CRISPR/Cas9 Workshop & Some Final Thoughts

On Saturday morning TAGC held a number of interesting workshops. You could learn about functional genomics for gene function discovery, how to find a job in academia, how to utilize NCBI databases for researching model organisms... And almost twenty more! There really was something for everyone. I decided to attend the CRISPR-based Genome Engineering workshop, and I am so glad I did. The first speaker, Alexandre Paix from Johns Hopkins University, started off with an explanation of the CRISPR/Cas9 system. This method of genome editing is based on an RNA defense system used by bacteria to protect themselves from viruses. By using this system, researchers are able to cut DNA at a precise location by using a guide RNA with the desired complimentary sequence to enable binding. What is so amazing is that not only can it be performed in a test tube, but it can also be done in the nucleus of a living cell! Another great presentation during this workshop was by Matt Schwartz from the University of Utah. He described SapTrap, a plasmid assembly pipeline that enables high throughput gene modification using CRISPR/Cas9. The audience was engaged and all speakers were asked a few questions after their talks. I was going to attempt to describe the details of SapTrap, but this abstract does a really excellent job. 

After the workshop, it was time to say goodbye to TAGC 2016, goodbye to Orlando, and goodbye to the amazing people I had met these past few days. Gathering my bags and enjoying the last sights and sounds of the conference environment, it was time to head to Orlando International Airport.

As I sat on the air-conditioned plane looking out into the bright Orlando afternoon, my head was a whir of thoughts and ideas. This conference was bigger than I imagined, and although I knew it would leave a positive impact on me, it was abundantly better than I could have dreamed. There were the big things that made it excellent - the passionate speakers, the educational workshops, the scientists from around the globe, the beautiful location... But there were also the little things that tied it together and made it one for the books - my conversation with Lifang about ciliate genetics, the hour-long friendly debate/discussion about fluconazole and anti-fungal resistance with Alex and the learned postdoc, the authenticity of the speakers at the Women in Genetics Networking Event, getting to know many fellow undergrads, grad students, postdocs, the endless rows of quality research posters in the grand Crystal Ballroom....

I feel extremely blessed to have had this opportunity, and I am so thankful for everyone that organized it (thank you GSA!), supported me with funding (thank you UFV!) and gave me the opportunity to do research in the first place (thank you Dr. James Bedard!) 

I think that when people get together for an event like this, great things are bound to happen. Who knows what connections were made and what ideas were sparked that will bring new projects and discoveries to fruition in the upcoming years and decades? 
I hope you have enjoyed this snapshot of my experience at TAGC 2016. Thank you for reading and following along. It has been a blast! 

- Vivienne 

P.S. If you have any questions or comments, feel free to leave them down below! 

Chromatin, Human Disease Models, and *Friendly* Yeast Debates

Friday was full, diverse, and wonderful! I headed down just before 7am to avoid the breakfast traffic jam, and met the most wonderful postdoc student originally from China named Lifang, now doing his postdoc work in the states. His research is in ciliate genetics, and prior to his postdoc position, he taught undergrads in China. So for the duration of breakfast, I got a free tutoring session on all things ciliate genetics. Score! He started from the beginning, describing the macro- and micronuclei, and went into more complex aspects as I ate my oatmeal and he munched on a blueberry muffin. After his explanations, I understood the ciliate talks that I attended on Thursday much better, but definitely could have used another hour to hear about his own research! 

After this lovely breakfast/learning session, I headed to the glorious Palms Ballroom for the Chromatin & Epigenetics session from the Drosophila community. The first talk was given by Sarah Elgin from Washington University. She discussed her work into the role of repetitious elements driving gene silencing. This was probably one of the most complicated talks I attended all conference long. I had to look up a few things just to understand the abstract! One of the most memorable parts of her talk was the discovery that the extent of a particular form of gene silencing depends on temperature. At lower temperatures, a loss of silencing was observed. This was confusing for Elgin and her colleague in a different lab; while Elgin observed the flies at 18 degrees Celsius, her colleague observed them at 25 degrees Celsius, and the two saw different phenotypes! This initially confusing difference turned out to be a great discovery. 

