Sapana Vora, PhD Candidate

Only July 7th, 2009, I successfully defended my thesis proposal and became a PhD candidate in Cancer Biology at the University of Chicago. The process was both informative and a little nerve wracking, and I'm glad it's over. My committee is smart, thoughtful, and truly engaged with my project and I am grateful to have them all signed on until the bitter end. Unlike at my prelim, I was able to amicably banter with my adviser and another prof and truly felt at ease the whole while, even when they asked me questions I couldn't answer. We did find the gaps in my knowledge and I have vowed to fill them to overflowing before my SRP (student research presentation) next February and certainly before my next committee meeting sometime next summer.

So what's my thesis project? In short, a case-control genome-wide association study of genetic susceptibility for the development of therapy-related acute myeloid leukemia (t-AML). What it basically means is that I'm going to genotype the germline DNA (what you're born with) of patients who are treated (more or less) the same way for the same primary cancer and see what's different between the people who develop t-AML (cases) and those who do not (controls). In terms of genetics, I'm primarily interested in SNPs (single nucleotide polymorphisms) and CNVs (copy number variants) found across the genome (genome-wide). It's the differences we're interested in, because they could potentially serve as markers or beacons representing susceptibilities to developing t-AML, a secondary, treatment-related cancer.

For those not familiar with the whole PhD process, it typically goes something like this:
Year 1: Take classes and rotate through labs (usually 10-weeks apiece).
Interim: Take some preliminary/qualifying exam to test knowledge and confirm student is ready to continue in the program. Join a lab for the thesis project.
Year 2: Take any remaining classes and fulfill TA requirements.
Interim: Assemble thesis committee (adviser+ at least 3 other profs, at least two of which are within one's department). Successfully write + present = defend thesis proposal.
Years 3-?: Conduct thesis research. Fulfill any class/TA requirements remaining. Meet with thesis committee at least once a year. Attend conferences, meetings, etc.
The End: Successfully write + present = defend thesis. Send copies to the five people who will ever read it. Graduate and put "Dr" in front of name. Figure out what to do with rest of life.

I am currently in the second "interim" stage. Now, all I need are my cases, controls, and data before I can move on. You know, small things.

California Dreamin'

[The last time I posted was June 9th. This is rather sad. I vow from here on out to post at least once a week, hopefully on interesting things going on in my life and barring any dearth of such news, at least interesting thoughts going on in my head.]

The past two months have been rather exciting though anxious at times. First the trip to California. On June 11th I flew out to California to celebrate Saket's graduation from Stanford. The flight was horribly delayed and I joined my family hours late, only to arrive exhausted to some terrible news. My Dad's mother's health had taken a turn for the worse and our greatest fears rapidly darted to the front of our minds. We promptly canceled our weekend at Yosemite (quite a shame, since my dad loves Ansel Adams' photography and longed to see the subjects in person) and started searching for the earliest flight to India. Unfortunately, my dad didn't have his passport with him (something I've made a personal point to always have with me when I travel, just in case...) so trip planning was slightly complicated. Our friends and neighbors, the Shahs, were a tremendous help in packing Dad's things and getting him to and from the airport as quickly as possible. We really owe them. He left on the 12th, just a day before Saket graduated.

The graduation ceremony was fun, though the sun was a bit intense (the tan lines have only just fully faded). We got to meet a lot of Saket's friends, tour the gorgeous campus, and enjoy a performance by the (in) famous Stanford band (tree included). Pictures are up on facebook.

The next couple of days were spent in the City. We toured the Marin Headlands with had incredible views of the Bay. We visited the fabled Berkeley campus where Greek architecture is the style of choice and meeting places and cafes just scream *liberal*. Just walk along the streets bordering campus and you'll inhale more than fresh, left-slanting air. We also ate at this great little Thai restaurant and basked in the glory that is Thai iced tea (half tea, half half-and-half, and half sugar).

