Thursday, July 20, 2017

How to Make the Most Out of Your Lab’s Move

“The lab is moving!” I must confess, when I heard these words from my mentor about a year and a half ago, my heart dropped. Lab relocation experiences are some of the worst horror stories that you hear from fellow researchers: precious samples lost, mouse colonies never recovered, months spent re-establishing protocols. Moreover, it also meant I would have to leave San Francisco, a beautiful city that I loved to live in, and where I found many friends. Being a scientist often means not having much choice of geographic location of your work. The choice of a particular subject or even broad field usually requires a move to a new city, or even a new country. Moving with the lab means making this choice again – do I leave my project and all the progress behind, or do I accept the delay in my research and go ahead. Now, two months after our move to New York, I would like to reflect on my experiences and that of my fellow lab members on our cross-country relocation from the trainee perspective.

Be ready before you have to be ready. The process for an established PI to change institutions is a long process that could take months or even years, so when you are applying for a PhD/postdoc position, you could simply ask your potential mentor whether he/she is considering changing institutions in the near future. Moreover, this process doesn’t happen in a vacuum – so you are likely to hear from other people in the field that a certain person is considering relocation.

Make your choice early. I guess, the best advice I got from my friends in science was to decide early. Whether one settles on joining the lab on a journey or decides to stay in a new lab, or even move to an alternative career, the quicker you make this choice the easier it will be for both you and your mentor. If you decide to not to move, it will give you enough time to wrap up your things and possibly transfer them to someone new. If you choose to go with your mentor, it would let you focus on things that need to be accomplished while you still have your reagents, equipment and safety of your old research isle. Which brings me to the next point…

Try to accomplish as much as possible before the move. While the last few months at UCSF were extremely intense, my colleagues and I got a lot done. I wouldn’t want to keep such an intense work tempo forever, but I managed to get a number of big experiments completed.

Make time to learn about your new institute and your new city (or maybe a new country?). When choosing the location for my postdoc, I spent a great deal of time learning about the cities where I might eventually live so I could make an informed decision about my quality of life during my postdoc. And, while there is not much time to explore a new place when you are rushing to finish your last experiments, it is important to do similar research before relocation. Coming from the Netherlands where I did my graduate research, I was absolutely clueless that different American states have different levels of taxation, and that New York City imposes an extra tax. Moreover, medical coverage and other work benefits differ dramatically among academic institutions. Getting this information can definitely help in having informed negotiations with your boss as well.

Prepare for a disaster scenario. The scary lab-move stories are there for a reason. It is inevitable that something will go wrong. When we were packing our last boxes, my mentor told me to consider that everything could be lost. Putting rolls of bubble wrap around the slides, and placing each box of eppendorph tubes in its own ziplock bag are real precautions, not exaggerated scenarios just to tell a good story. Apparently, our -20°C freezer broke somewhere mid-country, and thankfully the moving company had a reserve freezer plugged in for exactly this kind of situation. Two months in, we are still discovering that some reagent boxes are nowhere to be found. So if there is a crucial experiment needed for the paper, it is better to do it before moving.

Use the downtime to write or learn a new skill. As there will be a period of several weeks for the shipping of equipment/reagents/mice and overall re-establishment of lab normalcy, it is a great opportunity to use this downtime for writing or taking courses that you had never found time for in the past. Our reintegration in New York happened surprisingly quickly (I did my first experiment one week after the move, although finding things took a while), but the majority of my friends experienced gaps in their research.

Enjoy expanding your network and meeting new people. As our lab just moved, people in our new institute are very excited to have my mentor on campus. Accordingly, great students want to rotate or do internships in the lab, and it is easier to approach people with questions. I am also trying to see our relocation as a “two for the price of one” scenario. One of the exciting aspects of the move is the ability to experience two different research environments within one postdoc project. While I understand that I was lucky to move between two great cities and universities, I believe being exposed to a new scientific community helps you build scientific resilience.

Get to know how to start a lab. Re-starting a lab at a new institute is a lot like starting a lab, which is a very useful experience for those wanting to run their own group after completion of a postdoc. There are so many additional aspects to starting a lab: writing a new animal protocol and re-establishing a new inventory of all of your chemicals and equipment, to name just two. The lab move gives you an opportunity to see what it takes. I always took for granted some of the shared equipment we had in California, and not having it immediately available makes you understand how many little things you need to take care of as a group leader. In Dutch, the problems associated with starting something new are called kinderziektes – children’s diseases. And I hope that going through these diseases now will help me to acquire my immunity if I ever lead a research group of my own.

Moving with a lab is an undeniably difficult and stressful period. However, having survived it, I view it as a great learning opportunity that will help me in the future. While our settling in at Columbia University is far from complete, I have enjoyed this new opportunity. And, last by not least, I scored a new set of pipettes!







Evgenia Verovskaya
ISEH Publications Committee Member

Post-doctoral Fellow
Passegué Lab
Columbia University Medical Center
New York, NY, USA

 



Thursday, July 6, 2017

When people can…

As long as I can remember, there were people marching on the streets, either protesting or celebrating or even supporting the topic of the manifestation. It always fascinated me how powerful people can be, when they come together. In cases of manipulation of the public opinion this is of course not good. However, many times this can influence things in a positive way. Coming from a country like Greece, I have to admit that it was fairly frequent for me to see people getting together on the streets for a variety of reasons. Then, when I moved myself and my life to Boston, these events happened less frequently. I remember that I joined a protest in Boston once (although maybe this is not the right time to admit such a thing). It was about the Gulf war and people wanting their children to come back home. The subject of the protest was noble, however only a few people participated. Thus, it was to my great surprise and satisfaction when on April 22nd, 2017 the March for Science was organized, coinciding with Earth Day. A great symbolism could be seen in this coincidence…

The March for Science began hastily in January 2017 with only a few people. However, on April 22nd thousands of people around the world went out on the streets to show their support and simultaneously celebrate science… and life. People in more than 360 different cities on the six different continents were out there, on the same day, at the same time. I have to admit that I am not so knowledgeable about the history of these types of events. I have no idea if something like this has happened before. According to an article by Chris Mooney on April 22nd in the Washington Post*, this event was “pretty unprecedented”; individual scientists usually have strong opinions, but hardly was there before a movement concerning science that attracted so many people. There are very few causes that can actually unite and bring together many people and we all managed to make science one of them. 

