SPARK Blogs

“Here’s what you missed this summer on the show, Coats…” by Ranya Odeh

EPISODE I:  Pilot

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First Day of SPARK Internship

I walked into the UC Davis Institute for Regenerative Cures feeling excited and anxious to embark on the 8- week long journey that is the CIRM Spark internship. My fellow interns and I nervously trickled into the conference room to attend the weekly Monday morning lab meeting. I watched as each person entered, wondering who would be my mentor for the summer.  After being introduced to the (many) lab members by our lovely lab director Jan Nolta, we made our way into a smaller conference room to endure an important (yet slightly tedious) lab safety training.  Then, after our first lunch together as interns, we then attended a guest lecture about stem cell therapies for advanced peripheral artery disease. At the end of the day, the moment I had been waiting for finally came. I got to meet my lovely mentor: Dr. Fernando Fierro, who explained that I would be working on Mesenchymal Stem Cell migration on the wound team, with a focus on the differentiation capacity of MSCs when they are Enter a captiontransduced with certain lentiviruses. I didn’t know what that meant yet, but soon enough, I would find out.

EPISODE II:  The Hood

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Changing media to MSCs in a biosafety cabinet

It was only the third day of the internship, and it was my turn to learn how to change media to transduced MSCs. I put on my stiff, white lab coat and sprayed 70% ethanol on my purple gloved hands. As soon as I my hands entered the biosafety cabinet, I felt my heart pound, not only because I was scared, but because I felt like I was finally doing something worthwhile—that I was contributing to legitimate stem cell research.  My hands were shaking I peeled the pipet wrapper and prepared to remove media from the T225 flask. As a dispensed the old media into a waste bottle, I froze. Did I just throw the cells away? My mentor felt my tenseness, and luckily, I was reassured that the cells actually adhered to the plastic of the flask, and I was barely able to let out a relieved laugh. This media changing became a procedure that I repeated so often this summer that my mentor even coined it the “Ranya method.”

EPISODE III:  The Bench

Along with work in “the hood,” I completed some procedures on the lab bench. I remember the first time I did a staining experiment, I ended up staining the bench mat more than the cells; but  I got better with practice, thanks to my mentors who I will always credit with teaching me how to pipet the right way.

EPISODE IV:  The Bay

One of the most rewarding experiences of working in the Nolta lab was getting to know my lab team as well as my fellow interns. From catching Pokémon around the lab to anxiously watching my mentors load a western blot, to coming up with enough episode ideas for an entire season of a hypothetical TV show called “Coats” chronicling the lives of lab researchers, this summer has been one for the (lab) books.

EPISODE V:  The End

I can say with total confidence that the SPARK internship at the UC Davis IRC has been the greatest learning experience of my life. I am extremely disappointed that it has to come to an end, but I will remain forever grateful to have been a SPARK intern as I embark on a (hopefully stem-cell filled) future career. Stay tuned for the next season of Coats, (starring me: incoming scientist, Ranya Odeh) coming next summer to a TV screen near you.

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Posing with my completed poster!

 

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My amazing lab wound team.

 

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Posing in the GMP (good manufacturing practice) facility gowning room.

 

 

 

 

 

 

Stem Cells by Aaron Nguyen

Stem cells. The building blocks of life. The cure for the future.

Today, schools are educating students on basic knowledge of the world and skills that are needed to succeed. However, many of these skills are being questioned by students on how they will be applied to the real world. Seeing real life applications of stem cells that I had only learned about theoretically in my biotechnology class has really opened my eyes to how knowledge being taught at school is bridged to the real world.

Nguyen, Aaron bunny suitsWorking at the UC Davis Institute for Regenerative Cures inside the GMP facility, I learned a lot about sterile laboratory techniques that are required for cell culture to engineer therapeutics that are used to treat patients. Culturing cells is not only about technique, but it also requires time and patience. Being taught just basic knowledge of cells at school, learning about cell therapy was different than I thought it would be. I never really thought about how cells can be cultured in vitro with growth factors that allow them to develop and expand. I was surprised by the complexity of creating therapeutics that are used to treat patients at the hospital.