We also had 2.5 days schedule for Lake Tahoe and it was a splendid trip. We had heard much tell of the lake but never got around to seeing it, despite our many trips to the Great Bear Republic. Though the skies threatened rain the first afternoon, they promptly cleared for the next two days and we were showered with glorious weather. We took a few hikes, took lots of pictures of the lake, visited a Scandinavian castle, ate some of the best pizza I've ever had, found a delightful Thai restaurant with approximately 8,000 vegetarian choices, and in general enjoyed ourselves.

While I was busy having fun, a rather serious deadline was bothering me. My thesis proposal was scheduled for June 26th which mean the written part needed to be done by the 19th at the latest. I "worked" on it on and off but was starting to panic that I wouldn't get it done in time (poor vacation scheduling, eh?). Viewing the highly enjoyable Star Trek reboot with the sibs pushed the deadline further back but not forgotten. Sachi and Mom were scheduled to leave the next day (the 19th) and I was determined to just finish it all in one day. Then I got the email.

The stepmother of one of my committee members had passed away. Tim's, my friend and labmate, thesis proposal was scheduled for the 22nd and had to promptly be rescheduled. We decided it was best that he take my spot (since we share the same committee and the room was already booked) and that I reschedule to a later date. My new date ended up being July 7th, which meant I just received an 11 day extension. While my heart broke for my professor, part of me couldn't help rejoicing at the turn of events. Not quite schadenfreude, but too close for comfort.

With a deadline suddenly lifted, I found myself free to actually enjoy the last couple of days I had with my brother in California. We still worked in a student center for most of the 19th, though more or less relaxed the rest of the time. We played Smash Brothers with Nader until 3 a.m., toured the campus art museum (famous for its Rodin sculptures), attended a lovely BBQ with the people from DripTech (we got cool shirts too), attended an amazing farmer's market, and of course got more froyo (frozen yogurt for the uninitiated). I was sad to leave Cali but am seriously considering finding a post-doc out there someday....

Something useful for PPT2007

Hate always starting with the Calibri font package in PowerPoint 2007? Wish you could go back to Arial or Times New Roman? Then look no further than this post! Just follow the simple instructions below to set your own default presentation theme or design a new one:

In order to change the default font for PowerPoint 2007, we have to create a base
template and save it in default templates folder. Please follow the steps mentioned
below to create and save a base template and see if that will meet your
requirements.

1. Start PowerPoint 2007.
2. Select View tab ; then select Slide Master
3. On the Slide Master (Slide Master: the slide that stores information about the design template applied, including font styles, placeholder sizes and positions, background design, and color schemes.), make the changes that you want to be
reflected in every new presentation. You have to make the changes to each slide of the slide master.
4. Then click Close Master View.
5. Click Office Button and then click Save As > Other formats
6. Pick PowerPoint Template from the Save As Type list box
7. Save the template as Blank.potx. PowerPoint will automatically chooses the folder as %Appdata%\Microsoft\Templates, so accept the default location. The default location would be \Documents and Settings\\Application Data\Microsoft\Templates.
9. Close the file and start a new presentation to verify the font.
For your testing, attached a sample Blank.potx file based on your requirement.

(Courtesy of: Office Deployment Support Team Blog at http://blogs.technet.com/odsupport/archive/2009/04/24/how-to-deploy-specific-fonts-in-office-2007.aspx)

Whoa, I've Moved and Other Stuff!

Wow, so it's been an inexcusably long time since I've posted. I really should model my blog more after Saket's. He does a better job of actually, you know, blogging.

So what's happened since the middle of March? Obviously, the rest of that month, April, May, and about a week of June. In that time I've completed both of my required TAships (to smashing successes), finished my last graded class EVER (at least for grad school), and MOVED! My new digs are downtown, just two blocks off Michigan Avenue (the Magnificent Mile stretch of that great street) along Ohio St. For those who know the city, I'm very close to the Northwestern Medical Campus. And Nordstrom's. And the Gap. And Eddie Bauer. Oh my....it's going to be fun come day-after-Thanksgiving sale weekend!!

