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Sackler students collaborate with Emerson College in science communication course

As graduate students, we all know what it is like to present our research to a scientific audience that is not familiar with our research topic and the accompanying task of making the research and larger implications relatable. Most likely, however, the majority of us are not familiar with presenting in detail our research topic to a general audience: those who don’t know what the difference between DNA and RNA is, or what ‘epithelial’ means, or how cell culture works.

This spring, a group of Sackler students were presented with the opportunity–or challenge–to do so through a collaboration with Emerson College. Seven graduate students from various programs were paired with undergraduate students–whose majors ranged from journalism, TV production, video production, and animation–enrolled in an upper-level science course focusing on science media/communication. The main goal was for the Sackler participants to serve as scientist contacts with whom the Emerson students would put together three science-centric media pieces. The first two were written, one being a profile piece on the graduate student scientist who the undergraduates were paired with and the second being an article reviewing, explaining, and reporting on the graduate student’s research topic and field. The information gleaned from both of these interview experiences also culminated in planning and executing a final project in video form. These videos ranged from animated science-explainer videos to mini-films profiling the scientist collaborator, showcasing the broad interests and talents of both student groups.

The course instructor, Dr. Amy Vashlishan Murray–who earned her PhD in genetics from Harvard University–is a strong advocate for comparing, contrasting, and combining science and media. Her passion for science communication started in college and grew deeper in graduate school where she participated in various outreach programs, including the Science in the News lecture series. When she started teaching at Emerson, she created this ‘Science in Translation’ course as a way for her–from the perspective as first a scientist and second a communicator–to make an impact on future contributors to media and communication fields. In particular she designed the course for depth, as it was one of the first upper-level science classes to be introduced to the curriculum at Emerson. She wanted to help art-focused students find “the place of science in their world” by facilitating a “peek behind the curtain” of scientific research.

In addition to teaching, Dr. Vashlishan Murray initiated Boston’s branch of the Ask for Evidence campaign. This program, which is sponsored by the organizations Voice of Young Science USA and Sense About Science, seeks to have members of the public investigate consumer-directed advertisements making science-based claims and test whether those claims are indeed accurate. This effort dually challenges the public to think critically about scientific claims while also challenges those who use scientific claims to do so more carefully and accurately. Her work related to Ask for Evidence helped  her win the 2014 Paul Shin award from the Washington, D.C.-based grassroots group Coalition for the Public Understanding of Science (COPUS), which honors trendsetters and pioneers in the science communication field.

Dr. Vashlishan Murray took a flexible and welcoming approach to the class, letting it serve the needs of her students and science collaborators in equal turn; she frequently took into account and implemented suggestions from both groups throughout the course. The Sackler students started off the semester by attending an improv class with the Emerson students to pull down any initial social barriers and to encourage critical thinking about how we communicate not just with words but with movement and facial expressions and how one-on-one versus group communication works. We also were invited to many of the course’s classes, some discussion-based and others in which guest lecturers spoke, including science communicators from Story Collider and Stat News. The tables turned when we were the ones presenting in the form of 8-minute research flash talks, which the Emerson students critiqued based on how well we communicated the science for a general audience.

The majority of our time for this collaboration, however, was spent working with the students themselves. The semester-long relationship of in-person interviews, email correspondence, planning and filming sessions for the final video project, and discussions following the completion of each media piece facilitated deeper understanding and engagement on both sides.

“I was pleasantly surprised by the enthusiasm (for the scientific content and for the cause of science communication) expressed by many, if not most, of the students in the class,” Melissa LaBonty, one of the program collaborators and a CMDB graduate student, commented when asked about her experience with the Emerson students.I was also happy to learn that given the correct information and background, a lot of non-scientists can become just as passionate about our scientific interests as we are!”

Dr. Vashlishan Murray was able to share some of the Emerson students’ responses and noted that the majority of them mentioned the collaborative aspect of the course as the most impactful. In particular, she highlighted that many of them described their experience this semester as finding “the humanity in science.”

As for what future iterations of the course will be like, Dr. Vashlishan Murray mentioned she’d like to delve deeper into communication theory in relation to science for the Emerson students. For the scientist collaborators, more feedback about their communication skills and more involvement with the guest speakers are things she’d like to expand upon. Both additions would strengthen an already engaging and transformative experience that this course provided, enriching the knowledge gain for both the science-focused and communication-focused student groups.

Tufts “Meet The Scientist” event builds bridges with local community

Inspired by a conversation between post-docs at a science and education conference, the Tufts’ TEACRS (Training in Education and Critical Research Skills) and TII (Tufts Innovation Institute) worked together to host a community outreach event this May. The “Meet the Scientist” event took place on the Medford campus and consisted of a science faculty-hosted panel session and an activity session, with attendees including local families and students from all levels of schooling. The panel session allowed community members to ask insightful and probing questions of Tufts faculty that facilitated an open, honest, and engaging conversation about science and science research. Following this, the activity session consisted of six stations hosted by TEACRS post-doc trainees. Children, teens and adults alike had the opportunity to play with silk and DNA legos, to look at flies and talk about circadian rhythms, to isolate some of their own DNA, and to watch how music played from a mobile phone could make a cockroach’s leg muscles move.

With a strong turnout and enthusiastic hosts as well as attendees, this event succeeded in strengthening bridges between Tufts’ scientists and the local community. This type of connection is a significant component in narrowing the gap between the public and their understanding of science and strengthening trust in scientists and the work we do.

