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.  
2.  Vale, R.D. (201). Accelerating scientific publication in biology.  PNAS, 112, 13439–13446

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.

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

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.


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.


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

Stylianos Lefkopoulos

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

Thursday, May 4, 2017

The long and winding road to success

As our last post highlighted, scientific success is not always a straight line. In this post, we want to highlight the journey of Dr. Kateri “Teri” Moore who is an Associate Professor of Cell, Developmental, and Regenerative Biology at Mt. Sinai School of Medicine, wife of Ihor Lemischka, and mom to Chris and puppy Finley Louise. A clear theme from Teri’s path is that a sustained love of science, finding your own opportunities, and staying in it for the long haul can yield great rewards. We hope you enjoy Teri’s story and advice on how to thrive when there are bumps along the road.  We thank her so much for taking the time to share her journey with us.

Career Overview:
I have been working in labs since I was 16. I first worked in a small clinical lab. I married very young and had a son soon after. Going to school became secondary, so I put my plans on hold. I worked as a phlebotomist and technologist at the local hospital. Later, I started working in the Veterinary Pathology Department as a technician. It seemed like I fell into my natural habitat. I was very successful there and published extensively. At some point I decided it was my turn and decided to apply to Veterinary School, as there were so many options after graduation. After my first year in Vet School my marriage fell apart, necessitating my return to my former job in my “spare time”. My son remained with me as my ex-husband soon left the state. Chris was a freshman in High School at the time of our divorce.

I continued to publish papers while I was working and still managed to graduate in the top 10% of our class. Our lab worked on animal models of hematological diseases, including glutathione deficiencies, red cell enzyme deficiencies, red cell membrane defects, and iron storage diseases. After graduation I decided to stay in science and found a post doc at Baylor College of Medicine. My son went to live with his father for his senior year in High School. My time as a post-doc was the first time I lived completely on my own and I loved it. I feel I was pretty successful; I had an NRSA Fellowship, published well and had the time of my life.

After 5 years I decided it was time to move on and interviewed with Ihor Lemischka at a Keystone Meeting where he ended up offering me a position. I had sought him out as he was doing everything I wanted to do: purifying stem cells, cloning molecules from HSC and investigating stromal microenvironments. I honestly thought I would be there for 2 years to gain some lacking skills but I ended up staying and entering a relationship with him. One cannot deny that this was a very successful partnership. My position at Princeton was a non-tenure track that allowed me to get grants and have my own people, but I had to pay my own salary, theirs and negotiate space from Ihor. Notwithstanding, I was successful and did some excellent and groundbreaking work there.

In 2007 we decided to “shake up our lives” and moved to New York to Mount Sinai. Initially this move was very hard on me as I had ongoing mouse experiments and a grant from the New Jersey Stem Cell effort and had to leave $100K behind. As a result I ended up getting scooped on the two major stories I had been working on. After my initially slow start I was able to publish my first New York-based study in 2011 and then followed up with the next in 2014. Even before that, things really started to take off with the publication of our direct reprogramming of fibroblasts into hematopoietic progenitors paper in Cell Stem Cell 2013. A Developmental Cell and Cell paper followed these papers in 2016. My absolutely fabulous graduate student has now followed with a Blood paper in 2017. I’ve been able to obtain an NIH R01 and a New York Stem Grant to support the reprogramming efforts. Now I am finally up for promotion to full tenured professor after being a non-tenured associate professor at Mt. Sinai for almost 10 years. Quite frankly I feel that I am in the most exciting phase of my career.

How well have you been supported throughout your career?
In general I feel that I have been very supported in my career. As stated above I started working in a lab when I was 16 and had two excellent supervisors both named Paul. In fact, I gave my son Paul as a middle name to honor these men. When I worked at the Vet school my supervisor was also very supportive. So supportive that he felt free to take off for a sabbatical shortly after I arrived. Luckily a brand new post doc slipped into that role and we did amazing things. The only one I lacked support from was my first husband. When our marriage broke down after one year in school my previous supervisor was more than happy to take me back and I continued to work while I went to Vet school. At this point I had very few supporters that were women, probably due to the fact that there were few to none following my path at the Vet school.

