Notes from the North – MMCRI mouse transgenic expertise from the comfort of your own bench!

Whether you’re hunting for an engaging and useful elective as a first/second year student or soaking up last minute knowledge before jumping into the job/post-doc market, I recommend considering Mouse Transgenic Models and Advanced Mouse Transgenic Models coordinated by Dr. Lucy Liaw of Maine Medical Center Research Center and Tufts Sackler. The aim of the modules is to deepen understanding of molecular biology’s most popular mammalian model organism and help participants design thoughtful and effective in vivo experiments.

The first module givinjectiones an overview of how to develop transgenic models of gene expression and gene targeting plus strategies for phenotypic characterization such models. When I took the course for transfer credit in spring 2015 we learned basic transgenic and gene targeting construct design, conditional and inducible systems, early embryonic mouse development in the context of pronuclear and blastocyst injection, and the effects of genetic background on models. We utilized what we were learning over the course of the module to develop a strategy for making a mouse model of our choice (construct design through phenotype characterization) with discussion of our design at the start of each class.

CRISPR

The second module focuses on cutting-edge techniques currently being used in academic and industry laboratories to generate transgenic animals. Last spring we reviewed genome editing via Zinc finger nucleases, TALENS, and CRISPR/Cas9. The assignment for this module was to revise our previous model employing the more recent techniques.

Both modules utilized lecture, discussion of primary literature, and project development/presentation to ground participants in mouse transgenic biology. The pace was rigorous; we met for 2 hours twice a week for 3.5 weeks per module, yet easy to integrate with benchwork.

These well established modules have been available through the UMaine graduate course catalog for four years and will be directly available to Sackler students starting spring 2017 (look up CMDB 0350 while browsing the Tufts SIS catalog). The UMaine Graduate School of Biomedical Science and Engineering students who have traditionally taken this course rely on a consortium of institutes across Maine for their training. Because of this, the Mouse Transgenics modules are designed to be highly compatible with teleconference style classrooms allowing excellent participant interaction and experience in telecommunication meetings (a skill not to be sneezed at in this era of global collaboration).teleconference

Tufts Advisory Partners mean business

Guest Post by Jen Shih, writer for TBBC

From Left to Right (Alexandra Taracanova, Ji Kang, Christina Hao, Valerie Larriau, Maddy Das, Mike Pereria, Michaela Tolman, Farrah Roy, Wendi Ni, Mike Jager, Geoff Gonzalez
From Left to Right (Alexandra Taracanova, Ji Kang, Christina Hao, Valerie Larriau, Maddy Das, Mike Pereria, Michaela Tolman, Farrah Roy, Wendi Ni, Mike Jager, Geoff Gonzalez

 

April 2016: The excitement is palpable as the three co-founders sat around the table and planned out their first session as part of the inaugural Tufts Advisory Partners (TAP), a pro bono consulting group made up of Boston-area graduate students and postdocs. Alexandra Taracanova, Michaela Tolman, and Ji-Yong Kang were meeting to plan out their first engagement, or client relationship. They had selected a team of consultants, and now it was time to get to work. Tufts was about to be put on the map as an institution with high interests and talents for consulting and business development.

TAP was largely inspired by the sudden explosion in interest for the Case Study Group at Tufts. Students at Tufts, as well as institutions in the area, were becoming aware that career choice options were growing, make it an ideal time for TAP to emerge. Realizing the unmet need for hands-on opportunities in life sciences consulting, the founders of TAP got together in January 2016 and came up with a solution. TAP provides strategy services to biotechnology companies to develop their business. In working with a potential client, TAP will consult on how to set up the business, help them expand, or provide market research and due diligence. What makes this new consulting group unique is the ability to build an organization from the ground up, recruit clients, make their own rules, and pick projects to work on–in other words, they are essentially a fully functioning, autonomous firm that will provide a real product that will impact the biotechnology market. However, another integral goal in creating TAP was to connect enthusiastic and committed grad students and postdocs with the opportunity to use their talents.

For their first engagement, TAP selected a mid-sized medical devices company from several options. They planned to spend six weeks on the engagement, working with two teams. Of the three partners, Ms. Taracanova would work primarily with the client, and Ms. Tolman and Ms. Kang would each lead one of the teams as an engagement manager. Before the engagement began, and even before they could release the identity of the client, the eagerness and enthusiasm from the TAP partners was obvious. In particular, Ms. Taracanova was excited by the prospect of teamwork in the engagement teams and “seeing the two teams work together and move forward to deliver the end product.”

