All posts by Nafis Hasan

Versatile PhD – a Non Academic Career Resource for Doctoral Students

Guest Post by Christina McGuire, CMP

Versatile PhD, a tool for graduate students to explore non-academic careers, began as a listserv while Founder and CEO Paula Chambers was finishing her dissertation at Ohio State University. Her goal was to create a safe space where PhD students could discuss non-academic career options without feeling pressured to go into academia. From this original idea, the company has blossomed into an active resource where PhD’s from all backgrounds can come together in a supportive environment to learn, discuss, and network based on their interest.

While most of the website content is unavailable without a subscription, the website still has much to offer for those beginning to explore career options outside of academia. The PhD Career Finder lists many career opportunities available to STEM and Humanities PhD’s with information about what the career entails, how to advance, what background is best suited for the career, and how best to prepare yourself and your resume for following that path. It is an excellent resource for those who are interested in exploring what their future options are.

Additionally, with a paid subscription you gain access to resumes and cover letters and narratives from of the hiring process from real PhDs. You can post questions to any of the Forums, and network with members within the Versatile PhD network. While Versatile PhD is a national business, they also run regional meetups, where you can network in person.

So how can this site help you as a Tufts student or postdoc? Come to hear Paula herself speak about the mission, founding, and resources that Versatile PhD has to offer on March 16. Additionally, we will be hearing from Tufts post-doc and Versatile PhD Volunteer Sarah Dykstra on how she uses and benefits from Versatile PhD.

Zika: Coming This Summer to a Mosquito Near You

Guest Post by Ila Anand, Micro

A startling number of viral epidemics have made major media headlines in recent years. In 2014, the Middle Eastern Respiratory syndrome coronavirus (MERS-CoV) was quickly brought to America’s attention after two reported cases in Indiana and Florida. 2015 was the year the world went into Ebola frenzy and U.S. hospitals took extreme precautions to manage suspected infected patients. This year, the Zika virus has caught the CDC’s eye and for good reason. As Zika continues to spread from Brazil through the Americas, its arrival in the U.S. this summer is inevitable. Although no vector-borne cases have been reported inside the U.S. yet, over 150 travel-associated cases have been reported. Public health departments across the U.S. should brace for the next likely step: the moment when Zika passes from traveler-infected blood to a local mosquito and then to another person.

The Zika virus was first isolated in Uganda in 1947 from the Zika Forest, where researchers from the Rockefeller Foundation were studying yellow fever. These researchers experimentally used rhesus monkeys that were set out in cages in treetops as bait for mosquitos carrying yellow fever virus. Ironically, instead of yielding yellow fever virus from the blood of these monkeys, the researchers discovered Zika and speculated the virus had been lurking chronically in African monkeys for millennia. The virus was later isolated from mosquitoes of the Aedes genus in the same Zika forest and Aedes has since been identified as the vector of Zika. Eventually, Zika virus was discovered to infect humans across the African continent as well as in South Asia and Southeast Asia. More recently, circa April 2015, the virus has spread to the South America.

In humans, the virus manifests infection known as Zika fever, which often produces no symptoms to mild symptoms, such as headache, fever, rash, bloodshot eyes, and joint pain. Recently, the spread of Zika in South America has been linked to the growing number of infants born with microcephaly in Brazil. Microcephaly is a neurological condition in which the brain and skull fail to grow at a normal pace, resulting in a significantly smaller head size. At first the link to Zika was purely correlation, however, a recent report published in Cell Stem Cell directly demonstrated that Zika is able to infect and kill lab-cultured human neural progenitor cells. These neural progenitor cells were derived from induced pluripotent stem cells (iPSCs) and scientists tested Zika’s “tropism” by comparing percent infection across four cell types: neural progenitor cells, immature neurons, embryonic stem cells, and human iPSCs. While less than 20% of iPSCs, embryonic stem cells and neurons became infected, up to 90% of neural progenitor cells contained the virus and Zika either killed these cells or slowed their proliferation significantly. These findings may begin to unearth some possible mechanisms to how Zika infects and damages fetal brain tissue. Since neural progenitor cells give rise to a larger population of neurons and glial cells in the brain, infection of these cells could impact the neurons they produce and possibly affect brain development. In addition to microcephaly, Zika has also been linked Guillain-Barré syndrome, a sickness in which the person’s own immune system damages nerve cells, causing muscle weakness and sometimes paralysis. However, clinical findings from Brazil are still preliminary and there’s a need for more compelling evidence.