I had initially thought that I would go to graduate school after Vet school until I interviewed for grad school. This time it was a woman who looked at me and looked at my CV and saw that I had 15 publications; she asked me if “I just liked going to school”. She also said why don’t I just pursue a post doc. This I did and I was able to secure one after a phone interview arranged through the help of a male DVM/PhD that I worked with at the Vet school. At Baylor as a post doc I interacted with both men and women, again all very supportive. Those were heady times in molecular biology and gene therapy (1987-1992)- everything was new and exciting. I had so many good experiences and opportunities to go to national and international conferences to present my work. In fact, the women scientists that I met at ISEH meetings over those years to now have really shaped my career. For this I will be forever thankful.

In some ways I cannot discount the fact that I got myself to somewhere I wanted to be. Deciding to work with Ihor Lemischka was one of them. I thought I would be there 2 years to acquire the necessary tools and then “get a real job”. Little did I know that I was starting on yet again another journey. At Princeton I was in a non-tenure track assistant professor position (although Princeton refuses to call the position that, I was a Research Molecular Biologist) to start with, and was promoted to the equivalent of a full Professor by the time I left. When I applied for a grant I had to get the department chairman to explain to the NIH what my position was. This is the first time I felt less supported. Nevertheless, I did obtain an R01, a competitive renewal of that R01 and a NJ Stem Cell Grant. Initially at Sinai I felt supported, although I did think that I should have been appointed at least an Associate Professor with tenure. It is just now after almost 10 years that I am finally going up for tenured Professor. I was approved for promotion the first of January but it took 3 months for the Chair to put together his letter. I had the rest of my package to him right away. It will probably be summer before the whole process is done and I get promoted. I seriously doubt that the Chair would have been so slow for an eligible male candidate. It has been worse for another female candidate, 6 months. I might also mention that we two will be the first females promoted to full Professor in the department.

How has the environment improved for women in science since you started your career? How have they gotten worse?
Basically things have gotten better but we cannot stop improving. We are not there yet. The fact that we cannot elect a women president in this country says a lot.

In an article about Joan Steitz she is quoted as stating that “If a woman is a star there aren't that many problems. If she is as good as the rest of the men, it's really pretty awful. A woman is expected to be twice as good for half as much.'' Do you agree with this sentiment? If so, can you give an example of how you saw it play out. If you disagree, can you comment on how different institutions or different scientific fields might have variable gender biases.
I do agree with her totally but let’s not forget that women can hold other women back. I’ve seen this play out over petty jealousies about appearance and success in our own field. I am not going to name any names but I feel that some women (not all) treat other women badly on study sections when we should all be supporting each other.

From your interactions with female colleagues in other scientific fields, do you feel the hematology field is better or worse than others when it comes to gender equality? Can you give examples.
I think that women are quite well represented in the Hematology field. I do not have numbers on the Department Chairs or Division Heads in Hospitals but I have observed many strong women in leadership positions in Hematology, especially at ISEH. Overall the numbers are not there and I doubt that we will ever achieve gender equality across the board. To me the biggest areas of concern are in getting women to stand up for themselves and make demands in terms of leadership positions, salary, committee appointments, etc. We need to speak out more and not exist in the background. There is an inherent gender bias that is rather insidious, men and the powers that be tend to give lip service to this, but not act.

As a successful female researcher married to a successful male in a similar field, has this impacted your career negatively at any stage of your career, and if so, how did you deal with any of the negative experiences?
The ability to separate my science from Ihor was definitely difficult. I do feel that people have probably intimated that he was the brains behind the work we first did together. We did publish together extensively and he has been a co-Investigator or co-PI on my grants and vice versa. It’s only been since we have been at Sinai that I have been able to separate my work from his and publish without him. I can explicitly remember getting grant reviews that questioned my independence from him. I happen to know of several couples who work quite closely together and run joint labs- it is not uncommon. There are also some dynamic couples in hematology that may not share labs but share similar careers eg. Connie and Allen Eaves and Thalia Papayannopoulou and George Stamatoyannopoulos. Overall, I feel that I have benefited greatly from my partnership with Ihor. I am the one who chose to stay in Princeton and work with him rather than leave and establish myself somewhere else. Frankly we’ve been awfully good for each other in terms of our science.

