All posts by Kayla Gross

Uncategorized

Five Things to Consider Before Attending a Conference

1 Comment
  1. Make a good poster.

To bring a good poster to a conference, you need to have an actual poster to bring, which means carefully planning when you assemble and send your poster for printing. Leave at least a few days, or even better a week, between printing your poster and the date of your departure or attendance.

Check for any poster guidelines provided by the conference; you don’t want to end up with a poster that doesn’t fit on the presentation board.

Think about how you want your poster to look, in regards to content as well as physical appearance. Find an organizational flow for your information and data that will allow readers and listeners to easily track your project through its various stages. While paper posters are format most researchers use, fabric posters are easily packed into a suitcase, making them a good option for airline travel. 

  1. Choose sessions to attend wisely.

Big or small, conferences have a lot going on. Daily schedules are packed, and with larger conferences, there can be a half-dozen or more sessions happening simultaneously. It’s easy to get overwhelmed, so be thoughtful about the scientific fields or types of research you want to experience while there. Pick a few sessions that are of high interest to you that you absolutely will commit to going to, and be engaged in those sessions: sit in the front, take notes, write down questions and papers to look up later. Aside from those key sessions–and depending on the size of the conference and its offerings–be judicious in how you add to your list so you can get maximum output from all of the input available there.

  1. Plan out a networking strategy.

Conferences can be as much about networking as they are about sharing and learning new science. During poster sessions, socials, career events, dinners, and coffee hours, you might be introduced to dozens of new faces. Figure out ahead of time what you want to get out of the social aspects of the conference beforehand. Do you want to find another lab to collaborate with? Is there a lab you are interested in applying to after graduate school? Do you want to get to know trainees from other institutions? Are there contacts in science-related careers of interest to you that will also be at the conference? Once you have a goal in mind for how you want to network at the conference, scan through the program to pick out events that will help you meet those goals and commit to attending those sessions.

  1. Prepare business cards.

If you meet a potential collaborator or career connection, having a business card to give them could make or break a follow-up after the conference. After all, we’ve all written down someone’s email on a note in our phones and then promptly forgotten about it until we find it again three months later. With a physical card, your information is in a more accessible and memorable format that shows you are both professional and prepared.

  1. Rest, rest, rest.

It is tempting to get wrapped up in the busy nature of conferences, but breaks are key to making it through without feeling completely exhausted by the end. Each day, run out for a quick coffee, go back to your room and take a power nap, or take ten minutes to just listen to some music in a hallway or quiet corner. Even a small pause in the hustle can refresh your brain and make room for even more great science 🙂 

articles, Mentoring & Outreach, October 2018

Coffee & Conversation with Dr. Laverne Melón

3 Comments

Written by Alyssa DeLeoNEUR. Coffee & Conversation is a series of informal chats with women faculty on campus, hosted by Tufts GWiSE. 

Our last Coffee & Conversation of the year featured Dr. Laverne Melón, a post-doctoral fellow in the Maguire lab and a TEACRS scholar. She will joining Wesleyan University as a faculty professor in neuroscience in the Fall. Laverne was born in Trinidad and moved to New York when she was 10 years old. In high school, Laverne helped establish the science club, which she insists was the most poppin’ after school extracurricular at the time, and she knew she wanted to work in research before even knowing what that was. The science club gave her and her peers the chance to support each other in the search for research experiences and ultimately lead her to volunteer in a cancer genetics lab at Columbia University. As she reflects on her first experience in science, she also acknowledges that it was also her first exposure to the sexism and racism that exists in scientific institutions. It’s difficult to turn a blind eye to these situations when all you want to do is put your head down and do the work in front of you. But, she didn’t let this taint her passion for the field and her experiences spoke to her resilience, which would be noted by several scientists later in her career.

Laverne went on to earn a BA in neuroscience at Middlebury College, a MS in Behavioral Neuroscience at Binghamton, and a PhD in Addiction Neuroscience at IUPUI after her lab at Binghamton moved. She lost a Binghamton fellowship in the move and had to teach at IUPUI, which she found frustrating as anyone does when they’re forced to do something. However, Laverne began to enjoy the process and her career path in academia became increasing clear. Laverne has been a post-doc in Jamie Maguire’s lab for the last 4 ½ years studying effects of stress on reproductive health and the role of the GABAergic system in alcohol addiction. As she moved into her post-doctoral years, she was really fueled by a research question which she presented to Jamie along with some data to score her current position. Now, she’s fielding multiple offers for faculty positions and learning to navigate this new part of her career.

As always, we chatted about how early life experiences brought our guests to their current positions, how crucial the role of mentors played in this trajectory, and the vital importance of self-advocacy. But, we kept coming back to this idea of producing good, reproducible science and how that is only possible if the field really cared about the people behind the data. It’s no secret that scientific institutions have not been the best advocates for the health of their workforce. Levecque et al. published a study in May of 2017 reporting one in two PhD students experience psychological distress and 1/3 of graduate students are at risk for a psychiatric disorder. An online survey of graduate students in a recent March 2018 study by Evans et al. reports graduate students are more than six times as likely to experience depression and anxiety compared to the general population. SIX times! It’s exceeding clear that health of scientists across fields and levels are struggling in this environment. This begins by hiring scientists that are more than a good researcher, but are inspired teachers, passionate mentors, and expert managers who are in touch the health of their lab.

As Laverne is beginning the next chapter of her career, she’s considering taking on an administrative position as a director of inclusion and diversity in addition to her faculty appointment. She intends to use her status to implement institutional changes to allow for better science through caring, supporting, and mentoring the next generation of scientists. When Laverne started to work in science, she admitted she tried to assimilate as much as possible, but it gets exhausting. It’s difficult to integrate into establishments and systems that have been hostile to the existence of women and minorities in science while trying to stick it out until you can get to a position to make changes. She’s been able to tap into her mentoring network over the years for support and instructed us to be vulnerable in our insecurities to allow these organic mentorships to grow.

