(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…


*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). 

**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.”


The Great Wave off Kanazawa Katsushika Hokusai












(Or It Takes Guts to Alter a Brain Part II)

The term gut microbiota-brain axis describes the multiple mechanisms involved in microbe-to-brain interactions. These mechanisms include endocrine, immune, and neural signaling. Last year I wrote a post entitled “The Vagus Nerve”, which examined the role of the vagus nerve (neural pathway!) in the gut microbiota-brain axis. To re-cap, researchers from the University of College Cork and McMaster University found that an anxiety-reducing probiotic failed to impact the behavior of mice lacking a functional vagus nerve. No vagus nerve = no microbe-brain regulation. While the vagus nerve serves as an important component of the gut microbiota-brain axis, this post highlights an interesting story regarding vagus-independent mechanisms.

Chronic gut inflammation has increasingly been linked with psychiatric disorders. Indeed, people diagnosed with inflammatory bowel disease have a much higher risk of depression and anxiety. For more information, check out the link to Foster and Neufeld’s Gut–brain axis: how the microbiome influences anxiety and depression (see below). In 2010, Premysl Bercik and colleagues reported that chronic gut inflammation increased anxiety-like behavior in mice. Mice with gastric inflammation had increased levels of cytokines. Produced by immune cells, cytokines are small proteins that drive inflammatory responses. In addition, these mice had decreased levels of brain-derived neurotropic factor (BDNF). BDNF is an abundant protein found within the brain that protects and maintains neurons. In addition, alterations of BDNF levels have been linked with depression. To examine how the inflamed gut microbiota impacted behavior, a subset of mice received a vagotomy (snipped vagus nerve). However, the vagotomy did not impact anxiety-like behavior! Next, researchers treated the “anxious” mice with anti-inflammatory drugs. Drug treatment reduced anxiety-like behavior and decreased levels of pro-inflammatory cytokines, but did not impact BDNF levels. Surprisingly, treatment with the probiotic Bifidobacterium longum also decreased anxiety-like behavior and normalized BDNF levels. This microbial therapy, however, did not impact cytokine levels. Weird, right?! So how does the inflamed gut microbiota impact the brain? And how did the bacteria B. longum change behavior and neural chemistry? Short answer—we don’t know the exact mechanisms and there are probably many mechanisms involved (immune—cytokines, neural—BDNF, and more…). Researchers are continuing to discover the ways that microbes impact our mental health. I’m excited to learn more.

Stay tuned: in Part III, I’ll continue discussing the microbe/brain connection. Happy Exploring!

Microbes and Depression:

Bercik 2010:



(Or Tips to Thrive During A Love/Hate Relationship: Part II)

While I have a love/hate relationship with writing, I have a like/dislike rapport with editing. Once I have something written down, the “writing” process begins. Former Supreme Court Justice Louis Brandeis once noted, “There is no great writing, only great rewriting.” I agree. While editing may not be as creative as writing the initial draft, I find the editing process equally lengthy, although easier. However I recently read the following quote, “Self editing is the path to the dark side” -Eric Benoit, author. Thoughts?* For the rest of this post, I’ll examine how to avoid the Dark Side of rewriting.

Tip 1: EDIT, EDIT, EDIT—I edit each piece of writing multiple times. I try to schedule short, but frequent, editing blocks. For example, I might edit a paper for one or two hours and return the next day to re-edit for a similar amount of time. The brain has an amazing ability to self-correct bad grammar and golss oevr seplinlg meisatkes without alerting our inner editor!

Tip 2: READ ALOUD/READ BACKWARDS—During undergrad, an English professor suggested “backwards editing” to catch grammar/spelling errors. This doesn’t mean reading each word backwards! Instead, read your paper backwards sentence by sentence: read the last sentence, then the second to the last sentence, etc. This breaks up the “flow” of text, improving editing focus.

Tip 3: ASK A FRIEND—An additional editor with a critical eye can spot forgotten grammar/spelling mistakes and also suggest tips to improve the clarity/quality of your work.