Another great talk in this session was by Emily Brown from the University of California, Berkely. She studied the lifespan of Drosophila with different genotypes (XX, XXY, XY, XO, and XYY) to determine the role of the Y chromosome in sex-specific ageing. Male flies with genotype XXY had the shortest lifespan, while female flies with genotype XO had the longest lifespan. Thus, a shorter lifespan was correlated with the presence of a Y-chromosome. Brown described how the Y-chromosome acts as a "heterochromatin sink" by acquiring heterochromatic factors from other regions of the genome. 

Here I am in front of the stunning pool. While some were soaking up sunshine, I was looking forward to soaking up all things to do with models of human disease! Right after the Chromatin & Epigenetics session, I made my way to the nearby Crystal Ballroom to attend my first session from the Mouse community. Throughout the seven talks of this session, it quickly became one of my favourite sessions of the whole conference. Michelle Southard-Smith from Vanderbilt University Medical Center gave a fascinating talk on a mouse model of neurocristopathies (pathologies involving cells that are derived from embryonic neural crest cells). In order to do this, Southard-Smith made a Sox10-COIN mutant. She showed videos of the mice so we could easily see just how affected their motor control was. These Sox10-COIN mutants can be used as a model to study diseases such as PCWH (or if you'd like to use the exceptionally long name: Peripheral Demyelinating Neuropathy, Central Dysmyelinating Leukodystrophy, Waardenburg Syndrome, and Hirschsprung Disease).

Suzanne Hartford gave a really interesting talk on the interaction between BRCA2 and PALB2 at the replication fork. The loss of PALB2 leads to an unprotected replication fork and a decrease in genome stability. Additionally, Hartford and her team at the National Cancer Institute in Maryland made the very first mouse model of BRCA2 with a point mutation that affects function! This is yet another example of the mind-boggling work in genetics being done in our lifetime - go Suzanne Hartford, go!

The final speaker, William Barrington, had an exceptionally clear talk on differing responses to a variation of diets between mice of different genetic backgrounds. Wow, was this talk eye-opening and very applicable. With his study, Barrington clearly showed that strains of mice with differing genetic backgrounds had highly individualized responses to four common human diets: American (greasy burgers and french fries), Mediterranean (lots of vegetables and olive oil), ketogenic (very high fat, moderate protein and little carbohydrate) and mouse chow as a control. The four strains of mice had very different levels of adipose, glucose responses... The list goes on! Barrington argued that based on these findings, genetic background should be a major factor when choosing ones' diet. Although his talk was amazing, he didn't discuss how, as humans, we can take our genetic background into account to eat the best way for our particular genotype. Nonetheless, this is ground breaking work and I am sure he will come out with some more amazing studies relating genetics and nutrition. 

During today's poster presentations I made my way through the endless knowledge and discovery and ended up in the Yeast Genetics section, where I spent a good hour at my new friend Alex's poster. I was planning on just a few minutes, but then a postdoc who was studying the same compound (fluconazole) as Alex came by and a healthy discussion ensued. Through this conversation I learned that Hsp90 has previosuly been shown to play a key role in facilitating resistance to fluconazole. Interestingly, however, when the postdoc added an Hsp90 inhibitor (that he made himself!) and another drug at any concentration in combination to fluconazole, the yeast cells lived. The cells had gained resistance to fluconazole, but the mechanism could not have involved Hsp90, since many experiments validated the specificity of the Hsp90 inhibitor! The two bounced ideas off like a game of intellectual ping-pong, and I asked questions throughout, feeling a bit like the moderator as these two yeast researchers questioned, challenged, and advised one another. 

During my time slot at my poster, I had a few different individuals and groups stop by and had some wonderful conversations. Over the course of about an hour, two graduate students from South Korea, two postdocs and one undergrad from Italy, and two PhD students from Memorial University in Newfoundland stopped by! 