Sackler Spotlight – Bina Julian, PPET and Jen Nwankwo, PPET

This spring, two outstanding Sackler students–Bina Julian (PPET) and Jen Nwankwo (PPET)–were awarded the Tufts Presidential Award for Citizenship and Public Service. Established in 1999 by former university president John DiBiaggio, this award honors both undergraduate and graduate students who have shown substantial commitment to and achievements in building community through service and leadership. To highlight these accomplishments, we interviewed Bina and Jen about the work that led to their nomination and eventual awarding as well as what they do at the bench as well (note: at the time of publishing, Jen was out of town, thus we will update this article once we get a chance to talk with her).

Can you tell us about the work that led to you being nominated for this award?

Bina: I have a really strong desire to help people achieve their goals by increasing their self-awareness and connecting them with opportunities. And a parallel desire to figure out how to scale that impact when something works well…probably because I’m an engineer. That’s what drew me to the Tufts Biomedical Business Club (TBBC).

Our TBBC team runs like a small startup. From the beginning, we all saw the potential to connect Tufts students with professional resources, the Boston biotech community and each other. So we each went out and made connections [see Collaborator List] and designed ways for our members to learn and practice the business of science [see About TBBC]. Soon opportunities started coming to us, external groups reached out to collaborate, and our members were being recruited for jobs. I’m really proud of what we’ve built and how many people we’ve helped over the years.

Receiving this award especially acknowledges the work past and present TBBC leaders have done to shape TBBC into a sustainable and engaging training ground.


 

Box 1: Tufts Biomedical Business Club

TBBC is a way for researchers to gain industry awareness and professional development.  Members get introduced to TBBC by attending our seminars featuring business leaders in several areas including venture capital (Bob Tepper, Third Rock), biotech startups (Sandra Glucksman, Editas), and consulting (Chris Von Seggern, ClearView).  Many take a step further and participate in one of our self-guided initiatives, like Case Study Group, Biotech Journal Club, Biotech Buzz or hosting a speaker.  Others gain critical business experience by competing in our Tufts New England Case Competition (TUNECC) or the Gordon Institute’s Tufts $100K New Ventures Competition.  Regardless of whether or not our members become PIs, entrepreneurs or consultants, we hope their time with TBBC empowers them with the network and perspective to pursue a successful career.

Recent TBBC Connections

Internal Connections: TUSM Advancement Office, Sackler Graduate Student Council, Sackler Dean’s Office, Gordon Institute, Tufts Entrepreneurial Leadership Program, Tufts Center for the Study of Drug Development, Tufts Clinical & Translational Science Institute, Tufts Entrepreneurial Network (of student leaders), Tufts Entrepreneur Society (undergrad group), Tufts Institute for Innovation, Tufts MedStart, Tufts MD-MBA Program  , Tufts Office of the Vice Provost Office, Tufts Postdoctoral Association, Tufts Tech Transfer Office, TUSM Public Health and Professional Degree Programs

External Connections: Venture Café, Biotech Connection Boston, Boston Entrepreneurs and Advanced Degree Meetup Group, Northeastern Biotech Entrepreneurs, Boston University BEST Program, Hopkins Biotech Network, MIT Biotech Group, Harvard Graduate Consulting Club, Yale Graduate Consulting Club

Guest speakers from: Back Bay Life Science Advisors, Biologics Consulting Group, Biomille, Brean Capital, BrightMed, Campbell Alliance, Center for Integration of Science and Industry, Bentley University, ClearView Healthcare Partners,Cowen and Company, Cyta Therapeutics, Decision Resources Group, Dyax Corp., Edits, Flagship Ventures, Foundation Medicine, Foundation Medicine, Genzyme, Google, Health Advances, LLC, Johns Hopkins Technology Ventures, LEK Consulting, MPM Capital, Novartis, NYU Entrepreneurial Institute, Polaris Ventures, Propel Careers, RA Capital, Simon-Kucher & Partners, T2 Biosystems, The Isis Group, Third Rock Ventures, Thomas, McNerney & Partners, Tufts Center for the Study of Drug Development, Tufts Gordon Institute, Tufts Institute for Innovation, Vaxess Technologies, Visterra, Inc.


How do you feel that your work connects to your current and future research/career goals?

Bina: I think it highlights the kind of impact I would like to have and scale up. I’d like my future career to bring together my skills as an engineer, a scientist, an educator and a “connector.”

What was the experience of being nominated like?

Bina: I actually had no idea I was being nominated. I have Jaclyn Dunphy and Julie Coleman to thank for going above and beyond to find this award and gather recommendation letters from current and former TBBC executives. When I got the award email and learned what they had done, I was incredibly moved and humbled.

[The Presidential Awards Ceremony took place on April 21st, 2016.  Awards were presented by Tufts University President Anthony Monaco, Tisch College of Civic Life Dean Alan Solomont and nominators.  Watch segments from the awards ceremony here.]

How would you like to see your work continued past your time at Tufts? How do you feel your efforts currently support that vision?

Bina: I hope that TBBC will continue to have an impact and that our connections within and outside of Tufts stay strong. It’s encouraging to meet engineering, policy, medical, dental, nutrition and even veterinary students at our events; they bring such different perspectives to our discussions and also connect Sackler students with opportunities happening at other institutions.

I hope future leaders extend TBBC’s mission with fresh ideas and diligently assess the needs of its members so TBBC stays relevant. Most of all I hope that future TBBC leaders make a conscious effort to not only hone their own leadership skills, but also invest in the professional development of their teammates.

