoral fellowships, and early career. The increase in responsibility that comes with becoming a peer as well as an advisee is not something I think consciously about very often, so this has been a valuable exercise in examining the evolution of these relationships. Recognition of this changing role can facilitate collaborative scientific work because it gives you confidence in your value to a project.

Interaction at a distance. The CMDB/Genetics retreat brings together students and faculty from four campuses in two states, making it imperative that we utilize methods of communication that are speedy and reliable. Now imagine if we were on different continents! For the most part this has meant heavy reliance on email, but we have also found it helpful to setup online video conferencing for regular face-to-face interaction. Meetings can be tricky to schedule for groups comprised of very busy individuals, and it is easy to fall into the trap of holding too many, however they are important for quickly refocusing the group after a period of productivity. Another tool we have made extensive use of that is suitable for both near and far collaborative efforts are online workspace platforms such a Google Drive that allow multiple users to work and edit simultaneously. This is especially helpful in generating a living record of how the group’s ideas and priorities change over time. I think one of the greatest lessons I have learned from helping to organize the retreat has been realizing the importance of keeping a centralized record of decisions. It has allowed the retreat planning committee to understand the logic that got us to a particular point, and then guided us as we moved forward on a number of occasions.

The best way to improve any set of skills is to go out and practice them, so look for those collaborative opportunities!

“The Prize” by Geoffrey M. Cooper, PhD is a thriller for the dramatic scientist in all of us

I was excited to learn a few months ago that my former PI from BU, Dr. Geoffrey Cooper, was publishing a fictional novel about the competitive world of scientific discovery and competition. I’m sharing a short review for you guys to hopefully inspire you to pick up a copy of your own to enjoy this entertaining and relatable thriller!

A fictional novel that tells the story of two professors racing to discover the first successful Alzheimer’s drug, written by Geoffrey Cooper PhD., a professor of Biology at BU. The story follows a chronological timeline to detail how the insatiable need to achieve a novel discovery can drive scientists to perform inconceivable acts. Pam Weller acts as the protagonist, a young assistant professor studying Alzheimer’s, vying for tenure at the fictional Boston-based research institute, the Langmere. Opposing Pam is Eric Prescott, a well-established and older professor at the Institute for Advanced Neuroscience in Cambridge, also a fictional and supposedly more established institute, compared to the Langmere. Whereas Eric is credited with the establishment of an Alzheimer’s mouse, Pam is building her budding career on a novel cell culture model of Alzheimer’s in which primary mouse brain cells grow plaques and die in vitro. Pam’s lab’s efforts are directed towards screening tens of thousands of compounds in her cell culture model in hopes of identifying a drug that can stop or reverse the formation of plaques to rescue the cells—a much speedier technique, compared to the screening of compounds in Alzheimer’s mice. With Pam’s tenure review coming up quickly, the pressure is on for her to make a truly groundbreaking discovery. When Pam’s postdoc Holly happens to identify the right compound, she greedily decides to keep the data to herself in hopes of advancing her own career. In an exciting and dreadful twist, Holly uses her discovery to team up with Eric to steal the drug, destroy Pam’s credibility, and walk away with all the glory and a Nobel Prize to boot.

This book is a true thriller as Pam works to uncover the truth and gain credit where it is truly due. The Prize is an easy-to-read page-turner. It’s an exciting and relatable story that is sure to entertain, especially for us, as we are deep in the trenches of scientific discovery!

That being said, hopefully none of us are resorting to tactics as evil and dramatic as Eric and Holly. It’s just a Nature paper and full tenure and the Nobel Prize… nothing worth murdering anyone over, right?

The Prize is available for purchase on

Humans of Sackler: Becca Silver, “Enthusiasm was contagious (no pun intended)”


I’m Ila Anand, a fifth-year student in the Microbiology program. I’ve recently taken over the “Humans of Sackler” portion of the Newsletter, which was originally pioneered by Andrew Hooper. In this issue I had the honor of getting to know our GSC president, Rebecca Silver, better known as “Becca.” It was a delight sitting down with this die-hard Bruins fan and discussing a variety of topics—from finding out she loves butter pecan ice cream and Figaro’s to discovering how she first broke into science. I hope you enjoy our conversation and are better acquainted with our GSC president!

