On the Importance of Being a Scientist

As a Graduate Student Researcher we can identify as a student, teacher, or even an employee. But do we ever identify as a scientist? And if not, why not?

On a whim, I introduced myself as a “scientist” rather than a grad student in front of a large group of non-scientists. After explaining my unusual school situation several times to non-scientists after moving to LA, saying “scientist” just seemed easier. Despite the word scientist not appearing in my job title, I didn’t think I was wrong. After all, I have 2 degrees in biochemistry, am working on my third, and my days are spent designing and conducting experiments. Additionally, graduate students and post docs carry out a large portion of the NIH and NSF funded cutting-edge research that continues to place America as an innovative leader. I do the things that scientists do, so why couldn’t I call myself a scientist?

So I was surprised when someone, after finding out that I am a 5th year PhD student rather than a fully employed “scientist,” responded with “Oh, I thought you were a real scientist.”

Real scientist, eh?

superscientist

I’m going to call this image “Super Scientist”…Me. Wearing a lab coat. Because that’s what real scientists do, right?

I wasn’t offended. Graduate student researchers walk a blurry line between student and employee—and that’s not necessarily well-known in other areas. While a masters student in accounting may spend his or her days taking classes and doing projects, a masters student in science usually does research and teaches college courses.

 

However, the comment did get me thinking about my identity as a student and as a scientist and how that has changed over the years. In graduate school, we identify ourselves by our current year in the program. Our year describes our experience, knowledge, and what challenges we might be facing in coursework, teaching, and exams. Saying I was a “first-year grad student” meant that I was drowning in coursework and teaching while trying to find a lab to call “home”—senior grad students took pity on me with a reassuring “if you can get through first year, you can get through grad school.” Because I was never expected to know how to do anything or work independently during that first year, I didn’t. And I was okay with that. I checked with my advisor or lab manager before every experiment and ran to one of them with every issue I faced rather than attempting to figure it out on my own. As a fifth-year student, I still don’t know everything, but the label comes with more confidence. People ask me where things are and how to perform protocols. They value my opinion for experimental design and interpreting results. I work more independently, trouble-shoot issues on my own, and sometimes even solve problems for others.

Yes, experience plays a large role here. But how much does our self-identification play into our ability to succeed?

In their book “Switch: How to Change Things When Change is Hard,” Chip and Dan Heath say to “cultivate a sense of identity and instill the growth mindset” when trying to instill change.1 This can be change within ourselves, others, or a company. They argue that when we label ourselves differently, making the change is much easier. For example, a student that is not doing well in math will never improve if they label themselves as “bad” at math. Instead, by instilling a growth mindset that says “Math is hard. But you are smart. And if you work hard, you will get better at math,” students are much more likely to improve. Similarly, if we tell ourselves that we are “only a first-year” or “only a student,” we may never push ourselves to be an independent researcher during graduate school. The reverse can also be true. If the label “student” is only applicable when in traditional learning environment, we would never learn new things and stop progressing.

How we identify ourselves and others can have a huge impact on our success. The next time you catch yourself saying “I’m only a student” or any other phrase that minimizes your knowledge and contributions, think about the implications. Yes, we still have a lot to learn, but we will always have a lot to learn. Use what knowledge you have now and let it grow—I bet you will be able to go a lot further.

1 Switch: How to Change Things When Change is Hard. Chip Heath and Dan Heath. Crown Business. 2010.

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Star Wars, Frodo, and Scientific Presentations

You may not know it, but a scientific presentation can be as thrilling to watch as Star Wars Episode VI! *gasp* Did she just say that?! How can that be? Science is boring! Scientists are boring! They can only speak in monotone voices! There is NO WAY science can be exciting. When you break down the common components of a scientific presentation, it can be easy to see how science can come across as boring.

  1. Introduction: Relevant background is introduced to set the context for the remainder of the presentation.
  2. Question: What scientific question are you asking in your research? What is your hypothesis?
  3. Results: Data that answers your question and supports your hypothesis.
  4. Conclusion: A summary of the results and how they support your hypothesis.
starwars_jd-hancock-creative-commons

Photo by JD Hancock under Creative Commons

But science IS exciting. A well-told scientific story contains all of the components of a dramatic film following an unlikely hero on an impossible journey (think Frodo and the Ring). Except the scientist is that hero—the protagonist on a quest to solve a problem so challenging that no one has been able to solve it before. What if we rewrite the common components of a scientific presentation with a little more storytelling flair?

  1. Introduce the characters and establish a backstory. This is important information for the audience to understand the context of the presentation Think about how quickly we learn about Luke’s unusual talents and his orphan status in Episode IV. What are the main things your audience needs to know to understand the rest of your presentation? Don’t forget to refer back to these things throughout the story as a reminder!
  2. Present the Quest. What problem are you trying to solve? Why is it important? What have other people done and how did they fail? What are you going to show us that is different?
  3. Begin your journey. You’ve presented your goal, now how are you going get there? Your plan of attack shouldn’t be a secret. Layout what you plan to do so the audience has something to follow—like a map with the trail marked. However, don’t feel like you can only talk about the positive experiments. Whether it is due to limited time or a scientist’s ego, many researchers only address the successful parts of their journey. No story is interesting without the hiccups along the way. A story that followed Frodo simply walking to Mount Doom with no challenges along the way would have been extremely boring. Although not ALL trials need to be addressed, a thoughtful presentation that includes some of the dark alleyways of failed experiments inherent to research adds color and intrigue to the story.
  4. Plot Twist! Along with number 3, the twists and turns of a scientific journey provide excitement. Did your original hypothesis change after a key experiment? Did a lab mistake result in a successful result therefore changing the trajectory of your research? Did you have an “Aha!” moment?
  5. The Happy Ending. No story is complete without a happy ending. Science is an ongoing multi-part series. Each episode has a feeling of resolution that leaves the audience feeling comfortable, but still a little excited for what comes next.