The team members for this first engagement hailed from three institutions: Tufts University, Boston University, and Harvard University. Throughout the engagement, team members collected information from key opinion leaders, analyzed the data, and presented recommendations on business strategy for the company. Both teams worked to develop market entry strategies for one of the company’s assets. As the members were from different institutions and departments, there was ample opportunity to network and get to know other students and postdocs who were interested in the consulting field. However, after completion of the engagement, it was clear that the team members first and foremost gained a valuable and rewarding experience. Christina Hao, a team member from Boston University, said of her experience: “I worked with TAP for six intense weeks on a consulting project, where I was able to gain hands on experience with solving business problems in a hypothesis-driven, structured manner, as well as honing my presentation and leadership skills.  The level of teamwork was incredible, and the engagement manager was very professional and genuinely cared about our learning goals.  TAP is hands down the most enriching, rigorous and fulfilling business experience I have experienced so far as a graduate student.” What was perhaps key to the consultants who participated in this engagement was the learning experience, and Michael Pereira, from Tufts University, reports that “as a first-time consultant, TAP exceeded all of my expectations. I learned more about the consulting profession in those six weeks than any number of books or classes could possibly teach me. It is an absolute must for anyone seeking a career in life sciences consulting!”

The team members were not the only people who had positive reviews for the first TAP engagement; the client, now revealed to be SteadMed Medical, also had encouraging comments. The CEO disclosed that “[he] was very pleased with the personal engagement and passion the entire team embraced throughout the project. The final report was clear, concise and supported with facts and data. [They were] excited to execute on the recommendations made.” The marketing manager of the company describes the TAP engagement with the following: “The quick uptake of our industry, its challenges, and our visions were outstanding.  From the first week, we felt there was a deep understanding of how to take our questions and deliver them back with tangible perceptions and directions for us to move forward.  At the next given opportunity, we will engage with TAP again to leverage their passion, knowledge, and ability to deliver promising direction with a message tailored to a market we thought only we knew so well.”

With the first engagement behind them and with success, no less, the TAP team is looking forward. They are looking to begin a second engagement in August, and to build upon this first experience to improve, further engage, and delve deeper. With the growing interest in life science consulting, they should have no problem recruiting more team members who are interested in venture capital, life science investing, and the life science business in general. And if the initial reviews are any hint to the future, the next client they select from their list of options will benefit enormously as well.

Applications for TAP’s second engagement open August 1st, 2016. If you are interested in applying or have a business that would benefit from TAP’s services, please contact tuftsadvisorypartners@gmail.com.

 

Editorial: Career Development Survey Results

In the April issue of the Sackler Insight, we published an editorial discussing the career development resources available for Sackler students, their effectiveness and how they could be better suited to the dynamic landscape of a post-PhD worklife. As a follow-up, the Graduate Student Council (GSC), in collaboration with the Dean’s office, developed a survey to hear from students about their needs. This editorial will focus on the outcomes and suggest recommendations to be implemented by the GSC and the Dean’s office.

The survey was conducted over a period of 2 weeks, and around 1/3rd of all Sackler students responded, with representation from all class years and programs. Majority of the respondents had either prior research experience in an academic setting or had come straight from their undergraduate institutions, as shown in the pie chart below. While career development opportunities were of varying degrees of priority among the respondents at their time of graduate school interviews, almost all respondents, regardless of class year, considered these opportunities as a high priority at the time of the survey.

The survey also asked the students to indicate how many career development events at Sackler they had participated in over the last 2 years and to rate their usefulness. This data has been summarized in the bar graphs below. The same was asked for any career development opportunities outside Sackler the students had participated in. The students were also asked to indicate reasons they were unable to attend the events at Sackler and what kind of events they would like to see more. Lastly, an open-ended question was posed to gather additional comments from respondents. After analyzing the data, we identified 3 premises that were prevalent among the responses.