After poster presentations I grabbed some lunch and made my way quickly to the Drosophila Models of Human Disease I. I thought it would be a great way to complement the morning session of disease models in mice. As I walked through the first floor to the session, I couldn't resist capturing the beauty of the day (above). This session included talks on insight into Alzheimer's disease, identification of proteins involved in stretching of squamous cells, and mutations in mtDNA. Overall, a session packed with a LOT of details and discovery. 

I ended my day off with the Women in Genetics Panel and Networking event. I had selected this event prior to the conference, and was excited to learn from top female scientists. Seated at my table was a diverse group of researchers, ranging from another undergrad, to a professor, and everything in between. Together, we represented British Columbia, Pennsylvania, Melbourne, and Ontario, just to name the ones I can remember! The two speakers were not only top scientists in their fields, but were also incredibly funny as they shared their journey as females studying science. What stood out to me the most in their presentations was the emphasis on putting yourself out there. They emphasized how science not only relies on what happens in the lab, but on the ability to communicate well and confidently. These two women certainly epitomized this. 

After another excellent day at TAGC 2016, the view from my room was yet again a beautiful sight to behold. This was my last night in Orlando, so I soaked up the peaceful view and looked forward to an exciting workshop happening the following morning!

- Vivienne 

Lectures galore, PhD wisdom, and more freebies!

My my, was Thursday a packed day here at TAGC 2016. I had an early start with the Genetics and Determinants of Health Joint Plenary Session at 7:45 am, and was very thankful for the coffee stations positioned strategically throughout the conference halls! Before the session, I had breakfast with two postdocs from South Korea. Their 12 hour flight made my journey seem like a breeze! Once at the session, I whipped open my program book to the handy note-taking section (see above picture). The first speaker was Leonard Zon from Boston Children's Hospital. Zon made the world's first model of nevi (moles) in zebrafish in order to model melanoma! From this, his team is looking to identify new drugs to treat melanoma. Next up was Amita Sehgal, a researcher who studies sleep by using Drosophila models. I am amazed at how much we can learn by studying model organisms. According to Sehgal, the same genes implicated in Drosophila sleep are also involved with sleep in humans. Interestingly, male flies also have more robust "afternoon siestas" than female flies, and adult male flies who were deprived of sleep early on in life show impaired courtship behaviours. Sehgal showed a video to show the comparison between adult males deprived of sleep early in life versus those who were not, and the difference in speed was significant! Apparently, the reason why young flies sleep more than adult flies is due to lower activity of certain dopaminergic neurons that facilitate waking.

The third speaker, Harry Dietz from Johns Hopkins University School of Medicine, described the characteristic progressive widening of the aorta in individuals with Marfan syndrome. As you can imagine, this can be detrimental and may lead to "extraction" of the aorta, where it basically unzips itself due to the bulge. In mouse models of Marfan Syndrome, 100% of mice died due to aortic aneurysm. Dietz and his team identified potential new treatments by studying this model - so amazing!

Next up was Francis Collins! I was very excited to hear him speak. He did not present any of his own recent research, however, but gave a talk with lots of graphs and charts showing where funding from the National Institute of Health (NIH) is going. Based on the data, almost half of NIH grants go towards mouse research. Additionally, while funding for Drosophila and C. elegans research is decreasing, the success rate for grant applications for studies involving these model organisms is high. Collins also addressed the emerging era of big data and expressed that we must "become data scientists or suffer the consequences." He stressed the need to come up with standards for model organism databases. Of course, this is a challenging task, but in the long run will be more efficient and user-friendly, especially when studying more than one model organism.

After the session finished, I had a great conversation with the lady sitting next to me. She was also from the Drosophila community, and after a couple decades teaching, became a bureaucrat. She was so encouraging wanted to hear all about my research project! 

