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THE SCIENTIST Part I

(Or, some thoughts on science and communication)

I’ve finished my first year of PhD studies! Upcoming adventures for  Grad Year 2  include a thesis committee meeting, new TA responsibilities, work on another Review, comprehensive exams, and more opportunities to participate in science communication! I’ve wanted to blog about my graduate application process for awhile. Here are some of my thoughts about the interview process (from an introvert perspective). Feel free to discuss/post comments below!

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As evidenced from the title, I am an introvert (Myers-Briggs type consistently INTJ: The Scientist/Architect*). I’m absolutely content to enjoy a quiet supper and good book** after returning home from the lab. Although I look forward to research retreats, conferences, and scientific workshops; networking can be draining. When I received the schedule for my first graduate school interview, I described the event as an “introvert’s nightmare”. In actuality, my interview process was an amazing experience. I had the chance to visit amazing laboratory facilities, meet leading researchers, and explore new cities. While these events vary by university, I was typically interviewed by 10-20 researchers, graduate students, or post-doctoral fellows during each visit. Here are some tips for surviving graduate school interviews.***

  1. Be prepared and be yourself: The quality (not the quantity) of your conversation will impress research faculty. Be prepared to clearly and concisely state why you are interested in program X, the research in X lab, and why you will make a strong addition to X department. Be familiar with the research and publications of the labs you visit and be prepared to share what you would be interested to study during graduate school. Interviewers often ask about previous lab experience. Practice short (30 second) and longer (2 minute) elevator pitches of your undergraduate research projects. Remember to describe why your research matters and how these experiences prepared you for X research. Also, be prepared to discuss your future career plans (although it’s ok to be unsure!). But you also need to…
  2. Ask questions: Ask (intelligent questions) about their research!! Learn about course and teaching requirements, publication and funding opportunities, program length, and your responsibilities. If you are meeting with a student ask what they like the best and what they dislike the most about the lab/graduate program.
  3. Communication doesn’t always involve talking: Dress and demeanor (friendly, professional, and enthusiastic) also communicate interest in graduate research. Don’t dress in jeans and sneakers, but there is usually no need to wear a suit and tie–think business casual. Wear comfortable shoes (avoid heels) to walk around campus. I suggest close-toed shoes if you intend to visit lab spaces. In addition, check the weather ahead of time in case you need an umbrella or coat.
  4. Introverts, it’s ok to take a break: Interview days are often packed with campus tours, social events, lab talks, and more! Participate in the events, but also look for spaces to decompress. Is there time before interviews to walk around the campus? Is there a mid-day break? If so, it is ok to take the opportunity to re-charge and re-focus before returning to the interview process. Lastly…
  5. Don’t Stress! The fact that you were offered an interview is a good sign! Remember, you are also interviewing the university. Is this program a good fit for you? Plan to get a good night of sleep before the interview/s and don’t overanalyze conversations afterwards. Stay in the moment and enjoy the journey.

Are any of you preparing for interviews this fall? Happy adventures everyone!

*Sometimes referred to as the Mastermind personality 😉 What’s your type? https://www.16personalities.com/free-personality-test

** currently reading Ron Chernow’s Alexander Hamilton (and listening to Lin-Manuel’s glorious musical!) –thanks Ray!

***based on my experience interviewing at Microbiology programs in North America

 

 

 

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LET THEM EAT DIRT

(Or, My Latest Book Recommendation)

Last Autumn I wrote an article entitled “Amaze-On Microbiota” (https://theskope.com/2015/09/07/amaze-on-microbiota/). Amaze-On discussed the hygiene hypothesis theory, which posits that the obsession with over-sanitation may actually harm our health. Humans don’t exist as a solo entity. Instead, as I hope you’ve realized, we are meta-organisms that thrive alongside (and due to) our trillions of microorganisms.  The human gut microbiota is one of the most diverse microbial populations found in nature. Altering this vibrant community impacts our digestive, immune, and neural health. How do antibiotics, putative probiotics, diet, and lifestyle impact the human microbiota? How can we maintain a healthy microbiota, but also eradicate microbial pathogens?