Sources –

 

Tufts Innovation Spotlight – March 15, 2016

Guest Post by Michaela Tolman, Neuro, GSC President

Next week Tuesday night, over 50 people have already signed up for a first-ever event. Have you? 

Tufts Innovation Spotlight is bringing together 5 panelists who have brought innovation to the academic, clinical, and industry settings. Their achievements and wisdom will be celebrated with this classy event hosted by the Graduate Student Council at Abby Lane, which is right around the corner (literally a 6 minute walk).

The event will begin at 5pm with passed hors d’oeuvres on the upper floor of Abby Lane. The program will begin at 6pm with a panel discussion. There will be an opportunity for questions throughout as well as open networking from 7pm on. The goal of the event is to generate a discussion among students and panelists about the challenges they have faced bringing innovation to each of their respective fields and how they would advise our students as they strike out on their own careers.

Panelists

 

Qiaobing Xu, PhD is an Assistant Professor at Tufts. He received his PhD from Harvard in Biochemistry, did a post doc at MIT, and now focuses on developing nanotechnology for the applications of drug delivery and tissue engineering. His lab has developed “lipidoids” for delivery of DNA, RNA, or protein for therapeutic applications. Their tissue engineering efforts have resulted in a scaffold built from decellurized tissue which is currently being used to guide tissue regeneration.

Richard T. Lee, MD is a Professor at Harvard University and Harvard Medical school, as well as an active clinician at Brigham and Women’s Hospital, founder, and Chairman of the Board of ProteoThera, Inc. Dr. Lee received his medical degree from Cornell University and went on to study a broad range of medical issues. Their approach is to, “understand human problems and design solutions in the laboratory.”

Arnout Schepers, PhD is a post doc in the Bhatia Lab at MIT. He received his PhD from Hubrecht Institute in Utrecht in Hans Clevers laboratory. Previously, he has characterized intestinal stem cells in malignant conditions. Currently, he is working on making a 3D tissue model for cancer research.

Retsina Meyer, PhD is a senior scientist at Resilience Therapeutics. She received her PhD from MIT, where she won numerous fellowships and excelled in the entrepreneurial arena, winning the OneStart America’s competition. Resilience Therapeutics is currently developing a target for treating post traumatic stress disorder (PTSD).

Luhan Yang, PhD is a Co-Founder of the biotech company, eGenesis. She received her PhD as well as a post doc position from Harvard. She was named on the list “30 under 30” in Forbes Magazine and helped develop the CRISPR/Cas9 system for use in mammalian cells.

We hope you join us on Tuesday, March 15th!

Upcoming TBBC Events

The Tufts Biomedical Business Club (TBBC) is a student run organization whose mission is to cultivate business leaders in the health and life sciences. TBBC is a growing community of graduate, medical, dental and nutrition students, postdocs, physicians, scientists and alumni. It provides members with opportunities to learn about consulting, business development, entrepreneurship, intellectual property and more.  We engage our members though a number of initiatives including a seminar series, Biotech Journal Club, Consulting Case Study Group, panel discussions, and most recently Biotech BUZZ. E-mail tuftsbiotech@gmail.com for more information

Upcoming events:

TBBC Case Study Group

Mondays – 5-7PM, Jaharis 508

Julie Hewitt Coleman guides students and postdocs through the case interview process. Practice solving cases, gain insight and tips, and learn more about the field of consulting.

TBBC Dr. Dave Greenwald

Tu Feb 9 – 5-6:30PM, Sackler 114E

Dr. Dave Greenwald, a 2010 Sackler alum, now Director of Business Development and Corporate Sponsorships at Johns Hopkins Technology Ventures, will give a career seminar titled, “Starting a Company: Practical Advice for a Precarious Pursuit.”