Science is Fun and Exciting! As scientists we can sometimes fall into the trap of boring presentation structures simply because that is how people have always done it. But we don’t have to! Your research is exciting. Just make sure other people know that as well.

When cells don’t need chemical signals to find a wound after injury

Evolution over millions of years has given us the ability to function in our environment with little conscious thought—our heart pumps blood throughout our body, our digestive system pulls nutrients out of food, and when we get a cut, our body magically heals itself. But what if these things didn’t work? What if we had to tell our heart to contract like we tell our biceps when lifting a heavy box? What if digesting food required conscious thought or wounds didn’t heal? We probably wouldn’t survive very long. Luckily, our “built-in” systems keep us alive and thriving.

One of these built-in systems is wound healing. After getting a cut we might worry about how much it hurts or how long it will last, but we don’t have to consciously focus on healing. In order to function automatically, the cells that work to heal the wound need a way to know (1) that the wound occurred, (2) where the wound is, and (3) the size of the wound. And they need to know quickly. Cells gather this information using sensors that look for specific damage signals called DAMPs (damage associated molecular patterns). DAMPs form chemical gradients that alert surrounding cells that damage has occurred and the location and severity of the wound. (You can read more about DAMPs in my previous post HERE.) But although it has been well established that chemical gradients created by DAMPS are used to alert cells of an injury, scientists in the Philip Niethammer* group asked whether a mechanical sensor that indicates tissue damage would also be possible.

chatty-cells

After an injury, cells need to communicate with each other in order to find and heal the wound.

Unlike chemical sensors, mechanical sensors rely on physical sensations such as motion, temperature, and pressure. One potential biological mechanical sensor is cellular swelling.¥ Cellular swelling can result from tissue stress such as wounding and has been associated with recruiting leukocytes (white blood cells that are essential to protect the body from infection, especially at the site of a wound) to the injury site. The current theory to explain how cellular swelling recruits leukocytes involves the swollen cells rupturing to release DAMPs into the extracellular space (like a water balloon that gets too full and breaks). However, recent studies have demonstrated that cellular swelling can still initiate a wound healing response without cell rupture. These studies bring to light the potential role of mechanical sensors such as cell swelling in wound healing.

The first thing that the Niethammer lab found was that cellular swelling increased calcium (Ca2+) levels in cells surrounding the wound. The increase in Ca2+ caused cPLA2, a type of lipid found commonly in wound response, to move from the nucleoplasm (part of the inside of the nucleus) to the inner nuclear membrane (part of the outer ring, or “skin”, of the nucleus). Using this knowledge, the Niethammer group hypothesized that cellular swelling was sufficient to cause cPLA2 movement within the nucleus.

cellswellingfig

Cellular swelling causes cPLA2 movement from the inner nuclear membrane to the outer nuclear membrane. This process attracts leukocytes to the wound.

To test this hypothesis, the Niethammer group developed a novel method to make synthetic nuclei. Using giant vesicles made from dried lipids, they were able to mimic the “onion-like” inner and outer layers of the nucleus. After adding cPLA2 to the giant vesicles in the presence of Ca2+, they changed the environment of the vesicles to induce swelling. As they hypothesized, when the vesicles began to swell, cPLA2 moved to the outer layer of the vesicle. This means that cPLA2 movement only requires cell swelling and calcium! By working with only the bare minimum, they were able to strongly support their claim that mechanical sensing is possible in wound response which recruits leukocytes to the wound.

These experiments from the Niethammer lab are significant for a few reasons:

  • They have strong evidence to support a mechanism for wound sensing that differs from the current theory for how leukocytes are recruited to a wound. Mechanical sensing for wound response provides an alternative mechanism that may explain anomalies in cellular signaling. Furthermore, different areas of the body may require different sensing mechanisms. When thinking of wounds, you probably first think of wounds that happen on the outer layer of your skin, or your skin epithelial cells. However, there are epithelial cells throughout your body lining your organs and blood vessels to separate and protect them. Cellular swelling as a sensor is applicable to wounds such as those that occur in the digestive tract where the cells are in a hypotonic environment.¥
  • They developed a novel method to mimic nuclear layers that can be used to test how different extracellular environments can affect a cell. The giant vesicles are especially interesting because they reduce some of the complications that come from working with entire cells or organisms. Although it is important to take this complexity into account, a simplified approach allows researchers to isolate specific factors.
  • They show how simple biology can be. One of the beautiful things about biology is that, although constantly evolving to survive in ever-changing environments, it often takes the path of least resistance. That is, sometimes the simplest answer is the correct answer. Although other tissues may require more complicated sensing, biology takes advantage of instances when simple mechanical sensing is sufficient to relay an appropriate response.

*Enyedi, B.; Jelcic, M.; Neithammer, P. The Cell Nucleus Serves as a Mechanotransducer of Tissue Damage-Induced Inflammation. Cell. 165, 1160-1170, (2016).

¥ Cells swell when the inside of a cell is exposed to a hypotonic environment, or environment that has more water than the inside of the cell. Biology needs balance, and in order to balance out the amount of water inside and outside of the cell, water begins to enter the cell—therefore causing swelling.

When Your Advisor Changes Universities….