If you’re interested in getting involved with GWiSE, follow us on Twitter @TuftsGWiSE, like us on Facebook, or email us at tuftsbostongwise@tufts.edu. Our next Coffee & Conversation is October 19th, 2018 at 5PM in Jaharis 913.

articles, October 2018

Green Labs: How to be environmentally sustainable in biomedical research

1 Comment

The main responsibility of a biomedical researcher is to produce novel, trustworthy science that will improve human health. We may not be doing enough towards this goal, however, if we consider our research results to be our only impact on the human condition. How we conduct our research is just as critical as the results of our research, especially when it comes to the environmental footprint that research laboratories leave behind on university and medical campuses.

In 2013, Tufts University published a campus-wide report to assist the university in building a sustainable future. Working groups focused on three relevant sustainability areas—energy and water use, waste management, and greenhouse gas emissions—to develop actionable goals for reducing Tufts’ environmental impact. Regarding how laboratories and medical facilities factored into this impact, all working groups came to the same conclusion: “[these spaces were] singled out…as the greatest source of opportunity for increased sustainability across all Tufts campuses due to their large production of waste and heavy use of water and energy.”

Tufts is not the only university facing these issues. Harvard University labs consist of  20% of physical campus space but account for 44% of their energy use, and MIT labs take up less than a quarter of campus space but account for up to two-thirds of their energy use. So, if scientists like to talk the talk when it comes to best practices in advocating for governmental and community support of sustainable practices, how can we commit to similar support within our own institutions?

Many universities, including Tufts, have implemented Green Labs initiatives in order to develop environmentally friendly research laboratories using a classic sustainability framework: reduce, reuse, recycle. Based on resources from Tufts’ Green Labs Initiative and similar programs at other institutions, here are some starting points for making laboratories and research facilities more sustainable.

REDUCE

Energy: Labs can significantly reduce energy usage by maximizing the efficiency of their ultra-low temperature (ULT, or -80°C) freezers, as in one year, a single ULT freezer uses the same amount of energy as an average American household. Frequent de-icing, regular upkeep, and maintained organization all decrease the amount of work and time (and thus energy) required by freezers to decrease temperature to the set point. To encourage these approaches, Tufts joined the International Freezer Challenge in 2017, which “rewards best practices in cold storage management”. Of note, three Sackler labs–the Munger lab, the McGuire lab, and the Bierderer lab–participated. Additionally, a less universally advertised, but possibly more effective, approach to reducing energy usage by ULT freezers is changing their set temperature. The University of Colorado at Boulder has accumulated a significant amount of information demonstrating that maintaining ULT freezers at -80°C may not be necessary, as many sample types are capable of being stored at -70°C without any significant loss of quality. Though seemingly trivial, this ten degree difference has huge implications for lowering energy usage , which also translates to reduced energy costs (Figure 1). By rough estimation, Tufts could save close to $50,000 per year on electricity if all ULT freezers in Jaharis, M&V, Stearns, South Cove, and Arnold were adjusted from -80°C to -70°C.

†Number of ULT freezers was calculated by presuming 5 freezers per floor in Jaharis 6-9 and 10 freezers per floor in Jaharis 3-5. This estimate was extended to the remaining buildings on the Sackler campus.

Figure 1. Yearly energy expenditure & cost savings for ten-degree increase in ULT freezer temperature.

Closing and/or turning off chemical fume hoods when not in use also mitigates electrical expenditure. At the Medford campus, undergraduate student Emma Cusack led a “Shut the Sash” initiative last year in order to reduce energy use and cost. Based on consultations with the Tufts’ Office of Sustainability about her work, it is estimated that lowering sashes of all 123 chemical hoods on the Sackler campus from 18” to 6” when not in use would result in yearly energy expediture savings of around 40,000 kWh and energy cost savings of over $200,000.


Figure 2. Yearly energy expenditure & cost savings for reducing sash height of chemical hoods. 

Lastly, powering down non-essential lab equipment overnight and incorporating timers into power sources are also simple but meaningful methods of lowering energy usage. The latter method is especially helpful to maintain convenience along with energy efficiency, as incubators and dry ovens are shut off overnight but can still be ready-to-use upon arriving in lab, for example, if set to turn on in very early AM.

Water: A traditional autoclave requires 45-50 gallons of water per minute when in use, and this massive usage is due to the need for continuous addition of water for cooling steam condensate before draining into sewers. Equipment like Water-Mizers use real-time monitoring of drain temperature to add water for cooling only when needed, reducing water usage by at least half. Also, being mindful of when sterilization is actually required for equipment and using dishwashing services as an alternative also contributes to lowering water usage.

Within labs, addition of low-flow aerators to faucets and switching vacuum sources for aspirators from faucet-style to vacuum-style can also can significantly reduce water usage. Finally, being conscious of when it is really necessary to use distilled or deionized water, as the process wastes water that does not pass the filtering thresholds, can also contribute to making water usage by labs more efficient.

REUSE

Materials: Styrofoam shipping containers and freezers packs can accumulate quickly in labs, given the frequency at which supplies are ordered and received. However, they are not necessarily easy to get rid of in sustainable ways. Many labs end up reusing some fraction of the styrofoam boxes and freezer packs they receive for experiments, which seems to be the most common and easily practiced alternative to throwing these shipping components away.

RECYCLE

Materials: Another approach for sustainable disposal of styrofoam and freezer packs is recycling them. A handful of life sciences companies do sponsor recycling programs for styrofoam containers, including Sigma-Aldrich, Qiagen, and New England BioLabs (which has run such a program for over thirty years), but most companies do not, given the cost of such programs. Alternatively, for-hire companies specializing in styrofoam recycling can be contracted by universities, but again the associated cost can be a deterrent. Even rarer are return programs for freezer packs, as the combination of contamination concerns and the cost of re-sterilizing seems to discourage their implementation.