Do you have any advice for the younger female researchers whose partners are also male researchers on how to balance life/home and deal with any bias that might arise, especially if they work closely together?
We all have strengths and weaknesses. The challenge is recognizing them and then building on each other’s strengths. Do not dwell on the small stuff; learn to let things go. The balance thing is something you have to work on constantly and I admit readily that I do not have it figured out. Most tasks seem to be leaning in my direction. I am very good about making things easier for him. Unfortunately, the vice versa is not there, especially in our home life.
Do you have any advice for those who cannot accept that a female researcher can be the brains (or driving force) behind the research?
Just call them on it. In this day and age such discrimination should not be allowed.

Stay tuned for our next installment when we will hear the advice of Dr. Connie Eaves, a woman who can surely share the above sentiment of being outspoken and calling things like she sees them.

Teresa V. Bowman, PhD
Publications Committee Member
Former Chair, New Investigators Committee

Assistant Professor, Department of Developmental & Molecular Biology
Assistant Professor, Department of Medicine (Oncology)
Albert Einstein College of Medicine
Bronx, NY

Louise E. Purton, PhD

Associate Director, St. Vincent's Institute of Medical Research
Co-Head, Stem Cell Regulation Unit 
Associate Professor, Dept. of Medicine SVH, The University of Melbourne
Melbourne, Australia

Thursday, April 27, 2017

Thriving in a Two-scientist Household: Lessons from Those Who Went Before.

Being in a relationship with a fellow scientist can be an amazing experience. First and foremost, they understand your passion for research. You can discuss your science thoroughly as they have the knowledge to understand the work, the frustration, and the joy, as well as an interest in science to enjoy the conversation. You can commiserate about the ups and downs of experimental foibles, and jointly celebrate manuscript acceptances and grant successes. But there can also be downsides. At times, your partner could be credited for your work merely based on gender differences. If you choose to have a family you need to find the balance between work and home life perhaps even more than families in which only one partner is the scientist (it can be hard to stop talking science at times!). Furthermore, you may end up competing for the same funding opportunities.  Two scientist households are not uncommon, and have been the subject of a number of news features in Nature over the last decade that are worth reading, the most recent here: Dance, A. Relationships: Sweethearts in science. Nature 542:261-263, 2017.

In this part of our series on women in science, we interviewed prominent, successful women who have thrived in a two-scientist household. We hope you enjoy learning about their personal journeys as much as we have and also gain some insight into how to maneuver through your own situation.

In the first installment, we will share the experiences of Thalia Papayannopoulou, the Elo Giblett Endowed Professor of Medicine, past ISEH President, recipient of the 2016 Donald Metcalf Award and Wallace H. Coulter Award, mother of John and Alexi, wife to George Stamatoyannopoulos, and grandmother of 3 grandchildren. Thalia also answers some questions on tactics to being a successful woman in science and offers her perspective on how things have changed. 

Stay tuned for more stories from the women of ISEH.

Career overview:
I entered Medical School in Athens in my teens and throughout my 6 years of training, I received the grades I deserved and did not experience gender discrimination. After completing my residency, my husband (George Stamatoyannopoulos) and I went to the USA for specialty training and research opportunities. George had already lined up a position with the Medical Genetics Division at the University of Washington and I was planning to join the Hematology Division for my training. Both Hematology and Medical Genetics were Divisions in the large Department of Medicine and according to an existing regulation, husband and wife could not be appointed in the same Department (!). I therefore joined the Pathology Department for a couple of years and after the previous law changed, I moved to the Hematology Division under Dr. Clem Finch. Retrospectively, the diversion to Pathology turned out to be fortuitous as I gained experience in cell culture, histochemistry and enzyme biochemistry; skills, which served me well later.