Nguyen, Aaron hoodThe introduction to stem cells class that my mentor, Gerhard Bauer, is teaching has changed my perspective on stem cells and medical research in general. At school, I only learned about how stem cells have the potential to differentiate into other cells. In this class, we learned about the different types of stem cells (hematopoietic, mesenchymal, embryonic, and induced pluripotent) and how they can be applied clinically to improve the quality of life and reduce suffering. Guest lectures from notable doctors and researchers have also broadened my scope of the applications of stem cells. Cardiologist John Laird taught us how stem cells could be used to treat cardiovascular diseases, and neurologist Vicki Wheelock taught us about Huntington’s disease and the potential for stem cell treatment in other neurological diseases.

Stem cells really have broad potential to treat diseases, disabilities, and conditions in which no therapeutics exist.

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Behind the Scenes of Gene Therapy by Kelly Hongkham

 

“Gene therapy” – what is the significance of these two words?

For many, it spells out hope for a cure, for a chance at a healthier life, but at the Nolta lab, it is that and more. Here, the creation of gene therapies is a major basis of all the hard work and research that the Nolta team has dedicated their time to for over 30 years.

The ultimate goal is to treat currently incurable diseases and disorders through the manipulation of genetic material.

Simple enough, right?

Of course not.

Creating a successful gene therapy requires much more than targeting a defective gene and inserting a corrected one. In fact, just thinking about the multitude of research that is done every day in order to get just a little bit closer to a solution is simply amazing.

So, how does it work?

Over the past 8 weeks, I was given the incredible opportunity to peek into this world of research through the CIRM SPARK program, an internship which allows high school students to gain valuable experience working alongside professionals in a state-of-the-art research facility.

In all honesty, I was a bit overwhelmed. From day one, the other interns and I were taught all the ins and outs of working in the lab: what to do, what not to do, where to find this, where to store that, who to contact if something goes wrong, and, of course, the number one rule – ALWAYS wear your personal protective equipment. At first, I was worried because, knowing me, I would be the one to forget something and make a mistake. However, I quickly came to understand how friendly and supportive the Nolta team is and in no time, interning there became the perfect balance between hard work and fun.

At the Nolta lab, I had the honor of working in the Karyotyping Core alongside my amazing mentor, Catherine Nacey. From her, I learned the techniques for chromosomes analysis. Karyotyping is just one of the many molecular assessments important for quality control.

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For me, the most challenging part of the karyotyping protocol was learning how to identify each of the 23 pairs of human chromosomes. Now, even though you might think that they could be identified just by length, it definitely isn’t that easy. Believe me. However, fortunately, my mentor was very patient with me and within 2 weeks, I went from “Well… that’s definitely a chromosome” to “That’s an 11, I mean look at that wide heterochromatic region. And those dissipating bands on the q arm, come on it’s so obvious”.

Okay. Maybe I’m exaggerating just a little, but my mentor definitely has that level of confidence. Even now, I am still amazed by how rapidly she is able to identify chromosomes on even the worst-quality metaphases.

So, what happens from there?

After quality control, what’s the next step?

I could tell you briefly about how other research works, but it would not be as in depth as what I could tell you about karyotyping from harvesting the cells, to making the slides, to the final report. Even with all that I have learned this summer about gene therapy research, there is still so much that I do not know, and after getting a taste of what it is like, I want to know more. I have been inspired by all these passionate researchers and I look forward to being a part of the exciting gene therapy breakthroughs that will occur during my lifetime.

 

 

#CIRMSparkLab by Jamey Guzman

When I found out about this opportunity, all I knew was that I had a fiery passion for learning, for that simple rush that comes when the lightbulb sputters on after an unending moment of confusion. I did not know if this passion would translate into the work setting; I sometimes wondered if passion alone would be enough to allow me to understand the advanced concepts at play here. I started at the lab nervous, tentative – was this the place for someone so unsure exactly what she wanted to be ‘when she grew up,’ a date now all too close on the horizon? Was I going to fit in at this lab, with these people who were so smart, so busy, people fighting for their careers and who had no reason to let a 16-year-old anywhere near experiments worth thousands of dollars in cost and time spent?