A personal anecdote of my decision to move to a new university with my PhD advisor

Things have been pretty hectic here in the Wollman lab for the past few months, and especially the past couple of weeks, as we pack up our personal lives and lab benches and head north to the other side of Orange County (as my advisor, Roy, likes to say). When Roy first announced to us in May that our lab was moving from UC San Diego to UC Los Angeles in August (only 3 months away) I experienced emotions ranging from excitement to fear to denial. I began to scour the internet searching for advice on whether to remain physically at UCSD or follow Roy to UCLA, but all I found were personal anecdotes of other graduate students in similar situations. What I realized was that the decision to stay or move is highly personal and depends on a number of factors. So, here I add my personal anecdote to the conglomeration of internet information. Hopefully my story will be helpful to fellow graduate students facing similar situations.

So you’ve done it. You’ve been admitted to a PhD program, joined a research group, and are chugging along in the research process when your PhD advisor announces that they are moving to a different university. Ugh. It’s not unusual for professors to change universities throughout their career. However, the mixed student/employee status of a graduate student can make the decision to follow your professor to a new university sticky.

Although many graduate students have a tense or otherwise negative relationship with their PhD advisor, my relationship with Roy has been very positive. He has been very supportive throughout my time in his lab of my goals and outside-of-lab endeavors. I can openly discuss my career plans with him without fear of backlash for hoping to leave academia following graduate school. He is patient with me as I learn new techniques and thinking methods. At the time of his announcement I was at the end of my 4th year of grad school. Two weeks prior we had discussed me graduating at the end of my 5th year. When the announcement came my first thought was “I’ll just graduate faster and not have to leave!”. Being this far along in my PhD meant that switching labs would be impossible, meaning if I want to graduate I need to stay with Roy. I didn’t want to leave behind my relationships with friends and colleagues that I had built for the last 4 years, not to mention my beautiful condo just minutes from campus and the beach. LA has more traffic, LA is more expensive (a big deal on graduate student stipend!), LA has too many people etc. I was upset. I wasn’t ready to leave San Diego. Up until this point I had been the decision-maker when it came to moving: I chose to attend BYU for my undergraduate degree and I chose to attend UCSD for graduate school. Furthermore, despite being accepted to both UCLA and UCSD for graduate school, a variety of reasons led me to choose UCSD. Being forced to live in Los Angeles did not make me happy.

That afternoon I spoke with Roy about graduating sooner. As usual, he was understanding and supportive. We outlined a plan where I could defend my thesis in December and work remotely from September to December after the lab had moved. Since UCLA is only a 2 ½ hour drive from San Diego (without traffic, that is), I could still come up once a week to check-in with Roy and the rest of the lab. The plan was to complete a few key experiments before the lab moved and spend my remote time analyzing data and writing papers and my thesis. Leaving that meeting I felt good about this plan. I already had a first author paper in a notable journal in addition to a first author review paper. I moved my anticipated graduation date up by 6 months and would still be able to squeeze one more paper out of my PhD. Sure, the following few months would be crazy as heck, but that’s grad school right? Most importantly, I wouldn’t have to leave San Diego. And that made me happy.

But, there was a problem. What about after graduate school??

At the beginning of my graduate school career I decided to try and follow the advice some older graduate students had given me: Work your butt off until you advance to candidacy. Then, during your last couple of years, reap the rewards of your hard work and let your research do its thing. Use your spare time to pursue other interests that will build your resume, figure out what you want to do after graduate school, look for jobs, etc. I liked this plan and did my best to follow it. My 5th (and final *crosses fingers*) year of grad school was meant for figuring out what I ACTUALLY want to do with my life and finding a career. Speeding up my graduation timeline would mean giving up the luxury of taking time to find a job, pursuing other interests, and spending time traveling over the summer with my sister (I’ve been in school a long time dangit! I want to take some time off J ). Furthermore, the results for my second paper were turning out to be less exciting than originally anticipated. It would be nice to spend some extra time to finish my PhD project on a high note.

And so, I decided to move with Roy to UCLA. After all, it would only be for a year. I have the opportunity to meet new scientists and expand my network. UCLA is only 2 ½ hours from San Diego. The beach is still close and the weather is warm.  And who knows what new opportunities I will find here?!

Officially I am still a UCSD student. Since I have already advanced to candidacy I am not able to transfer to another school. Instead I am considered a “University of California Intercampus Exchange Student”. Basically this means I still have the perks of being a UCLA student, but my tuition is paid to UCSD. Our lab space is completely new and beautiful. My apartment is close to campus. My dogs and I are starting to settle in. So far I’m happy with my decision to follow Roy, even though I miss the familiarity of San Diego. We’ll see what new adventures are ahead!

lajollaoverlook_2016sept07

One of my favorite spots in La Jolla. Only a 10 minute walk from my lab, I would come here when I needed a minute to clear my mind or take a quick break. Of course, I’m in my usual lab uniform of leggings, T-shirt, and a bun on top of my head. I make no claims to be a fashion blogger. 

 

I am a Scientist AND a ___________.