At the end of my Hematology training, and upon completing my state license exams, I exhausted the limited support available from a Hematology Training Grant and I was asked to write an NIH grant to support my salary. I was given a copy of another NIH grant from the Gastroenterology Department, which at this point served as my only advice/assistance on grant writing. Not surprisingly, I did not get the grant and was soon without a salary and had to leave the Hematology Division. During this period, I volunteered in an outpatient Hematology Clinic at the Old Marine Hospital in Seattle. The desire to do research was still with me, however, and I realized that my prior research experience in cell culture and hematopoiesis could be useful to some of the projects being undertaken in the Medical Genetics Division. I was hired to do such research in a Program Project Grant (PPG) in Medical Genetics (full disclosure here, the PI of that PPG was George- I am still grateful today!). I love erythropoiesis and the research I did under this PPG did very well with papers and meeting presentations.

I then wrote an application for a Research Career Development Award (RCDA, customary at that time) for my subsequent incorporation into the Faculty of the Department of Medicine. The grant was not funded and I was not appointed (the department did not want me in its Faculty at that time!). However, my subsequent individual grant applications were successful, and a Faculty appointment followed (not as prompt as would occur for a male candidate). I had support from the Head of Hematology (John Adamson) and many of my Hematology colleagues at that time. As a Hematology Faculty member, I did my Hematology attending duties (inpatient and outpatient), participated in teaching the Hematology course to medical students and for 15 years I was the PI for the Hematology Training Grant. I subsequently chaired the Full Professors promotion committee for the Department of Medicine (quite ironic for a department that originally did not want me in its Faculty!). I also participated in many ASH activities, (Scientific Committees, Nominating Committees, as an executive committee member) and in NIH activities (three terms as a Study Section member, as an NHLBI Council Member and participating in workshops). In addition, I regularly attended ISEH Scientific meetings to keep up to date with the latest in experimental hematopoiesis.

How has the environment improved for women in science since you started your career? How have they gotten worse?
I recounted my early steps (in a very abbreviated form) to convey some comparisons between then and now, to show how much the situation has improved today (thankfully) for women physicians in Academic Medicine, and to emphasize that academic life is a very long process with several ups and downs on the way (unless you are extremely lucky). During my training period, women in Medical Schools were ~5% of the students and it was the time when women were viewed “as assistants to somebody else (a man)”- the prevailing axiom was “men take charge, women take care”. There was a rather “unconscious” non-guilty bias by men that prevented the promotion of women in science. In one of my clinic appointments, after I had introduced myself to my scheduled patient, he told me “I would like to see a male doctor” (!).

Thankfully Academic Centers now have more transparent policies for salaries and promotions and there are more women at the Assistant and Associate Professor level. However, women still lag behind at the full Professor level, despite women accounting for over 50% of the graduates from Medical Schools and nearly 50% of those receiving STEM doctorates. So we continue to witness the “leaky pipeline“ for women in academia. There are several reasons for that: a) an increased burden of family responsibilities at the same time as career development, b) lack of many role models combining career and family responsibilities, c) lack of research funding, d) poor mentoring, e) a male-based environment and f) lack of assertiveness in women in negotiating salaries or new positions (and note that a woman showing such assertiveness in negotiations is viewed differently than their male counterparts). Overall, however, there is a lot to celebrate. For example, the University of Washington (UW) boasts the highest percentage of female Faculty in the College of Engineering, which is amongst the top 50 engineering schools in the country. Further, the number of female Faculty in 19 STEM departments across 3 UW colleges has almost doubled (from 60 in 2000 to 112 in 2015), and more than half of the female faculty are now Full Professors with tenure. In our Hematology Division, there are seven female full professors: one was the President of ASH, two have won ASH awards and one is a Chair of Medicine in a large affiliated Hospital. So we have been lucky both at UW and specifically in our Hematology Division, with several women at the Full Professor level to foster a supportive environment for our younger female Faculty.

Recognizing the “women-related” realities, several Academic Centers have introduced family-friendly policies and many of the Scientific Societies recognize and appoint women in leading positions and strive to facilitate networking among the members. The presence of successful women either in the immediate environment to provide a supportive ”niche” or even outside the field has been an important parameter for motivational support.