The only way any of this vision will survive is if everyone gets involved – students, faculty, administration, alumni, and the biotech community at large.  We’re a completely student run organization with a multi-year, personal commitment to produce high quality events and initiatives for our members. Whether its volunteers, event ideas, business workshops, speaker connections, conference discounts, alumni mentorship, job/intern opportunities and of course financial support – the executive team welcomes donations in all forms!

Last but not least, can you tell us about the work that you do in the lab?

Bina: I’m a Pharmacology and Experimental Therapeutics grad student working with Dr. Alan Kopin, who directs the Molecular Pharmacology Research Center at Tufts Medical Center. The Kopin lab studies G Protein-Coupled Receptors (GPCRs), a superfamily of 7-transmembrane receptors known for modulating a wide array of intracellular signals in response to extracellular stimuli. These cell receptors are considered highly “druggable” as they are targeted by nearly 40% of FDA approved drugs.

Cells use GPCRs to sense cues in their environment and make decisions. I study a GPCR subfamily of chemokine receptors, whose primary function influences decisions surrounding cell migration. My thesis work characterizes a rather understudied chemokine receptor called CCR6. Notably, CCR6 is highly expressed on and influences the migration of Th17 cells – an immune cell type whose aberrant recruitment to inflamed tissue is associated with several chronic inflammatory diseases. Many are interested in the therapeutic potential of CCR6, yet few tools exist to tease apart and modulate CCR6 receptor signaling.

In the lab I’ve developed molecular tools and assays that can enable screens to identify and characterize CCR6 modulators.  Most recently I established a Bioluminescent Resonance Energy Transfer (BRET) assay to measure beta arrestin recruitment to CCR6.  Most people know that GPCRs signal through G proteins as their name suggests, but they have an alternative pathway mediated through beta arrestin.  The BRET assay allows me to observe dynamic protein-protein interactions with CCR6 and tagged signaling molecules.  We are also interested in how naturally occurring variations in CCR6 affect signaling and if these alterations could predispose individuals to disease.

CCR6 plays a complex role in inflammation at the level of individual cell types and the field needs tools to tease apart its influence. And unlike the reputation of its GPCR superfamily, chemokine receptors have had little drug development success (only one FDA approved compound modulates the migratory function of its chemokine receptor target). Overall I hope the insights from our study of CCR6 variants as well as the genetic constructs and assays we’ve developed can be used by both immunologists and pharmacologists to translate this work to help patients.

Adenine Methylation in Mammals: N6-mA is the new 5mC

Guest Post by Ila Anand, 3rd year, Micro

The advent of the epigenetics field occurred more than a decade ago and has since rapidly revolutionized our understanding of disease and inheritance. The term epigenetics encompasses any molecular switches attached to DNA that turn “on” or “off” the expression of genes. In germ cells, these molecular motifs can be passed onto the progeny. Although several types of epigenetic markers are known to exist, two types have been well characterized. The first one being histone modifications, which indirectly impact gene expression by altering nucleosome structure, and the second one being direct methylation of the DNA. The prevailing dogma in the field is that mammalian DNA methylation exclusively occurs on the fifth position of cytosine (5mC). However, the Xiao lab at Yale recently confirmed in the March issue of Nature that adenine methylation (N6-mA) can also occur in mammalian embryonic stem cells (ES cells).

Historically, adenine methylation has been known to predominantly occur in prokaryotes. Dam methylase, the bacterial enzyme responsible for methylation, has been heavily studied in E. coli since the 1970’s and controls mismatch repair of DNA, DNA replication, and gene expression. It was only until recently that several groups reported N6-mA occurring in the invertebrates, such as Drosophila, C. elegans, and green algae. Interestingly, N6-mA in these “simple” eukaryotes was implicated in activating gene expression. This is in striking contrast to 5mC, which represses gene expression in mammals. In December, a research team at the University of Cambridge published the discovery of N6-mA occurring in mouse and human cells, albeit at several orders of magnitude less frequently than cytosine methylation. However, this team was not able to identify the consequence of N6-mA on mammalian gene expression.

The Xiao lab at Yale elaborated on this discovery by finding that N6-mA represses genes on the X-chromosome of ES cells. First, the team confirmed adenine methylation was occurring in ES cells using SMRT-ChIP and mass spectrophotometry techniques. Next, they identified the demethylase enzyme Alkbh1 to be responsible for controlling N6-mA by generating a homozygous Alkbh1 knockout line. In this knockout cell line, they found increasing N6-mA levels on the X-chromosome of ES cells, indicating that adenine methylation is misregulated without Alkbh1. Intriguingly, the team found N6-mA to correlate with the silencing of LINE-1 elements. These elements are retransposons that are enriched at the X-chromosome. Although the majority of LINE-1 transposons have lost the 5’UTR and other proximal regions, several full-length “young” LINE-1 transposons exist at the X-chromosome and can be autonomously transcribed. The researchers found N6-mA to accumulate on “young” LINE-1 elements but not older, aberrant elements. Furthermore, N6-mA accumulated and silenced neighboring LINE-1 genes. These neighboring X-chromosome genes are known to play a role in cell fate decision.