Embrace the AND: Work-Life Balance for Women in STEM to Promote Equality in the Work Place

Today is National Women’s Equality Day (apparently it is also National Dog Day, which makes this female scientist with 2 dogs very happy). I consider myself very lucky as a female PhD student in a STEM field in 2016. Female scientists before me have sacrificed in ways that I do not need to and have paved the way for acceptance and encouragement of PhD seeking females. My female role models throughout my many years of school have been in all stages of life from single to married to mother. All are intelligent women who have made great contributions to society in their roles as scientist AND woman/wife/mother/mentor/sister/aunt/etc. All of my research advisors (2 during my undergrad and my PhD advisor) are male. Each has been supportive of my career goals as a woman in STEM. In fact, my PhD advisor once told me “You don’t have to go into a specific career if you don’t want to. Just make sure the reason you aren’t pursuing it isn’t because you think you can’t because you’re a girl”. Still, as a PhD seeking woman, I often get asked the question “What are you going to do when you get married and have kids?”.

science AND

Perhaps it is this question that makes women wonder early on whether they will be able to fulfill roles as scientist AND mother. Maybe this is what makes many women feel that they need to choose one path over the other. A career in science has been traditionally thought of as one that requires COMPLETE devotion. Even many men (whereas most men never need to choose between fatherhood and a career) have forgone families in order to dedicate their lives to science. Although more women are earning PhDs than ever before (41% of STEM PhDs were awarded to women in 2009), the number of female scientists pursuing careers in academia does not hold the same proportion. * Further examination into the personal lives of these women has revealed that unmarried women and women without children are more likely to pursue and hold tenure-track positions in academia than married women or women with children. These statistics indicate that the lack of work-life balance in academic and STEM fields may be causing women to leave science.

Stereotypes and “traditional” attitudes are not the only factors preventing women from achieving a work-life balance. Policies regarding maternity and paternity leave in the United States force many parents to choose between a career and childcare. The United States is the only developed country with no guaranteed paid maternity or paternity leave. California was the first state to have a paid leave program for new parents and large companies such as Netflix, Facebook, and Virgin Airlines are working to offer more flexible plans to help new parents. These policies work to create a better work-life balance to recruit and keep talent. But can these same types of policies be applied to careers in science? After all, 36% of researchers with children report a negative impact on their career if they pursued a work-life balance. ǂ Statistics such as these beg the question: are we losing talented female AND male scientists who want to have a family or a more balanced career and life?

The National Science Foundation (NSF), a major funder of scientific research in the US, is working to incorporate policies to support a healthy work-life balance. Specifically, they aim to increase the placement, advancement, and retention of women in STEM disciplines. Some of these policy changes include¥:

  • Flexible deadlines and extensions for submitting grants
  • Supplemental money in grants for research technicians
    • In labs where the majority of experimental work depends on graduate students who do not cost very much money, an experienced research technician can be a valuable asset if the advisor is unable to devote all of their time to the lab. Research technicians are rare in new labs that have limited funding. However, this is the time that many people may want to start families and need to devote time to their personal lives.
  • Incorporate family-friendly practices and policies in NSF’s CAREER (early development program for professors), all post-doctoral programs, and graduate research fellowship program.

Basically, as a leader in science in the US, the NSF is working to lead by example to other funding agencies, universities, and scientists to change what it takes to be a successful scientist. These policies will hopefully take unnecessary pressure off of early-career researchers who have or hope to start families while trying to succeed in the world of academia.

But, when all is said and done, how do you actually improve your work-life balance?

The Association for Women in Science conducts a workshop to develop a personal plan to achieve the work-life balance that you want. Here are a few recommendations from the AWIS to achieve your own work-life balance, or, as they define, “the level of personal fulfillment and professional success that are right for you”:

  • Define your situation. Work-life balance is a personal decision. Define what your own values and priorities are that will constitute your own balance.
  • Develop a strong support system. Family, friends, and close colleagues can all serve as support, coaches, and mentors when trying to achieve your balance.
  • Plan and prioritize. Keep your focus on your pre-determined priorities and learn to say no to non-priorities. I love Galit Lahav’s article “How to Survive and Thrive in the Mother-Mentor Marathon” where she advises others to “compartmentalize your brain and calendar”. When you are working, be at work. When you are at home, be at home. Don’t worry about home when you’re at work and vice versa. This will make you more efficient and productive in the end.
  • Learn to say “no”. This one seems to be especially difficult for females compared to males with 55% of females struggling to say “no” compared to 47% of males in science. And saying “no” doesn’t only apply to tasks and favors colleagues, friends, and family ask of you. You might be saying “no” to doing your own laundry or cleaning (you can pay people to do that) or to how well a project needs to completed (is there a “good enough” point?).
  • Set guilt-free boundaries. If you need to leave work early to pick up a child from daycare, then come in early so you don’t need to feel guilty. Make others aware of your situation by setting clear boundaries from the beginning rather than feeling guilty later.
  • Recharge your batteries. Remember that you have to take care of yourself in order to be of any use to anybody else. Sleep well, eat well, take breaks, exercise, and do activities that you enjoy.

“Every time we are saying ‘yes’ to something, we are saying ‘no’ to something else.” –Tara Teppen of the University of Illinois, Chicago


*National Center for Education Statistics 2010-028; NSF SRS InfoBriefs 08-208, 11-305

ǂAssociation for Women in Science Work-Life Balance Executive Summary

¥ Balancing the Scale: NSF’s Career-Life Balance Initiative

Illuminating biology with biological glowers

Utilizing Biological Phenoma to study Biology: Bioluminescence

Quick: Is the glowing water in this picture photoshopped or real?

bioluminescent waves

Phil Hart [Copyright Phil Hart under a Creative Commons attribution-noncommercial-share alike 2.5 license]

The correct answer is real! Yes, there is such a thing as naturally occurring glowing water. And it is made possible by a phenomenon called bioluminescence.