In my point of view, this is very important mainly because such movements also have a political meaning. Especially in the present times with the terrorist attacks and the huge wave of refugees, people have become afraid. This fear has many political consequences, as can be observed by the rise of radical left and right parties in many different countries. Nations have become more nationalistic and less open to global communication. It seems like most of the progress we have made as humanity since World War II, is suddenly disappearing and we quickly go back to where we started. That is why a gathering of people brought together by Science, happening at this present time, is a historical moment.

To better understand the importance of this happening, it is crucial to remember some of the goals of the March for Science. To give an idea of what this was about, in my eyes, I selected a few goals to discuss.  This manifestation was just as much a celebration, an encouragement, a support as well as a protest. It was a celebration of “passion for science”, and the “many ways science serves our communities and our world”; an encouragement for “public to value science”, but also for scientists to “listen and reach out to the communities”. It was a support for education and well being, since “science teaches people to think critically, ask questions and evaluate the truth based on the weight of evidence”. And, it was a protest against “policies that ignore scientific evidence” and characterize “science as a partisan issue”. (The goals can also be read on the March for Science website (https://satellites.marchforscience.com/) and their Facebook page (https://www.facebook.com/pg/marchforscience/posts/?ref=page_internal).

All these reasons and many more made the March for Science a day to remember. A day on which Science came closer to the people and a day on which people envisioned scientists as one of them. Undoubtedly, no one knows if there will be any direct outcome as a result of the March for Science. However, without doubt many people went to bed a bit happier that day, with a sense of fulfillment that is only given when fighting together for a common cause. We should thus remember this day and repeat the manifestation again when needed. Because people can…

*https://www.washingtonpost.com/news/energy-environment/wp/2017/04/22/historians-say-the-march-for-science-is-pretty-unprecedented/?utm_term=.8f2cf3e651bb



Eirini Trompouki, PhD
ISEH Publications Committee Member
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51, 79108
Freiburg, Germany

http://www.ie-freiburg.mpg.de/trompouki

Thursday, June 29, 2017

Science in the Time of Google and Smartphones

Today, we do business, communicate and thrive online. Smartphones have made the use of the internet affordable, quick and easily accessible. In a decade (if we consider the first iPhone launched in 2007), almost 9 out of 10 people in South Korea (the country with most users) and 7 out of 10 Americans now have a smartphone. How has the internet and the use of smartphones impacted the way we do science?

We use smartphones daily and have them on 24/7. We all have used the services of a technology company; however, the scientific community has not fully benefited from its use as other areas like business, marketing, music and television. But is there something we can do to increase our productivity or even better our science using the models of technology companies?

In order to get more perspective on this topic, I interviewed Vince Garcia, VP Travel & Lifestyle Services from American Express (AMEX), to get a corporate vision of this new “Google era” and smartphones.

How has business evolved with the use of Internet?

Vince commented, “There are several ways business has evolved. Social networking has enabled companies to interact directly with customers and engage with them in ways that were not previously possible. Apps have made it easier to interact with companies, through e-commerce, customer service, and loyalty. Mobile market research sent out by companies is now more readily answered via mobile-friendly surveys, promoting brand engagement. Geolocation enabled smartphones to provide for a greater degree of local personalization, GPS directions, and on-demand deals.”

What are the lessons to be learned from e-commerce and young entrepreneurs?


According to Vince Garcia, there are three lessons to be learned from this “Google Era”,

1.- “Creativity and Innovation”
“The key to the success of these new ventures is driven by creativity and innovation that disrupts the status quo and is first to market.” Google, for example, has different “out of the box” strategies to promote it.

Google Cafés: places that encourage the interaction between employees from different teams, where they can engage in conversations about work in a “relaxed” environment. Does your seminar room look something like this?

Google Conversations: weekly meetings where employees can talk and ask questions directly to the company’s leader.

Google 20%: a strategy to work 20% of your time on an idea that interests you but that is not your project. Most of students and postdocs work several years on one or two projects, but what would happen, if they can spend 20% or 10% of their time helping on projects from other lab members, or even from other labs?

2.- “It does not have to be perfect at launch”
“An online product does not have to perfect to launch, but has the stickiness to stay relevant and gain followership as it continues to improve and work out the bugs.” I am not suggesting publishing unfinished papers, but this statement got me thinking about post-publication peer reviewing, “that calls for continuous moderation of the published research” (
http://about.scienceopen.com/what-is-post-publication-peer-review/).

3.- “Investors know that most of the business ideas could fail”
“50% of online business survive past 5 years”, however, new startups are being created each day, so failures are part of the investment. Before Travis Kalanick (Uber’s CEO) revolutionized the transportation industry, he had two start-up failures. In science, there is almost no tolerance for failures, there is no room for negative results. Imagine a research center with a 50% successful rate or a researcher with two failed grants. I am not advocating to support bad ideas, but I think we have a bias towards the previous success of a researcher. Can we trust in a scientist with previous unsuccessful grants?  Our fear to fail is an impediment to submit risky, but innovative projects.


