Category: main_pub

Microtubule motors read MAPs

On September 6, 2018

Author: Hongyan Hao

Editors: Anna Feitzinger | Emily Cartwright, Keith Fraga, Jessica Huang, Sharon Lee, Yulong Liu, Linda Ma

Long distance cargo transport in neurons is facilitated by microtubule motors kinesin and dynein. In vivo, microtubules are crowded environments covered by different kinds of microtubule associated proteins (MAPs). How do motors react when they encounter MAPs? A recent work entitled ‘competition between microtubule-associated proteins directs motor transport’ published in Nature Communications by Ph.D. student Brigette Monroy in the Biochemistry, Molecular, Cellular, Developmental Biology (BMCDB) program explored how different MAPs directs motor movement on the microtubules.

My ability to write this article depends on my nervous system formed by numerous cells called neurons. Neurons communicate with each other through a long cable-like projection termed an axon, and branched cellular extensions called dendrites. The axons of our motor neurons can extend all the way from the spinal cord to our toes, which can be 1 meter in length. Thus, neurons are faced with the significant challenge of transporting proteins, vesicles and organelles over long distances to maintain cell polarity and the connection between neurons.

Hollow tubes called microtubules (MTs) are the highways for effective intracellular transport from the axon or dendrite to the cell body. Motor proteins kinesin and dynein are the trucks traveling along the MTs. Polarized with two distinct ends, i.e. a plus end and a minus end, MTs are one-way-only tracks for both motors. Kinesin-1 is plus end directed while dynein moves towards the minus end of MTs. Thus, the organization of the MT is essential for directing cargos to their correct destination.

Microtubule (MT) plus-end motor kinesin-1 and kinesin-3 are inhibited by tau patches, while tau has little effect on the MT minus-end motor dynein. MAP7 outcompetes tau and specifically enhances kinesin-1 movement. Similar to tau, MAP7 inhibits kinesin-3 but allows for the dynein movement.

In axons, MTs are highly organized into bundles with plus ends directed out towards the cell periphery, and minus ends oriented inward towards the cell center. In contrast, MT orientation is mixed in dendrites (1). In vivo, MT organization and dynamics are highly regulated by microtubule associated proteins (MAPs). For example, the MAP tau binds to the MT lattice and stabilizes axon MTs. When detached from the MT, tau proteins form aggregates, which is one of the hallmarks of Alzheimer’s disease (2). Another MAP, MAP7, also known as ensconsin or EMAP-115, binds to MTs at axon branch sites to positively regulate branch formation (3). As the MTs are decorated by different kinds of MAPs in axons and dendrites, how do the motors dynein and kinesin behave when they hit MAPs?

MAPs are not just rocks on the road that block motors. In fact, the two motors will respond differently depending on which MAP they encounter. For instance, previous studies have shown that kinesin-1 motors will stop and fall off when they encounter tau, while tau has little effect on dynein (4, 5). In contrast, MAP7 enhances kinesin-1 movement (6, 7). How do these different motors and MAPs coordinate with each other to achieve effective cargo transport in axons and dendrites?

A recent publication by BMCDB student Brigette Monroy and her colleagues from Kassandra Ori-McKenny’s lab at UC Davis explores how motor movement might be regulated by different MAPs coating the MTs (8). Consistent with previous reports, Monroy et al. found that tau is restricted to axons, but MAP7 was localized to both axons and dendrites in the Drosophila peripheral nervous system and tissue cultured mouse neurons. Using Total Internal Reflection Fluorescence (TIRF) microscopy, which allows for visualization of molecules on a single stabilized MT in vitro, the authors found that MAP7 strongly excluded tau from the MTs. Although bound to MTs more rapidly than MAP7, tau is displaced by MAP7 over time. This is most likely due to MAP7’s higher MT-binding affinity and longer dwell time on the MT lattice since purified MAP7 and tau do not bind to each other (8).

It is striking that MAP7 kicks tau off the MTs, but what are the physiological functions of MAP7/tau competition? Overexpression of MAP7 in Drosophila larval dendritic arborization (DA) neurons caused increased branch number while tau overexpression led to a decreased branch number. Overexpression of both MAP7 and tau led to more branches in DA neurons, consistent with the observation that MAP7 outcompetes tau (8).