Bioluminescence is a chemical reaction that happens in a living organism to produce a beautiful glow. Last month a few of my friends were swimming at La Jolla Shores and noticed that the water around them lit up with every movement of their bodies. What made the water glow? Phytoplankton emitting light when agitated—every movement from waves, currents, fish, or, in this case, swimmers, sent colorful flashes throughout the water. Wanting to witness it for myself, we went out again to experience the “glowing waves”. Unfortunately, we were too late in the season to experience the full beauty of bioluminescent plankton lighting up the waves, but by rapidly swishing our hands underwater, we were still rewarded with small sparks of light. Although my encounter with bioluminescence fell short that evening, I do get to see it in action every day in the lab.

Today I introduce how scientists utilize bioluminescent properties to study biological phenomena at the molecular, cellular, and organism level. Throughout history humans have benefited from the natural glow produced by bioluminescent organisms such as the use of dried fish skins as a source of light in coal mines instead of lamps. Usage of these organisms has led researchers to ask the question: what makes these organisms glow? Seeking to understand bioluminescence at a molecular level has led researchers to produce fluorescent “tags”. These “tags” can be attached to an unlimited number of molecules and proteins to answer fundamental biological questions.

Bioluminescence is a chemical reaction that takes place in a living organism to produce light. Although the most well-known organism to produce this glow might be the firefly, the majority of bioluminescent creatures are found in the ocean. Different organisms may vary in how they produce their unique glow, but the basic mechanism involves the enzyme* luciferase reacting with the light-emitting compound luciferin to produce light.

The beauty of naturally-glowing living organisms led researchers to investigate the underlying chemistry of this unique phenomenon. One researcher, Osamu Shimomura, began a lifelong relationship with bioluminescence when he found the structureǂ of luciferin in 1955. What followed was a quest to discover how different organisms produced their own unique glow. While investigating the bioluminescent jellyfish Aequorea victoria, Shimomura discovered green fluorescent protein (GFP). This discovery, and the consequent development of GFP, revolutionized biology. Scientists could now attach fluorescent proteins, such as GFP, to a molecule of their choice and literally watch biology in action by watching the fluorescently tagged molecules. In 2008, Shimomura, along with Martin Chalfie and Roger Tsien, received the Nobel Prize in Chemistry for their discovery and development of GFP.

Since the discovery of GFP, fluorescent proteins have been developed in a wide variety of colors for an extensive number of molecules and proteins. Although both fluorescent proteins and bioluminescence produce light, they work very differently. Rather than using a chemical reaction, fluorescent proteins produce certain light colors by using energy from other specific wavelengths of light. Fluorescent proteins create their unique glow when they are “excited” by a wavelength of light specific to the protein.¥ For example, GFP

GFPexcitationandemissionemits green light at ~510 nm after shining blue light at ~490 nm on the protein. By manipulating the protein, these light patterns can be optimized to produce different colors!

bioluminesenceTsien

Source: Tsien Lab

Researchers can use these proteins to image biological events in real-time and real-space. This process is called fluorescent microscopy. Fluorescent microscopes work by first hitting a sample with an excitation light. A camera attached to the microscope then catches the light emitted from the sample. When specific molecules (proteins, compounds, parts of cells, etc) are tagged with different fluorescent proteins, researchers can watch, analyze, and quantify what is happening—whether this is of molecules by themselves, inside of a cell, or even inside of an organism. Advancing technology in fluorescent proteins, microscopes, and other emerging biological approaches are pushing the limits of how small we can go (can we look at very specific interactions inside of a cell?) and how many things we can watch at the same time (can I see 6 things inside of a cell at the same time rather than only 3?). These advances are enabling us to find answers to critical questions such as:

  • Why do some cells act differently than others, even when treated the same? This question has applications in cancer research, healing responses, and why certain drugs work for some people and not others.
  • Can we predict the movement patterns of cells in response to a specific stimulation? Take a look at my previous post on wound response to see an example of the importance of understanding cellular movement.
  • What are the differences between the actions of a single cell and the actions of a population of cells? Single cells do not always act the same, and yet, a population of cells has a very predictable response. Why?

Although still young, the use of fluorescent proteins in biology is an exciting and continually improving field. By applying fluorescent microscopy to quantitative biology methods, we can better understand biological events to answer some of the most complex biological questions, such as those listed above. Most importantly, the resulting images provide a snapshot into the hidden world of biology by providing a new level of detail into how we function as living organisms.


*An enzyme is a protein that accelerates chemical reactions. Here, it accelerates the chemical reaction that makes luciferin light up.

ǂ In order to understand how things work, scientists often need to first find the structure of their molecule or protein of interest. Structures can be found using a variety of methods.

€ A wavelength of light is a unit of measurement in a light spectrum. That is, each color of light that we see has a specific wavelength—this is the visible light region (390 nm –780 nm).

Light Spectra

¥ Each fluorescent protein has a specific excitation spectrum and emission spectrum. A spectrum is a pattern consisting of peaks and valleys at different wavelengths across the visible light spectrum. This spectrum is unique for every fluorescent protein. For example, the spectrum of GFP has an excitation peak at ~490 nm and an emission peak at ~510 nm. ­ The emission spectrum consists of a peak that emits the color for that wavelength – the green that you see in GFP. This happens only after a specific wavelength of light, or the peak found in the excitation spectrum, excites the fluorescent protein.

GFP spectrum

 

Part 3: So you want to be a Scientist?? (or doctor, or dentist, or physical therapist, or lab technician, or…….)