 

 

1. Alumni network building

 

Majority of respondents to the survey advocated for more networking opportunities and information regarding alumni’s current jobs. The comments section also focused on the disconnect between alumni and the current students. While there are no Sackler specific alumni databases, as is true for other Tufts schools, it should be noted that Tufts does maintain a database of all alumni through the Advancement office. Individual schools can request alumni information through the advancement office and vice versa. There is already an existing network of Tufts alumni called Tufts Online Community (OLC) that allows Tufts alumni and students to establish and maintain connections. More info on the OLC and how to register for it can be found here – http://tuftsalumni.org/who-we-are/faqs/#community-what-is. Additionally, the Dean’s office, who keeps track of the Sackler alumni through social media services such as LinkedIn for training grant application purposes, also update the alumni information on the Sackler website (can be found here – http://sackler.tufts.edu/Student-Life/Career-and-Professional-Development/Career-Outcomes). Given that this existing database can be effectively used for networking, we urge the Sackler students to utilize this resource for their benefit. We also urge the GSC and the Dean’s office to hold a workshop to showcase this resource and guide the students on how to use it most effectively. A stronger alumni network can also be made possible through student organizations such as TBBC, who have been able to form a tight-knit group of peers across programs and class years.

  1. Full-time Career Development Office

There have been requests for a full-time career development resource to be made available for the Sackler students. However, due to the small size of the school, and the cost associated with hiring new employees and setup, it is difficult to be justified considering that PhD-track Sackler students do not pay tuition. However, if there could be a collaboration between the PHPD programs in the TUSM and the Sackler school, it could potentially provide a critical mass to warrant a full-time career office to serve all the schools on the Boston campus, albeit for broader services such as resume reviews. The changing landscape of the post-graduate work opportunities also indicate that there is a need for alternative career options, related to the healthcare and biomedical professions, which can be addressed through collaborative efforts between the various schools on the Boston campus. For example, last year the Sackler GSC collaborated with the Friedman nutrition school to host a career fair. Even if a full-time career resource center on the Boston campus is not possible, it’d serve the students well if the GSC, the PDA, and the Dean’s office could organize a few resume review workshops for students and post-docs throughout the year.

  1. Career Development Events & Resources

The bar graph showing the usefulness of the various career development events and resources indicates that most respondents find the seminars organized by Career Paths, TBBC and PDA to be most useful. However, some respondents commented on the focus of these seminars to be heavily biotech or industry-centric, which could undermine the needs of students who are not looking into get into such fields. While in general there might have been an increased number of events with such a focus, it should be noted that the GSC have sought to put out a diverse group of seminars, panels and workshops to help students pursuing any non-academic career path. Historically, the career paths committee of the GSC have focused on non-academic careers since that was the gap that needed to be filled – the Sackler faculty are well-equipped to provide advice on academic career paths, but that is not necessarily true for non-academic ones. In addition, a clear distinction needs to be made between the seminars organized by the various student groups – TBBC seminars will be focused on the biotech industry whereas the GSC seminars are more likely to include a diverse group of topics, based on their mission statements. This being said, it would also serve the GSC well to have a standardized version of event flyers for easy recognition. It would also help to showcase their previous events through the blog so students unable to attend such events can follow-up on what was discussed and presented.

In the last year, the PDA, GSC and TBBC have all worked closely together to host events that have been well-attended and lauded, and this is a trend that should continue to aid students and post-docs alike. However, more visibility and promotion of these events are required for a well-rounded attendance, as indicated by some survey respondents.

MyIDP was indicated to be really useful by the respondents who had used it, although this resources was not used by majority of the survey users. This shows that there is a need for a myIDP workshop that would help guide the students on using the valuable resource, which was deemed to be more useful than talking with thesis advisory committees. This workshop can potentially be done at the beginning of the academic year in September, to help the incoming and the rising students. Recent graduates should also be invited to a panel on different careers as mentioned in myIDP. This would further aid to establish connections between current students and alumni. Additionally, grant writing workshops should also be organized for both students and post-docs, as requested in the survey.

 

This survey was conducted to gauge student interest in career events and resources and how the existing ones can be tailored to better fit the needs of the Sackler student population. While valuable data was obtained from this survey, it should be noted that this data is inherently biased since the respondents are more likely to seek out career development opportunities within and outside Tufts, and are likely to be more active in participating in events and workshops. Even with these limitations, it can be safely said that Sackler students have laid down a strong foundation of career development resources and events through their own enthusiasm and efforts and grassroots organization. And it is to this collaboration between student organizations and the Dean’s office that we should turn to ensure proper career development resources are made available for Sackler students and post-docs.