Publications, grants, lab managing, supplies and collaboration are areas that we can improve in science. We need innovation and creativity, and new avenues that can help close the gaps between leader groups, new investigators, and under-represented groups. Technology start-ups succeed in changing the way we do business, we listen to music and live our lives. I think is time that we see a change in the way we do science.

Acknowledgments
I want to thank Vince Garcia for his time spent on helping me with this blog, and Eirini Trompouki, PhD and Peter van Galen, PhD for their edits and comments.



Eugenia (Kena) Flores-Figueroa, PhD
ISEH Publications Committee Member

Oncological Research Unit at the
Mexican Institute of Social Health (IMSS)
Mexico City, Mexico



Thursday, June 15, 2017

Making the Leap, Part 4: Addressing the Two-body Problem

All of us in the sciences have heard about the "two-body problem," a term often used to describe situations in which both life-partners or spouses are simultaneously seeking equivalent academic positions (i.e., faculty positions). How such couples can go about addressing this issue and gain employment for themselves is worthy of more than a single blog entry. A common variant to this situation is a dual-career couple where the spouse or partner works in an entirely different field. Depending on what the other individual, sometimes referred to as a "trailing spouse" does for their career (I'm personally not a fan of that term as it implies an inequality in the decision making between the employee and their partner), the ability of an institution to facilitate that person's employment varies widely. Frankly, the ability of an institution to facilitate employment for the partner can vary greatly regardless of the partner's field. This is based on the formal or informal resources an institution possesses to assist dual-career couples. In this post, I'll discuss some of the experiences my wife Bridget (she is a pediatric speech and language pathologist who works in a hospital setting) and I had during my faculty recruitment process, and provide some broader insights and guidelines on how to approach this version of the two-body problem, based on subsequent discussions I've had with other faculty and other recruits.

During my interview process, Bridget and I encountered a variety of institutional programs geared toward dual-career couples. On one side of the spectrum was the absence of any defined institutional program for facilitating spousal/partner hires whatsoever. In two of these cases, the faculty members and stakeholders in charge used (or tried to create) informal connections to circulate Bridget's resume to the children's hospital associated with the institution. Importantly, Bridget also did her due diligence; she used her own professional network to circulate her resume among potential employers both inside and outside the institutional umbrella. One of the institutions actively volunteered to fly Bridget out for a week to help facilitate her job interview process. Other institutions have more formal assistance programs. One of the institutions we considered had a defined dual-career couple job placement program, which provided logistical assistance for job placement and interviewing. Other institutions can even go beyond placement programs and provide financial support for the “trailing spouse”. The institution where I took my faculty position has a program that facilitates spouse/partner hires at the university by providing up to two years of 'bridging' money to help pay the individual's salary. This program was developed based on the recognition that funding is often a major sticking point in opening a position for the other individual. In this case, the children's hospital was passed Bridget's resume by one of the stakeholders of my hire, and was able to create a position for her because of the funding from the program. Bridget was flown out to interview and she was hired. This was certainly welcome news; the other institutions' hospitals where we looked were very impressed by her resume but had no funds to create a position for her. However, it is worth noting that Bridget is a truly skilled clinician in an in-demand field looking for a job within the same institutional umbrella.  It’s not clear how representative her scenario is with respect to employment outcomes through the ‘bridging’ program. The other institutions that presented offers to me could not find a position for her internally, and on her own she was often unable to find positions outside the university, owing in part to the size of the cities (and therefore the patient population) where the institutions were located.

The bottom line is that spouse/partner hiring is complicated. There is really no uniformity as to what an institution (or you and your partner) can do to facilitate a dual-career hire, or what you can reasonably expect from the institution to do. The situation becomes even more complicated for international couples, since work visas and other regulations may make it close to impossible to find a position for both within a short timeframe. So how do you wrap this into your decision making process, both as an individual and as a couple, as you prepare to make the leap?

Know yourself and know each other. Ultimately, where you go for a faculty position will be a decision made jointly by you and your spouse (if you have children, particularly of school age, obviously additional considerations come into play in choosing a new location for yourselves). It's likely that you have applied or will apply to a broad mix of institutions with varying job prospects for your partner. Knowing and, most importantly, agreeing ahead of time as a couple about values, needs, and expectations with respect to the outcome of the job search process is critical. Is your partner equally dedicated to their career outcome as you are? How much financial and/or career risk are you as a couple willing to take by moving to institutions or areas where your partner may be unemployed or under-employed for a time? Where are the points of compromise and negotiation for you both? What points are non-negotiable? Constraints such as where you both feel comfortable and happy living, in terms of climate, culture, city size and amenities, and, frankly, country, are also extremely important to discuss and agree upon. Indeed, Los Angeles, Boston, Cambridge and Frankfurt are going to be vastly different cities with unique aspects, opportunities and drawbacks that are critical to consider. You and your partner may have very distinct preferences on where to go, some of which will be negotiable and some of which will not. For this reason in my experience it is useful to have the conversation early and revisit it frequently during the interview and recruitment process to ensure you and your partner are on the same page. Bridget and I had mutually decided that we would go where she was able to find a sufficiently challenging position to maintain her career track; we felt this was important for our financial security and, most importantly, our happiness as a couple. We also wanted a city with certain amenities (music, outdoor activities, craft breweries, affordable housing). She was willing to compromise on issues such as salary, and I was willing to try another round of interviews if the environment or employment prospects for her were poor all around. This was the equation for the two of us; yours may be very different depending on your needs, values and priorities. It's worth acknowledging that time to go through further interviews can itself be a matter of luxury depending on your mentor's (or your) funding and time frame for you to move on; hence taking into account external forces that impact your decision, such as timeframe and whether you have one or more than one offer are also critical.