IA: Hi Becca! Let’s start with what were you doing before you started graduate school?

RS: I was having a good time in college at the University of Maine in Orono! Besides the academics, my favorite part of college was having my friends nearby and being able to spend time with them whenever I wanted. I had a pretty diverse group of friends in college and I still keep in touch with them. I’m originally from Portland, Maine and spending time with close friends was also a big part of my childhood. My favorite memories are from Fourth of July when my friends and I would hang out at a lake house. The lifestyle in Maine is generally much more slow-paced. That is actually one of the biggest differences I noticed when I started grad school—there’s much more of a “rush” in Boston compared to Portland, where the people are more laid-back.

IA: Sounds like there are definitely some cultural differences between the cities. Where else have you traveled to in the past?

RS: I’ve mostly traveled on the East coast. I’ve visited the majority of the North East and I’ve also visited Georgia and Florida. I’ve actually never traveled to the West Coast but if I had the opportunity to attend a conference I would totally go. I also really want to ski in the mountains of Colorado at some point in the future. Outside of the U.S. I’ve traveled to Canada and Bermuda. I visited Bermuda when I was fairly young (ten years old) and I vividly remember that time period because two weeks before the vacation I had pneumonia. At the time it was awful because I missed school and was trying to recover (I had a lot of Pediasure!), but in the end, because I also went on vacation, I ultimately took a month off of school and my teachers didn’t assign me any extra homework. You could say that was my first introduction to the infectious disease field!


IA: That does sound awful! So when did you actually become interested in pursuing research and studying science?

RS: Well, I was a bioengineer back in college and honestly pursuing research was a decision I made on the whim. I took an immunology elective class my junior year of college and quickly realized I really like immunology. The class was much more interesting than any of my bioengineering classes- the lectures were awe-inspiring! The professor really emphasized infectious disease clinical examples like super gross rashes all over the body, etc. The professor was so excited and his enthusiasm was contagious (no pun intended). After taking the class, that summer I took the GRE and applied for grad school the fall of my senior year. It was literally a 6-month turnaround from being a bioengineer to wanting to be an immunologist!


IA: What was your first experience working in a lab?

RS: My first experience doing lab work was during a Co-Op internship at Idexx, which is a veterinary biotech in Portland, ME. I interned at Idexx during the summer going into my junior year of college. I was involved in developing a lateral flow assay that is similar to an ELISA and this rapid immunoassay detected digging worms in infested dog feces. It was a triple detection assay so it was able to detect whipworm, roundworm, and hookworm. My internship involved developing positive and negative controls for the assay. My boss at Idexx played on the same recreational hockey team that I did in Maine and she was a Tufts alumnus. Later, when I decided I wanted to go to grad school, I reached out to her for a reference and she’s the one who influenced me to apply to and attend Tufts Sackler.

IA: That’s really neat that you play rec-hockey. How did you get into that? What else do you like to do outside of bench research?

RS: I picked up hockey in high school when I was fourteen. My friend asked me to try out for the school team because they needed more people and now it’s one my favorite activities to do. I currently play on a Greater Boston rec-team called South Shore Women’s Hockey League. We have a lot of fun! In addition to hockey, I like to run. I run with a group in Jamaica Plains called the Forest Hill Runners and my favorite spot to run is in Peters Hill in the Harvard Arboretum. It has the best view of the whole city, in my opinion. I also like to cook and play video games—specifically strategy games, like Civilization 6. As GSC president, I’ve also been heavily involved in planning the Sackler relays. Our plans are kind of top secret but I can tell you that this year we’re going to have relays in June rather than July and we’re going to have an awesome raffle. Of course, my favorite part about relays is winning- go Immunogenetics!