Undergraduate Research at a Small University

Finding undergraduate research opportunities when you’re at a small university, primary undergraduate university (PUI), or community/ junior college can be challenging.  Professors at community/ junior colleges, and even at most PUIs, likely do not conduct independently funded research. Furthermore, if there is a research presence at the university, research options might be limited to a few disciplines with small research groups.

womeninscience_wikimedia commons

(Photo courtesy of NIH National Cancer Institute accessed via Wikimedia Commons.)

But don’t worry! Your future research dreams are not over just because you are attending a university or college with little or no research. In fact, there are quite a few advantages to being in this situation. Below is a list of the advantages of attending a non-research focused school in addition to some tips that may help you find a lab to work in during your undergraduate career.

  • Small university/college=small class sizes. Smaller class sizes mean that your professors will be able get to know you better (and vice versa). Good letters of recommendation can only come from professors who have had the opportunity to get to know you, which is more difficult in large class sizes. Additionally, professors at universities that are not focused on research do not have to devote as much, if any, time to research. That means they can devote more to the students.
  • Professors have connections. Even if professors aren’t currently conducting independent research, they most likely have conducted research in this past, either at the Master’s or PhD level. These experiences are valuable to learn from, and they may still have connections to former colleagues who are currently conducting research. Because your professor has been able to get to know you (see point 1!) they may be able to recommend you for research positions. Additionally, they will still have valuable advice and expertise on how to get into research, how to get to your next goal, etc.
  • Don’t fret about your research focus! One of the big secrets about undergraduate research is that your research emphasis doesn’t really The purpose of undergraduate research is to get a taste of what research is like, learn some basic skill sets, and start to learn how to think like a researcher. Therefore, just because you aren’t researching string theory or cancer or whatever else you think you might want to do for the rest of your life isn’t going to be the end of the world. My undergraduate research started in adiabatic calorimetry after which I moved to bioinorganic protein research. Neither of these have ANYTHING to do with quantitative biology or wound response, but they still gave me the experience I needed to get started on my research path. Even more, you may discover new interests by trying to research something you hadn’t considered before.
  • Summer opportunities are bountiful. Take advantage of summer opportunities at cool places! There are programs at larger universities specifically for students at colleges without research. Try e-mailing professors at a nearby university that has a heavier research component. Just because you aren’t a student there doesn’t mean you can’t work in a lab at that university. You can also look at national labs and opportunities abroad. Bonus: a lot of these are paid!
  • Taking time off between degrees is 100% okay! If you still feel you aren’t able to get the research experience you would like as an undergrad, take a year or two off after you graduate and find a “grown-up” research job. There’s no rush to start graduate school or any professional program. Take the time to figure out what your limitations are and get a taste for what science and research are like outside of a textbook. This will also strengthen your resume if and when you do apply for a higher degree program.

Don’t feel limited in your undergraduate research choices just because you aren’t at a major university. There are plenty of options to fulfill your research experience needs that may be more beneficial to your career in the end.

Special thanks to Katherine Nadler for providing insight into undergraduate research at a small university.

This is Part 3 in a series of posts for advice on doing undergraduate research. Find Part 1 HERE and Part 2 HERE.

 

How do cells find a wound after injury?

How do cells know where they are? It’s an important question we often take for granted, especially in situations like wound healing where cells that are closer to the wound need to respond differently than cells that are farther away. If cells don’t respond correctly it can lead to chronic wounds (wounds that don’t heal), excessive scarring, and even cancer. Here I highlight a study recently published in Currently Biology that demonstrates how hemocytes*  find their way to a wound. The Paul Martin Lab at the University of Bristol and the Michael P.H. Stumpf** group at the Imperial College London worked together using a combination of in vivo (meaning, experiments done in a living organism) wound data and computational simulations to answer the question of how hemocytes know which direction to travel following an injury in Drosophila (fly)*** embryos.

HowDoCellsKnowWhereTheyArev3

One way that cells figure out where they are is by using information from the wounded cells themselves. Injured cells release DAMPs (damage associated molecular patterns) which tell the neighboring healthy cells how far they are from the wound. To illustrate how DAMPs work, imagine you are sitting in the stands of the Shamu show (or what used to be the Shamu show, at least) at SeaWorld and you want to figure out how close you are to the tank. It should be easy enough, but here’s the catch: you can’t open your eyes and you can’t move. One way you could figure out how close you are is by measuring how wet you get when Shamu splashes the audience. If you are close to the tank, you will get soaked. If you are farther from the tank, you will stay dry. DAMPs work in a similar way. Cells that are closer to the wound receive a lot of DAMPs, and cells that are further away receive less. However, scientists still aren’t sure what exactly these DAMPs are and how they travel across cells to activate them to initiate a healing response. Here, Martin and Stumpf determine how DAMPs lead hemocytes to an injury.

Following an injury, hemocytes travel to the site of the wound to begin the healing process by following a gradient of DAMPs. However, the specific identity of these DAMPs and how they travel remains unknown. Since the technology to physically measure gradients formed by DAMPs is yet to be fully developed, the Martin and Stumpf groups developed a mathematical model to predict how the DAMP gradient forms based on how hemocytes traveled to a wound following an injury. They began by injuring flies and quantifying how hemocytes moved towards the wound. Quantifying hemocyte movement involved several parameters including how long it took the hemocyte to reach the wound, when the hemocyte began to move after the wound, and how many times the hemocyte changed directions while moving towards the wound.

The results of their experimental data combined with the computational model show 3 main points that differ from the current theory of DAMPs.