Once I get my act together and blog from home (I'm on my school comp right now), I'll post pictures. In short, I can see: the Chicago River, the Trump Tower, the Sears Tower (a sliver), and the skyscrapers bordering Millennium Park. I'm also about five blocks away from Navy Pier, so I'll be attending a lot more WBEZ events.

So what's next? Before June is over I'll have traveled to California to celebrate Saket's graduation from Stanford (CONGRATS), celebrated my Dad's 64th birthday (insert Beatles song here) and Father's Day, visited Yosemite National Park and Lake Tahoe, and both written and succesfully defended my thesis proposal. I will actually have a laptop on that trip so I promise to update in a more timely fashion.

Until then, my sweets, farewell!

Science Olympiad at COD

In high school my friends and I were perennial participants in Science Olympiad, a national organization dedicated to getting students engaged with science and engineering. Having won several medals at both the regional and state levels and enjoyed nearly every minute with my team in and out of competition, I have since tried to help out with SciOly competitions nearly every year since graduating.

My specialty was the big-ticket biology events, namely Cell Biology (basically general biology), and Designer Genes (genetics/genomics), and I've been privileged to write tests for these events for both North Carolina and Illinois competitions. This year I wrote a Cell Bio test for the Illinois regional tournament held at the College of DuPage (COD). I find it tougher each year to write an age- and skill-appropriate test, though I think I did pretty well this time. The highest percentage result I had on the Designer Genes test I wrote two years ago was 60% from NCSSM (an elite, nationally-ranked science and math school for 11th and 12th graders). Those numbers are slightly worse than what you see on graduate exams! This time my highest was right around 80% while the lowest was about 25%.

It's interesting to interact with science-oriented high schoolers after so long. I'm always amazed by the great range in knowledge there is. I heard one student from a team exclaim confidently that while the cell they identified was from a plant it was definitely prokaryotic too. I just smiled and tried not to laugh. I put some tough questions on there that I didn't really expect anyone to get right, but some were total gimmies. I just wish I had a copy of the exams I took so that I could try to make mine as fair and reasonable as possible. Maybe next year...

I didn't attend the tournament alone. Kevin drove me and Nikhil (a housemate) there and we met up with Yan, another material sciences student at NU who went to UC as an undergrad (a connection to each of us!) While those three managed the Chemistry Lab event (which Kevin also wrote), I handled Cell Bio mostly on my own (they helped set up and brought me pizza for lunch). Overall we had a pretty good time, though I have to say our location in NC (Garner High School) was much better.

After getting all of scores in (and checking them twice) we left around four. It was an odd time between lunch and dinner and we were kinda hungry but unable to pick a place to eat, despite my GPS giving lots of choices. I missed a Culver's and couldn't find another, so we settled for Baskin Robbins. Turns out the one the GPS pointed us to was in a mall, so we ended up getting different choices from a food court to make everyone happy. For a poor economy and a late Saturday afternoon the place was absolutely packed. We made it back to Hyde Park around 6 where I caught up a bit with Bonnie and Jeffrey before messing around on my computer. Great day!

Radio City Skating Ya'll

When I moved to Chicago about 18 months ago, I only really knew one person here. Since then, other friends from times recent and past have moved to the city. I really need to find the time to hang out with more of them and haven't done a great job so far. Fortunately, Kevin's been a help here. He came up with the idea of bimonthly/monthly meals that he, Megha Bisarya (our Cary friend from high school), and I could share. Genius! After some deliberation we decided that today would be the day.

As you might know I'm not exactly the most social person, and thus my Friday evenings are typically low-key. Thus it was weird to suddenly have four different places I wanted to be on a Friday night: 1) dining with Aneta, Jeff, and Tim, 2) watching Tropic Thunder at movie night, 3) watching Battlestar with Matt, and 4) attending WBEZ/Chicago Public Radio's open house followed by ice-skating and dinner with Kevin and Megha. Naturally, I picked option 4.