The amount of plastic materials that biomedical research labs use are also quite high, though recycling used materials such as pipette tips, serological pipettes, conical tubes, or microcentrifuge tubes is often not convenient or feasible due to biological contamination. However, containers for materials (i.e. cell culture media bottles, pipette tip boxes) can be sterilized and disposed of much more easily. In the case of pipette tip boxes, several companies–such as Fisher Scientific, USA Scientific, Corning, and VWR–do sponsor programs where discarded boxes are collected or received via mail for recycling.

While achieving greener laboratories first requires implementation of sustainable practices like those listed above, the success of such efforts ultimately depends on institutional support and researcher engagement. Even if such resources and programs are offered by companies or research institutions, scientists need to be made clearly aware of their existence to take advantage of them. Accordingly, university- or departmental-level promotion of and encouragement for sustainable practices could substantially increase researcher interest and participation. Implementing reward-based systems, including financial incentives, for labs that ‘go green’ could also help motivate investigators to commit to practicing sustainable science.

In being more conscious of the environmental footprint that biomedical research leaves behind, scientists can clean up our own backyard and stand on firmer ground when encouraging others to do the same.

Thank you to Tina Woolston and Shoshana Blank from the Tufts Office of Sustainability and to Stephen Larson and Josh Foster from Tufts Environmental Health & Safety for providing information and resources on chemical hood numbers, energy usage, and costs.

Resources

Tufts University: http://sustainability.tufts.edu/get-involved/tufts-green-labs-initiative/

http://sites.tufts.edu/tuftsgetsgreen/2017/07/28/the-green-labs-initiative-an-overview/

University of Colorado: https://www.colorado.edu/ecenter/greenlabs

EPA Greenhouse Gas Equivalencies Calculator: https://www.epa.gov/energy/greenhouse-gas-equivalencies-calculator

Laboratory Fume Hood Calculator: http://fumehoodcalculator.lbl.gov/index.php

 

 

articles, Community, Events for Students, September 2018

Career development initiatives, curriculum design, & building networks discussed at Sackler Community Meeting

2 Comments

This past June, around seventy-five graduate students and faculty members joined Dean Dan Jay and Associate Dean Dan Volchok in the DeBlois Auditorium to reflect on the previous year’s progress and endeavors at the Sacker School. Various community leaders briefly presented on topics that reflect the Deans’ new mission of training to career excellence followed by open discussion between all attendees. Following the larger meeting, attendees continued to engage in these topics in smaller groups over lunch to continue pushing these goals forward in the coming year.

Jay opened the meeting by reviewing the results of career development “trial balloons” that the new administration worked towards last year. He celebrated the high interest and positive reactions from trainees for the new short courses, including Introduction to Drug Development (50 attendees), Navigating the Corporate Environment (22 attendees), and the R Programming Workshop (34 attendees). Building on this positive momentum, additional short courses will be offered in the coming year. A ‘science storytelling’ workshop and an entrepreneurship short course have been developed for the fall semester, with a teaching short course planned for the spring. There are also plans to develop the Introduction to Drug Development course into an official Sackler-wide elective for the spring semester. In addition, two career counseling workshops by Sarah Cardozo Duncan will again be offered in the 2018-2019 for students and post-docs who are interested in industry-related careers.

Not all career development endeavours in Sackler last year had such immediate success, however. The initiative to place students who have completed Year 1, Year 2, or their thesis requirements in summer industry internships encountered several difficulties, including reluctance from potential partner companies. That reluctance mainly stemmed from aversion to such a short internship time period (3 months), as several companies in conversation with Sackler administration requested at least a 6-month full-time commitment from students. Meeting attendees generally agreed that this length of time would be difficult for both PIs and students to commit to without serious disruption to research progress. However, there was at least one successful internship negotiation and placement, suggesting that the program may still be developed but not in as broad a manner as originally intended. A case-by-case determination was concluded to be the best approach moving forward, with the requirement for extensive conversations and mutual agreement between student, PI, and hosting company on timeline and degree of commitment being emphasized.

In reiterating his desire to see Sackler become a leader in career training for biomedical graduate students, Jay described his aspiration to develop a tuition-bearing, two-year master’s program in Biomedical Leadership. Matriculating students would have the opportunity to train for various career tracks related to biomedical research, and their curriculum would include current and future career development short courses or electives offered within Sackler. During the group-wide discussion session, the possibility of offering a 4+1-style master’s program in collaboration with the undergraduate branch of Tufts University was put forward and positively received.

Another main topic of the community meeting was the state of graduate research training at Sackler. Opening discussions involved debating the merits of switching from the current program-specific curriculum design to a single core curriculum that all first-year graduate trainees–regardless of program–would take. Across programs, students generally were opposed to a core curriculum in regards to scientific content, emphasizing that most seek a graduate education specifically to specialize in a particular area. They did support the suggestion that any core courses in scientific content should be ‘nanocourses’, instead of full required or elective courses. In contrast, developing a skills-focused core curriculum that included classes such as research methods, quantitative biology & bioinformatics, and statistics seemed to have wide support from both students and faculty.  In addition to curriculum content, the possibility of expanding the MERGE (Medically-Oriented Research in Graduate Education) beyond the Immunology and Molecular Microbiology programs was discussed. The MERGE program trains participants in clinical aspects of their research area during the summer prior to their first graduate year at Sackler. During this time, they are also paired with a clinical mentor who provides them direct contact with patients and clinicians and serves as a thesis committee member during their research training. Given the proximity of Tufts Medical Center, it was advocated for the Sackler School to take advantage of the opportunity to give more PhD students training in regards to the clinical impact of their research. Genetics and Neuroscience were considered as programs which MERGE could expand to, but no specific plans for that expansion were discussed.