I could talk for hours about the experiments that I worked to master; about the rush of success upon realizing that the tasks now completed with confidence were ones that I had once thought only to belong to the lofty position of Scientist. I could fill pages and pages with the knowledge I gained, a deep and personal connection to stem cells and cell biology that I will always remember, even if the roads of Fate pull me elsewhere on my journey to a career.

The interns called the experience #CIRMSparkLab in our social media posts, and I find this hashtag so fitting to describe these last few months. While there was, of course, the lab, where we donned our coats and sleeves and gloves and went to work with pipets and flasks…There was also the Lab. #CIRMSparkLab is so much more than an internship; #CIRMSparkLab is an invitation into the worldwide community of learned people, a community that I found to be caring and vibrant, creative and funny – one which for the first time I can fully imagine myself joining “when I grow up.”

#CIRMSparkLab is having mentors who taught me cell culture with unerring patience and kindness. It is our team’s lighthearted banter across the biosafety cabinet; it is the stories shared of career paths, of goals for the present and the future. It is having mentors in the best sense of the word, trusting me, striving to teach and not just explain, giving up hours and hours of time to draw up diagrams that ensured that the concepts made so much sense to me.

#CIRMSparkLab is the sweetest ‘good-morning’ from scientists not even on your team, but who care enough about you to say hi, to ask about your projects, to share a smile. It is the spontaneity and freedom with which knowledge is dispensed: learning random tidbits about the living patterns of beta fish from our lab manager, getting an impromptu lecture about Time and the Planck Constant from our beloved professor as he passes us at lunch. It is getting into a passionate, fully evidence-backed argument about the merits of pouring milk before cereal that pitted our Stem Cell team against our Exosome team: #CIRMSparkLab is finding a community of people with whom my “nerdy” passion for learning does not leave me an oddball, but instead causes me to connect instantly and deeply with people at all ages and walks of life. And it is a community that, following the lead of our magnificent lab director, welcomed ten interns into their lab with open arms at the beginning of this summer, fully cognizant of the fact that we will break beakers, overfill pipet guns, drop gels, bubble up protein concentration assays, and all the while never stop asking, “Why? Why? Why? Is this right? Like this? WHY?”

I cannot make some sweeping statement that I now know at age 16 exactly what I want to do when I grow up. Conversely, to say I learned so much – or I am so grateful – or you have changed my life is simply not enough; words cannot do justice to those sentiments which I hope that all of you know already. But I can say this: I will never forget how I felt when I was at the lab, in the community of scientists. I will take everything I learned here with me as I explore the world of knowledge yet to be obtained, and I will hold in my heart everyone who has helped me this summer. I am truly a better person for having known all of you.

Thank you, #CIRMSparkLab.

Gerhard and SPARK Class

SPARK Research…on Gene Therapy Vectors! by Lauren Duan

It’s been a crazy couple months. We started where every budding scientist starts, with little knowledge but lots of curiosity. Now that we’re near the end of our time in the CIRM SPARK program, it feels incredibly rewarding to be able to see that we can walk out of our respective labs knowing a little bit more about the world of regenerative medicine and a lot more about what research truly entails.
My experience during this internship was a bit different from others: my project didn’t even involve true stem cells, but rather focused on gene therapy vectors. Whereas my peers could talk about their MSC, hESC, or iPSC cultures, I could only nod and be glad we learned enough about these stem cells in our graduate-level Bio225 class to hold a conversation. I work with HEK293T cells that come from a line of transformed cells that originated from human embryonic kidney cells. They’re mostly used as producer cells for things such as viral vectors, which can be used for gene therapy to insert new functionaDuan, Lauren IMG_3170l genes to cure currently incurable diseases!

The main focus of my project was to find a more efficacious way to purify viruses, specifically adeno-associated virus, from all of the other cell debris. The two methods I tested are purification through Zeba desalting columns and fast protein liquid chromatography (FPLC). At the end, we found out which one works better by “counting” the relative amounts of DNA in the same volume of sample using qPCR, which should correlate in a 1:1 ratio with the amount of virus, since each virus has one single strand of DNA. The method with the highest amount of DNA would then be the most effective at purification! By finding the best way to purify the virus, I’ll be able to contribute to creating a more effective method of delivering virus-mediated gene therapy.