Know the institution and its environment. If an offer has been made to you by an institution, then the question of your partner's gainful employment and which programs or infrastructure the institution has to facilitate job searches or hiring becomes fair game. Following an offer, I felt at liberty to openly discuss Bridget and her employment needs, with discussions occurring often at the invitation of the faculty member(s) in charge of the hire. Up until the point of an offer, spouses, partners and family status really aren't a good topic of discussion for two reasons: 1) it can be an invitation for potential employers to discriminate against you, either consciously or unconsciously for any number of reasons related to family arrangements; 2) it simply isn't relevant to them yet and could come across as presumptuous by putting the cart before the horse. As far as how to approach the discussion, I found the best approach was to be straightforward and factual, and offer the relevant details of Bridget's career and employment needs. I also used the conversation to find out about what spouse/partner job placement or assistance programs existed at the institution, whether there were certain eligibility requirements for this assistance, and what limitations might exist for the programs in terms of time, degree of help, or funding. Lastly, I used these discussions to investigate as much as I could firsthand about the local job and real estate market (sometimes a second or third visit includes a half day with a local real estate agent or broker to see houses or apartments), to help assemble a picture of the financial and employment prospects for Bridget beyond our own research on the topic together. If and when I was asked for her resume, I furnished a PDF of a resume Bridget had updated for this purpose to my faculty handler(s) via an email, so it could in turn be easily circulated to any relevant parties. Not everyone knew where to send her resume; in this case Bridget was able to supply some ideas ahead of time based on her professional network (in all cases, prior to having an offer letter signed both by me and the institution, we asked that Bridget's job search be kept confidential so it wouldn't go back to her current employer). Indeed, depending on what your partner does for a living, as well as which programs or informal connections are in place, there are always distinct limits to what the institution can do, which brings up an important point:

Define your expectations (for yourselves and the institution). Academic institutions and the people in them are not necessarily miracle workers. If your partner has a career well outside the academic or biomedical sphere, say as a professional dancer, real estate agent or criminal lawyer, there may be very little to nothing anyone from the host institution can do to find your partner an internal position, let alone create one for them. There may be little the institution can do for you as a whole, if it doesn't have a job placement assistance program for dual-career couples. Even when your partner's career seems relatively 'easy' for a major biomedical research institution to find a spot for (i.e., a clinician if there's an associated hospital, or an art professor at a major university), an absence of money available to fund the position may prevent your partner from being employed there. Offering a new position is expensive, particularly if there wasn't necessarily an immediate need for a new hire in that department or organizational unit. As such, it is very important for you as a couple to define your expectations as to what 'success' will look like and how attainable it is given your partner's career, the local economy, size of city, and ability of the institution to intercede on your behalf. For instance, does your partner have to start in a job with the same pay rate and characteristics right away, or maybe able to settle for some level of 'starting over' at a lower level position? Does it mean moving to a sufficiently sized city so there are job prospects available in a realistic time frame? Does it mean you both need jobs within a short commute, or is it okay for one of you to make a longer commute to another city for work? Perhaps 'success' is being a single-income couple or family for a time. Or perhaps your partner could use the move as an opportunity to take on a new career instead. The key is that when dealing with the institution, these expectations are kept in mind. Don't expect every institution (or any institution) to work a miracle on your behalf. At the same time, if you have set expectations consistent with your comfort level/aspirations as a couple and the institution has the infrastructure to assist, find out how you and/or your faculty handlers can best make use of it, and keep a running dialogue with all parties to assess progress or lack thereof. It's important to keep your expectations reasonable but also not to back off from them. This doesn't mean waving them in the institution's face or using ultimatums ("either my spouse gets a job here or you can forget about the whole thing") but instead engaging in a respectful and honest dialogue to keep the process moving, and accepting that not every institution can assist in the way you may want. Your partner also will have their own legwork to do in looking for positions for themselves, regardless of what the institution may or may not do to help. Additional resources, such as alumni or professional groups you and your partner are associated with, may also be of some use. Ultimately, it will be a joint decision between you and your partner, and perhaps other family members, on where you land; it is important to know from the beginning what you collectively want out of this big career change, and to understand that your needs and expectations as a couple for careers and quality of life can be just as important as where you can do the best science.

In the next post, we'll get down into the finer points of negotiating your faculty startup package.



Eric Pietras, PhD
ISEH New Investigators Committee Member

Assistant Professor
Division of Hematology at the University of Colorado Anschutz Medical Campus
Aurora, CO, USA

Thursday, June 8, 2017

The cost of a postdoctoral experience and its impact on STEM diversity

Academic diversity in the biological sciences isn't what it should be.  At the most basic level, representation by underrepresented groups in the top research universities in the United States is less than 5%1.  Despite gains in enrollment of underrepresented students in the biological sciences at the undergraduate and doctoral levels, these gains do not extend to the tenure-track realm, where representation has changed very little over the past three decades. 

At another level, because of the ferocious degree of competition in science today - for publication in high impact journals, for limited grant funds, for fewer tenure-track positions -- one might argue that academic diversity is slowly been shaped by a "1%" mindset.  Perhaps more than ever before, the institution you come from-- even the lab you come from-- influences where you will publish, whether you will attain funding, and ultimately whether you will succeed. My purpose here is not to grumble; I'm sure there are many arguments that can be made on either side of this opinion. However, here I argue that the nature of the postdoctoral experience further links the attainment of a tenure track position with the availability of financial resources needed to endure that experience, and therefore that academic success does not depend on talent alone, but also on economic resources. I think undoubtedly one of the most unfortunate consequences of this is that it continues to negatively impact faculty diversity.