At 10am (it's amazing how much can happen before 10am here!) I headed to the Drosophila plenary Session I. One of my favorite talks from this session was by Ingrid Lohmann, who described the role of a particular hox gene transcription factor in the motor control of feeding in Drosophila. Another fascinating talk was by Annette Schneck. I appreciated how her talk was clear and easy to follow, as many speakers go at lightning speed. She focused on the role of habituation as a fundamental form of learning and a pre-requisite for higher cognitive functioning. Apparently, in many intellectual disability disorders, habituation is impaired, and therefore, the basis for higher cognitive functions (such as the ability to filter stimuli) is impaired. Through a series of experiments, Schneck and her team identified 98 novel genes required for habituation!  

This was my view while I ate lunch with another undergrad student named Alex from Stanford University. He told me about what he is doing studying yeast and anti-fungal resistance, and I gave him a synopsis of my research with Drosophila genetics. I asked him why he chose Stanford University, and he said he wanted to attend a school that had strong departments in addition to a strong science department. Hear, hear! I think it's great that he wanted to take his education to a whole new level by expanding his horizons beyond science.

Next up were the poster presentations! Here I am with Sami, fellow bioinformatics and Drosophila undergrad researcher from UFV. This photo was taken the night before at the Opening Mixer. Unfortunately photos weren't permitted during the poster presentations. I had the opportunity to talk with lots of PhD students, postdocs, and a few fellow undergrads! 

Following the poster presentations I headed to the Plenary Session and Workshop for Undergraduate Researchers. I am so glad that I attended this session. Not only were the speakers exceptionally good, but there was also a panel of PhD students who answered questions and gave copious amounts of advice. Their backgrounds and interests were all slightly different, making it a very well-rounded panel, and it was clear that they loved what they were doing. Some questions they were asked included: Does it look bad to take a gap year after undergrad? (Most said no - as long as you are doing something productive, interesting, or helps you grow and mature as a person) If you could change one thing about your journey to grad school what would it be? To this many said they would network more, be bolder, and believe more in themselves! One of the first speakers presented on why Drosophila sperm are so long - 28 times the length of their body to be exact! The main school of thought is that sperm and female seminal receptacles (SRs) are co-evolving, and therefore, longer sperm are selected for in the case of females with bigger SRs. 

After the session I took the speedy elevator down to the cafeteria to grab a quick dinner. I read through my notes, a few abstracts, typed some thoughts and memories on this good ol' blog, and chowed down on my sandwich. After dinner I made my way to a session on Ciliate Genome Stability and Dynamics, maneuvering my way through swarms of conference attendees. I wish I had more background knowledge on ciliate genetics before heading into this session, because, as I found out later, ciliates are unique in that they have two nuceli, one called the micronucleus and the other the macronucleus. All of the speakers in this particular session studied a ciliate called Tetrahyhemna thermophila. What I appreciated about one of the speakers in particular was her complete honesty. After reporting a strange finding, the speaker said, "I don't know what's going on... just yet." I liked how she was honest, but ended on a positive note that, although they may not possess the knowledge YET, each experiment beings them one step closer!

Also! The picture above shows one of the cool freebies included in our welcome package: a genetics themed deck of cards!

Unlike the glorious sunshine lighting up this photo, by the time I made it back to my room it was dark and I was ready for some sleep (And a time to recharge my brain after a day full of talks!) Friday will no doubt be just as packed as today, and I'm really looking forward to the Women in Genetics Panel in the evening. Until then folks! 

- Vivienne 

Mixers, Exhibits, and New People!

Yesterday was a very exciting day. The Marriott is now fully covered in GSA posters, signs giving directions, and almost everyone I see has the easily identifiable conference attendee name badge. It's a common site to see people looking quizzically at maps of the convention center while sipping on a coffee or typing away at a laptop.  