 

Humans of Sackler: Jaclyn Dunphy, “Good Things Come to Those Who Waitress”

I’m Andrew Hooper, a fourth-year student in Dr. Jamie Maguire’s lab in the Neuroscience program.  For as long as I can remember, I’ve been fascinated by the stories of how scientists came to be scientists.  Where are they from?  When did they recognize their passion for science?  How did they get their foot in the door?  What is it about their topic of interest that so captivated them?  And what breakthroughs just over the horizon would most excite them?  There are as many compelling, eye-opening answers to these questions as there are scientists, and I decided to highlight the diversity of backgrounds and perspectives at the Sackler School by gathering and sharing some of these stories.  Inspired by the format of Brandon Stanton’s wonderful “Humans of New York” blog, I called this project “Humans of Sackler”.

Recently I had the opportunity to sit down with Jaclyn Dunphy, a fourth-year Neuroscience student in Dr. Phil Haydon’s lab.  We discussed the questions above and many more, and I’m very happy to share with you a small sample of our conversation in this, the first issue of “Humans of Sackler”.  Enjoy, and please look me up if you’d like to share your story and be the next Human of Sackler!

 

Humans of Sackler, 15 June 2016

Jaclyn Dunphy, Neuroscience, Fourth-Year Student: “Good Things Come to Those Who Waitress”

Humans_Image1
Graduating from the Masters program at Kent State NEOMED

AH: Did you come into college with a biology major, knowing that that’s what you wanted to study?

JD: I wanted to be a teacher when I started college because I had a really great biology teacher in high school. I went to Xavier, a private Catholic college, so I also thought I might want to be a religion teacher. For the first couple years I took biology, education classes, and theology classes. But I had a ‘coming to terms moment’ with what my major was going to be around sophomore year, and so I just went through the bulletin of all the courses that were offered and picked the ones I liked the best – and they tended to be related to biology, so I figured that’s what I should be doing. I didn’t know what I could do with the degree. I had never heard of graduate school until after I graduated!

Humans_Image2
At an air show with dad

AH: Were your parents interested in science, or did your interest develop totally independently from family?

JD: I think my interest in science definitely goes back to roots that I have with my dad. He has a workbench in the basement, and some of my earliest memories of us spending time together were us building rockets in the basement. He was very into space and stuff, so we would build rockets down there. Also, I was in this program for gifted students when I was in fourth and fifth grade, and we were assigned weird projects – like if you’ve heard of the ‘egg drop’ project, where you have to drop an egg off of a roof and get it not to crack? I would get assignments like this and take them home. I was really excited about them, but my dad was even more excited! So we would work on those things together, and I would go back to school with something that was, like, 80% his idea and 20% mine. So in those couple of years we had five or six things we worked on together in the workshop downstairs, and that was really fun… We built a bridge with Popsicle sticks, and I could stand on it. I could stand on it to this day! We made I-beams – not my idea. I’d never heard of that, but he was like ‘We need to build I-beams!’ We even sanded them – it was intense.

Humans_Image3
After a day of kayaking on the Charles

AH: After you finished undergrad, what did you do for work and how did you transition eventually to grad school?

JD: I was working at an upscale restaurant called Bistro on Main, close to Kent State’s campus, where Kent State professors take their seminar speakers out for dinner. So I had seen a couple groups of them come through, but one night I was waitressing for a table of four people: three people from NEOMED/Kent State and their invited speaker, Wendy Macklin. When I came to the table they were talking about prion disease, and I said, ‘Oh, that’s odd dinner conversation’. And they asked ‘How do you know what that is?’ in a very accusatory but jovial tone, and I said ‘Well, I just graduated with a degree in biology’ and they were like ‘Then what are you doing here?’ and I said ‘Waiting on you, what does it look like?’ So after that, all four of them took turns harassing me, they asked ‘Do you need a job?’ and I said ‘No, I have a great job, I’m making a lot of money doing this, I’m just trying to figure out what I want to do.’ And they said ‘Well, if you figure it out, then here’s my card.’ They put the card in the bill and they said, ‘Give us a call if you want to work as a technician.’ And I didn’t even know what that meant. At that point, I thought I was going to be cleaning rat cages. So I interviewed with one of the professors at the dinner, Bill Lynch, a few weeks later. It was the worst interview I’ve ever had, it was terrible! He’s a virologist: he asked me whether viruses are living or not. I didn’t know it at the time, but that’s a controversy among virologists. So I just picked a side, and then he argued me all around in circles until I switched sides, and then he asked me why I switched sides..! I left feeling so defeated; it was the first experience I’d had of someone who really, really questioned my thought process. I felt terrible, I felt like I had done such a bad job. But he ended up offering me the job because he liked that I didn’t give up, he liked my enthusiasm.