I will use myself as an example:  I barely survived my six-year postdoc. My starting salary was under 40K.  When I finished, after almost 15 years of postgraduate education and experience, I was making 52K.  I lived in one of the most expensive regions in the country.  I had two young children, and I lived nowhere near family. I'm not ashamed to admit that I was broke, and I was ready for a real income.  But my paper was under revision!  In order to be successful, I knew I had to hang in there to see my paper published in a high impact journal and await the score on my resubmitted K award application (a process which took almost two years).

Unfortunately, my struggle is not unique, but I was very privileged to have had family assistance and support that allowed me to continue pursuit of my goal. My mom loaned me money on occasion, and would come up to help my partner watch our young kids when I traveled to meetings. This support was not only financial; both my mom and my partner understood that this (long, unpredictable) period of training and low wages would ultimately lead to greater success and stability, and encouraged me (and allowed me) to persist despite my financial situation.  Without their support, I am confident that I would not have made it to a tenure-track position. Nonetheless, I applied for numerous industry jobs in the last months of my postdoc, as my family wouldn't have survived another year on my salary.  


For many postdocs, this long, unpredictable, and financially difficult pathway to academia just doesn't add up. Individuals coming from disadvantaged backgrounds, that don't have economic resources or family support to persist in an underpaid position with an undefined tenure, are at a true disadvantage in the slow race for a tenure-track position.  It can be difficult, or even embarrassing, to explain to your family that you can barely pay your rent when you have an advanced degree, particularly if you are among the first in your family to attend college.  I believe that several factors that currently define the postdoctoral experience, at least in the United States, contribute to implicit bias that undermines the representation of under-represented scientists at top research institutions and is reflected in the leak of those scientists from the academic pipeline.

Tenure-track success means a longer postdoctoral fellowship.  While the average postdoc in the sciences is still roughly 5 years, one might argue that the average postdoc for those that reach the tenure track is longer.  Little data exist for this kind of metric, but the best estimate is that there is at least a 1-2 year gap between the postdoc length for industry or other jobs and postdoc length for a tenure-track position.  Why would that be the case?  As the merit list for a tenure-track job grows longer, so does the tenure of your postdoctoral fellowship.  Publication in a high impact journal typically requires an immense amount of work; as an example, the average number of figure panels and authors in papers published in Nature and Cell has risen 2-4 fold in the last 30 years2.  Furthermore, multiple submission and revision cycles can take years before acceptance.    Applying (and often re-applying) for independent funding tells a similar story -- awaiting reviews and grant cycles can take a couple years.  Together with graduate education, these numbers mean that it can take over 12 years before you attain a "real" job in academia. 

The cost of a successful postdoc experience makes it difficult to sustain.  Many postdocs experience financial difficulties that only worsen over time.  Relatively low salaries that, until recently, have remained essentially stagnant3, often aren't enough to support individuals, much less families.  Many of the top research institutions -- the institutions that churn out the most prospective tenure-track applicants -- are also in the most expensive cities -- Boston, New York, San Francisco, London. In these cities, housing costs alone often gobble up the vast majority of a postdoc salary.  Most often, moving near family does not factor into choice of a postdoctoral lab, so help nearby is not an option.  If you are a postdoc with a family, forget it -- exorbitant childcare costs, at least in the US, can gobble up the rest of your salary. Moving costs alone can put you thousands of dollars in debt. Attrition under these circumstances is almost undeniable -- it can become a choice between career and survival.

The "1%" and implicit bias
Underlying several of the aspects I've mentioned above is the less obvious but pervasive influence of what I previously referred to as a "1%" mindset. In the search for qualified tenure track applicants, many institutions employ explicit bias by filtering through applications for candidates that come from top research institutions, prominent labs, with publications in high impact journals.  And to some degree, this make sense -- these applicants are typically bound to be competitively trained, hardworking, and highly competent.  But these standards are also implicitly biased against applicants from less prominent institutions with publications in less prominent journals that are no less competent.  For many of the reasons described above, these applicants may be at smaller institutions in less expensive cities, because it allows them to continue their scholarly pursuit in ways that are affordable.  They may publish their work in less prominent journals to demonstrate productivity in a reasonable amount of time, or simply because being at a less prominent institution makes it more difficult to publish in a high impact journal.   The 1% bias thereby weaves its influences into the many factors that influence tenure-track desirability, and implicitly biases the tenure-track process towards applicants that can manage to sustain life as postdoc at all costs in order to achieve success. 


There is no easy fix to this problem. The University of California, along with several other institutions, recently adopted a much higher pay rate for postdocs.  Perhaps leveling the economic playing field will help equilibrate the experience for underprivileged scientists.    Furthermore, by acknowledging and openly addressing how the cost of the postdoctoral experience implicitly excludes underrepresented scientists, perhaps we can shake off some of our own implicit bias and challenge those around us to consider how these factors shape our scientific community.  
     