Tip 4: ACTIVE VOICE—Always choose a precise, effective verb. When possible, utilize the active voice.


Although no writer is perfect, poor editing can result in tragic consequences. I received approval from a friend to share his story. Many years ago, **Alex** applied for a competitive summer internship at **The Ice Cream Factory of Awesomeness**. After carefully editing his application and impressive resume, Alex submitted the paperwork. Several weeks later, Alex received an e-mail stating, “You are now hired by The Ice Cream Factory of Awesomeness. Thank you for your application…” Success! Alex informed his previous summer employer that he would no longer be available to work. Alex looked for housing near his new job. And then Alex waited. Alex waited. Alex waited. Alex waited, but never heard more from The Ice Cream Factory of Awesomeness. Mildly alarmed, Alex called the company. After a brief investigation, the Ice Cream Factory of Diminishing Awesomeness sent out a mass e-mail to the internship applicants, apologizing for a spelling typo in their latest e-mail. The corrected e-mail now read, “You are noT hired by the Ice Cream Factory of Awesomeness. Thank you for your application…”**

Don’t be like The Ice Cream Factory of Questionable Awesomeness. Be like Louis Brandeis: Supreme Court Justice, Harvard Law graduate, champion for social justice, author, and advocate for the power of great rewriting. Happy Editing!

*Apropos, as I recently saw the latest Star Wars.

**Alex went on to accomplish many successes 🙂

*** For more information about improve scientific writing, check out the following link. It is an old article, but a great one! 





(Or Happy 2016!)

January is more than halfway over and the Skope is returning after a holiday hiatus. On New Year’s Day my family reminisced about our favorite memories in 2015. For me, 2015 was a year filled with travel. I realized that roughly 80% of my trips were related to Microbiology/graduate studies. Even better, over half of these journeys were to places I had never visited before: Georgia (the Country), California, Toronto. Travel is an important component (and perk!) throughout the career of a researcher: conferences, college visits, collaborations, grad school interviews, laboratory workshops, international post-doc positions, global summits, lecture series, and more. Networking during these events provides valuable opportunities to exchange ideas, share research, learn from experts, and develop contacts—the topic of an upcoming Skope post. New posts coming 🙂

I’m grateful for opportunities to travel, learn, network, blog, and research in 2015. Thank you. These are some of my favorite science-related 2015 memories (both in Canada/US and abroad).

Scope 2015

Here’s to new adventures for all of us during 2016. Happy Exploring!



(Or Tips to Thrive During  A Love/Hate Relationship: Part 1)

For the last month, I’ve spent many days writing: reports, reviews, term papers. I’m tired of writing! However, after a few days on holiday and some Florida sun, I think it is time to add another blog post. And I’ve decided to write about writing.


Vermeer A Lady Writing a Letter 1665

I enjoy writing. I probably wouldn’t have started a blog unless I did. But I also absolutely detest writing. There is nothing quite like the horror of a blank page. And I am a very slow writer. Filling a page with sentences sometimes feels like using my head to bash a hole through a 3-ft concrete wall.

Or, as Gene Fowler, the American journalist and screenplay writer, noted,

“Writing is easy: All you do is sit staring at a blank sheet of paper until drops of blood form on your forehead.”

Earlier this month, someone asked me about my personal writing method. Here is a short list I compiled about my writing process “Before/During” and “After”* I finish a solid draft (of an academic paper). Perhaps some of these ideas are obvious, but I hope that one or two are useful for you.


