Monday, December 14, 2009

Priorities

The order in which I get things done (roughly) when sorting through a massive to-do list.

1. Quals. I had a written qualifying exam recently (we had to write a paper critiquing a journal article) and basically dropped everything else to work on it. I mean, if I mess this up, they kick me out of grad school, so I'd better take it seriously. (I've since heard back from the DGS that I passed. Woohoo!)

2. Teaching responsibilities. In general, I'm more likely to do work when someone else is depending on me than when only my own butt is on the line. This is especially true when the dependents are a bunch of undergrads, with whom I feel a special kinship because I used to be them. It's been wonderful working with the students this semester, and I'd hate to let them down in any way, so I'm very diligent about grading, preparing review sessions, and answering questions over email or the course message board. I'm also quick to volunteer for teaching-related tasks when my supervising professor asks around the pool of TAs. I find it rewarding. While there are many things that I don't know, I thankfully have a firm grasp of undergraduate level neuroscience, and I enjoy putting that knowledge to use. Especially when failed experiments have left me feeling like a useless moron.

3. Coursework. A lot of my coursework this semester has been seminar-based. This means listening to my classmates give a talk and providing them with feedback. I like hearing what they're up to, although I'm occasionally intimidated by all the super-smart folks in my program. I do everything I can to help them out, because they're my friends, and they've done the same for me. Classes also provide me with a lot of distinct, attainable goals (study for this test and ace it, research and write this paper, make this presentation and give the talk), unlike labwork, where the carrot seems to be constantly dangling just out of reach. When I finish my work for a class, it's really finished, and I can move on to other things.

4. Experiments. I'm still struggling to find the best strategy for Getting Things Done in the lab, especially as I juggle items 1-3 on the list above. Next fall, I'll be finished with quals, teaching, and courses, so it will be easier to plan my lab time. As it is, I'm trying to stay organized and break things into manageable chunks that can fit in around other obligations. My adviser has helped with this by encouraging me to think of smaller tasks (like, "order primers" rather than "complete Aim 1 of my NRSA") and to plan things out far in advance so I don't get overwhelmed. I've started adding these smaller action items to my calendar, and I feel very industrious when I have a full agenda (even if it contains things like "make LB/agar plates"). My labmates have also been extremely helpful, suggesting new things for me to try and training me in techniques. I have a long list of experiments planned for January. If all goes according to plan (hey, a girl can dream...), I should have lots of fresh data to play with in the next month or two.

5. Extracurricular activities. This is how I'd describe my work with Emory Women in Neuroscience (EWIN), Graduate Advocates for Work-Life Balance (GAWB), the Third Culture Journal Club, and other side projects (like organizing an event for Rebecca Skloot at Emory -- everything is coming together, so keep your eyes peeled for more information about that!). I find these projects inspirational when they're in the planning stage, and immensely satisfying when things work out. Even if the end product is nothing more than a successful meeting, I feel like I've done a good thing. I've concluded that I really like working with people on projects like these, and I'd like to keep it up when I move on to my future career. As it is, I don't have a ton of time to devote to these things, but I'm slowly building a network of people who have given me lots of help in bringing my (our) ideas to fruition.

6. Social life. Most of my local friends are fellow grad students, so even when we're swamped with work, we find some time to catch up over lunch on campus. My program is full of really fun people who can sometimes coax me out of my office and into a fabulous party. And, my live-in partner provides me with constant companionship and emotional support when I'm freaking out about a deadline. I struggle to make time for all of these important people (as well as the ones who aren't local -- my family, my friends from college and beyond...) and I hope I do a decent job. My partner and I eat a home-cooked meal together almost every night, and my friends and I keep in touch through Facebook when we don't have time to meet up for shenanigans.

7. Housework. Man... you don't even want to know how much laundry I have piled up right now.

8. Blogging. Sorry, guys.

Looking forward to checking more things off my list in 2010! I hope you all have a lovely holiday season and a restful break between semesters.

Thursday, November 12, 2009

PhD Diary, Year Two: November, 2009

The fall semester is starting to wind down. I'm currently working on an experiment that has been carefully timed to end the day before Thanksgiving, so I can visit family in Florida for the holiday. Hopefully, nothing will go awry. It will be nice to see my relatives again -- I haven't seen them since last Christmas!

The past month has been busy (aren't they all?), but satisfying. I had one week that seemed really overwhelming when I was looking at my calendar: grading the second exam for my TA assignment, meeting with a famous scientist who'd been invited to give a talk at Emory, trying to organize things for my own invited speaker(s), and presenting a short version of my proposed dissertation work (which I will be writing up for a pre-doctoral NRSA next semester) in my advanced graduate seminar. I was freaking out about these things, but somehow I managed to stay organized and get everything done. I even managed to have a little fun (if grading exams during commercial breaks of a football game can be considered 'fun'). I also scheduled a fabulous dinner date at Cakes & Ale for the end of the week, so I had something to look forward to. Although the grad student workload can be a little insane, I actually get a perverse thrill out of getting all of these things done. It's a boost to my self-confidence when I'm able to complete a seemingly daunting task. I may have to be careful about what I get myself into, though -- I keep hearing about cool extracurricular opportunities (undergraduate mentoring, graduate school organizations) and signing up for things. Eventually I will surely come to a point at which I cannot take on more work and expect to retain my sanity.