1.
http://ucd-advance.ucdavis.edu/post/nelson-diversity-surveys
2.  Vale, R.D. (201). Accelerating scientific publication in biology.  PNAS, 112, 13439–13446
3.
https://report.nih.gov/NIHDatabook/




Anna Beaudin, PhD
ISEH Publications Committee Member

Assistant Professor
UC Merced

Thursday, May 25, 2017

Dissecting biological systems at the level of single cells

A major focus of technology development over the past years has been on increasing sensitivity to work with low cell numbers. The ultimate goal for many cell biologists is to assay cells individually. The desire to do so is in part fueled by the increasing appreciation of extensive heterogeneity in many tissues. For example, tumors are very heterogeneous, and often include not only different tumor cell clones, but also differentiated cells, infiltrating T-cells, macrophages, and fibroblasts. In the hematopoietic system, it has become apparent that even the most sophisticated flow cytometry sorting scheme has limits: highly purified hematopoietic stem cells still exhibit heterogeneous behaviors when assessed using single-cell transplantation assays (Dykstra et al., 2007; Kiel et al., 2005). In this blog, we will outline some of the most exciting developments and state-of-the-art technologies that stand to transform our understanding of tissue organization.

Next Generation Sequencing of single cells
Many single-cell assays start with isolation of individual cells. There are several ways to approach this. The most widely used method is fluorescence-activated cell sorting (FACS), in which single cells can be deposited in 96- or 384-well plates using a flow cytometer (Figure 1, panel A). For example, Smart-Seq2 deposits cells directly into lysis buffer, followed by enzymatic reactions to reverse transcribe and amplify the mRNA (Picelli et al., 2014). Smart-Seq was one of the first single-cell RNA-seq protocols and has the distinct advantage of capturing whole transcripts, as opposed to other technologies that are 3’ biased. Microfluidics can also be used to capture cells in tiny droplets, followed by molecular barcoding of molecules in the droplet (Klein et al., 2015; Macosko et al., 2015) (Figure 1, panel B). Microfluidics enables processing of thousands of cells per experiment, resulting in much lower cost and labor; however, current protocols only capture the 3’ end of the transcript. For example, the companies Fluidigm, 10X Genomics and 1CellBio all offer single-cell RNA-seq technologies based on microfluidics. Recently, researchers at MIT have isolated single cells in slides with ~86,000 subnanoliter wells (Gierahn et al., 2017) (Figure 1, panel C). Single cells are captured together with beads, followed by sealing using semipermeable membranes, cell lysis and hybridization of the mRNA to barcoded oligos on the beads. This technology has the potential to further reduce cost and increase accessibility of single-cell RNA-seq, but is currently not offered by a commercially available platform. Following cell isolation and capturing of nucleic acids of interest, the material needs to be amplified using enzymatic reactions. RNA-seq generally starts with reverse transcription of RNA into DNA, whereas genomic DNA protocols, such as ATAC-seq and ChIP-seq, begin with amplification using PCR or T7 RNA polymerase (Buenrostro et al., 2017; van Galen et al., 2016; Rotem et al., 2015). Illumina adapter ligation, Nextera or PCR are the most common approaches to prepare the DNA for Next Generation Sequencing.

Figure 1: Single cell isolation for nucleic acid sequencing can be performed using flow cytometry (A), microfluidics (B) or subnanoliter wells (C).
 
Data analysis
With single-cell sequencing technologies, vast amounts of data are generated, and data analysis presents a formidable challenge. Demultiplexing, alignment, quality checks and duplicate filters can influence all downstream steps of the analysis. Some technologies incorporate unique molecular identifiers (UMIs), which tells you whether two similar sequencing reads were derived from the same or different starting molecules. Some protocols include linear amplification by T7 RNA polymerase, which can increase sensitivity, but can affect how duplicate sequencing reads should be collapsed. Setting a minimum number of detected transcripts is a common method to filter low-quality cells, but may inadvertently exclude cells that have less mRNA (such as hematopoietic stem cells). After quality filtering, cells are often clustered using dimensionality reduction methods such as Principal Component Analysis (PCA) or t-Distributed Stochastic Neighbor Embedding (t-SNE). These methods can be influenced by artifacts such as read depth and batch effects, that have to be carefully controlled. Considering these variables before starting a single-cell RNA-seq project is essential (Grün and van Oudenaarden, 2015). Many laboratories are working on the computational challenges in analyzing single-cell data, and investigators such as Dana Pe’er, Peter Kharchenko and John Marioni have published packages that can help with analysis.

Single-cell imaging
Since measuring averages of heterogeneous populations often mask unique properties of rare cell types, such as adult hematopoietic stem cells, it is evident that single-cell analysis is a prerequisite for unbiased understanding of cellular and molecular behavior (Schroeder, 2011). The single-cell sequencing approaches mentioned above have significantly improved our understanding of cellular and molecular heterogeneity. However, there is another layer when studying biological processes lasting days/weeks (i.e. lineage commitment of embryonic or adult stem cells); the temporal dynamics. Over a given timeframe, both developmental and cell-cycle stage might influence the profile of individual cells. Since high-throughput sequencing requires lysing cells prior to downstream analysis, such methods are limited to a static picture of cell’s properties, and therefore lack temporal resolution. Live-cell imaging, ideally in an in vivo setting, could provide such data. Advances in non-invasive in vivo imaging allowed observation of entire zebrafish embryos for periods up to 2.5 days (Keller et al., 2010). Unfortunately, technical challenges such as optical tissue properties (most embryos are less transparent than zebrafish), size, accessibility to relevant structures (i.e. bone marrow imaging) and inability to long-term immobilize living animals pose significant obstacles. This limits in vivo imaging to few compatible tissues and to short time frames, and thus to events with rapid kinetics. In vitro time-lapse imaging offers an attractive, but technically challenging alternative, requiring expertise in a number of hardware and software components. It enables monitoring fates and dynamic molecular properties of individual cells and their progeny before, during and after a certain change occurs for periods up to 2 weeks (Kokkaliaris et al., 2016). Specialized software can then be used to attribute specific properties to individual cells and reconstruct the kinship within a colony in multidimensional lineage trees post-acquisition (Skylaki et al., 2016). When coupled with endpoint gene expression methods, it can retrospectively identify cell-state transitions (Hormoz et al., 2016). However, in vitro time-lapse imaging is currently limited to tracking few proteins simultaneously and cannot substitute the need for observing biological phenomena in their physiological environment. Although its usability depends on the biological question, in vitro time-lapse imaging can be a powerful approach for high throughput screenings or monitoring signaling dynamics over time.