  1. The Martin and Stumpf labs found that DAMPs are released from the cells immediately surrounding the wound. This differs from prior predictions that DAMPs are released from the wounded cells themselves. The current theory of DAMP release is kind of like a water balloon that explodes when punctured. All of the water comes and gets anything in close proximity wet.
  2. The model revealed that there is only a single “wave” of DAMPS that lasts for only 30 minutes (as opposed to multiple releases over an extended period of time). This is significant when you think about how long a wound takes to heal-days and even weeks! That’s like taking a 2-week long road relying only on directions given to you in the first 30 minutes.
  3. DAMPs that recruit hemocytes to a wound travel by diffusion. That is, the healthy cells surrounding the wound do not use any sort of active mechanism to ensure that the DAMPs travel to the appropriate distance.

The Martin and Stumpf groups were also able to use their model to determine how hemocyte recruitment changes with multiple wounds, closely spaced wounds, and large wounds.

Multiple Wounds. For multiple wounds, they found that hemocytes become desensitized, or no longer respond, if the wound takes place less than 3 hours following the first wound. This makes sense when you think about how an organism needs to efficiently allocate its resources. If all of the hemocytes went to the new wound, then the old wound would not be able to continue healing. However, this might imply decreased healing for wounds occurring close to the first wound within a short time period. They also examined how hemocytes travel to wounds that are varying distances from each other.

Closely Spaced Wounds. Wounds that are very close together are essentially seen as “one wound” by hemocytes whereas wounds that are far apart are seen as two separate wounds. However, wounds at an intermediary distance displayed an interesting hemocyte behavior. Here, hemocytes between the wounds struggled to decide which wound to travel to, resulting in a decreased number of hemocytes at both wounds. It would be interesting to study whether this behavior causes wounds located at intermediary distances to heal less efficiently, but as of yet, no one has.

Large Wounds. The Martin and Stumpf groups studied the effects of very large wounds on hemocyte recruitment. Interestingly, they found that some large wounds healed appropriately while others did not. This is similar to clinical observations where chronic wounds cannot always be determined at the initial stage of wounding (meaning, you can’t tell if a wound is going to be chronic based simply by looking at it). This is the first time that a chronic wound model has been shown and will be of interest to future scientists to study what factors impact whether a wound will be chronic or not.   

So what does this mean in the broader world of science??

One of the most interesting thing that the Martin and Stumpf accomplished here was their ability to develop a mathematical model to predict the formation of the DAMP gradient. Mathematical models, although used heavily in other sciences such as physics and chemistry, have been slow to be adopted in biology. Biology can get messy, and therefore mathematical models can be difficult to implement. However, when technology to directly observe biological phenomena is still lacking, mathematical models can be a powerful tool. Although their model cannot tell you what the exact DAMPs released from the wound are (that will require more experiments), it provides a lot of clues to where researchers should be looking. This is a great example of the power of quantitative biology to solve biological problems.

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*Hemocytes is the term for blood cells in invertebrates. In this case the invertebrate is a fly. Hemocytes are a part of the immune system and are required in the wound healing process.

**Weavers et al., Systems Analysis of the Dynamic Inflammatory Response to Tissue Damage Reveals Spatiotemporal Properties of the Wound Attractant Gradient, Current Biology (2016), http://dx.doi.org/10.1016/j.cub.2016.06.012

***Why flies? The use of Drosphila embryos as a model is common in wound studies. They are transparent, making them easy to image under microscopes. Furthermore, flies are easy to genetically alter and, as far as immune response goes, work similarly to humans.

Part 2: So you want to be a Scientist?? (or doctor, or dentist, or physical therapist, or lab technician, or…….)

Practical Steps to Get Started in Undergraduate Research

Great Naomi. Thanks for Part 1 on getting started in undergraduate research. But how do I ACTUALLY find a lab??

Finding a lab to work in for the first time can be a little intimidating. How you go about doing this will depend on a few different factors including, but not limited to, research emphasis, university size, time limitations, pay vs volunteer preferences, etc. No matter your situation, here are a few steps to get you started in your journey to undergraduate research success.

    1. Come up with a list of professors to contact. The size of this list will depend on the size of your university where smaller universities will have fewer options than larger universities. Here are a few ways to come up with this list:
      • Write down some of your favorite classes and what you liked about them. Did you like the content of the class? Structure? Were the assignments interesting/fun/engaging? Is your opinion of the class based on the instructor? Based on this list, write down a list of professor’s names to contact. If you have had interaction with the professor, even better! (sidenote: always make an effort to have in-person interaction with any professor you take a class from. Even if the class has over 1000 students try to meet with the professor a few times over the course of the class)
      • Talk to your peers/upper classmen mentors/TAs. Ask which professors are taking undergraduate students and what the expectations are for undergraduates in the lab. Talk to your graduate student TAs (if you have them) and whether the lab they work in has undergrads and what the expectations are for them.
      • Go through your department directory and read professor bios/websites. Professors are notorious for not keeping updated bios or websites, but this will at least give you a general idea of the type of research a professor does. You can also see if they have a list of people in the lab and see how many undergraduates are working in the lab. Try looking at newer professors (at the associate professor level). These professors generally have more time to mentor students and may give undergraduates more responsibility than more established professors.
    2. Contact your list of professors. Simple enough, right? This might actually be the hardest part. If you have had interaction with the professor before, great. This will make contacting the professor 108, 439, 789 times easier. The next best thing is getting an in-person introduction from someone you already know in the lab. If neither of those 2 options is possible, go for the cold e-mail. Keep the e-mail short. Introduce yourself and tell them your major, year in school, GPA, pertinent classes you have taken (and the grades you earned in them), and a short sentence about why you are interested in doing research in their lab. You can also attach your resume/CV, but they might not read it. The best time to send cold e-mails is in the early afternoon (during or just after lunch) on a Tuesday or Wednesday. That way your e-mail won’t get lost in the abyss of e-mails professors wake up to in the morning (especially on Monday) and you won’t be forgotten over the weekend.
    3. And try again. If you don’t hear back from anyone within a week, try e-mailing them again as a “follow-up”. If you still don’t hear back, pick a few of your favorites and try catching them in their office. Professors aren’t as scary as you might think! Remember they are totally normal people…who happen to be really busy. If they are working at a university it means that a part of them enjoys teaching and mentoring. If you show that you are motivated to learn, professors will likely be more than happy to take you on.