And speaking of taking on extra work, I'm also trying to organize an event for Rebecca Skloot on campus. Ms. Skloot is promoting her critically-acclaimed new book, The Immortal Life of Henrietta Lacks, which I think has broad appeal not only for biomedical scientists, but for many other members of the Emory community. If you're a fellow Emory person and you're interested in helping me scare up some funding, please contact me.

Presenting an abbreviated thesis proposal in seminar really helped me organize my plans for the research I hope to accomplish over the next few years. My adviser and my labmates provided a lot of input, of course. But, most importantly, the assignment forced me to start thinking through my arguments for performing each experiment, what the possible results might be, and what each result would mean in terms of my central hypothesis. It was also the first presentation I've given in grad school using the word "I" (instead of "we" or "they") when referring to the creator(s) of some cool science.

Next semester promises to be even crazier than this one -- I'll be taking four or five classes, including an intensive grant-writing course. I'm not sure when I'm supposed to get anything done in the lab. But, after this year, I will have fulfilled all of my coursework requirements, and I'll be free to set my own schedule (within reason... sometimes, my tissue culture cells end up setting my schedule, and they don't respect weekends). Definitely something to look forward to. In the meantime, I'll have lots to keep my occupied.



Tuesday, November 3, 2009

Visualize your CV

My friend Liz shared this neat trick from ClueWagon: Paste your resume or CV into a word cloud generator like Wordle and see what comes out. Here's mine (click for larger version):

Friday, October 23, 2009

SfN 2009: Recap

As many neuro-bloggers have noted, it is very difficult to keep up a good blogging regime during SfN. With lectures, symposia, and poster sessions all day followed by social activities all night (we closed down a bar on more than one occasion), the conference is pretty relentless. I returned to Atlanta Wednesday night, and I've been trying to synthesize the rest of my conference experience. I also managed to keep up a running commentary about some SfN events on my Twitter account (when I could find wifi at the convention center), so check that out if you're interested in 140-character summaries.

Some highlights from the conference: The SfN tweet-up, where I met other dual science/internet nerds and dragged a bunch of my fellow Emory students along for the ride; a special lecture by Dr. Ben Barres during which he gave an extended sub-lecture about diversity in science (and referred to a previous talk, "Some Reflections on the Dearth of Women in Science," which I was lucky enough to attend last year); a special lecture by Dr. Eric Kandel, who literally wrote the book on neuroscience; several jam-packed symposia in Theme A; evening socials with free beer (I sort of crashed a party intended for University of Iowa students, who welcomed me with typical midwestern hospitality); discovering some extremely relevant posters in my field of research; networking with dozens of fellow scientists from around the world (we are totally Facebook/Twitter/etc. friends now!).

So what have I learned from my first major conference experience? The first major lesson came in conquering my tendency toward shyness. I found most of the people I met at the conference to be quite friendly, but it took me a while to get over my feelings of intimidation when approaching other scientists. This was especially true at the poster sessions, when I initially hesitated to ask questions or discuss someone else's work due to my lack of experience with the subject material. I got over this after a few days, and although a few people treated me in a dismissive manner, I had some really good conversations about other peoples' science. I also learned a lot by example, noticing which posters were easiest to understand and which speakers had the most professional attitudes when presenting.

The second lesson involved time management. With dozens of events happening each day, it's impossible to do everything. After a few days of struggling with the schedule, I decided that it was okay for me to hop from symposium to symposium, catching the short talks that were most interesting to me and then moving on to other things. I did always make a point to wait until each speaker finished his or her presentation before I left, though. I found it irritating when people would stand and walk out during the acknowledgments slide, before the speaker received their applause. I know we're all busy, but couldn't you wait another 30 seconds, in the name of politeness? I also tried to leave myself some flexible time for wandering around posters and vendors, taking a coffee break, or following a new acquaintance to a recommended event.

The third lesson: Pack a lunch. Convention center food is shamefully overpriced, unhealthy, and not particularly palatable.

It's good to be home. I'm giving lab meeting next week to share what I've learned from SfN (I was the only member of my lab to attend -- the rest of the students and postdocs are more geneticists and cell biologists than neuroscientists, and my PI was too busy with a study section to go to the conference). I found two really cool posters that dovetail nicely with our work, but I have a lot of background reading to do before I can put those results into the proper context.

Since returning to the lab, I've also noticed that SfN seems to have given my contact information to a bunch of vendors. Last month I didn't even have a department mailbox, and the first piece of mail I received at the lab contained my credentials for the meeting. This week I noticed a pile of catalogs, flyers, and other promotional materials. That was a little disheartening. I may keep some of the catalogs for my coffee table, though -- I'm sure non-scientist houseguests would be amused by the listings for various rodent mazes, which featured some very cute mice.