Conclusions
Recent advances in single-cell analysis have significantly improved our understanding of cell behavior in homeostasis and disease. Sequencing RNA or DNA from single cells poses great engineering and computer science challenges. The innovations in this field are fast-paced, and future breakthroughs will enable higher capture efficiencies of molecules within cells, with robust protocols that are accessible to more investigators. Such technologies are already contributing to a reconsideration of the hematopoietic hierarchy (Nestorowa et al., 2016; Paul et al., 2015; Villani et al., 2017; etc.). Coupling gene-expression assays with in situ live-cell imaging adds another dimension enabling detection of local differences between similar or anatomically distinct regions of the same tissue (Silberstein et al. 2016). As methods become more sophisticated and multiplexed, unraveling complex tissues at the level of cellular resolution will make a lasting contribution to our understanding of biological systems in health and disease.




Peter van Galen, PhD
Publications Committee Member
Massachusetts General Hospital
Broad Institute of MIT and Harvard, USA
Konstantinos D. Kokkaliaris, PhD
Publications Committee Member
Department of Biosystems Science & Engineering, ETH Zurich, Switzerland

Citations
Buenrostro, J.D., Corces, R., Wu, B., Schep, A.N., Lareau, C., Majeti, R., Chang, H., and Greenleaf, W. (2017). Single-cell epigenomics maps the continuous regulatory landscape of human hematopoietic differentiation.

Dykstra, B., Kent, D., Bowie, M., McCaffrey, L., Hamilton, M., Lyons, K., Lee, S.-J., Brinkman, R., and Eaves, C. (2007). Long-term propagation of distinct hematopoietic differentiation programs in vivo. Cell Stem Cell 1, 218–229.

van Galen, P., Viny, A.D., Ram, O., Ryan, R.J.H., Cotton, M.J., Donohue, L., Sievers, C., Drier, Y., Liau, B.B., Gillespie, S.M., et al. (2016). A Multiplexed System for Quantitative Comparisons of Chromatin Landscapes. Mol. Cell 61, 170–180.

Gierahn, T.M., Wadsworth, M.H., 2nd, Hughes, T.K., Bryson, B.D., Butler, A., Satija, R., Fortune, S., Love, J.C., and Shalek, A.K. (2017). Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput. Nat. Methods.

Grün, D., and van Oudenaarden, A. (2015). Design and Analysis of Single-Cell Sequencing Experiments. Cell 163, 799–810.

Hormoz, S., Singer, Z.S., Linton, J.M., Antebi, Y.E., Shraiman, B.I., and Elowitz, M.B. (2016). Inferring Cell-State Transition Dynamics from Lineage Trees and Endpoint Single-Cell Measurements. Cell Syst 3, 419–433.e8.

Keller, P.J., Schmidt, A.D., Santella, A., Khairy, K., Bao, Z., Wittbrodt, J., and Stelzer, E.H.K. (2010). Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy. Nat. Methods 7, 637–642.

Kiel, M.J., Yilmaz, O.H., Iwashita, T., Yilmaz, O.H., Terhorst, C., and Morrison, S.J. (2005). SLAM family receptors distinguish hematopoietic stem and progenitor cells and reveal endothelial niches for stem cells. Cell 121, 1109–1121.

Klein, A.M., Mazutis, L., Akartuna, I., Tallapragada, N., Veres, A., Li, V., Peshkin, L., Weitz, D.A., and Kirschner, M.W. (2015). Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell 161, 1187–1201.

Kokkaliaris, K.D., Drew, E., Endele, M., Loeffler, D., Hoppe, P.S., Hilsenbeck, O., Schauberger, B., Hinzen, C., Skylaki, S., Theodorou, M., et al. (2016). Identification of factors promoting ex vivo maintenance of mouse hematopoietic stem cells by long-term single-cell quantification. Blood 128, 1181–1192.

Macosko, E.Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas, A.R., Kamitaki, N., Martersteck, E.M., et al. (2015). Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell 161, 1202–1214.

Nestorowa, S., Hamey, F.K., Pijuan Sala, B., Diamanti, E., Shepherd, M., Laurenti, E., Wilson, N.K., Kent, D.G., and Göttgens, B. (2016). A single cell resolution map of mouse haematopoietic stem and progenitor cell differentiation. Blood.

Paul, F., Arkin, Y. ’ara, Giladi, A., Jaitin, D.A., Kenigsberg, E., Keren-Shaul, H., Winter, D., Lara-Astiaso, D., Gury, M., Weiner, A., et al. (2015). Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors. Cell 163, 1663–1677.

Picelli, S., Faridani, O.R., Björklund, A.K., Winberg, G., Sagasser, S., and Sandberg, R. (2014). Full-length RNA-seq from single cells using Smart-seq2. Nat. Protoc. 9, 171–181.

Rotem, A., Ram, O., Shoresh, N., Sperling, R.A., Goren, A., Weitz, D.A., and Bernstein, B.E. (2015). Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat. Biotechnol. 33, 1165–1172.