Strengthening the Sackler community was also a significant theme of the meeting. During a discussion about building diversity and inclusion at Sackler, students expressed the need for more structured support from the school. They expressed that while student-led initiatives such as SPINES (Students Promoting Inclusive Excellence at Sackler) provide excellent resources and opportunities for underrepresented minority (URM) students, the responsibility of delivering such support should not fall so heavily on the trainees themselves. Through this discussion, it was emphasized that bringing more URM junior faculty–from Tufts or other institutions–to speak at graduate seminars could help build networks for students to rely on. In addition, hosting a greater number of Sackler-wide events during the year, especially during recruitment, could foster a greater sense of community and provide more school-directed opportunities for URM individuals to connect across programs. Another discussion about community building focused on developing stronger alumni networks. The career development short courses were one way in which the Dean’s Office started on this initiative already. Various alumni contributed their expertise and their time to the courses’ development and operation, which was key to their success; this arrangement also provided a structured environment in which students could take the opportunity to develop professional connections with alumni in their career areas of interest. Given the positive outcomes from this year using this approach, there are plans to build on this foundation for similar endeavours in the future. Dean Jay also discussed his efforts over the last year in reaching out to Sackler alumni for fundraising, which he had done in collaboration with Roxanne Beal from the School of Medicine’s Office of Advancement and Alumni Relations. To broaden this effort, faculty were encouraged to reach out to their former trainees, and the group supported the idea of current students reaching out to alumni for an annual fund.

Overall, the morning and lunchtime discussions provided great insight into the past year’s success as well as highlighted what aspects of graduate training at Sackler still need to be strengthened, and the dialogue between students, faculty, and staff generated actionable items for the administration to take on in the coming academic year.

november 2017, Techniques

Top Techniques: Single-Cell RNA Sequencing

1 Comment

Image from Papalexi E & Satija R, Single-cell RNA sequencing to explore immune cell heterogeneity. Nat Rev Immun (2017).

As scientists ask increasingly focused and nuanced questions regarding cellular biology, the technology required to answer such questions must also become more focused and nuanced. In the last decade, we have already seen several significant paradigm shifts in how to process data in a high-throughput manner, especially for genomic and transcriptomic analyses. Microarrays gave way to next-generation sequencing, and now next-generation sequencing has moved past bulk sample analysis and onto a new frontier: single cell RNA sequencing (scRNA-Seq). First published in 2009, this technique has gained increasing traction in the last three years due to increased accessibility and decreased cost.

So, what is scRNA-Seq?

As the name suggests, this technique obtains gene expression profiles of individual cells for analysis, as opposed to comparing averaged gene expression signals between bulk samples of cells.  

When and/or why should I use scRNA-Seq compared to bulk RNA-Seq? What are its advantages and disadvantages?

The ability to examine transcriptional changes between individual cells uniquely allows researchers to define rare cell populations, to identify heterogeneity within cell populations, to investigate cell population dynamics in depth over time, or to interrogate nuances of cell signaling pathways—all at high resolution. The increased specificity and subtlety given by single-cell sequencing data benefits, for example, developmental biologists who seek to elucidate cell lineage dynamics of organ formation and function, or cancer biologists who may be searching for rare stem cell populations within tumor samples.

Practically, scRNA-Seq often requires far less input material than traditional bulk RNA-Seq (~103-104 cells per biological sample, on average). The trade-off for this downsizing advantage, however, is because of the lower input, there is often more noise in the output data that requires additional filtering. Also, as with any rising star high-throughput technique, standardized pipelines for bioinformatics processing of the raw output data are still being finalized and formalized. As the same type of growing pains occurred when bulk RNA-Seq rose to prominence, no doubt a more final consensus will also eventually be reached for scRNA-Seq.

What platforms are used for scRNA-Seq?  

The three most current and common workflows to isolate single cells for sequencing are by microplates, microfluidics, or droplets.

Microplate-based single cell isolation is carried out by laser capture of cells, for example by FACS, into wells of microplates. This approach is useful if there are known surface markers that can be used to separate cell populations of interest. It also provides the opportunity to image the plate and ensure that enough cells were isolated and that it was truly a single cell isolation. Reagents for lysing, reverse transcribing, and preparing libraries are then added to individual wells to prepare samples for sequencing.   

Microfluidics-based single cell isolation consists of a chip with a maze of miniature lanes that contain traps, which each catch a single cell as the bulk cell mixture is flowed through. Once cells are caught within the traps, reagents for each step of the sample preparation process (lysis, reverse transcription, library preparation) are flowed through the chip lanes, pushing the cell contents and subsequent intermediate materials into various chambers for preparation, followed by harvesting the final material for sequencing.

Droplet-based single cell isolation also uses microfluidics but instead of traps it involves encapsulating, within a single droplet of lysis buffer, (1) a single cell and (2) a bead linked to microparticles, which are the reagents necessary for sample preparation. The advantage of this approach is that a barcode can be assigned to the microparticles on each bead, and thus all transcripts from a single cell will be marked with the same barcode. This aspect allows pooling of prepared samples for sequencing (decreasing cost) as the cell-specific barcodes then can be used to map transcripts back to their cell of origin.

The other significant consideration for designing scRNA-Seq experiments is what sequencing method to use. Full-length sequencing provides read coverage of entire transcripts, whereas tag-based sequencing involves capture of only one end of transcripts. While the former approach allows for improved mapping ability and isoform expression analyses, the latter allows for addition of short barcodes (Unique Molecular Identifiers, UMIs) onto transcripts that assist in reducing noise and bias during data processing.    

So, which platform should­ I use?