One possible mechanism is that MAP7 and tau affect DA neuron branching by regulating the intracellular transport of the Golgi outposts. Golgi outposts are important for branch formation by nucleating MTs at branch sites (3, 9). The increased branching observed with MAP7 overexpression may be due to increased kinesin-1 mediated cargo transportation since Golgi were found to be enriched in the plus ends of MTs in DA neurons.

In vivo studies have revealed positive regulation of kinesin-1 by MAP7, but the mechanism has been unclear (7). Using in vitro single molecule motility assays, where the movement of a single fluorescently labeled motor protein on the MT is observed under TIRF microscopy, Monroy et al. found that both human and Drosophila MAP7 directly affect kinesin-1 by enhancing the motor landing on the MT. This may be due to 34 conserved amino acids in MAP7 which may facilitate kinesin-1 recruitment through a weak, ionic interaction with kinesin-1. Kinesin-1 motors stop and fall off the MTs when they encounter patches of tau. Would the presence of MAP7 overcome tau’s inhibition on kinesin-1? The answer is yes. MAP7 can not only replace tau on the MT and recruit kinesin-1 onto the MT, but also restores the ATPase activity of kinesin-1 inhibited by tau.

Tau has little effect on dynein motors. What about MAP7? Interestingly, just like tau, MAP7 barely affects the mobility of the dynein active complex in vitro. So, does MAP7 only affect plus end MT motors? Kinesin-3 family motors are also plus end directional. In contrast to kinesin-1, MAP7 inhibits kinesin-3’s landing on the MT as well as its mobility. However, tau inhibits kinesin-3 in a similar way as kinesin-1.
Cells have very complex environments and it is challenging for in vivo studies to provide clear and detailed mechanisms of how proteins work with one another. On the other hand, in vitro results can be difficult to interpret because simplified systems introduce biases not present in cells. In this paper, the Ori-McKenny lab illustrates how powerful it is to combine in vitro and in vivo studies to investigate the mechanism of cellular processes.

MTs are essential to maintain the shape, polarity and intercellular transport in our neurons. The findings suggest that MAPs on the MTs coordinate with each other and that MT motors can interpret MAPs, which allows for the regulation of cargo transport. Monroy’s story only discussed MAP7 and tau, but MTs are also occupied by other MAPs. Also, MTs can be post-translationally regulated to favor or inhibit motor mobility. I am grateful that our neurons have a system to coordinate cargo transport, which makes up a powerful neural system that enables me to ponder the relationship between different MAPs, motors and how they are doing their jobs together on the MTs! I am excited to see what Monroy and Ori-McKenney come up with next! A more complex map about motors and MAPs is yet to be revealed!

Now, after sitting here for a while, I have decided to walk out to get a cup of iced tea. I suppose that the kinesin and dynein motors made their ways to the right destination and the long motor neuron axons delivered the message to my toes, since I made it to the long line and am enjoying it now.

References:
1.         Burton PR (1988) Dendrites of mitral cell neurons contain microtubules of opposite polarity. Brain Res 473(1):107-115.
2.         Ballatore C, Lee VM, & Trojanowski JQ (2007) Tau-mediated neurodegeneration in Alzheimer’s disease and related disorders. Nat Rev Neurosci 8(9):663-672.
3.         Tymanskyj SR, Yang B, Falnikar A, Lepore AC, & Ma L (2017) MAP7 Regulates Axon Collateral Branch Development in Dorsal Root Ganglion Neurons. J Neurosci 37(6):1648-1661.
4.         Ebneth A, et al. (1998) Overexpression of tau protein inhibits kinesin-dependent trafficking of vesicles, mitochondria, and endoplasmic reticulum: Implications for Alzheimer’s disease. Journal of Cell Biology 143(3):777-794.
5.         Dixit R, Ross JL, Goldman YE, & Holzbaur EL (2008) Differential regulation of dynein and kinesin motor proteins by tau. Science 319(5866):1086-1089.
6.         Barlan K, Lu W, & Gelfand VI (2013) The Microtubule-Binding Protein Ensconsin Is an Essential Cofactor of Kinesin-1. Current Biology 23(4):317-322.
7.         Metzger T, et al. (2012) MAP and kinesin-dependent nuclear positioning is required for skeletal muscle function. Nature 484(7392):120-+.
8.         Monroy BY, et al. (2018) Competition between microtubule-associated proteins directs motor transport. Nat Commun 9.
9.         Ori-McKenney KM, Jan LY, & Jan YN (2012) Golgi Outposts Shape Dendrite Morphology by Functioning as Sites of Acentrosomal Microtubule Nucleation in Neurons. Neuron 76(5):921-930.