Notes from the Library…LabArchives


Notes from the Library…LabArchives

Tufts has an institutional license for LabArchives, an electronic lab notebook.  Your lab may already be using this tool, but if not, read on for information on what LabArchives is, and how you can use it in your work.

What is LabArchives?

LabArchives is a web-based electronic lab notebook, designed to replicate and enhance the features of a traditional paper notebook.  LabArchives allows you to electronically document your experiments, store files, search content, manage version history, and collaborate with others.

How do I access to LabArchives?

While LabArchives is designed as a collaborative tool for research labs, anyone at Tufts can contact Tufts Technology Services to request access:

Once a LabArchives account has been created for you, then access the login page from your preferred browser (Chrome, Firefox, Internet Explorer, or Safari):  Select ‘Tufts University’ from the dropdown menu (if you are on campus, then this option will already be selected), click ‘Go to Your Institution’s Login’, and enter your Tufts username and password.

LabArchives is also accessible via a mobile app for Android and iOS devices.

Tell me a little more about what I can do in LabArchives.

Like any tool, LabArchives is what you make of it.  Here are a few things you can do in LabArchives:

  • Create multiple notebooks
  • Organize information into folders, pages, and entries
  • Enter text, structures, or calculations, and upload files, to a page
  • Develop templates for common protocols and methods
  • Tag content to facilitate searching in your notebook
  • View changes made to, and revert to old versions of, your notebook

What types of files can I store LabArchives?

Any type of file can be stored in LabArchives.  Files up to 15 GB can be uploaded to a notebook page.  If you need to reference a file that exceeds this limit, then you can store the file elsewhere (e.g. Box, research storage drive) and link the location path to your notebook.  Your LabArchives at Tufts account has unlimited storage.

Can I view and edit files in LabArchives?

LabArchives is integrated with Office Online and GraphPad Prism, which allows you to view and edit Word, Excel, PowerPoint and Prism documents from within your notebook.

In addition, an Office plugin enables you to save documents to LabArchives while working in Word, Excel or PowerPoint on your desktop.

Most image files can be viewed and edited in LabArchives.  PDF documents can also be viewed in LabArchives.

Can LabArchives be used to store personally identifiable and/or medical data?

No.  LabArchives does not meet the standards necessary to comply with Health Insurance Portability and Accountability Act (HIPAA) or Family Educational Rights and Privacy Act (FERPA) standards.

How does LabArchives allow me to collaborate with others?

You can share an entire LabArchives notebook or an individual folder, page or entry with other LabArchives users, at Tufts or other institutions.

As a notebook owner, you can choose whether you provide read/write or read-only access to your content.  Permissions can be changed at any time.

How can I access my LabArchives notebooks when I leave Tufts?

Prior to leaving Tufts, you should confer with your PI about transferring ownership of your LabArchives notebooks to another LabArchives user in your lab.  In order to continue to have access to your notebooks, you will need to create a free individual LabArchives account or, if you are going to another institution with LabArchives, an account at that institution.

You can also download either an HTML or PDF version of your notebooks, for offline reading and storage.

What are the next steps if I want to start using LabArchives?

To request access to LabArchives, contact Tufts Technology Services:

For quick start guides, frequently asked questions and troubleshooting, go to the LabArchives help page:

For help with data management best practices, such as file structure, naming and metadata, contact me: laura.pavlech@tufts.eduLabArchives

On the Shelf…

For Work

 SpringerNature Experiments

Springer Nature Experiments

Location: Access from link in Sackler Biomedical Sciences Research Guide

Springer Nature Experiments, which I featured in my October post is now available.  This platform searches four protocol and method resources simultaneously: Springer Protocols, Nature Protocols, Nature Methods, and Protocol Exchange, providing easy access to more than 50,000 protocols and methods.

Unique indexing means that you can quickly find protocols and methods for a particular organism, common and emerging techniques, or videos.  When you find one that works, then you can click through to the full text, available through Tufts Libraries.