The implications of the Xiao team’s findings are numerous. First, adenine methylation of LINE-1 elements appears to have evolutionary significance. N6-mA at these sites silences LINE-1 expression and neighboring gene expression and this is exactly opposite to the role N6-mA plays in invertebrates. The researchers hypothesize that controlling LINE-1 expression safeguards the active transcribed elements from reintegrating into the genome and creating genomic instability. Additionally, since neighboring genes are silenced by N6-mA, the epigenetic marker could play a salient role in embryogenesis. Although Alkbh1 cells are capable of differentiating, the Xiao team found that these knockout cells have an imbalance in cell fate decision. Another implication of N6-mA on the X-chromosome is that it could be the mechanism of X-inactivation in females and ultimately control sex ratios, since LINE-1 elements are enriched at the X-chromosome. Finally, because LINE-1 elements are also enriched in tumor cells, N6-mA sites can give us some more insight into oncogenesis. In conclusion, the Xiao lab’s findings enhance our understanding of the mammalian epigenetic repertoire and open new avenues to therapeutic design for a range of diseases.

 

References:

DNA methylation on N6-adenine in mammalian embryonic stem cells

Wu, Tao P., et. al.

Nature 532 (7599), 329-333

 

http://www.the-scientist.com/?articles.view/articleNo/45710/title/New-Epigenetic-Mark-Confirmed-in-Mammals/

 

https://www.genomeweb.com/sequencing-technology/researchers-identify-methylation-mark-previously-uncharacterized-mammalian
http://news.yale.edu/2016/03/30/sex-baby-ancient-virus-makes-call

EDITORIAL: Career development resources for non-academic paths (Part I)

This two-part editorial by the Insight team seeks to open a discussion between faculty, students, postdocs and the school administration about whether the school is prepared for meeting the changes in the future of PhD holders. The first part will address the current available resources and the unmet needs of the students/postdocs, and will also explore some possible solutions. The second part, to be published in the next issue of the InSight, will carry the opinions of all parties involved collected through a survey and communication, which will serve as a stepping stone towards meaningful changes that will benefit us all.

Editors’ Note, 4/11/16, 1:30 pm – The article has been modified to include corrected information regarding the BEST award application by Sackler. Previously it had stated that Sackler had applied for the BEST award and was not awarded due to lack of proper infrastructure. However, after communicating with the Dean’s office, we have learned that Sackler had applied in conjunction with other Tufts graduate schools and it is speculated the application was not funded partly due to complex administrative structure and evaluation and dissemination plans. The changes are reflected in the article. 

The Doctorate in Philosophy (PhD) is a degree awarded to recognize original contributions to collective human knowledge. Thus, it is no surprise that the next step after getting a PhD is to join the bastions where such knowledge is curated and cultivated, i.e., to pursue an academic career. However, given the current structure of an academic job and the nature of academic tenure, a bottleneck in academic positions have taken firm root in the last years. According to Nature, the number of postdocs have jumped by 150% between 2000 and 2012 while the number of tenured or full time faculty positions in the US has either remained stagnant or fallen. While the debate on how to improve the lives of postdocs and other non-faculty PhD holders rages on and restructuring of federal funding for scientific research is ongoing, the increasing number of PhDs leaving the traditional path and venturing into other professions is readily apparent.

Postdoctoral appointees, by field
Adapted from Powell 2015 Nature
Employment of doctorates
Adapted from Cyransoki et al 2011 Nature

In recent years, the PhD degree has been developed as a marketable asset with a accompanied with a powerful skill set — the ability to think critically, solve problems and troubleshoot, be organized and detail-oriented. The idea that the skills required for obtaining a PhD are also recognized as required to be successful in any other profession, and is now being echoed by career counselors. While industry research positions were once spoken about in hushed voices before, these positions are now not only coveted, but other non-research jobs are also becoming more prominent in seminars and career advice panels for biomedical graduate students and postdocs.

This trend is also evident within the graduate student population here at Sackler School of Biomedical Graduate Sciences, where more than half the alumni have pursued non-academic careers. As the funding climate struggles to recover and academic positions become more scarce, the question arises of whether the existing model of career development for student and postdoctoral trainees is sufficient to ensure future success and achieving their goals. It is apparent that career development training outside of academia is required, but the support for this by the curriculum and administration at the Sackler School seems to lag behind our peer institutions, and even our colleagues on the Medford campus have access to the Tufts Career Center and the students in the Fletcher School have their own Career Services office.

Resources currently available for students at Sackler interested pursuing non-academic careers are mostly driven and organized by the students themselves. These student-led initiatives have produced a full roster of seminars and workshops focusing on such career options held nearly weekly between the Career Paths Committee of the Sackler Graduate Student Council (GSC) and the Tufts Biomedical Business Club (TBBC). These groups have become increasingly active over the past few years, with their efforts growing into independent events like the Tufts New England Case Competition (TUNECC), as well as collaborations with the Tufts Postdoctoral Association and student groups in the School of Medicine. Additionally, the Tufts Mentoring Circles group has provided students peer guidance and spaces to discuss such career options among themselves. Every student initiative listed here has sought more interactions with Sackler alumni, but the information to facilitate that exchange is not readily available. Student leaders at Sackler have expended great effort to build the career resources the student body needs, but these efforts are reaching the limit of what they can achieve and will only be short term and partial solutions without additional resources and support infrastructure. Some of this could be built by students, like shared repositories for maintaining records and thus institutional memory so energy is expended solving new problems instead of rehashing old ones. The most important piece, however, cannot be done by students alone: an accurate, current database of Sackler alumni and their occupations that is accessible and searchable.