TBBC Dr. Lauren Linton

Th Feb 25 – 5-6:30PM, Sackler 316

Dr. Lauren Linton, Deputy Director of the Tufts Institute for Innovation, formerly co-Director of the Sequencing Center at the Whitehead Institute and Associate Director of the Center for Genome Research at the Whitehead/MIT, will give a career seminar titled, “Don’t Be Afraid to Experiment.”

TBBC Biotech Journal Club

F Feb 26 — 12PM Noon, Jaharis 155

BJC will meet to discuss current topics in the biotech industry. To join the mailing list, email tuftsbiotech@gmail.com with the subject line: BJC

Recent Events:

TBBC Biotech Journal Club

F Jan 29: Townsend Benard gave a presentation on the Innovative Medicines Initiative, Europe’s largest public-private effort aimed at speeding the development of better and safer medicines for patients.

TBBC Sackler Speaks

Th Feb 4: TBBC partnered with the Graduate Student Council to host a flash talk competition among Tufts students. Eleven speakers gave 3-minute presentations on their research; Jess Davis-Knowlton took home first prize.

TUSM Faculty takes steps to unionize

On December 11, 2014, tenured and tenure-track faculty members of the Tufts University School of Medicine (TUSM) filed a petition to the National Labor Relations Board (NLRB) to hold on-campus union elections. If this election is allowed by NLRB, then the 70 members of the TUSM faculty will join the ranks of their Medford colleagues in the Faculty Forward union at Tufts, a division of the Service Employees’ International Union (SEIU) Local 509 (1). As mentioned, this is not the first time Tufts-affiliated faculty have filed for unionizing.  In February 2015, majority of the Medford/Somerville campus faculty had voted in favor of unionizing in an effort to improve working conditions (2). And even before that  in 2014, adjunct faculty members on the Medford campus, rallying under the Adjunct Action division of SEIU, negotiated a significant raise in their pay (3) that is set to be completely in effect by September 2016 (4).

http://www.seiu509.org/files/2015/02/IMG_0487_580p.jpg
Tufts University Medford Faculty vote to unionize. Source – SEIU Local 509

The TUSM faculty appears to be motivated for similar reasons; in a joint email to Tufts Daily, Dr. Karina Meiri, Professor of Developmental, Chemical & Molecular Biology (DMCB), and Dr. Henry Wortis, Professor of Integrated Physiology & Pathobiology (IPP), mentioned issues regarding salary and research funding as major sources of motivation. They elaborated in the letter that while faculty members are trying to get funding in an increasingly competitive environment with diminishing sources, the university is putting on additional pressure on them by providing “negative incentives”. Drs. Meiri and Wortis mentioned, “If faculty were unsuccessful, [in their application] as they were pretty much bound to be, given the odds, their salaries would immediately be cut, often by very significant amounts.” They also pointed out that many faculty felt that their ability to speak their minds on administrative decisions was being limited. Drs. Meiri and Wortis believe that through unionization, financial transparency and partial restoration of decision-making ability, job security and stability can be achieved for the faculty. To quote, “Our strong belief is that the educators and researchers at a university need to be deeply involved in decisions that shape its mission and that unionization will provide a path towards…the return of collegiality”.  It seems that majority of the TUSM faculty are in favor of unionizing, as almost 60% of them had voted in favor of holding on-campus elections. The ones who did not vote, either did not do so because they do not want a union or they do not feel strongly enough for the need of one, as Drs. Meiri & Wortis explained in their letter.

Faculty unions are not new in this part of the country – if the TUSM faculty are allowed to hold elections on campus, they will join their colleagues at Northeastern, BU, Lesley and Bentley Universities (5). There is also an increasing trend of faculty unionization throughout the country, and Drs. Meiri & Wortis believe it to be a reactionary movement to the increasing adaption of a for-profit model by universities. They explained in their letter, “Many universities have chosen to save money by shifting the burden of teaching to part-time untenured…adjunct faculty members. Others have increased the cost of enrollment to plug financial holes. University priorities are increasingly being set by financial rather than academic agenda. Across the country whenever universities are being managed as corporations rather than collegial institutions faculty are increasingly looking towards unionization as a means to re-assert the original model of shared decision-making.”