How clean is too clean?

Dr. B. Brett Finlay (my mentor) and Dr. Marie-Claire Arrieta (a new assistant professor at University of Calgary) wrote a phenomenal book, Let Them Eat Dirt, that explores these questions and provides practical steps to protect your family’s health. If you want to learn more about gut microbes and the crucial impact of the human microbiota in development, read LTED!

For more information see: http://letthemeatdirt.com 

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Alaskan Adventures

(Or More Posts to Come after the Holiday Hiatus)

Hello everyone! I hope that you are enjoying a beautiful July. I wanted to share an update on my graduate school progress: classes are finished, a new teaching assistantship starts this September, and research continues!

I’ve recently returned from a very rejuvenating (and nearly internet-free) family vacation. My family went somewhere we always wanted to go–ALASKA! We enjoyed glaciers near Juneau, berry-picking in Sitka, kayaking in Ketchikan, and, on our way back, I visited Vancouver Island for the first time. More microbiome stories to follow this upcoming week. Stay tuned! How’s your summer?

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AN AMERICAN IN AMERICA PART II

(Or Reflections from Washington, Washington)

Last weekend I spent a day in Seattle, Washington. This marked the first time I’ve visited downtown Seattle since I arrived in Vancouver (yikes! I thought I would visit the US more). Our group travelled south to watch a baseball game as an early farewell celebration for an amazing labmate (come back and visit O!). Somewhat sadly, the home team lost to the Texas Rangers, but it was still an entertaining, sunshine-filled afternoon. After the game, we meandered through the Pike Place Market and I enjoyed a summer smoothie and gyro (not typical Seattle fare, although we did play count-the-Starbucks on the way back).

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In many ways, it was the quintessential American Sunday afternoon—baseball game, players in blue and white, and a rendition of “God Bless America” during the seventh inning stretch. We even listened to a podcast on American history and politics as we travelled to the stadium.

Recently, a historical microbiome moment occurred in Washington DC. In case you haven’t heard, President Barack Obama unveiled the National Microbiome Initiative (NMI). Check out the White House Announcement here (https://www.whitehouse.gov/sites/whitehouse.gov/files/documents/OSTP%20National%20Microbiome%20Initiative%20Fact%20Sheet.pdf). The NMI follows a nationwide call to action for microbiome research issued earlier this year. In 2016/7, US Federal agencies will invest $121 million dollars in interdisciplinary, multi-ecosystem microbiome studies. Moreover, the NMI announcement also included some serious microbiome funding from academia, industry, and private sectors, including…

(1) $12 million for the Center for Microbiome Innovation (UC San Diego)

(2) A public microbiome data bank from One Codex

(3) $100 million from the Bill and Melissa Gates Foundation

While hundreds of millions of governmental dollars have already been invested in microbiome research (think the 2007 Human Microbiome Project, NIH-funded and NSF-funded research), the NMI highlights both the continued importance and interest of microbiome research. Proposed projects range from examining oceanic microbes to the study of extraterrestrial microbes in the solar system, human microbiome research and examination of plant-microbe interactions, development of computational tools and fostering of public knowledge. The future is bright with research possibilities. Let’s explore!

PS: Thanks A for transport and E for planning!

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AN AMERICAN IN AMERICA PART I*

(Or Reflections from Washington DC)

I returned to Washington DC to spend the Memorial Day weekend with family–although my parents had no idea that I was coming home! The mastermind behind this surprise family reunion was my brilliant younger sister—Khelsea**. As Khelsea arrived later but still wanted to witness the unannounced arrival, we coordinated my entry to occur as she Skyped our parents. 2,900 miles (4667 km), 20 texts, and .5 Skype calls later, I walked through the front door and greeted my completely bewildered parents and a very excited goldendoodle.