We appreciate that the Dean’s Office has recently increased its support of these student efforts, but believe that more can be done. An increased contribution to co-sponsorship from partial funding of one or two events with the GSC annually to a series of three annual workshops and career panels over the past two academic years, and the interactions between a handful of students with Sackler alumni through the new “Day in the Life” program are good starting points. However, the student body and Sackler as an institution would derive greater benefit and return on an investment in career development and advising staff, similar to those available at the Fletcher School and the Medford campus, but scaled for Sackler. It would be mutually beneficial, as it works to the advantage of a school to have an engaged student body that will recognize and appreciate the school’s support in shaping their careers as alumni. Furthermore, this infrastructure could be a common point for alumni to rely upon and connect with students and each other.

The lack of formal career development resources at Sackler has been identified by peer reviewers as an area for improvement, and puts us at a competitive disadvantage for student recruitment and securing grant funding. Prospective students actively seek graduate programs that provide career development, and among the recommendations made by the review committee for the newly-merged CMDB program were formal non-academic career training options and an expansion of extramural internships through the alumni network and faculty connections. Funding agencies such as the National Institutes of Health (NIH) evaluate grant applications on this aspect of graduate training as well. For example, F31 grant applications to support graduate students require descriptions of career training and development; the proposed changes will essentially strengthen the Sackler students’ applications and may increase the number of extramurally funded students, alleviating the pressure on the school.  A more recent example includes the NIH Broadening Experience in Scientific Training (BEST) awards, a funding opportunity established in 2013 in response to the state of the biomedical workforce and to prepare trainees for diverse career paths that utilize their PhD training. Boston University received a BEST award in 2014 for its biomedical research programs in part because of its existing career development and support infrastructure. It should be noted that Sackler, along with other graduate schools at Tufts, had applied for the BEST award. While the reviewers had found the application to be strong in certain areas and to have “potential for high impact”, they also noted weaknesses that included “complex administrative structure and the evaluation and dissemination plans”, which could partly be responsible for the award not being funded (source – email communication with Sackler Dean’s office). These issues can be addressed with the establishment of the proposed infrastructure development and can further strengthen such grant applications in the future. 

The faculty mentor plays an important role in shaping a mentee’s future career — the mentor’s support and guidance are essential for the mentee’s career development. While Sackler faculty are generally supportive of students and postdocs, it is critical for them to come forward and actively support mentees’ who choose to pursue careers outside of academia and research. The Greater Boston area is known as a hub for biotechnology research and business, with companies specializing in everything from drug development to consulting. Many recent and local alumni maintain a connection to Tufts through their faculty mentors absent a career development office at Sackler, and both students and postdocs would greatly benefit if the faculty mentors shared these connections, and offered guidance and support on leaving academia.

The current funding climate and the stagnation of academic positions, along with the burgeoning postdoc crisis, amount to conditions favorable for a paradigm shift. We cannot just keep focusing on the academic jobs traditionally held by PhDs. In order to better adapt to this changing landscape of post-doctoral work, the students, postdocs, faculty, and administration need to work together to bring about improvements to the environment at Sackler, specifically:

  1. Developing an accessible, searchable, up-to-date database of Sackler alumni that can be used by students, postdocs and faculty looking for career advice and connections.
  1. Faculty support in the form of guidance and connections in developing non-academic careers.
  1. Career development support staff for students from the Tufts and Sackler administration, so as to cultivate an engaged alumni population.

Comments, suggestions, and other feedback on this editorial can be left on either the InSight blog or via this online form: Anonymous feedback form: http://goo.gl/forms/PXEfcLfgeX

A survey to collect more detailed data from the student body will be conducted by the Sackler GSC in the coming weeks.

 

Resources for learning how to code

Last month, I put together a small script that made the calendar from the Sackler website accessible to calendar software such as Google Calendar, Apple Calendar, Outlook, and others, that a majority of people now use. This little simple bit of code solved a problem of the Sackler website that has existed for years and requires no further intervention on my part. I’ve put the source code online on GitHub for anyone who is interested in seeing how it works (https://github.com/danielsenhwong/sackler). For anyone who is interested in learning how to code or, like me, would like to develop their skills beyond the introductory undergraduate level, I’ve compiled a list of resources that may be useful.

Getting started

This is in many ways the most difficult part about learning how to code. Many resources exist, but it’s difficult to know which is the most approrpiate for your current skill level. You may already be somewhat familiar with some specific coding techniques or languagees, but significant gaps may still remain in your knowledgebase. Such gaps could include understanding how to set up a coding environment on your computer, which language is most suitable for your work, or how to interface with a database instead of just reading data from a file generated by your plate reader. As biomedical scientists, our familiarity with computers and code is limited compared to more computationally-intensive fields, but not compeltely absent, and our field is rapidly becoming more computational.

practicalcomputingFortunately, there is a book specifically intended for biologists who are interested in developing their computing skill set: Practical Computing for Biologists, by Steven Haddock and Casey Dunn. The book introduces basic concepts of coding while also providing a thorough walkthrough of how to set up a suitable environment on your computer before moving on to practical applications of coding and tools for data analysis, including working with databases and best practices for working with graphics and generating figures for publication. The companion website for the book makes much of the example code freely available, along with some other extras, including the reference tables, which are extremely useful while you’re still learning the commands: http://practicalcomputing.org/

lynda_logo1k-d_72x72Tufts Technology Services (Tufts IT) also has some resources available for free to the Tufts community, including access to Lynda.com, which hosts self-paced online tutorials for a number of different topics, including coding as well as software-specific training (Adobe Photoshop, Illustrator, InDesign, etc.). Additional details can be found on the Tufts IT website: https://it.tufts.edu/lynda

Integrating coding into your work

It can be difficult to learn how to code if it’s siloed away as a separate skill you’re trying to learn, so one effective technique is to integrate it into your normal workflow. One example would be to use R (r-project.org) in place of Excel or Prism to perform your statistical analysis. A good book for learning how to get started is Introductory Statistics with R, by Peter Dalgaard. A PDF version of this book is available for free through the Tufts library or heavily discounted for purchase: http://link.springer.com/book/10.1007%2F978-0-387-79054-1

Sackler Spotlight – Wei-sheng Chen, CMDB

As part of a new endeavor to highlight exciting and groundbreaking work done at Sackler, we are now interviewing current students about their science and themselves.  