Best of luck in your journey to find an undergraduate research lab home!

This is Part 2 in a series of posts for advice on doing undergraduate research. Find part 1 HERE and Part 3 HERE.

 

Part 1: So you want to be a Scientist?? (or doctor, or dentist, or physical therapist, or lab technician, or…….)

General Advice to Get Started in Undergraduate Research

The importance of undergraduate research experience on a resume is increasing as acceptance into graduate school, any healthcare related profession education, and employment opportunities in the scientific industry become more competitive. That is, as an undergrad, you NEED undergraduate research experience if you want to go to graduate school, go into a healthcare related field, or even to work as a laboratory technician in scientific industry. Although each situation is different (school size, what kind of program you want to go into, research interests, etc) here are a few pieces of advice to get you started in your pursuit of getting research experience as an undergraduate:

  • Get started ASAP! The sooner you get into a lab, the better. It’s okay if you don’t know what your EXACT research interests are yet. At this point, you probably need to get your feet a little wet to even figure out what type of research you enjoy. Science can sound a lot cooler in textbooks than it is on a day to day basis. Get in a lab. Learn some techniques. Start learning how to think like a scientist. After all, most graduate/professional programs aren’t looking for someone with experience doing XYZ, they’re looking to see if you have the capacity to analyze data, learn new things, and think like a researcher. Starting earlier will give you more time to contribute to the lab and hopefully get your name on a paper or two. Furthermore, you will have more time to develop a relationship with the professor which translates into a GOOD letter of recommendation.
  • Don’t be TOO picky…. At this point you don’t have very much, if any, research experience- especially if you want to join a lab earlier in your undergraduate career. Don’t fret if you aren’t doing research to cure cancer yet! Start by thinking about the classes that you have enjoyed the most and ask those professors if they have any space in their lab. If they don’t, look and see who is in their division/track/department (ex. if you really enjoyed molecular biology, look at the professors who teach molecular biology courses or are in the molecular biology division). Chances are you will be able to start learning basic techniques that will give you the foundation you need to succeed later on in your research career.
  • ….but choose your lab carefully. Be careful not to join a lab simply to get a letter of recommendation and be able to have it on your resume when all you did was wash dishes. Sure, sometimes you need to start at the bottom, but make sure that your time spent paying your dues will lead to research projects in the future. In the long run getting hands on experience is much more beneficial.
  • Find a professor who is willing to mentor you. Find out from your peers or upper classmen which professors are more likely to take on undergraduate students and actually mentor them. You might start by looking at associate professors who are generally more motivated to get research going and, therefore, may give you more responsibility. Younger professors also generally have more time to devote to training and mentoring. This can be beneficial not just for learning how to do research, but developing a relationship with a professor can be valuable for the rest of your career. As an undergrad you will most likely work closely with a graduate student or postdoc, but make sure that the professor knows who you are and how you contribute to the lab.
  • Record everything. Write everything down. Take pictures, videos, etc. Keep everything in a lab notebook to refer to later on. There is a steep learning curve when starting research and you will want to refer back to these notes later on. Keep everything as neat and organized as possible to make it easier on yourself later on. You may try writing things in lists while in lab and then going back later that day or week (but not too long afterwards or you will forget) and filling in the details of what you did. Keeping a good lab notebook is a skill that even the best scientist lacks. Believe me. Science will be So. Much. Easier. if you learn how to keep an organized lab notebook from the beginning.
  • Ask questions. Don’t be intimidated to ask questions. It is better to ask a question BEFORE breaking an instrument or ruining an experiment. However, don’t run to your grad student/postdoc/professor with every little thing. Spend ~15 minutes trouble shooting (Google is great!) by yourself and write down what things you tried before asking for help. This will help you start to think more like a scientist!
  • Try to work independently. Similar to number 6, try to work as independently as possible. You will probably still work closely with someone with more research experience, but don’t always rely on simply doing what people tell you to do. Try and get a small project as soon as possible (maybe after learning a few basic techniques in the lab). You may have to “prove” yourself first (for some professors, this is as simple as actually showing up to lab and wanting to do work) and it will definitely require more time and commitment, but in the end the ownership and pride you have over completing a project will be worth it!

Remember, your time as an undergraduate is meant to be spent learning and preparing for a future career. Don’t look at undergraduate research just as a requirement, but take the time to reap the benefits of having the opportunity to gain experience in a lab. This is one of the few places as an undergrad where you get to enjoy learning for the sake of learning and not just to cram for an exam or pull an all night-er to finish up a paper. Enjoy!

Stay tuned over the next few weeks for more advice on joining a lab as an undergraduate! I’ll be giving step-by-step tips to find a lab, research at a small university, research at a large university, and more!

Special thanks to Jessie Peters, Jamie Schiffer, and Katherine Nadler for input