  1. READ, READ, READ–Before I start to write, I always spend a significant time reading about the subject. I read not only to learn/find sources, but also to study writing styles. What words are typically used to describe a phenomena/technique/concept? What clichés should I avoid? What is the tone of a particular journal/field? What are effective transition phrases? Sometimes I use a different highlighter to mark a particular passage or phrase that I enjoyed for its literary value. Later, I review these “good writing-highlights” –what about that phrase did I enjoy? Why did I think that passage effectively summarized an idea?
  2. Use There are many words/phrases that I use too often-“noted” “moreover” “interest/ed” “theme” “use”. When I am writing a draft, I search through my document to see whether I am using a particular word/phrase in excess (CTRL-F). Sometimes seeing the word/phrase highlighted makes me more aware that I’ve used the word “use” more than three times in one paragraph. Then, I use an online Thesaurus to swap these offenders…perhaps “utilize” instead of “use”. Plus, utilizing an online Thesaurus or Thesaurus app definitely enriches my vocabulary (just don’t go overboard, seriously).
  3. Try Different Outline Methods: When I write I make a general outline in Word. Then, I fill each section of this outline with all the sources I plan to use and a sentence fragment about each source. After, the general outline is completed, I work section by section. I open a new Word Document and copy/paste a section of the general outline. I keep organizing the source+sentence fragments until the notes are in the order I plan for my draft. Working off this more complete outline, I write a draft version in the initial general outline document. –something like this (completely false sources)Screen Shot 2015-12-20 at 2.52.22 PM
  4. Save Multiple Versions: Every time I work on a draft, I save a new version (Report 1, Report 1.1, Report 1.2, Report 1.3…). If I make large changes in one version and the next day I decide I like the original better, I have the older draft saved! Sometimes, I return to an early draft just to remind myself about the overall flow of the paper.
  5. Use a Tool to Manage Bibliographic Data: Zotero, Mendeley, Standalone….definitely worth using one of these programs!!!

Hope these ideas help. *Part II (After Tips) will be online soon.







(Or 300!)

I recently returned from a microbiome conference. It was an amazing experience to listen and learn about the impact of the human microbiota on health, development, and evolution. The speakers included leading microbiologists, immunologists, geneticists, anthropologists, ecologists, and developmental biologists. The vital functions of microbial symbionts remained an overarching theme throughout each wonderfully unique and informative talk. While at the conference, I was reminded of the following quote:

“Life would not long remain possible in the absence of microbes.”—Louis Pasteur, circa 1883.


Untitled*contemplating microbes and Pasteur during a conference break…

Almost one year ago, PLOS Biology published a thought-provoking, conceptual piece by Drs. Jack Gilbert and Josh Neufeld. The article, entitled Life in a World without Microbes examined Pasteur’s statement. I won’t spoil their conclusion, but I’ll list a few of their comments:

  • Microbes produce vitamin B12 for half of the phytoplankton*
  • Humans depend upon gut microbes to produce amino acids and essential vitamins
  • Without microbes, biogeochemical waste would accumulate rapidly—think about it…

Stay tuned for more gut microbiome-brain posts later this year.

PS: Thank you to the 300 visitors from 25+ countries that have viewed, subscribed, and shared this the Skope! Cheers and Happy Microbial Exploring!

* phytoplankton form the base of many aquatic food chains and produce much of the world’s oxygen

Check out the Source: 



Or It Takes Guts to Alter a Brain PART I

vagus Henry Gray (1918) Anatomy of the Human Body

The longest and most extensive cranial nerve in our body, the vagus nerve connects the brain to the lungs, heart, and gastrointestinal (GI) tract. Within the lungs, the bronchial branch stimulates the bronchi, while the cardiac branch impacts heart rate. The vagal fibers that reach the GI drive peristalsis, the wavelike, muscular contractions required for food to pass through the digestive system. And amazingly, this neural connection also provides a link in gut microbiome-brain interactions.

First, a little history…

The record of gut-brain interactions has an ancient history. Rufus of Ephesus who lived in the 2nd century, noted that the snipping of the vagus nerve (a vagotomy) stopped peristaltic movements within the stomach. Galen of Pergamum, the great physician and philosopher, identified the vagus nerve in his De Anatomicis Administrationibus (On Anatomical Procedures). Relatively recently, a vagotomy was considered an important therapy to combat peptic ulcer disease. But what about the gut microbiota?