As with most advanced techniques, determining which platform to use depends on the biological question being asked. A microplate-based platform does not accommodate high throughput analyses but does allow for specificity in what types of cells are being analyzed. So, for example, it would be a good choice for investigating gene expression changes within a rare population of cells. It also does not require particularly specialized equipment (beyond a FACS machine) and thus is a relevant choice for researchers without access to more sophisticated options. Microfluidics-based platforms are capable of more throughput than microplate-based while retaining sensitivity, but they are more expensive. Finally, droplet-based platforms provide the greatest amount of throughput but are not as sensitive. Thus, they are most appropriate for elucidating cell population composition and/or dynamics within complex tissues.

How can my scRNA-Seq data be processed, and is it different than bulk mRNA-Seq data processing?

Performing computational analysis on scRNA-Seq data follows a similar pipeline as bulk RNA-Seq, though there are specific considerations required for scRNA-Seq data processing, especially during later stages of the pipeline. One of the major considerations is significant cell-to-cell discrepancies in expression values for individual genes. This effect occurs because each cell represents a unique sequencing library, which introduces additional technical error that could confound results when comparing cell-specific (and therefore library-specific) results. This effect can be mitigated during data processing by additional normalization and correction steps, which are included in most of the publicly available scRNA-Seq processing pipelines.

Finally, the types of interpretations drawn from scRNA-Seq experiments are also technique-specific and question-dependent. Common analyses of scRNA-Seq data include clustering, psuedotime, and differential expression. While clustering is done with bulk RNA-Seq data, clustering scRNA-Seq data allows for assessing relationships between cell populations at higher resolution. This aspect is advantageous for investigating complex tissues—such as the brain—as well as for identifying rare cell populations. Given the large sizes of scRNA-Seq data sets, performing clustering of scRNA-Seq often requires dimensionality reduction (i.e. PCA or t-SNE) to make the data less noisy as well as easier to visualize. By coupling clustering results along with differential expression data, identifying gene markers for novel or rare populations is made easier. Psuedotime analysis is particularly useful for scRNA-Seq experiments investigating stages of differentiation within a tissue. Using statistical modeling paired with data reflecting a time course (for example, various developmental stages of a tissue), this analytical method tracks the transcriptional evolution of each cell and computationally orders them into a timeline of sorts, thus providing information relevant for determining lineages and differentiation states of cells in greater detail.  

Where can I do scRNA-Seq in Boston?  

Tufts Genomics Core here at Sackler has a Fluidigm C1 machine (microfluidics). Harvard Medical School (HMS) has several options for single-cell sequencing platforms. HMS Biopolymers Core also has a Fluidigm C1 system that is available for use on a for-fee, self-serve basis after training, with reagents purchased and samples prepared by the individual, as well as a 10X machine (droplet). HMS Single-Cell Core has a inDrop machine (droplet) that includes for-fee full service with faculty consultation.

What is the future for scRNA-Seq?

Bettering the way in which samples are processed and data is analyzed is a priority for scRNA-Seq experts. Specifically, ongoing work seeks to improve library preparation and sequencing efficiency. The programs used to process scRNA-Seq data are also still in flux so as to provide better normalization and correction tools for increasingly accurate data. On a larger scale, developing technology to analyze other biological aspects (genomics, epigenomics, transcriptomics) at the single cell level is of high interest, especially when considering how powerful combining these other forms of single-cell analysis with transcriptomics could be for understanding both normal and disease biology.

Resources:

  1. scRNA-Seq software packages: https://github.com/seandavi/awesome-single-cell
  2. Review of bioinformatics and computational aspects of scRNA_Seq: https://www.frontiersin.org/articles/10.3389/fgene.2016.00163/full
  3. Practical technique review: https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-017-0467-4
  4. Start-to-finish detailed instructions on scRNA-Seq: https://hemberg-lab.github.io/scRNA.seq.course/biological-analysis.html
articles, September 2017

New Sackler leadership envisions training to career excellence

1 Comment

The beginning of this academic year has seen a shift in the leadership of the Sackler school with the retirement of both the Dean & the Associate Dean. Dr. Naomi Rosenberg’s decision to retire from her role as the Dean of Sackler after 13 years of dedicated service was received with a mixture of surprise and trepidation, which was compounded by Associate Dean Kathryn Lange’s retirement decision around the same time. The dynamic duo left large shoes to fill and the search committee spent the summer choosing candidates who would have the school and its constituents’ best interests in mind. To that end, Daniel Jay, Ph.D., a faculty member of the Developmental, Chemical & Molecular Biology department, and Daniel Volchok, Ed.D., previously the Assistant Dean for Graduate Student Life at Northeastern University, were chosen to fill the positions of the Dean and Associate Dean, respectively. Both of these individuals bring their extensive experiences to the table. Dean Jay has mentored numerous graduate students and has served as the post-doc officer for the school prior to his appointment as the Dean, and Assoc. Dean Volchok has worked with both undergraduates and graduate students across multiple disciplines that range from medical schools to business schools.

For Dean Jay, a fortuitously timed conference on graduate education solidified his commitment to throw his hat in the ring, while Assoc. Dean Volchok found that beginning his position simultaneously with a new Dean was a wonderful opportunity to build a fresh vision for Sackler from the ground up. Aside from similar serendipitous timing, Jay and Volchok also developed convergent objectives for how to keep Sackler and its associated graduate programs a competitive academic institution. Of particular interest regarding these new goals is that they grew directly out of interactions with students.

“In my interview, with the students I met with, they all talked about career,” Volchok recalled. “It was very important to the students. It turned out they were right…career focus is part of the life here.”

Jay states that their new mission for Sackler is one of “training to career excellence”, which encourages high distinction not only at the bench for students, but also in less traditionally academic contexts, such as in the boardroom or at the news desk. “The reason for that,” Jay explained, “is that 80% of our trainees go on to careers beyond academia…and we need to train all of those individuals in addition to the small number that do go on in academia to compete, to excel, and to lead in areas of whatever their chosen career passion.”