For Leisure

 Manhattan Beach

Manhattan Beach, by Jennifer Egan

Location: HHSL Leisure Reading Fiction E28m 2017

This historical novel tells the story of a woman who becomes a diver at the Brooklyn Naval Yard during World War II, and her father’s entanglements with the mob.  One of The New York Times 100 notable books of 2017.

Sci-Art Contest 2017: And the winner is…

Last month the Sackler Insight hosted a contest to find the best science-based art (“sci-art”) at Sackler. All twelve entries were posted to the Sackler Graduate Student Council Instagram account (@SacklerGSC) and the Sackler student Facebook group. The winning contributor will receive a $25 Visa gift card!

The results are in! 174 voters from both Instagram and Facebook weighed in on their favorite pictures. Our lucky first place winner is Mary H. from Microbiology with her photo “An enteroid supernova,” which received 65 votes. Runners-up included Rana A. from PDD with “Making the best of a bad Western” (61 votes) and Rob C. from CMDB with “Monday Blues – Screening One-Bead-One-Compound Peptide Libraries” (39 votes).

Congratulations Mary, and thank you to everyone who participated! You can check out the pictures below:

Notes from the North – CMDB first year visit to MMCRI

We frozen few doing our thesis work in the CMDB and genetics programs are always looking for ways to highlight some of the excellent resources we have at our institutes. Last month I had the pleasure of hosting the CMDB first year students and introducing them to the Maine Medical Center Research Institute in Scarborough, Maine. They heard from the faculty here about potential rotation projects, but perhaps more importantly about the larger on-going projects that could become collaborative efforts between Maine and Boston. Here are some pictures of their visit and a link to the updated MMCRI website in case you too are interested in finding out about current MMCRI research.


Left to right CMDB first years Brittany Ahlstedt, Alexander Hu, Alice Meng, and Jackson Fatherree at Portland Head Light at Fort Williams Park.


Left to right CMDB students Alice Meng, Brittany Ahlstedt, Jess Davis-Knowlton, Jackson Fatherree, and Alexander Hu at Duckfat in Portland.

Lessons from #GradStudentTax

The recent tax reform bill passed in the House caused much uproar in the academic community as it removed the provision in the current tax code that waives the students’ school tuition. This provision, known as qualified-tuition-reduction provision (section 117(d)(5)), allows for the waived tuition to be exempt from taxable income; removal of this provision would therefore add to the tax burden of the students, who are already living marginally with an average income of ~$30,000/year. Sackler students, who currently receive $33,500, would see their taxable income increase by ~$20,000 (annual tuition) which would push them to a higher tax bracket (15% to 25%). It should be noted that this tuition waiver provision does not affects students in their 6th or higher year of study at Sackler as tuition is not charged past the 5th year.

Fortunately, the Senate’s version of the new tax bill retains this provision, for now. It remains to be seen whether the merged version of the bill will keep or remove this provision. In the meantime, graduate students have been organizing nationwide; the Sackler graduate student council organized a call your representatives event last Tuesday. If you haven’t gotten a chance to make your voice heard yet, consider signing onto FASEB’s letter to Congress asking them to protect the waiver provision.

The fight to protect this provision has raised other questions among grad students, particularly, why do universities bill tuition and then waive it? It appears that the waiver is not done in the same manner across all private universities. For example, Cornell University considers its tuition waiver as a qualified scholarship, which is tax exempt and not affected by the removal of the provision in the House bill. But this still allows for the question to be asked as to why universities just don’t charge $0 for tuition or if they can NOT charge it after 5 years, why they can’t do it for the years before. The answer seems to lie with the fact that universities are using the billed tuition as a way to generate revenue, especially in the sciences. This may sound sinister, but the reality is more complex. As scientists & trainees supported mostly by government grants, we are all aware of the overhead & indirect costs that are involved with doing research and that a percentage of every grant awarded to a faculty member at the university is matched by the NIH and given to the university administration. This support is necessary for maintaining a research environment, but it also begs the question of whether taxpayer money should be used to fund administrations of private universities with large endowments, particularly at a time when budgets for scientific endeavors are being slashed. Additionally, given that private universities, which enjoy a non-profit status, are behaving more and more like for-profit institutions, one is left to wonder whose interests are being represented at the administrative level.

