April 2016, articles, Community, GSC career events, Mentoring & Outreach

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.

 

April 2016, articles, Techniques

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

April 2016, articles, Community

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”.

April 2016, articles, Community

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

April 2016, Library, Notes from the library

Notes from the Library…Measuring Research Impact: Author Metrics

At some point in your career, you will be asked to demonstrate the impact of your work.  You may be asked to do this for a grant application, progress report or renewal, or on a CV for a job application, promotion, tenure or performance review.  Traditionally, this has meant providing a list of publications you have authored, and perhaps the number of citations that those publications have received.  Alternative methods of demonstrating research impact will be discussed in a later post.

How can I create a list of publications that I have authored?

You can do an author search in any bibliographic database, such as PubMed (see this month’s PubMed tip), Web of Science, or Scopus.  It may be necessary to search more than one database to generate a complete list.  Once you have run the search, you can save the results within the database (for example, send results to the My Bibliography section of My NCBI in PubMed) or export them to a citation manager.

Where can I find how many times my articles have been cited?

Several databases provide the number of times an article has been cited.  Traditionally, Web of Science has been used to obtain citations counts; recently, Scopus and Google Scholar have emerged as alternatives to Web of Science.  Each resource provides a different citation count because each indexes (or, in the case of Google Scholar searches) a different set of journals over a different period of time.  Web of Science remains the best choice for authors with a long publishing history because Scopus indexes articles published from 1996 to the present (although older content is being added).  Google Scholar is a moving target because it “generally reflects the state of the web as it is currently visible to our search robots and the majority of users” (https://scholar.google.com/intl/us/scholar/citations.html – citations).  Regardless of the source that you choose, it is important to always cite that source.

How can I create a citation report in Web of Science or Scopus?

A Web of Science or Scopus citation report provides aggregate statistics for a set of search results.  See the library’s ‘Measuring your Research Impact’ guide for step-by-step instructions on generating a citation report in Web of Science and Scopus.

What is the h-index? 

You may have heard of, or noticed on your citation report, a metric called the h-index.  The h-index is the number of papers (h) in a set of results that have received h or more citations.  For example, an author with an h-index of 10 has 10 articles that have each received 10 or more citations.  This metric is an attempt to measure both quantity (number of publications) and quality (number of citations).  Therefore, it is considered a measure of the cumulative impact of an author’s work.  For a recent discussion of the h-index and other measures of academic impact, see Anne-Wil Harzing’s ‘Reflections on the h-index’: http://www.harzing.com/publications/white-papers/reflections-on-the-h-index.

April 2016, arts & culture, Library, On the Shelf

On the Shelf…

For work…

Essential Science Indicators

Electronic Resource: Essential Science Indicators

Location: Search for ‘Essential Science Indicators’ in Databases search box on the HHSL homepage (http://hirshlibrary.tufts.edu/).

This research analysis tool, integrated with Web of Science, provides performance statistics for authors, journals and articles for 22 subject fields.  Essential Science Indicators can answer questions like: who are the most-cited authors in my field; what journals publish the top papers in my field; what is the average number of citations per article in my field; or what is the minimum number of citations that my article needs to receive to be in the 10% percentile in my field?

And leisure…

All the Light We Cannot See

All the Light We Cannot See, by Anthony Doerr

Location: HHSL Leisure Reading, Sackler, 4th Floor, Fiction D652

Winner of the 2015 Pulitzer Prize for fiction and numerous other awards, this book tells the parallel, and eventually intersecting, stories of a girl in France and a boy in the German army during World War II.

April 2016, Library, PubMed Tip of the Month

PubMed Tip of the Month: Author Search

Go to the Advanced Search Builder by clicking the ‘Advanced’ link under the PubMed search box.

Choose Author from the All Fields drop-down menu (just Author, not Author – Last, Author – Full, or any of the other options). Enter the author’s last name, followed by 1 or 2 initials with no intervening punctuation (for example: Jones EA). If you are unsure about the inclusion of the second initial, then do not include it.