As a successful female researcher married to a successful male in a similar field, has this impacted your career negatively at any stage of your career, and if so, how did you deal with any of the negative experiences?
Despite the long list of improvements at several levels, there are still special challenges to balance academic work and family responsibilities when both partners are in academic positions. In addition to routine daily needs for every family (school schedules, child care assistance, rides for activities, etc), families in academia face additional and unusual needs. These include unusual work hours in a day and the instability in funding. Many academic centers have significantly expanded their faculty base relying on outside funding to support their salaries (a good recipe for disaster when there is an abrupt restriction in funding). This can put couples at odds for negotiating new positions after every career step (the so-called “two-body” problem). This atmosphere can result in imbalances in career trajectories, as moves might be good for one not so good for the other, etc.

There are additional hurdles for couples in the same discipline of academic work. When they publish together, the usual perception is that it was the man’s idea that the woman worked on- all the credit goes to the male of the family. Indeed, this issue came up during my promotion, but the defense by my colleagues in the Hematology faculty prevailed. Therefore, it would help if they have independent publications, or if one of the two diversifies to a different research area (if possible). In general, to face all of the above challenges, and especially for women with their added burden in family affairs (i.e small chidren), a supportive partner is of paramount importance. Plans for one to slow down and support the other partner (man or woman) with a good advancement trajectory can be a good family decision. When both partners are competing at the same time, this creates a high level of stress. Every successful woman with children that I had the opportunity to observe in Medicine had a supportive partner to save the family from unpredictable child-related events and other family emergencies, in addition to the financial burden for child care.

What advice would you offer other women in science?
Despite the evolution in academic research, what is perpetually important, both then and now, is the quality of mentoring a trainee receives and the local scientific environment. Successful mentoring requires that the mentor is interested in what you are doing and he/she is committed to your success, putting your career development ahead of his/her own. There is a continuous exchange of ideas and a continuous learning process for both the mentor and the mentee. In my opinion, besides the scientific input, the personal virtues and character of the mentor and mentee are particularly important for developing good relationships. Mentoring is also particularly effective when the mentor insists that the mentee expresses his/her ideas in writing. This exercise is extremely useful for writing papers or grants. Another important factor is to prepare the mentee(s) for the failures that will inevitably come along the way, either at the bench, or after a paper or grant is rejected. For me, I remind them of my own failures. The successes are easy to celebrate. Mentoring should be an enjoyable process for both the mentor and the mentee. Both should cherish the memory later. The mentor should rejoice and celebrate the mentee’s upward success and the mentee should cherish the inspiration and support he/she received. It is a gift for both.

We hope that you have found Thalia’s story as inspiring as we have, and may it give hope to those who are currently experiencing any of the difficulties she has encountered. We thank her so much for taking the time to share her journey in research with us. In our next post in this series, we will hear from Teri Moore, Associate Professor (soon-to-be Full Professor!) at Mt. Sinai.

Teresa V. Bowman, PhD
Publications Committee Member
Former Chair, New Investigators Committee

Assistant Professor, Department of Developmental & Molecular Biology
Assistant Professor, Department of Medicine (Oncology)
Albert Einstein College of Medicine
Bronx, NY

Louise E. Purton, PhD

Associate Director, St. Vincent's Institute of Medical Research
Co-Head, Stem Cell Regulation Unit 
Associate Professor, Dept. of Medicine SVH, The University of Melbourne
Melbourne, Australia

Thursday, April 20, 2017

Q&A for Upcoming ISEH Journal Club

The New Investigators Committee is excited to announce the second ISEH Journal Club, which will run next week (24 - 28 April). We'll be discussing a recent paper in EMBO entitled Osteopontin attenuates aging‐associated phenotypes of hematopoietic stem cells with the paper's first author, Novella Guidi.  Starting 24 April, you can ask Novella any questions about the paper through the ISEH Facebook group

As before, to help introduce this paper and start the discussion, we conducted a Q&A with Novella. This recent publication came from her PhD research with Dr. Hartmut Geiger at the University of Ulm. Novella is currently a postdoctoral fellow with Dr. Valter Longo at the University of Southern California.