Duan, Lauren IMG_4022 cropIf I said I work with highly concentrated viral vector suspensions everyday while wearing a full body suit, two pairs of gloves taped to my sleeves, and a face mask, it might seem like I’m doing something extremely dangerous. However, if all goes well and the gene therapy vector works as it should, I really would only be at risk of being cured of a disease! Working in the Good Manufacturing Practice (GMP) facility at the UC Davis Institute for Regenerative Cures means that personal protective equipment (PPE) really does protect both me and the product.

The GMP is like no other place I’ve ever been. With fewer than 10,000 particles larger than 0.45 microns per cubic foot per minute in each manufacturing room (while the outside air has around 35,000,000 on the same scale), I’ve never been in a place so clean. Working with the GMP employees, being able to see and participate in clinical-grade manufacturing, has been absolutely invaluable. It’s really allowed me to connect all of the experimental science done in the basic and translational research labs to the actual therapies that go into patients during clinical trials.

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I can’t say enough how grateful I am for this opportunity to see research from the eyes of a real scientist. Even though I’m young and liberated from most responsibility and commitment, I can safely say that my future in science is as sure as can be.

 

 

A Day as a SPARK Student By Diana Ly

 

There is no such thing as a typical day for a CIRM SPARK student intern at the UC Davis Institute for Regenerative Cures. Because my mentor, Whitney Cary, is not only in charge of the Stem Cell Core, but is also the lab manager, my day usually begins with restocking the lab. This is a very important step to start off the day because all the people in the lab use the common materials that we supply. Not to mention moving these boxes has helped me gain some arm muscle (I did not expect that a science internship would require muscles)! The next task that is needed to be completed daily is to make 70% ethanol (which is when I get to use my favorite 4000 mL graduated cylinder!), fill the Nanopure water, and make 1XTAE to supply the lab with those common fluids.

Ly, Diana IMG_4044 cropUsing a huge graduated cylinder to make a large amount of 70% ethanol that is used to clean everything in the lab, which is very, very important!

After restocking and making fluids, it is time to work on my project! Cells are traditionally grown on a feeder layer called mouse embryonic fibroblasts (MEF) which supports the cells by keeping them pluripotent. However, scientists are moving towards xeno-free substrates, which do not contain any animal byproduct, for clinical use of these cells. This is a huge advantage because it prevents contaminants (pathogens, etc.) from the MEFs from transferring into the human body along with the cells. Many scientific companies have created different xeno-free substrates, and my project is to test one of them called Vitronectin which is used with Essential 8 Medium. We are hoping that Vitronectin will support the cells like MEFs do.

I first began by culturing H9 human embryonic stem cells (hESC) on MEFs. During this process I change media and observe the cells on a day to day basis. Then, when the colonies have grown big enough, I would manually passage these cells. This means that I would scratch off the undifferentiated cells and divide them upon new MEF plates and continue culturing them. After a few passages on MEFs, I transferred the cells onto Vitronectin, where I continued to change media daily and manually passage them when they were ready. Everyday, I would enter the lab excited about how my cells have been growing. I am the most excited when I am looking through the microscope and scanning the plate to visually see the cells’ growth.

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After working on my project for the day, I usually have other tasks to do in the tissue culture room such as making media and aliquots. When making media, there is a recipe that needs to be followed where we add the components stated and filter them through the media filter. When all of this is done, there is a Stem Cell Core tradition where we have to draw a picture on the media bottle with a permanent marker.

Ly, Diana MEF mouse picture“No MEFs, please!” : A picture of a mouse that I’ve drawn on my Essential 8 Medium bottle. Essential 8 Medium is used to culture stem cells on a xeno-free substrate called Vitronectin.

At the end of the work day, I always look forward to returning the next morning, not only because of the wonderful work that I get to do but also the amazing people that I get to work with. I can’t believe that this internship is coming to an end, and I am extremely grateful for this amazing opportunity because it has really opened my eyes about stem cell research.