Humans_Image4
Demonstrating the Blind Spot at the Museum of Science, with Alex Jones (right)

AH: What was it about glial cells that made them so interesting to you?

JD: I fell for astrocytes – I liked that they were so abundant but they were so under-studied. There was so much to learn. What are they doing? There has to be more to the story. Later on, when I met Phil Haydon, he said that in the field of glia, there’s a lot of low-hanging fruit, and I felt like that was very much the case. Glia are… I hate the word ‘support’ cells, but they are support cells for neurons. Neurons are like actors in the big play that is the brain, so the glia are stagehands, directors, producers, writers – they’re the ones that actually control the show. But the ones that you see and you care about are the neurons.

 

On the Shelf…

For work…

Experimental Design for Biologists

Experimental Design for Biologists, by David Glass

Location: HHSL Book Stacks, Sackler, 5th Floor, QH 323.5 G549e 2014

This handbook is designed to teach the fundamentals of experimental design.  The author, who is the executive director of the Muscle Diseases and Aging Initiative at the Novartis Institute for Biomedical Research, held a workshop on campus in May.

And leisure…

The Summer Before the War

The Summer Before the War, by Helen Simonson

Location: HHSL Leisure Reading, Sackler, 4th Floor, Fiction S611s 2016

Set in an English village on the cusp of World War I, this novel tells the story of a woman selected to be the first female Latin teacher in the local school.  A little ponderous and predictable, but an easy summer read.

Notes From the Library…Author Identifiers

What are author identifiers?

An author identifier is a unique identifier that distinguishes one researcher from another, eliminating confusion in scholarly publication and grant funding.

Why do we need author identifiers?

If you have ever tried to do an author search a database, then you know how difficult it can be to find all articles by a particular author.  An author may have a common surname, publish under variations of the same name, change their name, or different geographical/cultural conventions for reporting their name.  Affiliation and field of study relieve some of the ambiguity associated with author names, but inclusion of this information in a search does completely eliminate the problem.  Two authors with the same name may work in the same field.  Like author names, there are often multiple ways to list the name of a department, school or university, and affiliations change as an author moves from one institution to another.  Moreover, some databases only provide the affiliation of the first author, or allow an author to list only one affiliation.  PubMed/MEDLINE did not include affiliation for all authors until 2014.  For these reasons, a simple search for articles by one author can easily become complicated.

What options exist for author identifiers? 

Over the past few years, one author identifier system has emerged as the frontrunner: Open Researcher and Contributor ID, or ORCID (http://orcid.org/).  ORCID is an open, non-profit community effort that provides unique persistent digital identifiers for researchers.  ORCID partners and members include universities, commercial research organizations, publishers, professional societies and funders, such as Nature Publishing Group and the National Institutes of Health (NIH).  Several publishers offer the option of including an ORCID ID when submitting an article, and some plan to make an ORCID ID mandatory for corresponding authors (http://blogs.plos.org/plos/2016/01/author-credit-plos-orcid-update/).

A few publishers have their own author identifier system.  For example, when researchers register for Thomson Reuters free online community, ResearcherID, they are assigned a unique alphanumeric identifier that can be used to track their publications and get citation metrics in Web of Science.  Authors of articles indexed in Scopus, an Elsevier database, are automatically assigned a unique identification number.

This sounds like one more account to maintain, do I really need an author identifier?

Yes, an ORCID ID is another account to create and maintain.  However, ORCID has gained traction amongst universities, publishers and funders, and if this pattern continues, then hopefully it will alleviate author ambiguity.