While it may seem reasonable to allow tenured and tenure-track faculty to unionize, it is not the case. The legal precedent set by the 1980 ruling in the NLRB v. Yeshiva University, which found the tenured faculty not eligible for unionization for their significant influence on administrative decisions, stacks the odds against the TUSM faculty’s hopes of holding on-campus elections. This precedent is also partially responsible for the opposition of the TUSM administration to the faculty’s petition at the NLRB. As the Executive Director of Public Relations, Kim Thurler, told Tufts Daily “that 1980 Supreme Court ruling … recognizes the substantial authority faculty members hold and their significant voice in determining curriculum, academic standards and policies. Many NLRB decisions since 1980 have followed this Supreme Court precedent.” (1)

Currently, the TUSM faculty waits on the NLRB’s decision on whether they will be allowed to hold elections or not. Regardless of this decision, the fact that this has become a trend across universities, institutions founded on principles of non-profit due to their increasing profiteering nature, is a great cause of concern indeed.

 

Drs. Meiri & Wortis’ quotes have been reproduced from their letter to Tufts Daily with their permission. The Tufts Daily article was published on Jan 29, 2016, and can be found here

 

Techniques – Go with the Flow

What is Flow Cytometry and what can it do for you?

by Stephen Kwok & Allen Parmelee

Flow Cytometry is something I never heard about in school, but once I learned about it, the possibilities seemed endless as to how I could use it as a tool to make work and research better. FACS (Fluorescence Activated Cell Sorting) Sounds like an office tool, not a state of the art piece of scientific equipment. In reality, it is like a multitude of fluorescent microscopes all working together to gather data at the same time. Wait, it gets better…you can actually physically separate your cells from one single cell per well on a 96 well plate, to millions of cells in a 15ml tube! The human eye has a habit to have bias; these machines convert the analog data into a digital plot or histogram that can’t be argued with! Is it 30% positive or 35% positive? Yes, we can actually tell the difference!

Let’s back up a step here. The technology is best used if you have markers for your cells. You can take fluorescently labeled antiboties to identify cells. Let’s say you are looking for stem cells. Cd34, SCA-1, and c-Kit are common for hematopoietic stem cells. Label these three, throw in a viability marker, and you have successfully identified these cells. You can move forward with your experiment and simply ANALYZE the cells. Or, you can try to isolate these cells by SORTING them. Fluorescent protein transfections with a GFP or RFP marker are common. Why grow cells in harsh selection media when you can simply pluck them out and put them into a plate? I need to do some PCR, but I have to figure out how to get 1 cell, 5 cells, 25 cells, 50 cells. Limited dilution is going to take me forever! In as fast as 30 seconds you can have those exact numbers of cells lined up into your pcr tubes or a 96 well plate.

At our facility we have cell analyzers available for use 24/7. We train people in basic theory, and then help them get started on how to run the instruments. Sorting, however, is a little more complicated and is done by the two intimidating guys running the facility: Allen and Steve. 

Steve & Allen, the Flow Bros (right to left)
Allen Parmelee & Stephen Kwok, the Flow bros (left to right)

 

There are always plenty of questions to answer about FLOW. How fast is fast? Well the Analyzers can run approximately 3,000 cells per second. The high speed cell sorters. 30,000 cells per second! This can translate to over 100e6 per hour. How sensitive are the machines? We can detect one cell in 10e6 cells! How many markers can I use? The most common is 4 different colors at a time, but we could do up to 17. Be wary, however, just because we said you can. Doesn’t mean you should. Work smarter, not harder! I have 4 different populations: can I sort them all at once? Yes! In fact, we can do up to 6 simultaneous separate populations at once.

How can I do good flow cytometry? The key is sample prep! Yes, they seem like magical boxes, but the experiment is only as good as the components. Titer your antibodies. TEST them with a positive control. Bring a negative or untreated control as a baseline. Would you run a gel without the markers? Find the correct markers, and look for the greatest separation. Cells need to be in Single Cell format. It is highly recommended to filter/strain your samples because the pathway for the cells are 70-150um in size, a clump of cells can clog the machines and render them inoperable.

Come by, check out the machines, ask us questions…we hope you’ll be pleasantly surprised at the possibilities.