In 2011, Drs. Javier Bravo and Paul Forsythe reported that Lactobacillus rhamnosus*  impacted brain chemistry and behavior via the vagus nerve. Researchers fed mice either a standard chow diet (SCD) or an SCD+ Lactobacillus rhamnosus diet. L. rhamnosus is a probiotic with anti-inflammatory properties. Later, the mice underwent a variety of behavioral tests. Mice fed the probiotic enriched diet exhibited reduced depressive-like and anxiety-like behaviors. Moreover, the SCD+ L. rhamnosus mice also displayed unique differences in GABA receptor levels. GABA, gamma-aminobutyric acid, is a major neurotransmitter. Deficits in GABA signaling are linked with depression. The mice that ingested L. rhamnosus displayed an increased expression of GABA receptors in the hippocampus and a decreased expression of GABA receptors in the amygdala and prefrontal cortex**. This suggests that a microbe within the gut modulates the brain—an organ far, far, away. How?! The exact mechanism is unknown, but when researchers snipped the mouse vagus nerve the L. rhamnosus diet no longer altered behavior or GABA expression. Gut microbes produce many modulatory molecules, including neurotransmitters, these molecules may stimulate the vagus nerve, impacting brain and behavior. Remember: the vagus nerve is only one of many pathways involved in gut-brain communication.***  Could gut bacteria be a useful tool to treat depression? What do you think?

Interesting work Dr. Bravo and Dr. Forsythe!

*The lactic acid bacteria are typically found in our guts and yogurt!

**Hippocampus: brain region associated with learning, memory, and much more // Prefrontal cortex: the ‘smart’ brain region associated with cognitive thinking and much more // Amygdala: brain region associated with fear

***I’ll post about vagus-independent gut-brain communication later!

Sources + Additional Information:

Vagus Nerve:


Johnson, Leonard R., Ed. Physiology of the Gastrointestinal Tract, Two Volume Set. Elsevier Limited: Oxford, 2012.

The Bravo et al. study:

For a Great Review on Gut-Brain Interactions, click:


Zombies Among Us

(Or Time for a Halloween Post: How Microbes Shape Behavior)

A couple weeks ago I volunteered with the UBC Let’s Talk Science Team for a Zombie-Themed Science Day at Science World. I did not know about the Let’s Talk Science (LTS) Organization until I came to Canada. LTS STEM*  volunteers create and share exciting science-focused learning programs. For more information about LTS check the link below. And if you are a student or teacher in a STEM program I encourage you to volunteer with LTS!

Zombie Day

Our team discussed brain anatomy with young Science World visitors–we even got to decorate awesome brain-shaped cookies. Plus, we received complimentary zombie make-up for the day! Working at Science World reminded me about Amazonian zombie ants. When Cephalotes atratus ants get infected with the Cordyceps fungus, the insects begin displaying fatal, zombie behavior. Cordyceps spores infiltrate the ant brain and force the ant to climb nearby plants and stay put. The ant eventually dies and “a vigorous, silky, greyish-white mycelium* emerg[es] from the body joints and orifices” (Sampson and Evans, 1982). The Cordyceps are now in the perfect position to release ‘zombie’ spores, which drift down and infect more unsuspecting ants.

Did you know that microbiome communities can also shape behaviors? Researchers at the Karolinska Institutet in Sweden found that germ-free mice, which lack a gut microbiota (or any microbiota for that matter!) exhibited increased activity and less anxiety-like behavior compared with mice exposed to microbes. Moreover, researchers discovered that the germ-free mice showed elevated levels of important neurotransmitters, including serotonin and dopamine. Another research group at McMaster University in Canada found that antibiotic-treated mice displayed increased exploratory behavior. Very odd, considering that mice are neophobic (afraid of new things). The antibiotics had altered the gut microbiota composition. When mice were taken off antibiotics, the gut composition and strange behavior returned to normal. Researchers noted that the mice treated with antibiotics also displayed a decrease in brain-derived neurotropic factor, or BDNF. BDNF is a protein that promotes neuron growth and is important for memory and learning. Researchers think that shifts in microbial composition impacted BDNF levels, which changed mouse behavior. Complicated, right?