Over the weekend, our family visited Washington DC. We walked along the Tidal Basin, stopping by the Thomas Jefferson, Franklin Delano Roosevelt, and Martin Luther King Jr. Memorials. Next, we visited flower-adorned war memorials and walked alongside the grand Reflecting Pool, which links the Lincoln and Washington Memorials. Ten thousand US flags covered the lawn adjacent to the pathway, a temporary memorial to those who died in combat over the past decade. Each flag contained the name and biography of a fallen soldier. Family members, veterans, and visitors were allowed to walk through the flags—mourning, commemorating, remembering.

While DC has been swamped in the crazed and crazy election campaign, the Memorial Day weekend provided a much-needed respite and a time to honor American heroes and reconnect with family and friends. Last Memorial Day, I was preparing to start graduate studies in the fall. In fact, one of my first Skope posts discussed Memorial Day weekend (see HOLIDAY: https://theskope.com/2015/09/09/holidaze/). Many new adventures have occurred since those early posts—grad courses completed, a review written, and mountain trips with new friends. Grad school has definitely been a challenging (but rewarding) experience. I have no idea what new adventures will happen when Grad Year 2 begins, but until then, I’ll keep exploring!

*Part II coming soon—the blog post where I’ll share some exciting microbiome news from DC!

**also a big THANK YOU to AR, RR, and JB for transport, logistics, and secret planning! You’re amazing!

 

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LET’S CHAT ABOUT THE MICROBIOME

(Or an invitation to dialogue)

If you are around Vancouver next week, come out to Microbiome Seminar Series and Journal Club at the Djavad Mowafaghian Centre for Brain Health. Next Wednesday I will be presenting on my review–Microbes and the Mind: Emerging Hallmarks of the Gut Microbiota-Brain Axis.

For more information, check out the link below:

http://epims.med.ubc.ca/research/microbiome-seminar-series-and-journal-club/ 

Gotta make some slides now…

 

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MICROBES and the MIND: emerging hallmarks of the gut microbiota–brain axis

(Or…a Review!)

Interested in learning more about the gut microbiota-brain axis? Check out this Review by yours truly and the Finlay Lab! This paper discusses structures (including the vagus nerve) and neuromodulators that are involved in microbe-brain interactions. I hope you enjoy!

http://onlinelibrary.wiley.com/doi/10.1111/cmi.12585/epdf

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WOMEN and SCIENCE

(Or Our Voices Matter)

We must tell girls their voices are important.” – Malala Yousafzai

In the US, Women’s History Month is celebrated in March (and March 8 is International Women’s Day!). As March comes to the end, I thought I would share some of my recent experiences celebrating women in the sciences. On March 8 I attended the 2016 Wonder Women Networking Event at Telus World of Science. In addition to getting free pizza and watching a great IMAX presentation (Humpback Whales narrated by Ewan McGregor), I also chatted with some amazing female scientists. This event was sponsored and hosted by the Society for Canadian Women in Science and Technology (SCWIST). –PS See the latest header to check out my pic of BC Place from Science World

Later in the month, I attended a talk at UBC entitled “The Only Woman in the Room: Tales of a Female Ecologist”. Dr. Judith Myers, Professor Emerita in the UBC Zoology Department shared her career history and experiences as a female scientist.

During her talk, Dr. Myers related how she discovered her passion for ecology and conservation biology during early research positions. At one point, she planned to fulfill her dreams by marrying an ecologist and helping him in his research. However, she decided to pursue her interests though graduate work…in molecular biology. But this field wasn’t the right fir. She re-focused the research to include her ecology interests and hasn’t looked back. Throughout her career, Myers has examined tent caterpillar populations, invasive species, and biological control agents.

Similar pieces of advice from both events include:

  1. Do what you feel passionate about, but don’t worry about picking the perfect research/career fit. Just keep working!
  2. Life is full of surprises, many challenging and rewarding–enjoy the journey (Many researchers at the SCWIST event had major career changes and Myers later fulfilled her initial dream by marrying and collaborating with an ecologist!)
  3. It’s important to have a healthy work-life balance
  4. Support each other: speak up, ask for help when you need advice and be a mentor to others as well

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Me, hiking this month near Lynn Canyon Suspension Park. Yay for work-life balance!