The grad student tax debate has also raised the question of the role of graduate students in the workplace. Traditionally, graduate students have been considered as trainees rather than employees and a certain paternalistic relationship exists between faculty/administration & graduate students. However, since the National Labor Relations Board’s decision to recognize graduate students as employees, thus allowing them to unionize, this trainee status is being questioned more and more. Graduate students have faced obstructions from the university administrations when they have tried to unionize, and faculty have been divided on the topic of whether students should unionize (one professor going as far to tell grad students to focus on work rather than wages). Tufts currently has a graduate student union, but the Sackler school doesn’t have one at the moment, reasons for which lie with the content student body and the lack of a teaching requirement as part of the stipend.

It seems that the tax bill requires major revisions, for reasons separate from the grad student tax. This gives us, academics, time to organize around this issue and keep putting pressure on our representatives to protect the tuition waiver for graduate students. This also allows us to have a broader discussion about the roles of graduate students in the workplace, and how universities use funds that they receive from the public through the government funding bodies. Transparency from the administration’s side is likely to win them more supporters among students and faculty alike, rather than a nebulous state of operations.


On the Shelf…

For Work

Embase logo


Location: Search for ‘Embase’ in search box on Databases tab of the HHSL homepage (

This database indexes biomedical journal articles and conference abstracts.  The database includes thousands of journals not indexed by MEDLINE (PubMed), and is particularly robust in its coverage of pharmaceutical and medical device literature and conferences.  Unique indexing, through its Emtree controlled vocabulary, and search features make it easy to retrieve precise results.

Springer Nature Experiments, which I mentioned in my October post, is now available.  To access, click the link in the ‘Find Springer Nature Protocols & Methods’ box on the Sackler School Biomedical Sciences Research Guide

For Leisure

 Life After Life

Life After Life, by Kate Atkinson

Location: Tisch Library Book Stacks PR 6051.T56 L54 2013

A God in Ruins, by Kate Atkinson

Location: HHSL Leisure Reading Fiction A875g 2016

Life After Life is a novel about an English woman who lives through the events of the first half of the 20th century again and again, with small, but critical, changes each time, reminiscent of Ray Bradbury’s short story, A Sound of ThunderA God in Ruins is the companion novel to Life After Life, following the brother of the main character in the first novel through his experiences in World War II to the present day.

To request a book from another Tufts Library:

  1. Search for the book in JumboSearch, which is the default search on the Hirsh Health Sciences Library homepage.
  2. Once you find the book, click the title to view the record for that book.  Click the ‘Log in’ link in the yellow box.
  3. Log in with your Tufts username and password.
  4. Once you have logged in, click the ‘Request item’ link.
  5. Choose your pickup location (Hirsh Health Sciences Library) and click ‘Request’.  You will be notified via email when the book is ready for you to pick up.


Notes from the Library…Finding Gene Information in PubMed

PubMed is just one database from the National Library of Medicine (NLM).  The National Center for Biotechnology Information (NCBI), a division of the NLM, maintains several molecular biology databases.  These databases link to one another and to PubMed.  This month, I’ll describe how to find information about a gene in PubMed and the Gene database.

Which NCBI resource(s) should I use to find information on a gene?

You can start in either PubMed or Gene, a database of known and predicted genes for a several species.  Each record is devoted to a single gene and may provide information on nomenclature, chromosomal location, gene products, phenotypes, and interactions, as well as links to literature, sequences, and other NCBI and external databases.  Consider a Gene record a gene’s homepage in NCBI.