Say Cheese! A Snapshot of Microbial Communities on Cheese

By Staff

On August 9, 2018

In main_pub

Author: Jessica Huang

Editors: Keith Fraga, Hongyan Hao, Sharon Lee

I love eating cheese. If you set a block of cheese in front of me, I will probably not stop eating. One of my favorite memories from taking French in high school, besides singing a bunch of Disney songs in French, was the time my teacher brought a few different cheeses for us to try out. I have briefly thought about getting a cheese wedding cake if I ever manage to get married.

But what makes cheese so cheesy? The answer is, surprisingly, microbes.

How is cheese made?

Before we delve into the contribution of the microbial community within cheese, it’s important to know a bit about how cheese is made. The key component in milk for making cheese is the protein casein. Normally, casein is found in a micelle form in milk, which means that several caseins aggregate together into a spherical form. Since casein is negatively charged, the spherical micelles repulse one another. However, if acid is added, the negative charge is neutralized, allowing for coagulation, which is the thickening of milk into solid curds that are used to make cheese. Using this method alone will produce softer cheeses.

Comic about caseins coming together.

Another way to promote coagulation is to use rennin, which contains a protease called chymosin that breaks down κ-casein, a soluble protein that forms a protective and stabilizing layer around casein micelles. This formation of the solid milk curds is the first step in making cheese. The curds are then separated from the whey, which is a liquid byproduct composed of proteins that remain soluble even after acidification and rennet treatment. Whey can be used for several things, such as protein shakes. Meanwhile, the curds are processed in various ways to make different types of cheeses. The last step is the maturation of cheese, which contributes most to the distinct flavor of cheese and can last anywhere from several months to several years.

So where do microbes come into the picture?

While vinegar or lemon juice can be used to acidify milk, another common method is to use microbial starter cultures instead. Some of the most commonly used strains in starter cultures include Lactococcus lactis (used for cheddar), Streptococcus thermophilus (used for mozzarella), and the Lactobacillus species (used for Swiss cheese). These bacteria help acidify milk by converting lactate into lactic acid.

Microbes also play a significant role during the aging process of the cheese. During this time, bacteria added from the starter cultures begin to die off, while other microbes that were either already in the milk from the beginning or joined in from the environment along the way begin to flourish.

Sometimes additional microbes known as adjunct cultures are added. Their main purpose is to enhance the flavor or texture of the cheese rather than to produce lactic acid. One example is the mold Penicillium roqueforti, which puts the blue in blue cheese through its formation of spores. The unique flavor of blue cheese comes from the conversion of fats into flavorful free fatty acids and methyl ketones by lipases produced by P. roqueforti. Another example is Penicillium camemberti, which gives cheeses like camembert and brie their soft, gooey texture. Its preference for the surface of the cheese allows for the development of a characteristic soft, white, bloomy rind. The holey appearance of Swiss chese is thanks to Propionibacterium freudenreichii. These bacteria convert lactic acid inside the cheese into carbon dioxide, which becomes trapped and forms bubbles. Acetate and propionic acid are also produced as byproducts and contribute to the flavor of the cheese. P. freudenreichii is often used together with Lactobacillus helveticus, a strain that can also be used when making cheeses like cheddar and that helps produce a nutty flavor.


A) Spores formed by  roqueforti throughout blue cheese. B) Bloomy rind of brie formed by P. camemberti.

Of course, there are many other microbes present in cheeses. In addition to those that are added, there are also microbes that were present from the very beginning in the milk, as well as ones that were acquired throughout the cheese-making process. Furthermore, many factors such as pH, temperature, and salt content affect which microbes are capable of forming colonies in the cheese. The presence of the microbial community, the metabolic byproducts they produce, and their interactions with one another in turn produce the distinctive flavor, aroma, and texture of many different cheeses.

A cheesy model system?

Cheese is home to many different microbes, and the rind is especially rich in microbial diversity. This makes cheese a potential model system for studying microbial communities. One of the labs that uses cheese for research is headed by Rachel Dutton at UC San Diego. Back in 2014, her lab successfully sequenced 136 different rind communities and found that they are highly reproducible. They discovered that the composition of the microbial community on cheese rinds and the relative abundance of individual microbes is correlated with the type of rind. For example, the bloomy rinds of camembert have a denser population of fungi, as would be expected of rinds produced due to the mold P. camemberti. The environment that the cheese is exposed to as it ripens is important too, but surprisingly, where the cheese was made does not correlate with the composition of the microbial community.