Both Jay and Volchok believe that trainees are the key to Sackler’s success. To highlight the importance of student leadership, Jay mentions that “extracurricular programs, that didn’t exist 10 years ago, were developed by student leadership such as the GSC [Graduate Student Council], TBBC [Tufts Biomedical Business Club] and the PDA [Postdoctoral Association].” They both want to see this trend to continue as they would like students to take ownership of their career choices and approach the Dean’s office with their needs and wants to ensure their success. Jay believes that “we will be stronger and better if we are willing to change with the times to provide what students require for success.” He is also less concerned that faculty may not be on board with non-traditional career choices. He believes that most faculty are not opposed to career choices outside of academia, and he stresses that research excellence is still the first priority for any trainee at the Sackler school and will not be compromised

In his twenty years at Tufts, Jay has watched, as well as aided, the trainee community forge extracurricular programs and initiatives to fulfill these alternative training needs, despite, and more aptly because of, the shortage of accessible resources. To build upon this foundation, this fall semester the Dean’s office launched two new trial initiatives: a drug development short course, taught by alumnus Stefan Gross, and career counseling services provided by Sarah Duncan. In addition, Volchok is currently working on developing a business skills course based on his experience in Northeastern’s business school; such action speaks to the fresh perspectives he brings to Sackler through his extensive and varied educational and administrative experience. While this type of career training will remain supplemental in the short-term, they plan to eventually incorporate such training directly into the infrastructure of Sackler. This integration will run the gamut from admissions to available curriculum, such as proposed course offerings focused on business or transferable skills (eg – team building, project management, etc.), school-facilitated industry internships that are integrated into a student’s research plan, and possibly a two-year biomedical Masters program that would incorporate training in both research and non-traditional science career development.

The majority of these programs will be accessible not just for graduate students but also for Tufts postdocs as well. Jay’s role as the post-doc officer for the school has made him very much aware of the bottleneck effect of the current academic job crisis that these postdocs face. Therefore, he has stressed that programs be made open to the whole Sackler community whenever possible. He also proudly mentions the success of the PDA, which organized around 70 events last year, and affirms his faith in trainee leaders to build career-related programs. Unfortunately, industry internships will not be open to postdocs, but Jay hopes to work with industry contacts to improve that situation.

The success of these programs and the new vision, according to Jay, will be evaluated by whether “graduates have an easier time finding their first job.” He mentions that he developed this milestone after his conversations with alumni who wished they had learned particular skills before entering the job market. In these conversations, he also discussed building more formal engagement between the alumni and the school, such as the possibility of alumni acting as adjunct professors to teach aforementioned short courses and the development of a biomedical research interest group. He affirms that he has had a positive reaction from the alumni who have also expressed interest in hosting/organizing events. He also mentions that alumni would definitely be a part of the new branding strategy now that the Dean’s office has developed its new mission. As a key component to executing these varied goals, Jay and Volchok have also established and seeded a new Sackler career development fund, dedicated to financing the programming to come out of this new mission.

Jay and Volchok aim to use their first year to launch programs that would serve as “trial balloons.” The school is “small, so [it is] easy to make changes”, according to latter, and therefore, they would like to test out which programs can be expanded upon in the long term. “This year will test the viability and utility of these short courses that can be used to build upon for longer term goals, and student engagement and participation will be crucial to seeing these initiatives succeed,” Jay elaborated. This last point seems to be critical to the new administration, as “feet on the ground”, as Jay put it, will be the litmus test for whether these initiatives continue. Both seemed confident that the students will indeed engage, given how proactive the trainee community has been about this topic in the past, and are ready and willing to listen to individual feedback.

“We’re of the size that we can make sure students are successful,” Volchok observed. “We can work with individual students when we need to. Students can feel like part of the community and not just a number.”

While a small student body has organizational advantages and new approaches can be tested easily without much bureaucratic repercussions, there are also disadvantages. The current funding climate, along with the fact that Sackler is surrounded by heavyweight schools with similar programs, has led to a dwindling number of students recruited to our programs every year. In the light of such events, concerns regarding the continuity of Sackler as a successful graduate school are bound to rise. However, both Jay and Volchok believe that their new mission of a strong emphasis on career development will help Sackler stand out amongst the other schools in the area.

“I view this as our route to success…how do we define ourselves in a very competitive environment,” Jay said. “If we dedicate ourselves wholeheartedly to this mission, we would, in some ways, distinguish ourselves so that we are competitive, so that a student may choose us because they seek this path toward career excellence. We have to find a way to be relevant…I think the combination of being in Boston, of being small and mobile–if we can do it, we set the standard for the rest of the country. So that is exciting to me, and that’s making a difference, and this is why I’ve taken this job.”

Besides the strong emphasis on career development, the Dean’s office’s new mission also prioritizes community building both in and outside of Tufts. Jay mentions a great advantage that Sackler has by being surrounded by Medical, Dental and Nutrition schools, and being in the same university as a Veterinary school–all opening doors to an influx of opportunities for trainees and faculty to design their studies that could result in more collaboration within the school. As an example, he cites the Clinical & Translational Science Institute (CTSI) and their intentions of working more with the Sackler Basic Science programs (CTSI currently offers drop-in hours for statistics consultation and also offers a course on biostats, both of which are open to Sackler trainees). Jay is also looking forward to hearing individual programs’ changes to curriculum based on discussions between students and faculty mentors (CMDB is offering a bioinformatics class to its students after it was brought up in the program retreat). Additionally, Jay hopes to reach out to industry as well for more collaboration on various fronts.

Jay and Volchok are also tuned in to the social needs of the community to protect its members while reaching outside of their bubble. They are both advocates of the new student club Scientists Promoting Inclusive Excellence @ Sackler (SPINES), and stressed “increased awareness of diversity and inclusion” and building a tolerant community. In an effort to increase student engagement, Volchok has revised The Goods–a weekly digest of news, opportunities and events both on and off campus–delivered to the school community. He believes that “students have a good voice here” and are great resources on how the school and its environment can be improved. Both Jay and Volchok mentioned the need for more community outreach into middle schools, both in the Chinatown communities and the African-American communities in Roxbury. They would like the students to help with organizing and mentoring in these communities.