I left lab surprisingly early (3:45) in order to catch a bus to Navy Pier by 5. WBEZ is lucky enough to broadcast from the most visited destination in all of Chicago (and the state of Illinois for that matter). Tim, my lab mate, thought an hour to get to the Pier was a bit excessive, but given the stifling traffic we encountered on Lakeshore Drive (also called LSD, hah) it took a solid hour to go about 9 miles. Yeah.

It took some hunting to find the studios at the Pier, but at last I got there. The party was just getting started. There was a swag table set up and the first thing I thought was "buttons!" I picked up several of those along with a Wait, Wait, Don't Tell Me magnet, some bumper stickers, etc. They even provided bags to hold all the swag. How sweet. Mingling solo is easy for some people, but not for me. I just feel so awkward entering other people's conversations. I picked up a glass of 312 (brewed by Goose Island, a local brewery, and named after downtown Chicago's area code...click "no" for the 'are you over 21?' question on the website), and started wandering. I admired the (open) trophy case which housed an Emmy for This American Life, several Peabody awards, among other honors. Walked past the DJ from Sound Opinions and headed out onto the terrace to admire the view of downtown Chicago and Lake Michigan. Got over my awkwardness and joined a group of staffers. Talked to some people who work on fundraising and community outreach. Nice people!

Needed to warm up so I went back inside and started to see how far I could explore before someone said I shouldn't be there. Peeked into the lunchroom (nice vending machines) and as I passed some studios I saw a tour group heading into one. I slipped in behind the last person and got to visit a recording studio where live music acts play (complete with piano and fancily designed wood panelling for acoustics), another recording studio, and the main office area where pretty much everyone works. It's a giant cube farm with several nice flat-screen TVs posted around the walls. No one, not even the execs, has a doored office, just bigger cubes. It's a very egalitarian setup and apparently convenient for impromptu meetings. We got to meet Richard Steele, a longtime radio man and one of the hosts for EightForty-Eight (which I discovered just today was named after WBEZ's street address: 848 W Grand Ave). He talked about what it was like to work for WBEZ and some of the challenges the employees face by working (as opposed to just visiting) Navy Pier; food prices are astronomical, commuting can be a real pain, and all those tourists can be really annoying (and clueless) sometimes (example, people standing next to the ferris wheel and asking where it is). Seems a great guy.

I was supposed to meet up with Megha and Kev at 7 by Millennium Park so I left after the tour. It's a bit of a hike to get back to the Loop from the Pier, but it was a beautiful if chilly night and I had my camera. There's something about cities at night that I just love. The lights, the bustle, the way everything takes on this otherwordly look. Daytime means work, nighttime means play. I took my own sweet time walking down since I'm rarely downtown in the evening and just had to take advantage of the clear sky and shining moon. Please see facebook for the pics.

Finally met Megha at a Dunkin' Donuts where we chatted and waited for Kevin. By 7:15 we were at the skating rink in Millennium Park for its last week staying open (who knows, though, it might snow in April). The line was mercifully short and the rink not too busy so we got our skates and got laced up in no time (though Megha needed some help tightening hers). I don't consider myself a very good skater, Kevin's much better, but I felt good enough on the ice to move pretty quickly, smoothly, and confidently. I hate falling, while doing anything, so I'll never be great until I'm ready to get hurt. Oh well.

Skating was a blast. Kev thought it'd be a great idea to try swing dancing on ice and I agreed. Megha taped us with my camera and the result is hilarious if not terribly well executed. It's harder than it looks at the Olympics!

We stopped around 8:30, just before the ice was set to be zambonied, again, and took the El to Grand Ave to find a Mexican place, Su Casa, Megha suggested. We shared some dishes and had a nice conversation. There was a lot of food and while Megha and I were stuffed, Kev suggested we grab some ice cream from the Coldstone we passed on the way to the restaurant. We protested but agreed anyway, and naturally ate some of his minty chocolately delight (I don't remember what it was called but it was delicious). Coldstone kicked us out at 11 and we decided we should probably head to our respective homes.