The Dutton group also found that many of the dominant species can be isolated and cultured, allowing them to easily recreate the communities in vitro. Thus, they were able to study interactions between different species, and observe how they affect one another in pairs. One of their findings is that the presence of fungi may promote an increase in pH, creating an environment that is beneficial to some bacteria. Overall, it looks like they’ve succeeded in creating quite the tasteful system.

Cheese is grate

Cheesy pun aside, cheese really is quite wonderful. It’s the basis of many delicious dishes and makes for a great snack by itself. On top of all that, it’s also making cool contributions to science. You gouda love it.

(P.S. Cheese can still go bad. If you see mold that isn’t supposed to be on the cheese, throw it out if it’s a soft cheese. For hard cheeses, which have lower moisture content, you should be able to cut off the moldy part and keep the rest. Bon appetit!)

References

Button JE, Dutton RJ. Cheese microbes, Current Biology 22 (2012) R587-R589.
Wolfe BE et al. Cheese Rind Communities Provide Tractable Systems for In Situ and In Vitro Studies of Microbial Diversity. 158 (2014) 422-433.
https://www.cheesescience.org/microbes.html#lab

Mentoring and being mentored, the Graduate School Edition

By Staff

On April 2, 2018

In main_pub

Author: Sharon Lee

Edited by: Keith Fraga

I remember the day I walked into her office for an interview.

Dr. Tama Hasson, Director of the Undergraduate Research Center-Sciences at UCLA, had been doing this for a while and knew that a sure way to comfort a nervous student was her big, encouraging smile. Before I knew it, within the next fifteen minutes of our meeting, she laid out my entire academic plan and became one of my first mentors! At that time, I only knew about my interest in research. I had just joined a lab to satisfy my growing scientific curiosity. But I didn’t know anything about graduate school.

As a first-generation college student and the only one in my family pursuing a PhD, I am grateful for the support and guidance I received through the years from my mentors! Finding good mentors has been a skill I have tried to develop over the years and I hope to share a few things I have picked up about how to be mentored.

What is mentoring and how important is it to find a good mentor?

Image credit: “Piled Higher and Deeper” by Jorge Cham www.phdcomics.com

I like the definition of mentoring from the American Association of Pharmaceutical Scientists: mentoring is a relationship between two individuals (a mentor and a mentee) based on a mutual desire for development towards career goals and objectives.

In graduate school, the most important mentoring relationship is the one that develops between graduate students and their thesis advisor (research mentor). It is also one of the most sensitive relationship and sometimes, can be challenging to maintain.

As an undergraduate, all I focused on was the type of research I was interested in. When I was looking into labs to join, I prioritized the research topic over everything. It was not until much later that I realized finding a good faculty mentor is more important than working on a particular project. First-year graduate students tend to forget this when choosing their thesis labs.

Dr. Daniel Starr, Professor and former BMCDB Chair, agrees that a match between a graduate student and a faculty mentor is more important than the project. As scientists, we should be excited about a variety of different projects, but “the match is essential” for a successful and nourishing graduate career.

To collect some thoughts about mentoring from other faculty and students, I circulated an anonymous mentoring survey within the BMCDB graduate group. All 18 faculty who responded to the survey also agreed that good mentoring is very important for a graduate student’s training.

What is key for a successful mentoring relationship?

When asked what is key for a successful mentoring relationship, the response that I received from the majority of faculty and students was communication. Clearly communicating one’s expectations from a mentoring relationship helps to avoid any misunderstandings that may arise from unspoken assumptions about the roles and responsibilities of a mentor and mentee.

Dr. Starr, who has mentored 9 graduate students, also added that because “every student needs a different mentoring style”, mentors need to be “flexible and patient” with their students. It was encouraging to see that 94% of the BMCDB faculty surveyed were open to changing their mentoring style to meet the needs of their graduate students.

In addition to communication, Dr. Steve Lee, Graduate Diversity Officer from UC Davis Graduate Studies, believes an important factor for a successful mentoring relationship is self-awareness. Self-awareness is critical because both mentors and mentees need to recognize the way they best communicate their ideas and how they best receive feedback. A high level of self-awareness helps recognize when there is a dissonance between you and your mentor/mentee. It allows you to put aside your differences and work collaboratively to meet shared goals.