Of course, most of these ideas are still in the very early stages. “We’re at the very beginning of all this,” Jay said with a laugh. Even so, they seem to be off to a good start, as Jay and Volchok spent their first few weeks listening to the needs of the community before shaping their mission. Jay admits “…the level of concern and frustration of career path thing is here,” an issue frequently brought up by students in the past. Jay and Volchok are committed to listening to the needs of the trainees and helping them as much they can, but they also want the students to take ownership of their own career paths by being proactive. When asked what the students can do to help the Dean’s office, Volchok expresses his eagerness to work with students to improve their experience at Sackler. “Be open and honest with us. Come and tell us when things are going well. Come and tell us when things are not going well. If you have ideas and things we can do differently, let us know.”

articles, Events for Students, September 2017

An exciting new group, NEGWiSE, kicked off this summer with an Inaugural Retreat connecting New England area graduate women in science and engineering

by Siobhan McRee & Heather Tanner

There was an excited tension in the humid halls of Boston University the morning of August 19th, where women from eight institutions across New England were finally coming together under one roof. For months leading up to this day, representatives from each school spent many a late-night brainstorming, planning, and organizing, not just the Inaugural Retreat they were attending today, but the genesis of a new organization whose mission would be to unite, diversify, and advocate for women in science and engineering throughout New England. They had just founded NEGWiSE: New England Graduate Women in Science and Engineering.

The retreat kicked off with the keynote speaker: local entrepreneur, founder, and CEO of Seeding labs, Dr. Nina Dudnik. Her nonprofit company brings scientific equipment and training to underserved areas worldwide, and the theme of her talk was collective action. As she spoke, she acknowledged that tens of thousands of protesters were currently marching on the Boston Common to protest racism and hate speech, and many in the audience had cut their marches short to hear her speak. Protest signs littered the aisles as Nina pointed out that by taking the time to support fellow women here and now, when there were other pressing and important issues, strongly demonstrated the passion and dedication of everyone in the room. Continuing to echo the national conversation, Nina emphasized that the time for talking is over, and she urged, to many a nodding head, now we must act.  

Nina talked about her time as a graduate student at Harvard Medical School, where she overcame extreme gender imbalances to find mentors and advocates, and ultimately changed the demographics of her department to hire more women. She spoke of how we as women in science must work harder, be more productive, and walk a fine line to be just the right amount of outspoken but likable – feminine but firm. She said that often we, as women, do this with an apologetic meekness that we must shirk to accept full ownership of our accomplishments. Her advice: practice saying the words “My name is…and I am an expert in…”  because this is something we consistently feel shy about, regardless of our achievements or awards. But we can help each other do this too. Nina encouraged us to amplify each other’s voices; whether in meetings, in lab, or online, me must give and receive credit. We must also repeat, reinforce, and validate other women’s viewpoints so their voice, and our collective voices, can be heard. We can build an ‘old girl’s network’ of our own. This is a kind of power we can harness to act on, to affect change, and keep improving.

Nina reminded us that we as women are already working overtime; here we are choosing to spend our Saturday, not on the couch watching TV, but actively working to both question and improve the status quo, all the while standing in solidarity with other women. But as a new group, Nina stressed, it is important we distinguish ourselves, to find a niche among the multitude of women’s groups in the Boston area. As her keynote wrapped up, the room was uplifted with a common hope and strength. Nina put words to the thoughts we all had- that together we have the resources not just to talk but to act, and facilitate important and sustainable change.

Building off the groundwork laid by Nina, the next part of the retreat featured short presentations from each school about their GWiSE groups, where representatives from Tufts, Boston University, MIT, Northeastern, Harvard, Brown, Boston College, and Dartmouth all talked briefly about their strengths and resources, and how they could benefit from a consortium like NEGWiSE. While Tufts does not have a dedicated GWiSE group (yet!), the Tufts Mentoring Circles stood in to represent Tufts, and will also be supporting the development of a Tufts GWiSE group that’s currently in the making.

The bulk of the afternoon was dedicated to several “Breakout Sessions.” These focused discussions were brainstorming sessions on topics such as the organizational structure of NEGWiSE, the role of men, increasing diversity, outreach, and advocacy. Tufts’ own Dr. Ayanna Thomas, professor of Psychology, led the diversity discussion to brainstorm how NEGWiSE could facilitate enhancing diversity, both regarding incoming graduate student demographics and within high level graduate education positions. Likewise, discussion was held about how other GWiSE groups at other universities can help Universities such as Tufts to create their own internal GWiSE group.

However, one Breakout session that received a lot of traction was Advocacy. Attendees, added to the momentum started by Nina’s keynote speech through eager discussion of action items affecting graduate students and consideration on how NEGWiSE could implement change. Several issues rose to the top as important within the STEM graduate community, including parental leave policies, mental health, domestic violence, and student/advisor dynamics. In fact, NEGWiSE decided to take on resource gathering about parental leave policies for comparison across universities, with the goal of proposing a standard policy for graduate student parental leave that can be proposed directly to each administration. This timely issue is the first action item that NEGWiSE will be tackling, but it will not be the last. Through the breakout sessions, the mission of NEGWiSE was refined to include graduate student advocacy as a central tenant, especially for issues relating to women in STEM. It was strongly felt that NEGWiSE will distinguish itself among Boston area groups in this way, while also best serving the needs of multiple universities across New England.