This month’s spotlight is on Wei-sheng Chen (CMDB) who earned his PhD from Sackler last year and whose dissertation work will be published in Nature Communications.  

 

What is your research focused on?

My research focused on the role of galectins, a family of carbohydrate binding proteins, in the ocular diseases. During my Ph.D., I investigated (i) the role of galectins in modulating angiogenesis and lymphangiogenesis, (ii) effect of inhibiting galectin-3 and galectin-8 on corneal and choroidal neovascularization, and (iii) therapeutic opportunities of treating glaucoma.

What are some of your major findings?

My thesis project is to study the role of galectin-8 in modulating the process of lymphangiogenesis. Compared to blood vessels, lymphatic vessels were considered less important, invisible, and thus largely neglected by scientists and clinicians. Only in recent years, subsequent to the identification of lymphatic-specific markers (such as podoplanin), it is becoming increasingly clear that lymphatic vessels do not just serve as passive conduits for interstitial fluid and cells, but is actively involved in the pathogenesis of numerous diseases. In addition, the role of carbohydrate recognition system in the regulation of lymphangiogenesis is poorly understood. For my thesis project, using the avascular cornea as a canvas, I demonstrated that galectin-8 is a key mediator of crosstalk among VEGF-C (vascular endothelial growth factor-C), podoplanin and integrin lymphangiogenic pathways. Also, this is the first report demonstrating that podoplanin is a key player in VEGF-C-induced lymphangiogenesis.

What short- and long-term implications does your research have in your field?

In this study, we demonstrated that in the mouse model of corneal allogeneic transplantation, galectin-8-induced lymphangiogenesis is associated with an increased rate of corneal graft rejection. In addition, in the mouse model of herpes simplex virus keratitis, corneal pathology and lymphangiogenesis are ameliorated in galectin-8 knockout mice. Targeting galectin-8 can be a potential novel therapy for corneal graft rejection and herpes simplex virus keratitis. In addition, these results have broad implications for developing novel therapeutic agents to treat numerous diseases, including, but are not limited to, lymphedema, tumor metastasis, cardiovascular diseases (myocardial infarction, hypercholesterolemia, and hypertension), inflammation and immunity, obesity, glaucoma, dry eye disease, and allergic eye disease.

What initially got you interested in science in general, as well as your current field, and this project(s)?

I began my scientific career as a part-time undergrad student in a cardiovascular lab in National Cheng Kung University, Taiwan. My job was to purify plasminogen from human plasma, and further process the protein enzymatically to generate different forms of anti-angiogenic angiostatins. I guess ever since then, I have been fascinated by vascular biology.

During my first year at Tufts, I was looking for a lab studying vascular biology and have done different projects related to the field. Fortunately, I joined Prof. Noorjahan Panjwani’s lab at Ophthalmology Department in 2011 to start my thesis project. During my Ph.D., I have learned a lot about the diverse functions of glycans and glycan binding proteins. In addition, I was encouraged to attend regional and international conferences and have developed great interests in pathogenesis of ocular diseases such as glaucoma and age-related macular degeneration.

Where do you see your career heading in the short or long term?

In the short term, I would like to learn more about the interaction between blood/lymphatic vessels and immune cells such as macrophages and T cells in the setting of eye diseases and/or cancers.

In the long term, I would like to become an independent scientist focusing on vascular biology in the hope to find new therapies for ocular and cardiovascular diseases.

Anything interesting that you do outside of lab or that is science-related but not connected to your research? 

I like to travel and try different cuisines. I especially like conferences that are held close to beaches. In my free time at home, I also like to watch food channel. Some of my favorite programs are “Chopped”, “Guy’s Grocery Games” and “Worst Cooks in America”.

Implicit Bias: A Conscious Discussion of Unconscious Actions

It is no secret that unconscious biases penetrate various realms of society; from hiring decisions (Lebowitz, 2015) to medical care (Blair, Steiner, and Havranek, 2011) and even foul calls in the NBA (Schwarz, 2007).

But what about implicit bias in our everyday lives? Does it really play a role in who we form relationships with, or the way we interact with others, or even the way we perceive a stranger?

Implicit bias refers to attitudes or stereotypes that affect our understanding, actions and decisions in an unconscious manner, according to the Kirwan Institute for the Study of Race and Ethnicity, which publishes an annual Implicit Bias Review . Unlike explicit bias, which reflects the attitudes or beliefs that one endorses at a conscious level, implicit bias is judgment and/or behavior that results from subtle cognitive processes that often operate at a level below conscious awareness and without intentional control.

Recent claims of overt and covert discrimination on college campuses and in policing raise the question: How does someone’s unconscious reaction to people of a different race, religion or sexuality influence their judgment and behavior? Psychologists and social scientists working within this field do not have a concise answer to explain how implicit bias manifests in everyday life, as it is hard to rule out alternative explanations.
In other words, implicit bias can and does happen, but it is complicated to prove.