Dr. Lee suggests that regular self-assessment is a good practice for graduate students to understand where they stand. Particularly for women and students from minority backgrounds who experience higher levels of imposter syndrome, communicating with one’s mentor can be intimidating. Self-assessment can be used as a strategy to overcome imposter feelings and take actions to move forward. Dr. Lee recommends for the students to mentor up!

What is Mentoring up?

“Mentoring up is a concept that empowers mentees to be active participants in their mentoring relationships by shifting the emphasis from the mentors’ responsibilities in the mentor-mentee relationship to equal emphasis on the mentees’ contributions.

This term was conceptualized by Dr. Lee with colleagues back when he served as the Assistant Director of CLIMB. They came up with this idea to encourage students to proactively engage with their research mentors for an effective mentoring relationship.

The core principles and framework of mentoring up is described in Chapter 7: Mentoring Up”: Learning to Manage Your Mentoring Relationships, in the book, “The Mentoring Continuum – From Graduate School through Tenure”. In this chapter, the authors provide strategies for mentees to consciously contribute and guide their mentoring relationships through difficult situations, avoiding passive patterns of behaviors that may limit their own success.

I highlighted below three of the seven core principles and strategies of mentoring up that graduate students (mentees) can use to foster their mentoring relationship:

Maintaining Effective Communication. It is important that mentors and mentees seek to understand each other’s communication styles and take time to practice communication skills, particularly when their preferred method of communication is different.
- Determine your mentor’s preferred medium of communication and acknowledge if it differs from your own personal preference.
- Schedule a regular time to meet with your mentor and prepare for the meetings by articulating specifically what you want to get out of the meeting.
- Keep track and share progress toward project and professional goals, both verbally and in writing.
Aligning Expectations. With clear expectations, mentoring relationships are more likely to be productive. Problems and disappointment often arise from misunderstandings about expectations. In order to avoid such misunderstandings, expectations should be clearly discussed and realigned on a regular basis as they may change over time.
- Ask your mentor for his or her expectations, and also share yours, regarding your research project, role and responsibilities of being a graduate student, and your professional career goals.
- Ask others in your lab about your mentor’s explicit and implicit expectations.
- Write down the expectations you agree to with your mentor and revisit them often.
Assessing Understanding. Determining how well you understand your mentor as well as how well your mentor understands you is not easy, but is crucial for a productive mentoring relationship. Develop strategies to critically assess each other’s understanding.
- Take a minute to consider any assumptions you have made about what your mentor knows or does not know about how well you understand your project.
- Ask questions when you do not understand something. If you are afraid to ask your mentor directly, start by asking other lab members and peers.
- Explain your project to someone who is not familiar with your field and help them to understand your project and its significance.

I asked my thesis advisor once to re-explain some concepts about my research project which I did not clearly understand. I was worried that he would be unhappy about having to repeat himself. But in hindsight, I am glad that I asked my questions because my advisor was equally pleased to have clarified my confusion. He actually appreciated my initiative to clear my misunderstanding.

We students so often assume that our advisor will react negatively to our mistakes and lack of understanding, which leads us to make an even bigger mistake of not openly communicating. 75% of the students surveyed reported that despite being not extremely happy with their thesis advisors, they did not talk with them about improving their relationships.

Image credit: “Piled Higher and Deeper” by Jorge Cham www.phdcomics.com

How to get the best of all worlds?

One of the common mistakes that graduate students make during their early years is to expect their thesis advisor to fulfil all the different roles and responsibilities of a mentor. They often need to be reminded that no one can do it all, that one mentor cannot provide all the guidance and support that a student needs. Effective mentoring is a community effort and thesis advisors should encourage and assist their students with finding other mentors with complementary skills and knowledge. Some examples of people who can make an excellent additional mentor include senior PhD students, postdocs in your lab, faculty you rotated with, and your thesis committee members. It is also a good practice to maintain your relationship with old mentors from previous institutions.

Graduate students can also actively seek out mentors on their own. As a woman in STEM, I look for opportunities to engage with female scientists and identify women mentors. I love this quote from The Atlantic about How Women Mentors Make a Difference in Engineering: “It’s not that having a female mentor increased belonging or confidence – it just preserved it.” “They act as a “social vaccine” that protects female students against negative stereotypes and gives them a sense of belonging.”