 

Additional Instagram posts about my experience:

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“Like a Small Boat On The Ocean, Sending Big Waves Into Motion” [1] by Sharon Burk

 

“Extract the RNA from our samples.” This seemingly small task could have a profound impact on the bigger picture. During this summer internship I had the opportunity to work with Dr. Kyle Fink and the other members of the Juvenile Huntington’s Disease team at the Nolta Lab in the Institute for Regenerative Cures. Huntington’s Disease (HD) is a neurodegenerative disease that is caused by a mutation in the Huntingtin gene. This disease is linked to a single cause that cannot be visible because it occurs at the molecular level and yet it leads to devastating consequences for the people and families affected by it.

Burk, Sharon IMG_4053 cropThe central dogma of biology states that DNA is transcribed into RNA which in turn is translated into a protein. These proteins are all different and serve different functions in the body such as making hair, or enzymes, or in the case of HD, making the mutant Huntingtin protein. All these proteins are derived from genes in our DNA. However, it is the expression of different genes that make a protein unique. While the exact function of the healthy Huntingtin protein is unknown, it is essential during development and serves many roles in the adult brain, such as assisting in the transportation of other proteins. In HD, there are additional nucleic acid triplicates, Cytosine Adenine and Guanine (or CAG) in the mutant Huntingtin gene that exceed what is normally found in healthy individuals. These CAG repeats encode for the amino acid, glutamine, and for this reason more glutamine amino acids are present in the mutant Huntingtin protein. This causes the proteins to mis-fold in a manner that inhibits its proper function. It is amazing to think that the fact that these proteins folded in an improper manner will cause someone to contract Huntington’s Disease. The folding of proteins devastates someone’s life and the people around them.

I was given the opportunity to work with an outstanding mentor and fellow team members. It is incomprehensible to think that what I am doing (something as small as extracting RNA) might help people with Huntington’s and their families. Researchers are collaborating to find a solution for this disease at the molecular level. Their work consists in identifying the mutant gene and turning it off using specialized proteins, so that those individuals who have received their life sentence might be able to live normal lives.Burk, Sharon IMG_4046 crop

Advancements in science have rapidly progressed over these past few decades and life-changing scientific developments are more likely to emerge in the years to come. In 1869, Friedrich Miescher identified a nucleotide. Almost a century later in 1950, Watson and Crick discovered DNA. In 1993 in Lake Maracaibo, researchers discovered the genetic cause for HD. The future seems so bright. Now, in the year 2016, we are developing ways to correct the genetic dysfunction of HD.  The goal of this scientific experiment is to restore hope and courage in those individuals affected who are struggling just because CAG repeats in their DNA

“Extract the RNA from our samples,” now that task doesn’t seem so small after all, but just might send “big waves into motion.”

[1] Platten, Rachel. “Fight Song.” Columbia Records, 2015.

 

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My SPARK Research Scholar Experience by Vincent Truong

So I am a complete klutz sometimes. It comes from my dad’s side, who, when coming overseas from Vietnam, attempted to push a sliding door. Needless to say, there wasn’t a sliding door left. I have this unintentional, destructive nature. Everything I touched would break, snap, bend, or is ruined in some way.

But I applied to the CIRM Spark program at UC Davis and was accepted to do actual laboratory work alongside others in the field. It was exciting, yet, it was absolutely terrifying. I was excited to learn and to do things I normally wouldn’t do as a normal high schooler like gel electrophoresis, but I would be scared to pipette the carcinogen, ethidium bromide, needed to make it. I paid extra attention to how things are done and asked my mentors constantly to check to make sure I would add the correct buffer in the correct amount at the correct time.

Truong, Vincent montageSurprisingly, no major accidents happened. Although I struggled with some of the lab work that required finer motor skills (seriously, some of the things scientist do requires like 5 hands), they did not turn out too bad; I didn’t have to wipe up shards of glass along with the 5 hours worth of work splashed all over the floor.

Until, I broke something. As I was afraid that I would be late to a test for the summer class that the SPARK Students at UC Davis have to attend, I rushed to put the 2L flask of bacteria transformed with VSVG into the shaker. The result: a ton of glass and a flooded shaker. With nutrient broth dripping out of the shaker, I ran to ask for help to fix up my mess and, after wiping up the spills on the floor, I hurried to class.

That next week really sucked. With the help from one of mentors, Kyle, we cleaned the shaker. I smelled strongly of broth and ethanol as I cleaned the shaker out. My lab coat sleeves were covered with ethanol and I had to walk away from the shaker because of the nauseating smell, even with a face mask on.