Schroeder, T. (2011). Long-term single-cell imaging of mammalian stem cells. Nat. Methods 8, S30–S35.

Silberstein, Lev et al. 2016. Proximity-Based Differential Single-Cell Analysis of the Niche to Identify Stem/Progenitor Cell Regulators. Cell Stem Cell 19(4): 530–43.

Skylaki, S., Hilsenbeck, O., and Schroeder, T. (2016). Challenges in long-term imaging and quantification of single-cell dynamics. Nat. Biotechnol. 34, 1137–1144.

Villani, A.-C., Satija, R., Reynolds, G., Sarkizova, S., Shekhar, K., Fletcher, J., Griesbeck, M., Butler, A., Zheng, S., Lazo, S., et al. (2017). Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Science 356.

Thursday, May 11, 2017

Making the Right Choice: Group Leaders vs PhD Students

Selection period has started! As a group leader, like Eirini Trompouki for instance, you wish to recruit the best graduate students. So you will have to ask yourself: Whom of all those candidate students should I choose for my lab? On the other hand, as a graduate student, like Stylianos Lefkopoulos, you wish to earn a PhD and need to choose the appropriate supervisor and lab. Thus, you would have to ask yourself: Whom of all these mentors should I trust for my education and training? Although the choices on both sides might sometimes be difficult and tricky, there are certain general criteria that could help you choose the right candidate or supervisor.

GROUP LEADERS

As a group leader you essentially always look for the following features of your future graduate student:

Motivation/Passion: No matter what you decide to do in your life, you ‘d better be passionate about it, for only then do you have chances of succeeding and satisfying both yourself and the people you cooperate with. Given this together with the persistence that research demands, you should look for a graduate student who loves research and science and really wants to do a PhD. Candidates who are seeking to obtain a PhD as a stepping stone for an alternative career, have low chances of succeeding, because their drive and ambitions are related to something else than research.

Creativity and logic: In science, it is all about being creative and able to think, as we call it, “out of the box”. Should you consider all the amazing scientific discoveries so far, it is evident how important it is for a graduate student to be able to think and muse on the project question and take it one step further to the answer. This certainly demands a broad way of thinking. At the same time, logic and common sense are equally important, to keep things solid, under control and focused.

Organizational skills and independence: These two features are crucial for a successful graduate student. Organization leads to efficient time management and avoidance of past mistakes and repetitions. Independence, on the other hand, can assure you that science will progress even in the absence of your mental or physical interference. It also builds trust between the graduate student and the supervisor, which is important for your professional relationship and interaction.

Team player/personality: Working with a group of people means that not only you as a mentor should get along with the people in your lab. They should also get along as a group, both regarding the common good of the lab and their individual work. Choosing a joyful personality with a mentality, more or less, close to the one already established in the lab, will keep things balanced and create a happy working atmosphere in your team.

STUDENTS

But, what if you are on the other side, being a student looking for a lab to do your PhD in? As for every kind of relationship, a professional relationship is always bi-directional. So, what are the criteria you, as a candidate graduate student, take into account while searching for a prospective mentor?

Knowledge in the field/Successful past work: After you have chosen your scientific field of interest, one of the major things you should take into account before starting your graduate studies is the present and/or past contribution of your future mentor to this field. As a graduate student, you wish to evolve and succeed in your chosen field, in order to render your presence in the field and thus be able to aim for high goals in the future. Your mentor will play a crucial role in this since she or he will be your guide in this endeavor. Thus, your supervisor needs to be a scientist that you trust and admire regarding their knowledge and scientific impact. Admiring the person you work with will also highly motivate you and them, resulting in a constructive collaboration and successful work. 

Open mind/Willingness to discuss new ideas: Even though you are a trainee, your passion for science and basic knowledge acquired during bachelor/master studies may often lead you to the point where you come up with an idea of your own. Although this should be a feature highly appreciated by your supervisor, sometimes it happens that they might be particularly set in their ways and not open to new suggestions. Look for a supervisor who will be willing to discuss your new ideas and either allow you to explore them or explain to you thoroughly and with good reasoning why these ideas will not contribute to your project progress, so you can always benefit from it –remember, you are still a trainee.

Teaching skills/Interest in training: Although teaching and training should be taken for granted, you might not be the high priority of your supervisor –sometimes not a priority at all. PIs balance between their and your success, which do not always go together (especially in big labs, where the mentor might rely on 3 or 4 people to perform). It is, therefore, understandable that some of the group leaders cannot keep this balance, often neglect students who need help, and invest more of their time in experienced scientists (e.g. postdocs) who will produce more data and faster contribute to the lab progress. But you, as a graduate student, need someone who will be willing and eager to train you, spend time on you, believe in you and teach you thoroughly all you need to learn to gain experience. As such, it is of crucial importance to pick the right person.

All in all, making the right choice is very important for both sides. Apart from the criteria listed above, there are numerous other factors that one could take into account, like communication between the mentor and the graduate student, which at the end of the day might just be a matter of personality and mentality. The important thing to keep in mind, however, is that trying to make your choice by strictly sticking to your criteria list, might not be a very realistic solution. Most of the time, people you meet will only fulfill some of these criteria. Thus, estimate the situation on your own, based on the overall image of the person, the alternative choices you have and … your instinct!


Eirini Trompouki, PhD 
 ISEH Publications Committee Member

Group Leader
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51, 79108
Freiburg, Germany
http://www.ie-freiburg.mpg.de/trompouki



Stylianos Lefkopoulos

PhD Student
ISEH Member
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51, 79108
Freiburg, Germany