All in all, it was a fabulous evening and I hope to repeat it soon!

AAAS Annual Meeting: Our Planet and its Life, part I

This year the American Association for the Advancement of Science, better known as AAAS and the publisher of Science magazine, a world-class journal that contains papers from vastly different fields of science (from astronomy to anthropology, psychology to physics, neurology to nanotechnology, etc) held its annual meeting in my very own Windy City. I got wind of the meeting from a university email that announced the meeting organizers were looking for student "session aides" to keep things running smoothly. In return for at least eight hours of aid, the aides would have their registration (normally $70 for students) paid for. Naturally, I immediately applied and was got a position a few days later.

The day the meeting started I attended a brief orientation session to find out what exactly I'd be doing and when. Simple things, though some people had dumb questions (I believe there are such things). But that always happens. Brooke Sylvester, a 4th year in my program, kindly gave me a ride home.

Friday is when the real fun started. I wasn't scheduled to perform my aide duties until Sunday so I had Fri and Sat free to explore the massive Hyatt Regency, pick up free swag, and of course attend interesting seminars on all kinds of neat topics. I first attended a seminar discussing AAAS's plans for "Year of Science 2009," basically a program that works to get schoolkids and the public in general interested in science. Some interesting comments, including emphasizing to students the non-linearity of science, especially in terms of the scientific method. Science is not always hypothesis-->experiment-->gather data-->draw conclusions, then rinse and repeat. Insights can come from unexpected places and science is more like a web of interlinked pieces in which new connections are made all the time. A neat site that has a picture of the "real scientific method." Science education is a big passion of mine and I was interested to see what the panel and attendees, including journalists, researchers, teachers, and students, had to say about the subject. Another interesting group is COPUS, or the "Coalition on the Public Understanding of Science." I got an idea for a "Rock-It Science Concert" that could be fun to stage here at UC. The last neat thing I pulled from this seminar was more info on "Science Cafes" which are informal sessions between scientists and the public that occur in public, non-academic places like coffee shops and bars. Ben Wiche from NOVA and WGBH in Boston described going into bars with a scientist and how he could get the attention of the bar patrons and engage them in a science topic they normally would probably never discuss. Takes a lot of guts to engage the public in such a direct way, but the payoff would totally be worth it! I get to host my own "junior" Science Cafe in May at UC.

The first plenary lecture was delivered by Dr. Sean Carroll of the Univ. of Wisconsin at Madison. Dr. Carroll is a very talented and famous evolutionarily biologist who has written and lectured extensively on evolution and Charles Darwin. 2009 is a special year for scientists, and in particular evolutionary biologists. This year we mark the 150th anniversary of the publication of "On the Origin of Species" (by means of natural selection) by that great naturalist and celebrate what would have been his 200th birthday. As you can imagine, the meeting was something of a Darwin lovefest and Carroll's speech epitomized the reverence for the man, the theory, and as a nice touch, the other scientists, namely Alfred Wallace, and Henry Bates, who were friends of Darwin and supportive of his theory. Great lecture with some compelling stories about Bates and Wallace in particular (mishap- and adventure-filled treks through South America and Indonesia all in the name of science).

The headline for the evening was recent Nobel laureate and environmental champion Albert Gore. I'd already purchased tickets to see him at the Chicago Theater in April before hearing of this meeting, so I was thrilled to get a second chance to see Mr. Gore. I respected him as VP and like him even more for his campaigning on the behalf of scientifically sound environmental policy. Part of the lecture felt like Inconvienent Truth, Part II, while the rest was an impassioned and moving call to action to scientists to get them, rather us, more active in politics and their community. I've got videos posted on YouTube and some pictures on my Facebook page. Check them out!