Any researcher can register for a free ORCID ID.  You can use your Tufts username and password to register for, or link to an existing, ORCID ID.  To get started, go to this page: https://orcid.org/signin.  Choose to sign in using your institutional account and search for Tufts.  You will be prompted to enter your Tufts username and password.  Once you do so, select the ‘Register for an ORCID ID’ link.  For more information about creating and managing your ORCID account, see: http://support.orcid.org/knowledgebase/topics/32827-using-the-orcid-registry.

PubMed Tip of the Month: Saving Searches and Creating Alerts

You can save searches to your My NCBI account (see PubMed Tip of the Month for March 2016), and choose to receive daily, weekly or monthly emails when new articles meeting your search criteria become available.  To save a search, simply click the ‘Create alert’ link under the PubMed search box on any results page.  If you are not already signed in to your My NCBI account, then you will be prompted to do so.  Name your search and select whether or not you wish to receive email alerts.  Once you have saved a search, it will appear in the Saved Searches box in My NCBI, where you can see a list of your searches, the last time you ran a search and any new articles that have been added to PubMed since you last ran the search.  Saving searches saves time and frustration, and allows you to remain current on articles in your area of research.

Create alert link on PubMed results page
PubMed Create Alert

Notes from the North – The Science of Lobster

The other week my family and I were driving home from an afternoon on the beach playing in the waves, poking through tide pools, and eating seaweed (only Ronan indulged in this last pursuit) when we IMG_20160713_204129_894[1]made a spur of the moment stop at a local farm to pick up lobster and a couple pounds of steamers1. Standing at the counter in flip-flops and a swimsuit as the lobsterman weighed out our “bug”, I began to ponder this quintessential Maine summertime treat. In preparing and eating whole lobster the consumer becomes acutely aware of the animal’s physiology; an experience most of us are divorced from for most of the produce we eat.

 To start with, you have to decide as you are making your purchase whether you would like a hard-shell or a soft-shell lobster. A soft-shell lobster is one that has recently undergone ecdysis, a shedding of the exoskeleton. The lobster does this by inflating a newly grown exoskeleton with water within the old carapace causing it to pop open and expose the soft new shell. The reason these soft-shell lobsters cost less per-pound than the hard-shell lobsters is that a good proportion of their weight comes from that water rather than meat.

When you get your lobster home and are facing the decision of how to cook him or her2, you might begin to wonder “why on earth do I need to buy it live?” In part this goes back to the molting cycle again: powerful proteases (four members of the calpain family) induce muscle atrophy in the claws in order to reduce the volume of tissue that will need to be withdrawn from the old shell. When the lobster is dead, these proteases cause rapid degradation of the flesh. The other part of the answer lies in the presence of metabolites from micro-organisms. The combination means a much shorter shelf-life for raw lobster meat than you might otherwise imagine.

This inconvenient brevity of freshness forces the chef to consider the question of lobster nociception.  The avoidance behaviors (tail-flipping) exhibited by lobsters upon being placed in boiling water clearly demonstrate that at the very least lobsters have evolved to respond to noxious stimuli. Pain is typically understood to be comprised both of physical sensation and emotional distress, but since it is difficult to observe or define emotion in non-humans using only our experience of human emotion it seems reasonable to minimize the animals’ exposure to noxious stimuli. In Europe this is accomplished by electrocuting crustaceans prior to cooking, but the best compromise I have seen in the US is to make a cut through the lobster’s brain while it is still cold from the fridge before cooking.

There is a huge body of scientific literature out there both utilizing lobster as a model organism and studying it directly (the lobster fishery just in Maine is worth over $1 billion!), but I’ll leave you with just one last lobster physiology anecdote. Ed Kravitz, one of my grandmentors (mentor’s mentor) demonstrated that GABA is a neurotransmitter using lobster (the shell apparently makes a convenient receptacle in which to bath the muscle and nerves), but I was always told that Ed’s favorite part of studying lobster was the taste test!

  1. Scrumptious little soft shell clams that are cooked by steaming. In our family we bring the cooking brine to the table so we can rinse each clam clean of sand before dipping in butter to consume whole.
  2. The most infallible method to determine the gender of your lobster is by looking at the first pair of swimmerets that appear on the ventral surface of the animal where the tail joins the cephalothorax. In females these are soft and flattened while in males they are stiff and curve to form a tube through which spermatophores are deposited in the female during mating.Lobster anotomy