Tufts Laser Cytometry, Jaharis 5th floor. 

Special points of interest:

  • No Color Cloning
  • Bulk Sorting
  • Fluorescent work
  • Cell Cycle
  • Apoptosis
  • Ca+ Flux
  • Single Cell PCR
  • Rare Event
  • Bacteria
  • CRISPR
  • Stem Cells
  • Neurons
  • Transfections
  • Infections
  •  Libraries

 

Insight Essay Contest WINNER – Developing Resilience

Author: Matthew Kelley, 3rd year, Neuroscience, Moss Lab 

http://sackler.tufts.edu/~/media/Sackler/Page%20Images/Neuro%20Student%20Research%20Page%20Photos/kelley_matthew%20rp.jpg?&mh=160&mw=120
Matthew Kelley, 3rd year Neuro, Moss Lab

The pillars supporting a good scientist remain unbroken. They have changed little since Galileo dropped spheres in Pisa and Pasteur confirmed germs cause disease. It is the understanding and mastery of these core principles that should be the dominant focus of graduate training. The journey of a scientist is one of vistas and ditches. For the PhD student, so quickly can things shift from shining moments of discovery to the fierce harshness of figuratively banging their head against a lab bench after another failed experiment. Unless the student enters this land prepared, they will collapse in the first journey over the top. Discoveries require failures. Without resilience to failure, decisions are tainted by fear of failure. The process of gaining a PhD is overflowing with decisions of consequence including selection of advisors, scientific projects, and career paths. Resilience, the capability to adapt to diverse stressors, is critical to making these decisions with a clear and strong mind. Outlined here are four ways resilience can be improved during PhD training.

  1. Understand mental well-being.

We choose to go the moon in this decade and do the other things, not because they are easy, but because they are hard…”

In 1962, in the sun drenched football stadium at Rice University, President Kennedy declared why the American people must pursue this great achievement. But the path to the Apollo 11 landing on the moon was far from smooth. A raging fire consumed all three astronauts of the first mission, Apollo 1. There were many reasons to scrap the program. Yet America pressed on to reach the lunar surface due to the ultimate resilience of an entire team following Kennedy’s call. We do things because they are hard.

In order to achieve such resilience in science, the PhD student must understand their own resilience. Are problems avoided because of failure’s sting? Do roadblocks bring the desire to avoid difficulties all together? It is critical to understand how stress affects personal decision making. A healthy mind underlies balanced processing of information. The student must be guided to recognize when their thinking is warped by stress, resulting in a lost desire to pursue difficult problems. The watchful gaze of the student’s committee is critical, but can be supplemented with mental health counseling focused on developing introspective thought. When such self-awareness is gained, resilience becomes a tangible trait to personally and actively increase. Hard problems are no longer fearsome, but glorious challenges.

  1. Place failures in proper perspective

Great people fail, but understand the meaning of failure. Failure isn’t a worthless enterprise, a waste of time and resources. Far from it. Failure is the journey.

In order to develop resilience as a PhD student, it is important to understand what failure is. When an experiment fails, it is not a fatal loss. Negative data retains value. And failed experiments can be further optimized to better answer the chosen question. In the process of PhD training, negative results or outcomes must not be hidden away, but acknowledged by student, advisor, and committee as a critical part of scientific training. Once failures are defined as constructive parts of training, resilience to their sting becomes much easier to develop.

  1. Build skills to create positive experiences

Some of the most resilient people on TV appear on Junior MasterChef, a culinary competition of children under the judgment of Chef Gordon Ramsay. He presents ingredients and a goal, and four-foot tall competitors bring him their completed dishes, some terminating in crying defeat under his carefully worded criticism. However the winners don’t break. They remain resilient to the criticism and create beautiful dishes that ultimately wow both Ramsay and audience. What sets these children apart? It’s both resilience to criticism and a mastery of cooking technique. These kid chefs are so skilled in their cooking finesse, that when a challenge comes this confidence sets them up for success.