“Some biases seem obviously pilogowrong, like treating equally qualified people differently when hiring or promoting,” said Calvin Lai, director of research for Harvard’s Project Implicit. “Every day biases are hard to wrap our heads around because they’re so much more personal, and you can point to other reasons.”

Similarly, structural factors beyond your control might come into play. If most of your friends look like you, or you tend to date people of the same race as you, it could largely be just a reflection of the demographics in your community.

However, research shows that those relationships, along with the interactions and experiences that come from them, are key contributors of implicit biases. These biases begin forming at a young age and are easily reinforced into adulthood through social settings and mass media.

“When you think backwards, what you think is normal is really cultural pressure that pushes you into bias, implicit and conscious,” said sociologist Charles Gallagher, chairman of the Department of Sociology and Criminal Justice at LaSalle University in Philadelphia.

Hanging out with friends that look like you isn’t necessarily a bad thing, especially if they’re nice people! However, research suggests that implicit biases and stereotypes, both positive and negative, are maintained through persistent lack of contact with others beyond your “in-group,” that is people who share certain characteristics.

The good news? We are not helpless to combat implicit bias. It can be mitigated through intervention strategies, starting with recognizing where it might exist in your life and seeking exposure to people and experiences beyond your regular circles.
Psychologists and social scientist who study implicit bias are working to gather more data with the goal of making people more aware of their unconscious decision-making and its consequences.
Harvard’s Project Implicit features a battery of “implicit association tests” where participants can measure levels of implicit bias around certain topics based on the strength of associations between concepts and evaluations.

“The goal of the organization is to educate the public about hidden biases and to provide a ‘virtual laboratory’ for collecting data on the Internet.”

If you’re interested in measuring your levels of implicit bias (almost everyone displays bias in some way, according to the experts!), here are a few tests you can take:
Understanding Prejudice: Implicit Association

Test Look Different: Bias Cleanse

 

References
2015 State of the Science: Implicit Bias Review. (2015). Retrieved from; http://kirwaninstitute.osu.edu/my-product/2015-state-of-the-science-implicit-bias-review/
Blair, I. V., Steiner, J. F., & Havranek, E. P. (2011). Unconscious (Implicit) Bias and Health Disparities: Where Do We Go from Here? The Permanente Journal, 15(2), 71–78.
Grinberg, E. (2015). 4 ways you might display hidden bias every day – CNN.com. Retrieved from; http://www.cnn.com/2015/11/24/living/implicit-bias-tests-feat/
Lebowitz, S., Jul. 17, 2015, 9, 022, & 2. (2015). 3 unconscious biases that affect whether you get hired. Retrieved from; http://www.businessinsider.com/unconscious-biases-in-hiring-decisions-2015-7
Schwarz, A. (2007, May 2). Study of N.B.A. Sees Racial Bias in Calling Fouls. The New York Times. Retrieved from; http://www.nytimes.com/2007/05/02/sports/basketball/02refs.html

Top Techniques: Confocal Microscopy

by Alenka Lovy

What is confocal microscopy?

Reading and thinking about cell biology is very interesting no doubt, but I find that to be able to see biological processes by live microscopy just amplifies the questions at hand so much! Have you ever seen movies of cells dividing? I remember when I first did. It was hard to go from the picture perfect diagrams of the textbook to the real thing, but after a few times of watching the movies I saw the perfect (or not so perfect) progression through all the steps. Maybe it was the timing of it, or just being able to see the tangle of chromosomes trying to line up, and then the sudden division, I found it so breathtaking! Live cell microscopy has been my tool of preference to answer many biological research questions ever since.

Confocal microscopes in particular are powerful because they optically slice through a specimen (even live cells) and allow 3D image reconstruction in up to four different fluorescent channels. Confocals are built to scan point by point through your sample using laser light, and image just one particular plane of focus. This is very different to the standard fluorescent microscope which illuminates and images the entire sample at once, including out-of-focus light. The confocal is used to obtain clearer images of subcellular details that cannot be imaged with the fluorescent microscope and is especially useful for co-localization studies. There are many exciting techniques you can use with the confocal including fluorescence recovery after photobleaching (FRAP) with which you can observe protein mobility and recovery, fluorescence resonance energy transfer (FRET) which can show protein interactions, as well as photoactivation/uncaging studies.


BOX 1: What confocal can do for you (and your mitochondria)

Using a photoactivatable GFP targeted to the mitochondria to measure mitochondrial fusion is a nice demonstration of the precision and quantitation that can be achieved using a confocal. Mitochondria are amazingly motile and networked and look like spaghetti . They also undergo constant fission and fusion, which can be difficult to capture. The top panel in the figure below shows the mitochondrial network (z stack) labeled with TMRE in Hela cells imaged every 15 min for 1 hr. It is impossible to capture which mitochondria are fusing.

red

green

However, if a small portion of the network is photoactivatedand then imaged in z stacks over time, the signal can be monitored over time (bottom panel in the above figure). As the mitochondria fuse, the GFP protein becomes diluted in the larger volume of the network that has not been photoactivated, and the extent of dilution can be quantified and used as a measure of mitochondrial fusion.


What facilities does Tufts have for confocal microscopy and other imaging techniques?

The Tufts Imaging Facility has four confocal microscopes and most are equipped with the standard 405nm, 488nm, 561nm and 633nm laser lines, which is important to know when choosing fluorophores. Using the Fluorescence SpectraViewer online will help you determine if the emission spectra of your fluorophores overlap such that crosstalk between them can be minimized. We have two inverted microscopes equipped for live cell imaging, and two upright microscopes that are usually used for fixed samples and 3D reconstructions. While imaging living cells, you can use an automated focusing mechanism which employs an infrared laser that keeps track of the coverslip, and therefore your sample. If you’ve ever had to adjust the focus yourself over several hours, you know just how powerful this feature is!