If the author has a common last name, then you probably want to narrow your search by including an affiliation. To do so, choose Affiliation from the All Fields drop-down menu below the boxes where you have entered the author’s name. Enter the name and/or location of the institution with which the author is associated. Affiliation can become complicated if the author has been (or is currently) associated with multiple institutions, or the name of the institution has several possible variations. If the author has an uncommon last name, then first try searching without an affiliation.

Check the results to ensure that they authored by the person in whom you are interested.

If you have searched for your own name, then you can send the results to the My Bibliography section of My NCBI by clicking ‘Send to:’ in the top right corner of the results page.

Author Search in PubMed Advanced Search Builder
Author Search in PubMed Advanced Search Builder
articles, March 2016, Techniques

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.

Library, March 2016, Notes from the library

Notes From the Library…Citation Managers

What is a citation manager?

At their most basic, citation managers are software programs that allow you to store and organize your references, and insert formatted citations and bibliographies into documents.

What citation managers are available?

There are several citation managers available; the library supports EndNote (and EndNote online), Mendeley, RefWorks and Zotero, which are all popular and well-established programs. Other available programs include Papers, Sente and Paperpile.

Which citation manager do you recommend?

It depends! While all citation managers have the same basic features, some citation managers are better for storing and annotating PDFs, working on multiple devices or computers, and collaborating with others. If I had to choose one, then I would recommend EndNote. This robust, widely-used citation manager has a bit of a steeper learning curve but several nice features such as automatically finding full text for references, annotating PDFs on your computer or mobile device, and thousands of citations styles.  If you need help choosing a citation manager, then ask your colleagues what they are using, or ask me (laura.pavlech@tufts.edu).

How can I get a citation manager?

I will focus on the four programs that the library supports: EndNote, Mendeley, RefWorks and Zotero. All of these programs works on both Macs and PCs. An EndNote app is available for iPads; a Mendeley app is available for both Android and iOS devices.

EndNote: Available for installation on Tufts-owned or personal computer for anyone with a primary affiliation of student, faculty or staff in the Tufts White Pages. Bring your laptop to the Tufts Technology Services desk on the 5th floor of Sackler (Monday-Thursday 9AM-6 PM, Friday 9AM-7PM) or call 617-627-3376 for remote installation.

Mendeley: Freely available to anyone. Create account and download at: https://www.mendeley.com/.

RefWorks: Available to Tufts students, faculty and staff. Create account at: https://www.refworks.com/refworks2/default.aspx?r=authentication::init&groupcode=RWTuftsU

Zotero: Freely available to anyone. Create account and download at: https://www.zotero.org/

Library, March 2016, PubMed Tip of the Month

PubMed Tip of the Month: My NCBI

My NCBI is a personalized account for PubMed and other National Center for Biotechnology Information (NCBI) databases, such as Gene and Protein. This account allows you to:

  • Save searches and receive daily, weekly or monthly email alerts when new articles meeting your search criteria become available.
  • Save collections of references; in the My Bibliography section, you can save references to articles that you have authored. Collections, including My Bibliography, can be made publicly available, providing you with a URL to share with colleagues or use in grant applications.
  • Change preferences for how your results are displayed in PubMed, and select favorite filters.
  • Manage compliance with the NIH public access policy in the My Bibliography section.
  • Utilize Science Experts Network Curriculum Vitae (SciENcv) to help you create biosketches for NIH and NSF grants.

To create an NCBI account:

Click the ‘Sign in to NCBI’ link in the top-right hand corner of any PubMed page (or, click here).

Click ‘Register for an NCBI account’ link, or sign in with a 3rd party option, such as Google or eRA Commons (recommended for NIH-funded investigators who do not currently have an NCBI account). Note, you cannot user your Tufts username and password as a 3rd party sign in option.

My NCBI Sign In
My NCBI Sign In