Lastly (for this post), a recent Bioessays review article discussed whether our gut microbiota manipulates dietary cravings in order for us to eat (unhealthy?!) foods that promote microbial fitness. But feeding gut microbes high-fat and high-sugar treats doesn’t help our waistline! Describing the study, one journalist asked “Are we food zombies controlled by our gut bacteria?” I’m not sure, but maybe that is why I’m craving some Halloween goodies…

Stay tuned for more gut-brain research!

*Science Technology Engineering and Mathematics

**a mass of filamentous-like structures (the vegetative fungal growth)

Sources + Additional Information

Zombie Ants, Anyone?

Germ-free mice:

Antibiotics and Microbes:


(Thanks EY for the cookies!)



(Or every field needs a good dose of healthy skepticism!)

In 2013, experts of the emerging human microbiome field gathered at the National Institutes of Health (NIH) campus in Bethesda, Maryland. The NIH-sponsored conference entitled “Human Microbiome Science: Vision for the Future” highlighted both the successes and challenges of the microbiome field. Speakers noted that “A challenge in microbiome research is to move beyond identification of microbiota community structures that correlate with disease states to establishing a causal link between structural changes and the functions of microbiota in disease.” The “hype” of correlation studies, especially ‘hot topic research’ will always remain. Scientists need to be cautious when interpreting their results and presenting results to the public. In a 2014 Nature Comment, William Hanage lists five questions that microbiome researchers should ask when planning an experiment. I think these five questions also serve as a solid framework for readers (that’s us!) when examining microbiome research. I’ve listed the the questions below. For a more detailed read, check out the link to Hanage’s article.

  1. Can experiments detect differences that matter?
  2.  Does the study show causation or just correlation?
  3. What is the mechanism?
  4. How much do experiments reflect reality?
  5. Could anything else explain the results?

Lastly, I have to share with you this awesome article. Did you know that the microbiome totally caused the financial crisis in 2008!! What??! #Microbiomehype #SEC_NIHworkingtogetheratlast #BewaretheBacoTell


Thanks to NM for sharing, and great job EB representing at the NIH!


Human Microbiome Science: Vision for the Future Report:

Hanage’s Article: 

Financial Crisis and the Microbiome:


THE WILD LIFE OF OUR BODIES: Predators, Parasites, and Partners That Shape Who We Are Today

(Time for a Book Review: Or part of the reason why this blog exists)

My interest in microbiome research stemmed from an ecology class that was definitely more ecosystem-based than human-oriented. My professor, an avid reader and researcher, often suggested articles/books pertaining to the course material and our diverse professional interests (pre-dent, pre-med, teaching, research, physical therapy, nutrition!). One recommendation was Dr. Rob Dunn’s The Wild Life of Our Bodies. In WLOB,  Dunn notes our integral and inseparable connection with the gut microbes that reside on and within our bodies. Indeed, the ever-increasing separation from our microbial communities (extreme ‘clean living’) may contribute to heightened susceptibility to allergic and autoimmune diseases-the hygiene hypothesis concept.

I read about a young Navy technician who performed an appendectomy in a submarine during WW2 using floss and tea strainers. And I discovered the important role of the appendix in maintaining a thriving gut microbiota. I learned about the history of germ-free animals. And I read about how microbes shape the human immune system. I was hooked. I wanted to learn more about these beneficial gut microbes. The next year I applied for a summer internship studying the gut microbiota. Spending two months examining the impact of diet and antibiotics on the gut microbiota further cemented my interest in microbiology and decision to pursue graduate studies.

If you are interested in the importance of the gut microbiota and enjoy medical case studies, I would highly recommend Dunn’s book, but warning, you might become a microbiologist! PS-Dunn’s Lab at the University of North Carolina has published some exciting microbial research. If you are interested in the belly button microbiome or microbes in household dust-check out the link to the Dunn Lab website below!

(Shout out to JH, PT, RC, and CM!)