Do remember that building an effective mentorship takes time and maintaining it takes effort. Mentorship is a work-in-progress and a long-term investment! Practice humility and be willing to adjust or compromise to achieve your mentorship goals. However, if the relationship is not working, take charge and do something about it. I greatly appreciated when Dr. Starr encouraged students to do the same. He said that “students need to know that some matches don’t work, like a large percentage of matches don’t work” and it is fine to change labs and find a new mentor who can help you be successful. “Graduate school is hard enough as is … hopefully you find a match that makes graduate school fun, hard but fun.”

Resources:

National Research Mentoring Network (NRMN): NRMM is a nationwide consortium of biomedical professionals and institutions collaborating to provide trainees across the biomedical, behavioral, clinical and social sciences with evidence-based mentorship and professional development programming.
Questionnaire for Aligning Expectations in Research Mentoring Relationships: a tool to help beginning graduate students to align their expectations with their thesis advisors. Also helpful in assessing where you stand compared to other graduate students in the lab, among your cohort, and/or within the graduate group.

Let’s destigmatize the conversation about impostor syndrome!

By Linda

On March 1, 2018

In main_pub

All 26 BMCDB graduate student respondents self-identified as having experienced impostor syndrome

Author: Linda Ma

Impostor syndrome has been experienced by most students and academics to some degree, but rarely openly addressed. It is something that I have struggled with throughout my entire academic journey. My peers had always seemed so put together, so self-assured. In the meantime, I never felt good enough, never deserving enough. In short, I felt like an impostor.

Impostor syndrome is defined as being plagued by constant self-doubt and the fear of being found out as an ‘intellectual fraud’ (Villwock et al., 2016). Dr. Terrance R. Mayes, Associate Vice Chancellor of Diversity and Inclusion at UCI characterizes impostor syndrome as attributing one’s success to luck, to connections, to being in the right place at the right time, rather than due to one’s own merit.

I couldn’t put a name to my own feelings of impostor syndrome until the summer of my senior year in undergrad when I took part in a summer research program. The program coordinator sat us all down in a lecture hall and proceeded to describe me to a tee. In that moment, everything clicked.

Still, there was a stigma about discussing impostor syndrome with my peers. Putting a name to my feelings didn’t mean an immediate cure. In my first quarter of graduate school, more than ever, I was plagued by feelings of self-doubt. Balancing the course load with lab rotations was overwhelming, and I always felt like a disappointment. Nothing I ever did felt good enough.

Given how impostor syndrome is usually discussed behind closed doors, I was pleasantly surprised by how many students and faculty were willing to openly share their experiences with me.

I circulated an anonymous survey to the BMCDB graduate students and 100% of the 26 respondents reported that they have experienced imposter syndrome in some form. Respondents ranged from first years to sixth years.

While chatting with Dr. Steve Lee from Graduate Studies, he brought the Clance Impostor Phenomenon Scale (CIPS) to my attention. CIPS was developed by an Atlanta based psychologist, Dr. Pauline Rose Clance. CIPS numbers range from 20 to 100, with those scoring higher than 80 experiencing intense IP (impostor phenomenon) tendencies. Completing this short evaluation does not constitute an official diagnosis but may put your impostor syndrome into perspective. Taking the assessment helped me confirm the intense impostor syndrome that I’ve been experiencing for most of my life. Moving forward, I have found myself being a lot more open with expressing these feelings to my PI. I would be interested in knowing how members of the UC Davis and broader scientific community fall on this scale.

I was surprised to find that Dr. Anna La Torre (Assistant Professor), and Dr. J. Clark Lagarias (National Academy of Sciences Member, Distinguished Professor, and current BMCDB Chair) have both struggled with impostor syndrome. Strangely, this was reassuring to me that such successful professors have grappled with the same issues that I have been suffering from.

Dr. La Torre brought the following to my attention, “It affects women more than men and individuals from underrepresented groups are even more susceptible. So, if you are like me, a woman and a minority, chances are that you feel like a fraud.”

First year Abby Primack voiced similar views that “women, people of color, and other marginalized communities” especially feel this.

It’s important that graduate students and the broader scientific community know that impostor syndrome is common, and there should be no shame in owning up to it and having an open dialogue with your peers.

I have been coping with my impostor syndrome by confiding my fears to members of my cohort and those close to me. Secondly, my PI has been an unwavering force of support.