I’ll begin in PubMed because it is the database with which you are likely most familiar.  In the PubMed search box, you can enter either a gene’s name or symbol.  To activate the Gene Sensor (see next question), use the official gene symbol, which can be found at, the site for the HUGO Gene Nomenclature Committee (HGNC).  The HGNC assigns standardized names to human genes.

What is the PubMed Gene Sensor?

Gene Sensor checks the gene symbol that you enter against symbols in the Gene database and, if a match is found, displays links to information about the gene in NCBI databases at the top of your PubMed search results.  These links include: the records(s) for the gene in the Gene database; articles on the gene’s function (GeneRIF; see below); and tests in the Genetic Testing Registry.

Choose the link to the gene’s record in the Gene database.  The first option will be for the human gene, with links for other species, if available, following.

Gene Sensor results in PubMed
Gene Sensor results in PubMed

What if my initial PubMed search does not activate the Gene Sensor?

If you do not see the Gene Sensor box at the top of your PubMed results, then you can search the Gene database directly by selecting ‘Gene’ from the drop-down menu next to the search box.  Enter a gene name or symbol, species, or disease.

Gene database in drop-down menu
Choose Gene database from drop-down menu

How do I find information once I am in a Gene record?

Use the Table of Contents in the right-hand column of the record to navigate to specific information about the gene.  Scroll down to the ‘Related information’ section of the right-hand column for links to information about the gene in other NCBI databases.

Record in Gene database
Record in Gene database, with Table of Contents in right-hand column

So how does this help me find PubMed articles about a gene?

In the Related information section of a Gene record, you will notice several links to PubMed.  Each of these links retrieves a specific set of articles in PubMed:

  • PubMed: Articles that have been indexed with the Medical Subject Heading (MeSH) of the protein that the gene codes for, combined with the subheading ‘genetics’. For example: ‘Hemochromatosis Protein/genetics’[MeSH].
  • PubMed (GeneRIF): Articles that focus on the function of a gene. GeneRIFs (reference into function) are identified in three ways: by National Library of Medicine staff; by volunteer collaborators who submit a function, and article(s) describing that function (if you know of, or have authored, an article about a gene’s function, then you can submit a GeneRIF); through reports from HuGE Navigator, a human genome epidemiology knowledge base from the Centers for Disease Control and Prevention.  PubMed (GeneRIF) also includes articles that describes a gene’s interactions.
  • PubMed (OMIM): Articles cited in Online Mendelian Inheritance in Man (OMIM) records. OMIM is a compendium of human genes and phenotypes.
  • PubMed (nucleotide/PMC): Articles identified from shared sequence and PubMed Central links.

Each set of articles is continuously updated.  Use these links to retrieve the set of articles that best describes the type of literature you are seeking.

PubMed links in Gene record
PubMed links under ‘Related information’ in Gene record

What if I want to find all the literature on a particular gene in PubMed?

If you want to do a comprehensive PubMed search for literature on a gene, then use the Gene record and HGNC ( to identify the gene’s current and past names, symbols, and synonyms.  Use ‘OR’ to combine these keywords with the MeSH term for the protein that the gene codes for, with the subheading ‘genetics’.  Some genes, but not all, genes also have a MeSH term for the gene itself.

For example:

“BRCA1” OR “BRCC1” OR “FANCS” OR “BROVCA1” OR “PPP1R53” OR “breast cancer 1” OR “Genes, BRCA1″[MeSH] OR “BRCA1 Protein/genetics”[MeSH]

You may get a lot of irrelevant results with a comprehensive search because many gene symbols are not unique.  Therefore, this search would likely have to be combined with another concept, using ‘AND’.

For example:

(“BRCA1” OR “BRCC1” OR “FANCS” OR “BROVCA1” OR “PPP1R53” OR “breast cancer 1” OR “Genes, BRCA1″[MeSH] OR “BRCA1 Protein/genetics”[MeSH]) AND (“ovarian neoplasms”[MeSH] OR “ovarian neoplasms” OR “ovarian cancer”)