But the retreat was not simply all work and no play; after the brainstorming was over, the fun began! Moving from the classrooms of BU to the BU Beach, attendees met and networked with each other over delicious BBQ. A scavenger hunt encouraged people to talk to each other. Attendees needed to find a person who fit each condition from a list. For instance, items included who had run a marathon or who likes Dunkin Donuts better than Starbucks. The first few people to find answers to all those questions won some NEGWiSE swag. A fun photo booth with props got everyone laughing, while a DJ spun tunes, and a Facebook friending frenzy ensued.

The Inaugural retreat introduced the framework and mission of NEGWiSE, a new group to connect, support, and advocate for graduate women in science and engineering. Soon the NEGWISE will hold their own elections for this year’s committee which will follow with many more activities which will be announced at Tufts. Likewise, the Medford and the downtown campus are negotiating our own GWiSE group. If you want to get involved with the Tufts GWiSE group that is forming and will partner and collaborate with NEGWiSE, please contact tuftsgwise@gmail.com.  Also, you can follow NEGWiSE on twitter @NE_GWISE or on Facebook at New England GWiSE

articles, Library, September 2017

Library Roundup: A Review of Helpful Links, Tips, & Resources

Every month, librarian Laura Pavlech from the Hirsch Health Sciences Library helpfully provides us with invaluable tips and reminders about resources that are available to the graduate student population to help with their research and other academic needs. 

In appreciation for all of her hard work this past year, here is a look back at what she assembled for our use:

NOTES FROM THE LIBRARY

PUBMED TIP OF THE MONTH

Thanks again to Laura for assembling these wonderful aids!

 

Community, Events for Students, Mentoring & Outreach

New England Graduate Women in Science & Engineering Retreat, August 19th

NE GWiSE Inaugural Retreat!

New England Graduate Women in Science and Engineering (“N-E-G-wise”) is a new alliance between groups of graduate women in STEM from universities in Boston and across New England. We’re joining forces to address the issues facing graduate women in STEM. Join us for our first event, the NE GWiSE Inaugural Retreat, this summer! Details can be found below or at our website, https://negwise.wordpress.com .

Description: Come join us at NE GWiSE’s Inaugural Retreat- a day of connecting graduate women from different universities and collaborating to help make NE GWiSE an organization that can effectively address the issues we face and create change within our community.

We will start off the day being inspired by our opening keynote speaker (TBD). Next, we will have introductions by partner GWISE groups and breakout sessions to discuss how NE GWiSE will function. Finally, we’ll end the day with a scavenger hunt and BBQ social! This is a great opportunity to meet graduate women from different departments and universities, share best practices and recurring issues, and foster collaborations and friendships across the region. We hope to see you there!

Registration closes August 16th at 5pm so sign up now!

Date: Saturday, August 19th, 2017

Time: Registration is 12-1 pm, Opening Keynote starts at 1 pm, Event goes until ~7 pm

Location: BU College of Graduate Arts and Sciences and BU Beach

Coffee and snacks will be served throughout the event. Dress is casual.

 

 

April 2017, articles, Events for Students

GSC Committee & Club Updates: April 2017

Tufts Biomedical Business Club (TBBC)

from Aaron BernsteinCMP

Upcoming Events

TBBC Case Study Group: Mondays – 5-7PM, Jaharis 508

Practice solving cases, gain insight and tips, and learn more about the field of consulting.

TBBC Tufts Biomedical Alumni Speed Networking Night: Th Apr 13 — 6-8PM, Sackler 114

TBBC, in collaboration with the Office of Alumni Relations will be hosting a speed networking night! Meet fellow students and Tufts alumni who are working in the biomedical field from across all of Tufts campuses and programs, including Sackler, Fletcher, Medical, Dental, Nutrition, and the Gordon Institute. Mingle with old friends and new. We look forward to seeing you! Food and drinks will be served at this facilitated networking event.

TBBC Biotech BUZZ with Lily Ting: F Apr 14 — 9AM, M&V Lobby (Stearns 108)

Dr. Lily Ting is a life scientist and entrepreneur with 12 years of experience in academia and industry. Lily received her PhD from New South Wales University in Sydney and a post doc in the Gygi Lab at Harvard Medical School. After her experience leading projects in the academic sphere, Lily worked in a business development role at Athletigen and is now an Associate at PureTech Health. PureTech is a venture creation firm focused on bringing innovative solutions to the fields of neuroscience, immunology, and gastrointestinal diseases. She is also an avid dragon boat racer and just won gold, silver, and bronze in Puerto Rico!

TBBC Consulting Seminar Series: ClearView Heathcare Partners: Tu Apr 18 — 5-6:30PM, Sackler 507

Representatives from ClearView Healthcare Partners will speak to students about consulting and ClearView’s Connect to ClearView program for advanced degree candidates. 

TBBC, the Sackler Dean’s Office, GSC “Sackler Speaks” Flash Talk Competition: M Apr 24 — 5PM, Sackler 114

A well-developed flash talk is an effective tool to quickly and easily communicate your work to others. These take time to develop and usually evolve over a series of iterations. Sackler students will have a chance to give their scientific flash talks before a judging panel and other students. All presenters will receive helpful feedback and compete for nice prizes. This will be a low-key, fun event with appetizers and beer, and a chance to network with other students and professionals.

Recent Events

TBBC Biotech Buzz with Joel Batson, PhD, of RA Capital

F Feb 24: TBBC hosted Joel Batson, Science Project Manager at RA Capital. Joel introduced students to a new web-based tool he is developing and offered students the opportunity to collaborate with him and his team.

TBBC Career Seminar: Teresa Broering, Director of R&D, Affinivax

Tu Apr 4: Teresa Broering, current Director of R&D at Affinivax, a Cambridage, MA-based company developing a next generation approach in vaccine technologies, and former Director of Immunology at AbVitro as well as Senior Director of Product Discovery at MassBiologics, joined us for a discussion of her career path and her current role with Affinivax, and the current state of the biotech industry.