Truong, Vincent science buddiesAlthough I felt absolutely terrible about it, the people at the Institute for Regenerative Cures were understanding of the mishap. Karen, the person who I asked for help during the accident, told me that the shaker actually smelled clean after my mentor and I cleaned it, even with all of the bacteria inside of it.

My time at in the CIRM Spark program was amazing but it had its hectic moments to. Some days, there would be so many things happening at one time: 2 Maxi Preps, Splitting Cells and Transfecting them, along with a class that day. Even though I did not physically do all of these things, it just seemed overwhelming at times. But I learned a lot throughout the whole program, especially to slow down and do things right.

 

A successful Western blot…not too shabby!:

 

Truong, Vincent western blot

Clinica Tepati: “Fulfilled Clinic”, Fulfilled Trip by Jean Miriam Yasis

“Every person holds the right to health care” – Gerhard Bauer

Yasis gel loading
Gel electrophoresis

Every single day of being an intern at the UC Davis Institute for Regenerative Cures has been refreshing, exciting, and engrossing. Having the opportunity, over the course of these weeks, to witness the starting point and processes of finding potential cures to diseases that have long existed has conditioned me to a mindset of tangibility for change. Although my time interning has been short, changes in the ways of treatment, in techniques of experiments, or even in the mentality of a patient, researcher, or physician, have been made visible. The reasons for my goal to work in a lab have also changed as I continually realize the depth of research and clinical application. Working in a translational lab, we experience the transformation of ideas into treatments that clinical trials soon follow. Holding clinical trials as our goal throughout this process and being able to witness specific patient problems strengthen the personal objective to see the end result.

 

Yasis, Jean Miriam - Clinica Tepati imageDuring this internship, our cohort was able to take a trip to Clinica Tepati, a student-run clinic that accommodates uninsured patients. Here, I was reminded of my goal to discover ways to more efficiently eliminate the ailments commonly experienced, from diabetes to cardiovascular needs, by the patients seen and of the problems many underrepresented groups encounter when they are unable to receive healthcare due to financial and social hindrances. I realized society’s injustice when regarding healthcare for each person despite its efforts to promote the importance of good health throughout the nation. Today, a person does not truly receive complete medical attention unless he or she is capable of paying for treatment or going through a tedious process, not always guaranteed, to receive grants that will supply one with free treatment. It is not hard to picture a person in need in that certain situation as a friend, family member, or even oneself. Upon our visit, our internship director, Professor Gerhard Bauer stated simply, “Every person holds the right to health care”. This statement has since been molded into my mind as a personal challenge to see this idea applied because it holds true—no matter whom the person is or what his or her situation is, care should be granted without much deliberation.

Yasis clean roomAs a high school student, I am amongst the new generation that must maintain this concern of providing every person the rightful care he or she deserves and encourage the possibility of each person to receive an effective treatment to a disease. By continuing my goal to be an asset in a lab that makes reaching clinical application a top priority, I could apply my desire to see that all are granted easy access to an attainable treatment and protect the true aims to better the conditions of each patient. Contributing to the STEM field is far more than simply finding advancements in technology or curative therapy; it involves bringing attention to current, active issues and understanding that these situations can be acted upon with collective cooperation and returning to the original goals of making a healthy life an accessible, given right.

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Science Blogging & Social Media 101 for SPARK Research Scholars

The SPARK Research Scholars at UC Davis are in for a busy second week, blending laboratory and classroom training in stem cell biology with training in social media and science blogging.

Here are a few best practices for early career scientists getting started with social media professionally:

  • Remember – social media platforms are public and content may live forever online
  • Only post images or information that you would feel comfortable sharing with colleagues during a lab meeting, in the classroom (public spaces) or advertising on a billboard along the highway
  • Choose a professional, friendly profile photo
  • Think about the professional profile you would like to build and concentrate posts, comments and “likes” on a few related topics (in our case… stem cell biology and regenerative medicine!)
  • Do not overshare personal details or images… it is sometimes okay on Twitter and Instagram, seldom okay on LinkedIn
  • Respect the privacy of others – check with colleagues before posting their images or information about their work