A common theme among the faculty and students that I surveyed was that talking about our experiences with impostor syndrome was key in overcoming or managing our feelings.

Students surveyed were all very adamant about talking to professors, colleagues, advisors, older students, and “people who believe in you and support you and can bring you up when you doubt yourself.”

One third year student quipped that you need to “fake it ‘til you make it.”

When second year Anna Feitzinger gets overwhelmed and intimidated by graduate school she takes a deep breath and reminds herself of how far she has come, and that she got into graduate school for a reason.

An anonymous fourth-year student advised, “Make a habit of being courageous, taking risks and working outside of your comfort zone. You will likely realize that the community is more supportive and less critical of your competence than you are.”

Sixth year Matt Blain-Hartung says that the “only way to overcome this is to… push forward and stick up for yourself. Eventually you will win some arguments with your boss/ post-docs and remember that you deserve to be here.”

For Dr. Lagarias, Cognitive Behavioral Therapy and support from family and friends have been key resources. “It is easy to lose perspective when we are all trained to over-hype our own accomplishments to ‘be successful’.”

Dr. Lee believes that a balance must be struck between being too arrogant and being too encumbered by one’s impostor syndrome to be motivated.

However, there is no one-size-fits-all way to manage one’s self-doubt. Coping mechanisms which work for one individual may not work for another. It is important to find what works for you.

Dr. La Torre said something that really resonated with me and many of the student survey respondents, “Avoid comparing yourself with others. We are surrounded by amazing, talented and successful people. You don’t need to be Einstein to achieve your goals, so stop comparing yourself to that person. It’s important to admit that you had some role in your own successes. It was not all pure luck, and nobody belongs here more than you.”

This article by no means serves as a ‘how to guide’ for overcoming impostor syndrome. I mean it only as a stepping stone to an open discussion about something that most of us suffer from but are too afraid to talk about. Perhaps there is a way to bolster our scientific community and address the mental health issues that we face as academics. We, the meek scientists, must stop keeping our fears bottled up.

Edited by: Sharon Lee

Additional resources:

References

Villwock, J.A., Sobin, L.B., Koester, L.A., and Harris, T.M. (2016). Impostor syndrome and burnout among American medical students: a pilot study. International Journal of Medical Education 7, 364-369.

Finding Your Way: Choosing a Thesis Lab

By Staff

On February 2, 2018

In main_pub

Contributing authors (alphabetical order): Emily Cartwright, Anna Feitzinger, Keith Fraga, Hongyan Hao, Jessica Huang, Sharon Lee, Linda Ma

Congratulations, you’ve made it past the harrowing applications, nerve-wracking interviews, and awesome recruitment food! The first year in graduate school can be difficult, as you juggle coursework with organizing rotations and looking for the lab you’ll be dedicating the next 4-6 years of your life to. The question of which lab you will join is the question that you think about all the time, and rightfully so. The experience and relationships you make during your PhD are transformative. But there are many variables to consider and reaching a final decision on which lab to join can be a challenge!

All of us here at BioScope have gone through the same process, and we have some ideas that just might give first-year graduate students another perspective on deciding on a lab. In some ways, this is an advice column, but definitely not a “How to” article. We don’t know of a magic bullet that makes this decision easy. Part of the process is actually experiencing the process itself: all of the highs and lows, all of the epiphanies and backtracking, and the feeling of finally deciding. So let’s get started!

Getting through rotations!

Perhaps the first step in deciding on a lab is doing rotations. Granted, some disciplines and graduate programs do not operate on a formal rotation schedule. However, in general, there is a period of time during the first year where you will have the chance to rotate with a lab that you are interested in. The “Car Dealership Test Drive” analogy works perfectly here. What better way to experience a lab environment, the research they do, and how you work with the PI more than doing a rotation with them?

Specifically, here at UC Davis, many graduate programs provide great resources for finding faculty to rotate with. Don’t forget that you can look in other departments as well! UC Davis has diverse faculty, covering a range of fields that you will definitely find something that you’re interested in pursuing.

While shopping for a car, you can test drive as many cars as you want, which is not the case in graduate school. You can only participate in a limited number of rotations. Therefore, there can be a lot of planning and reflection that goes into who you should rotate with. There are two things we want to stress about managing rotations:

(1) Know what you want to study – or what you DON’T want to study – to a point where you can narrow down the labs you are interested in. Having the self-discipline to focus your interests is critical for decisive rotation decisions.