In the same way, the PhD student can be set up for scientific success by becoming a master in their chosen area of technique. If skills are mediocre, failures are sure to increase, to the point where the student gives up and quits. Resilience is hard to build when one is set up for failure. It is an important role of the student’s advisor and committee to critique student technique, because in its improvement lies the path to increased positive student experience. And mastery of technique brings certain confidence, because though an experiment may answer or negate a hypothesis, a clean result remains a beautiful thing.

  1. Create supportive relationships

Neil Armstrong stepping onto the lunar service was a culmination of years of rigorous work. Thousands contributed so one man could take one small step. Science is a team sport. Without a supportive network of mentors and peers, problems become harder and resilience difficult to sustain.

It is easy as a PhD student to become intellectually isolated in pursuit of a project. This can and should be avoided. In order to gain resilience and pursue the hardest of problems, guidance is needed from those that have been there before. Opportunities to present work provide an outlet for constructive criticism and guidance. The selection and pairing of mentors outside the student-advisor relationship serves as a platform for dealing with failure. Support networks can be facilitated, but ultimately are an active process on the part of the student. Such relationships should be encouraged during graduate training to build the resilience to the failures and press to the successes.

Conclusion

Resilience is a trait able to be learned and developed by anyone. When scientific resilience is gained, hard problems can be pursued resulting in a fulfilling PhD training experience. A fulfilling scientific life requires resilience to separate one from the psychological weight of failure. And resilience not only gives the ability to think clear and true in science, but throughout the hard and difficult decisions that are guaranteed to appear during the human life. Developing resilience in science should be a major focus of graduate training.

Biotech Startup Mixer, presented by GSC Career Paths

Shortly after returning from the holidays, the Career Paths Committee of the Sackler Graduate Council coordinated a biotech/startup mixer on January 6th, 2016 at the Field in Central Square. Representatives from bosWell, Neumitra, Genometry, Thrive Bioscience, as well as the COO of Editas Medicine donated their time to chat about their careers.  The event was remarkably well attended by PhD students, as well as a handful of post-docs and MD/PhD students.  Whether it was the draw of learning more about alternative career paths, or the casual venue, the event was an excellent success.

IMG_1328 IMG_1327

Notes from the North – MMCRI Transgenic Core

MMCRI transgenic core

The Maine Medical Center Research Institute (MMCRI) has partnered with Tufts to provide a professional core facility that has over 15 years of experience providing high quality services for the generation of mouse transgenic strains including the use of CRISPR/Cas, cryopreservation of mouse germ cells, and imaging, including MRI and microCT. Mice are generated in a full barrier, AAALAC-accredited animal facility in a transgenic production room that facilitates direct importation of mice into the Tufts barrier facility. Contact us to discuss your mouse and imaging projects.

Mouse Transgenesis

Source - MMCRI transgenic core
Source – MMCRI transgenic core

We provide microinjection to generate your mouse models. Services include microinjection of fertilized oocytes with traditional DNA transgenes, or microinjection of CRISPR/Cas. ES cell injection is also performed. Contact us to design your CRISPR mouse project – cost depends on type of modification, strain of mouse, and days of injection. We have a high surveillance production room that will allow importation of mice direct into some barrier facilities.

Contact – Lucy Liaw, Ph.D., liawl@mmc.org

microCT

Source - MMCRI transgenic core
Source – MMCRI transgenic core

We house a Scanco high speed in vivo microCT scanner X-ray system. Our microCT facility has extensive experience in bone imaging and quantification, and can work on other projects where tissues are provided, i.e., vascular imaging of samples perfused with microfil. We provide quantification and any 3D images of the samples as required. Contact us to get a project quote. Pricing is based on hours of scanning and analysis time.

Contact – Lucy Liaw, Ph.D. liawl@mmc.org

Small Animal MRI

Source - MMCRI transgenic core
Source – MMCRI transgenic core

Our MRI facility houses a Bruker Pharmascan 7T, 300 MHz imager with 100 μm resolution. Services include anatomical imaging of most organs, angiography, proton spectroscopy and localized spectroscopy, and cardiac imaging, including diastolic and systolic dimensions of the ventricle. We can house “clean” animals at our facility for studies requiring longitudinal imaging. Contact us for mor information.

Contact – Ilka Pinz, Ph.D. pinzi@mmc.org