Thanks to KH, LH, SV, and SW

For more on Judith Myers see: http://www.zoology.ubc.ca/person/myers

For more on Humpback Whales see: http://humpbackwhalesfilm.com

For more on SCWIST: http://www.scwist.ca 

For more on Science World: https://www.scienceworld.ca

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BARRIERS AND BUGS

Barrière hématoencéphalique
Blood Brain Barrier surrounding capillaries in the brain

(Or It Takes Guts to Alter the Brain Part III)

The lastest gut-brain posts have focused on the role of the vagus nerve in gut-brain interactions. The vagus nerve runs from the brain into the abdomen and may serve as an important neural interface between the gut microbiota and the central nervous system. This post examines another physical component of the gut microbiota-brain axis. Unlike the vagus nerve, this structure does not provide a link between bugs and brain, but rather acts (primarily!) as a barrier. The blood brain barrier (or BBB) is composed of tightly-linked brain cells. Proteins, primarily claudins and occludins, stitch these cells together, forming tight junctions. The BBB allows water and certain molecules to pass from the blood into the brain, while preventing the transport of harmful substances, including bacterial components.

A recent study from the Pettersson Lab examined the role of the microbiota in BBB formation and maintenance*. Researchers found that germ-free mice (lacking a microbiota) exhibited increased BBB permeability. Remember, the BBB acts as the ultimate brain bouncer-protecting our nervous system from toxic substances. Disrupting BBB permeability may significantly impair brain health and function.

To measure BBB permeability, researchers injected [11C]raclopride, a radioactive substance, into the bloodstream of both germ-free mice and conventionally-raised mice. Used in tracer amounts, [11C]raclopride does not harm the brains or health of the mice. Following injection, positron emission tomography (PET) imaging was used to track the radioactive substance. Germ-free mice had a higher uptake of [11C]raclopride within the brain compared to conventionally-raised mice. In addition, important tight junction proteins (occludin and claudin-5) were decreased in the brains of germ-free mice.

But could a gut microbiota fix the dysfunctional BBB? And if so, how?! To examine the role of the microbiota in BBB formation, researchers colonized germ-free mice with the microbes from the gut microbiota of conventionally-raised mice. The previously germ-free mice exhibited decreased BBB permeability and increased levels of occludin and claudin-5. Next, researchers gave germ-free mice short-chain fatty acids (SCFAs), small molecules produced by gut microbes. Even without the microbes themselves, SCFA-treatment decreased BBB permeability. While the effects of increased BBB permeability in germ-free mice remains poorly understood, this study demonstrates another complex interaction between the gut microbiota and brain health.

Stay tuned for upcoming posts on microbially-produced components (SCFAs, neurotransmitters, and more!) involved in the gut microbiota-brain axis.

Sources + Additional Information:

*http://stm.sciencemag.org/content/6/263/263ra158 

Pettersson Lab: http://ki.se/en/mtc/sven-pettersson-group 

 

 

 

 

 

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A MICRO HAIKU*

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(Or Thoughts While Running the Flow Cytometer**)

At the FACS machine

I left my water bottle

Forty more samples

 

Running more samples

I wish I had some music

Thirty-nine tubes left

 

Flow cytometry

Should have brought my phone with me

Thirty-eight more tubes

 

Something is not right

Where are my controls (?), blast it!

This is very bad

 

At the FACS machine

Day two: second round of flow

I forgot water…

#stayhydrated

*You probably remember the haiku from English class. Quick refresher: a haiku is an unrhymed poem. The form was developed in Japan (5 syllables first line, 7 second line, 5 third line). For some beautiful haiku poetry, check out the work of haiku master Takahama Kyoshi (1874-1959).

http://terebess.hu/english/haiku/takahama.html 

**Flow cytometry is actually an amazing tool. FACS or Fluorescence-activated cell sorting is a specialized type of flow cytometry. See “Micro-Defined: A hopefully useful, but definitely not über technical, microbial-related set of definitions.”

https://theskope.com/2015/08/13/micro-defined/

Painting:

The Great Wave off Kanazawa Katsushika Hokusai