Here I am sitting on the spiraling staircase ready to head into the undergraduate mixer, my first event of the conference! The first hour of the mixer involved hearing a panel give presentations and answer questions about applying to graduate school and pursuing academic careers. The first speaker, Anthea Letsou, represented the National Science Foundation (NSF) and explained the process of applying for research grants. She went into detail about the NSF's Graduate Research Fellowship (GRFP) and REU (Research Experience for Undergraduates). Unfortunately, these grants are only for US citizens so I would not be able to apply, but it was still interesting to learn about how students in a different country are able to gain research experience.

The name of the next panelist escapes me, but thankfully, his words do not! This panelist, highly experienced in grad school admissions, outlined the general process of applying to grad schools and the importance of specifically tailoring your personal statement to each program you apply to. What I found interesting was how much he emphasized addressing one's weaknesses head on in the personal statement. For example, in the case that someone had poor grades in undergrad, instead of ignoring this in their personal statement, he strongly recommended addressing it positively as something that they have overcome, and won't stop them from seeking higher education. He also helped our brains begin churning by encouraging us to ask questions such as, "Why do I want to go to grad school in this particular field?" and "Why this particular school?"

The third and final panel speaker was a PhD candidate from Izmir, Turkey named Hatem. I am so glad I had the opportunity to hear her describe her journey, and wow, what a journey! Hatem focused a lot on the importance of finding a lab with a PI (primary investigator) who you communicate well with, as she went through a long and bumpy process of finding a lab that was the right fit with her. Another thing I never thought about in length before was just how important ensuring funding is. Some PhD students are put in a very challenging spot when there isn't enough funding for them to finish their research. They then have to try and find another lab, another PI... According to Hatem, during grad school you really earn a "masters degree in life."

After the panelists presented there was a brief time for questions, followed by snacks and the opportunity to talk in smaller groups with the panelists, grad students, and of course, fellow undergrads! I met students from Kentucky, Illinois, Columbia, and more, some studying yeast, others Drosophila, and one running experiments with C. elegans. The research that these undergrads are doing is amazing - one student I talked with is studying a Drosophila model of autism spectrum disorders (ASD), and gave me a quick synopsis of the correlation of ASD with Fragile X Syndrome. I was very impressed! 

This is the registration, pick-up, and go-to desk in the case of any questions. Whoever did the graphics for this conference did an excellent job. Whenever I see the hexagons I immediately think of hexane and benzene rings... Haha oh organic chemistry!

After the undergrad mixer I headed to my first session of talks. I decided to attend the two hour session of talks from the zebrafish community focusing on Regeneration and Stem Cells. It took me a few minutes to decipher what the first speaker meant by "TREEs," and a quick read of their abstract on the TAGC app clarified these to not have trunks and green leaves, but to be "tissue regeneration enhancer elements." I am quickly realizing how many acronyms are used in genetics, and even all throughout biology. Hopefully more of these acronyms will become increasingly familiar by the end of the conference. The next speaker was from Boston Children's Hospital and discussed her work in screening for chromatin factors involved in the differentiation of hematopoietic stem cells, more commonly referred to as HSCs (see, another acronym!) She had excellent images showing how chromatin remodeling factors, specifically one called Ing4, are required for HSC specification. One of the other speakers that I found very interesting talked about cryopreservation of zebrafish spermatogonia in whole testis. When placed into female ovaries the spermatogonia differentiated into oocytes! This is fascinating, and my brain is trying to understand how exactly this works.

Following these fascinating talks was the Opening Mixer with Exhibits. This is where I picked up copious flyers, leaflets, pins, and learned about everything from aquatic systems for precisely controlling environments for zebrafish to minicube PCR systems. There was also the most amazing microscope with a built in needle for making transgenic embroys.  

The tightly regulated zebrafish tanks, with the control panel located adjacent to the tanks on the right side. 

The Minicube PCR machine! Now this is something that would look mighty good in our UFV labs... :) Each tube does a separate PCR reaction simultaneously with different temperatures, cycling times, target DNA.. you name it!