What was the motivation for studying hematopoietic stem cell aging?
What motivates me and the laboratory about studying the aging of hematopoietic stem cell (HSC) is that aging at the stem cell level is one underlying cause of aging-associated immune-senescence as well as leukemia. In fact upon aging HSCs undergo changes in function and structure, including skewing to myeloid lineages, lower reconstitution potential and loss of protein polarity, which influences health span. What is highly exciting about studying HSC aging is that the functional decline of aged stem cells may be reversible and that rational interventions to achieve HSC rejuvenation can be developed by targeting HSC aging mechanisms, thereby allowing for a more healthy aging.

What are the key findings of your paper?
The first important finding in the paper is that an aged-related decline of osteopontin (OPN) in the bone marrow niche microenvironment is able to extrinsically result in HSC aging, while so far mainly HSC intrinsic mechanisms have been considered to be the important driving force of the aging process. Secondly, exposure of aged HSCs to activated OPN fragments attenuated aging of old HSCs, resulting in increased engraftment, decreased HSC frequency, increased stem cell polarity and a restored balance of lymphoid and myeloid cells in blood. This nicely demonstrates how rescuing  osteopontin levels in the niche supports a more youthful HSC function.

How do you think your story will impact the blood field? What do you see as the important next steps?
I think our findings emphasize the importance and the contribution of the niche microenvironment in driving or exacerbating HSC phenotypes, and especially being considered when rejuvenation therapies are being established. Our study in fact points to exciting novel ways to improved immune system in old individuals and possibly reduction of oncogenic transformation upon aging, by therapeutically targeting the place where blood stem cells reside. Interestingly, osteopontin levels are not only low in the bone marrow niche, but also in the peripheral blood upon aging therefore as a next step we are aiming to use osteopontin replacement therapy in mice to reverse the influence of an aging niche. Our findings cannot at this stage be directly extended to clinical treatment of human patients, but the data provide interesting leads that one day could benefit human health by boosting the immune system of elderly people.

Are there members of our ISEH community that contributed to the context for your paper? How did he/she contribute to your research question?
Yes, there are few people of the ISEH community that contributed to my project development path. Most of all it was the work previously done by Dr. Susie Nilsson that inspired me in digging deeper into the osteopontin signaling pathway upon niche aging. In fact, she previously showed that OPN knock-out mice had an increased HSC pool size in vivo with markedly enhanced cycling, suggesting osteopontin as a key regulator of HSC quiescence. Moreover, work from Dr. Peggy Goodell showed how aged circulatory factors and the bone marrow cytokine RANTES are able to influence the HSC myeloid skewing phenotype and that heterochronic transplants of aged HSCs into young animal generate less myeloid cells. Altogether their data implied a critical role of a young and functional niche in supporting young and healthy HSCs and immune cell production, which directly inspired me to investigate the role of osteopontin in influencing HSC aging-related phenotypes.

Who would you particularly like to read your paper?
If I have to think about someone I would particularly like to read my paper this person would be Dr. Paul Frenette. His excellent work on unraveling the nature and function of the HSC niche microenvironment has always fascinated me. He elegantly demonstrated, based on distinct genetic mouse model and advanced high resolution imaging, that the perivascular area of the sinusoidal blood vessels is the region in which HSC mostly resides, surrounded by important niche cell types that further regulate HSC function and maintenance. The endosteal niche is highly vascularized, implying that the cellular components of the niche that regulate HSC function are interconnected. During the past years’ conferences, I got the chance to meet him a couple of times and I always loved discussing my data and findings with him. His critical point of view always inspired me to view, analyze and interpret my results critically. These conversations gave me the confidence that I was digging in the right direction. I would like him to read my paper because I am sure he would be highly critical by asking a lot of tricky questions, while he would have of course additional advice for the next steps in my research endeavor.

Thank you to Novella Guidi for participating in our 2017 ISEH Journal Club.  Please visit the ISEH Facebook group from 24 - 28 April to submit your questions and join the discussion.

Novella Guidi, PhD
ISEH New Investigators Committee Member

Postdoctoral Fellow
University of Southern California / Leonard Davis School of Gerontology