(2) Rotations are less about the progress you make in the short amount of time in the lab, and more about getting a feel for the lab. In the rotation, you receive a small project, and in the hopes of impressing the PI, the lab, and your peers, you devote a lot of energy to generating results. Striking gold during a rotation (such as getting results that will contribute to a manuscript) is rare, and not something to bet on. Instead, it is much more efficient to devote your attention to being in lab, experiencing the group, learning how you work with the PI, and gaining a solid grasp of the research program.

Honesty and Realism goes a long way

An important thing to remember when looking for rotation labs is to be realistic. You can’t be searching for a lab that studies microRNAs in brain development by day and cures Down syndrome by night. Even a lab with diverse projects maintains very specific and well-defined areas of interest. Having ambitious goals and ideas are great, but the key is to not pigeon-hole yourself to a point where every lab you come across doesn’t quite do everything you are excited about. Your perfect lab does not exist. You have to let your scientific interests grow and develop, and allow yourself to be mentored.

This goes to a deeper point about graduate school. It is not so much what you do, but how you do it and learning the skills to be a scientist. It is very common for individuals to work on something totally different from their thesis research after graduating. Doing a PhD helps you sharpen the tools to study a variety of problems. Getting a PhD is more about the training, and finding a lab is more about fit than it is about field.

Handling uncertainty is key

As mentioned above about rotations, knowing your interests is key to to deciding which lab to join. This is part of “Knowing yourself,” which consists of answers to questions like, “What am I interested in?”, “What type of research environment do I work best in?”, “Do I want a PI that is hands-on or hands-off?”, “What do I want to do after my PhD? And how can my thesis lab facilitate that?”, and many more. You can answer these questions by thinking back to labs you’ve worked in before and what you liked and didn’t like about them. With each rotation, you’ll be able to get a clearer idea of what your answers to these questions are.

Deciding on a thesis lab can be roughly split into concerns of two types: concerns that you can control, and concerns that are beyond your control. What we want to highlight is an appreciation of the difference between what you have control over (your attitudes, your interests, your effort) and things you cannot control or predict (how your relationship with your PI will develop, how funding will change, how experiments will go).

The major pitfall in deciding a thesis lab is being too worried about things that you cannot control. We are all concerned about choosing the “wrong” lab, becoming stuck in a situation where we need to switch advisors. In those cases, the relationship with the PI deteriorates due to a host of reasons. You cannot forecast these changes to your relationships. You do your best to address problems early on and find solutions. Appreciating the things that you can control gives you a tool in making your decision.

Things you should ask yourself

Choosing a thesis lab is a very personal process. It is about you, and you finding your way through graduate school. All of us here at BioScope arrived at our respective labs in different ways, and we pondered different concerns. However, we have recognized a few questions you should ask yourself. These are questions that you do not need the answer to right now. These are questions where your answer will change over time, maybe every 5 minutes! Nevertheless, these are some questions that are meant to get you thinking.

The Research

Do I love the science, and am I excited about the unanswered questions in the field?
Can I see myself truly enjoying reading papers in this field?
Am I willing to perform the literature searches necessary to fill in my gaps of knowledge?
Can I imagine performing the essential lab techniques on a daily basis, becoming an expert in the lab’s tools?

The Thesis Advisor

Can I see myself working with this PI for the next several years?
How comfortable do I feel communicating with the P.I.? Is it easy to have a conversation and brainstorm ideas?
Do I do better when the P.I. has an open door policy (questions always welcome), or can I be productive without meeting with my P.I. once a week?
What is the PI’s track record with other PhD students? What do other people say about the lab?
Is my PI supportive of my future goals?

The Environment

Can I have enjoyable and intellectual communications with the other students/post-docs, or do I feel like there are unpleasant interactions?
Do I prefer a lab that’s more social, or one where everyone goes into lab just to get the work done?

The grass on the other side is still just grass

Finally settling into a lab is a wonderful feeling; It’s like finally finding a home. And yet, we still have our difficulties. We still have our miscommunication. We still sometimes ponder if we made the right decision. It is very natural to have these questions because, like we said, there is no magic bullet, no recipe for doing this. And as scientists that strive for some degree of precision and exactness in our lives, this is hard to wrestle with. A lab is not perfect when you join. It takes dedication, patience, and communication to create a PhD training perfect for you. So keep calm, and carry on.