"Schedule at-a-glance" posters are located all throughout the conference area, listing the upcoming talks from particular model organism communities. 

Here is the spread of items I picked up from the exhibits and from the welcome package. I'm pretty excited to have a bright red hat reading "Rainbow Transgenic Flies," a stack of genetics themed cards, and a preeetty cool GSA tee shirt. 

At just after 11pm I headed back to my room from the exhibits. I could have easily spent another half hour there, but my copious yawns told me I needed some rest. Thankfully the exhibits are around for most of the conference so there is plenty of time to take another look.

So far, the Allied Genetics Conference has opened my eyes to some amazing research being done around the world, not only by research professors, postdocs, and grad students, but also by fellow undergrads. The talks so far have also confirmed just how complicated science is and how a nice, tidy answer wrapped up with a bow just doesn't happen. Science, and genetics specifically this weekend, is full of unanswered questions and dedicated individuals seeking answers. Although not said with explicit words, the passion in each speaker is so evident from the long days spent in the lab, the commitment needed to run experiment after experiment, the constant asking of questions, and the insatiable curiosity.

- Vivienne   

Vancouver --> Toronto --> Orlando

If someone ever tells you to hop on a plane to Orlando, Florida, hop on that plane with gusto and you will thank yourself! I am typing this from my hotel room at the Orlando World Center Marriott. My head is slightly fuzzy from being awake for so long, but the sheer excitement of being here and the beauty my eyes have taken in since arriving here has kept me awake and smiling.

So far I've seen conference attendees flooding quickly into the conference center. How can I tell, you ask? Well, the CRISPR shirt on one attendee and GENETICS written in bold print on another's backpack makes me pretty sure. :) 

This is the very first thing you see when entering the Marriott. The three black columns with abstract blue art are actually elevator shafts! There are stairs just below the globe-like structure that spiral down past a waterfall and lead into an expansive hallway that leads to the many (and I mean MANY!) conference rooms. 

Once you walk down the stairs and make your way to the ballrooms and meeting spaces, this is what you see. I took this picture before the people flooded in and the signs went up, and you can really see just how incredible this center is. According to the concierge, one of the ballrooms is one of the largest rooms in the entire world. This ballroom will hold all of the posters as well as the exhibits.  

Palm trees are present around just about every corner and along every street, flourishing in the balmy heat and daily rainstorms. This is the view directly out of a large window on the convention center floor. 

And more palm trees! This vegetation is so different to anything I've seen in the Pacific Northwest. Taking an ecology class here on a trip would be an excellent field study...  I would be the first to sign up... :) Studying the underlying genetic mechanisms that allow plants to flourish in extreme heat versus cold and winds would be very interesting, especially if students were immersed in the climates themselves! 

Another interesting plant enjoying the Orlando humidity and high temperatures. It was so humid outside that my camera lens began to fog up!

The glorious staircase leading down to the convention center rooms. If you look closely, you may be able to make out the marble of the stairs, which makes up most of the convention walkway's flooring (stunning!)

This is just a small part of the large outdoor pool area. Just look at the detailed structure of  the palm tree trunks. So cool!  

Banana trees (with no fruit, just yet!) make their home right outside the entrance to the food court.

And at last, the stunning view from my room. Every night when the sun sets and the evening breeze sets in the Marriott puts on a laser show, lighting up the pool with vibrant colors and music. It's so beautiful. The fireworks from Disney world can also be seen lighting up the sky at night, with some set off during the day as well.



I hope you have enjoyed this first post and introduction to the setting of the Allied Genetics Conference 2016. I will be posting every day during the conference, and will share stories of the talks, workshops, exhibits, people, and more that I experience. I know that I am going to learn a huge amount from the people I meet, the research I learn about, and the events I attend. After all, TAGC doesn't just stand for the Allied Genetics Conference, but also for the Totally Awesome Genetics Conference (kudos to the GSA for coming up with that!)

Stay tuned for more! 


 - Vivienne