The Nikon A1R inverted confocal has a resonant scanner capable of high speed imaging (500 frames/sec at 512×512 pixel resolution) suitable for ion imaging and is being used for calcium imaging in cardiomyocytes. It also comes in handy during very long tiled scans with z-stacks, and although the image quality is slightly sacrificed, depending on the resolution needed, the gain in speed may well be worth it.

The Leica SP8 inverted confocal has a HyD sensitive detector and can be used with very low laser powers allowing longer imaging of easily bleached samples. For example, measuring how quickly a photoactivated GFP spreads within the mitochondrial network every minute over an hour would bleach the signal before all the information was collected on a regular detector compared to a HyD detector.

Another good technique to avoid bleaching in live cell imaging is to use the total internal reflection microscope (TIRFM). On this microscope, you can adjust the angle of laser light with which you illuminate your sample. There is a particular angle at which all the laser light is internally reflected, except for a 100nm evanescent wave. With this you can then image processes close to the membrane, such as receptor insertion/cycling. Very often you can image a little bit deeper than the 100nm, and because the laser is at an angle, you will not bleach your specimen as fast. As opposed to confocal, the TIRF system has a sensitive EMCCD camera, enabling faster imaging (I have been looking at calcium sparks at 50 ms/frame).

The Leica upright microscope has water immersion objectives that have a large working distance and work well for thick cleared samples such as mouse brains or zebrafish embryos.

Finally, in addition to standard fluorescent microscopes, we also have the automated Keyence fluorescence microscope which can scan up to 3 slides and stitch large images together in four channels as well as in brightfield. If large tiled scans are needed, this may be the instrument of choice due to the speed and ease of use.

For more information about the instruments in the Tufts Imaging Facility, please visit our website. If you would like to use an instrument or need help planning an experiment please email me at:

Alenka.Lovy@tufts.edu.

If you’d like to learn more about microscopy in general, the Molecular Expressions Microscopy Primer is a great resource.

GSC holds first advertised open meeting in 3 years

On March 3, 2016, the Sackler Graduate Student Council (GSC) held an advertised open meeting and invited the Sackler student body to attend. While all GSC meetings are open, according to the bylaws, and club/organization leaders attend the first meeting of academic year, this was the first time in 3 years that the GSC meeting was publicly advertised. When asked about the motive behind this action, Michaela Tolman, current GSC President, stated “we serve the students, so we wanted to offer a way in which they could express their opinions while also giving them a flavor of what GSC does and how it is run.” While the turnout was modest, she did mention that it was more than what she had expected.

Traditionally, GSC meetings  mostly comprise of financial updates from the treasurer, different committees (career paths, social, newsletter, etc.) reporting on their previous events and discussing their future plans and setting up action items to be completed before the following meeting. This meeting  followed the same pattern and after the committee updates, the floor was opened up to the non-GSC attendees.

Most of the non-GSC attendees shared that they were curious about the inner workings of the GSC and had either been invited to the meeting by a GSC member to the meeting or attended on their own initiative; some of them were also interested in joining the council the next academic year. Almost all class years and programs were represented in the attendee group.

Given that a major focus of the GSC is to organize and hold events focusing on career building and networking, it was no surprise that most of the suggestions from attendees were focused on that topic. Suggestions were made for events to improve social media networking, seminars on data management and presentation skills and early stage career development, and most emphasis was placed on the interactive nature of the events and their diverse nature. Other suggestions included a consolidation of seminar schedule, especially student talks, across programs and departments, including the hospital seminars.

GSC’s commitment on serving students manifests itself in it’s quick response to the students’ feedback at the meeting. CMP rep Dan Wong, has already put together a google calendar program that allows consolidation of all seminars that are listed on the Sackler calendar and can be easily integrated with an individual’s calendar (here is how to do it).  When asked about the outcome of the meeting, Tolman mentioned “I had no idea what people would bring up – which shows that we always need to seek student input. Some things were helpful for directing our current efforts – career paths heard positive things about diversifying the type of events that they hold while also focusing more on skills. The coordination between programs was discussed, and I am really excited to put into action the student suggestions.” She also hoped that some of the attendees would join the GSC in the future, and that most, if not all, attendees would see GSC as “a fun and an exciting opportunity to take part in”.

Overall, the open meeting seemed to have served its purpose in getting student feedback. The necessity of such a meeting, at least once a year, was echoed by both the GSC President and the attendees; Tolman believes that a town hall style meeting will be more effective in increasing student engagement and getting more input from students as “it would help better direct what we do and better serve the students’ needs”. Attendees who were contacted as a followup of the GSC meeting agreed that this year the GSC has become more interactive and applauded the various efforts GSC has undertaken to integrate students better and become more interactive, such as through The Goods email format, the Instagram account and voting on the location for Relays.

The bylaws of the Sackler GSC clearly show that this organization is for the students and by the students, and therefore, there should be no doubt that increasing student engagement in not only its events, but also its governance should be made a priority. In the past, there have been GSC events where student attendance and engagement have fallen short of expectation, whether it be due to lack of advertising or a distancing of the GSC from the student body it represents. This publicly advertised open meeting is, in my opinion, a definite right step towards the actual fulfillment of this organization’s mission.