Sunday, October 18, 2009

SfN 2009: Day 2

The second day of SfN left me in a great mood. I opted to take the Metra to and from the conference center instead of relying on the shuttle, as I was pretty traumatized by last night's never-ending return trip. The Metra station at Millennium Park is about a mile from my hotel, so I started my day by walking through downtown Chicago in the stillness of an early Sunday morning. It was cold and clear. I was amazed at how beautiful the city is; just walking and taking in the sights has been a great experience. Stopped at a Dunkin Donuts on my way to get some food and caffeine, then continued to the train station.

The Metra ride went smoothly and I made it to McCormick Place in time for my first event, the Time Management Workshop on combining family and science. This was of interest to me because of my work with Graduate Advocates for Work-Life Balance. The panelists were all faculty at different stages of their careers, with different family configurations. I enjoyed hearing about how they achieved their own balance, and was pleasantly surprised to hear a lot of focus on the pros of being a working scientist and a parent -- their kids get to travel the world, and labs can become a kind of extended family, if you surround yourself with supportive colleagues. Brief talks by the panelists were followed by a Q&A during which the workshop organizer solicited suggestions for how the Society for Neuroscience can help its members achieve the balance they need. The suggestions echoed my own opinions -- that SfN should help trainees lobby for better family-friendly policies at their home institutions (maybe they can get Emory to comply with the NIH's policy on paid parental leave for training grant recipients...), and that similar panels with speakers at the graduate student and postdoc level would be helpful for the junior members of the society who are considering their choices for the immediate future. I also learned that other neuroscientists are lobbying for the creation of new family fellowships, to support individuals with family obligations that might make their scientific careers especially challenging. Email addresses were exchanged. It was overall quite a positive event, although I got the sense that some members of the audience were really struggling. Workshops are good, but we also need to be proactive about policy reform. We have to help people like the woman who stood up and said she was considering leaving science over her institution's failure to accommodate her family needs, or the woman who is afraid of losing job offers due to pregnancy.

With these thoughts running through my head, I had time for a quick lunch (I think the food court salad bar is one of the better options -- the $12 price tag is kind of ridiculous, but you can really load up your plate and share with a friend. Plus, it comes with soup!) before Dr. Thomas Sudhof's special lecture, "From Synapses to Autism -- Neurexins, Neuroligins, and More." I'd heard about the genetic studies implicating these key players in autism spectrum disorders, but I hadn't heard all of the details. Dr. Sudhof's lab has created mice with a mutant form of neuroligin 3 that recapitulates the version of the gene seen in some autistic children. The mice have social interaction deficits, but they are superior to wild-type mice in certain learning and memory tests. Further study shows that mutations in neuroligin 3 seem to shift the balance between excitation and inhibition in the mouse brain -- inhibition is heightened in the cortex, whereas excitation is heightened in the hippocampus. Dr. Sudhof proposes that the proteins that maintain the structure of the synapse (proteins in the presynaptic cell involved in neurotransmitter release, as well as postsynaptic factors that are important for receptor scaffolding) form a biochemical family that is a major player in the etiology of autism.

After Dr. Sudhof's talk, I hung around to watch the Peter and Patricia Gruber Lecture. Each year, the Gruber Foundation presents a neuroscience award to a distinguished researcher (or team of researchers) to commend their contributions to the field. This year's award went to Dr. Jeff Hall, Dr. Michael Rosbash, and Dr. Michael Young for their groundbreaking work on the molecular underpinnings of circadian rhythms. Dr. Hall and Dr. Rosbash were both faculty at Brandeis while I was there earning my BS/MS (Dr. Hall has since moved on to the University of Maine), and it was a treat to see people that I used to pass in the dim-lit hallways of the old Brandeis science building up on that stage. The three honorees presented a series of short lectures describing the history of their work on Drosophila neurogenetics and the winding path that led to the characterization of per, tim, and other genes that contribute to the daily cycle shared by all of your cells.

By then I decided to hop on the 4:15 Metra back downtown. I grabbed a sandwich and a cup of soup at a cozy little cafe, read the New Yorker, and enjoyed some quiet time away from the 30,000 neuroscientists at the convention. Strolling around Chicago by myself reminded me of living in Boston, when I would often go for long walks in the city to explore, window-shop, and people-watch. Atlanta doesn't lend itself quite as well to those little adventures, and I miss them. I'm glad I had this opportunity to visit a new city and get a little vacation with my science.

Tonight I'm headed to the SfN social media tweetup at LaSalle Power Company. It's at 7:00 PM. I'm looking forward to meeting some other internet nerds among the thousands of science nerds. A few of us have been busily tweeting away throughout the conference (albeit hampered by a Twitter outage this morning!). In the meantime, I'll be reviewing the conference itinerary for tomorrow. Feel free to suggest any talks or posters that you think I ought to visit.

SfN 2009: Day 1

Up too late hanging out in the hotel restaurant with new friends made on tonight's hellish shuttle ride (the bus driver got lost... it took me about an hour to cover the three miles between the convention center and my hotel). But, I had to blog about this:

A fellow Emory Neuroscience graduate student, Kim Maguschak, was recognized this year with SfN's Next Generation Award for her outreach work. Kim helps to organize the Atlanta chapter of the Society for Neuroscience, including most of the work for our large Brain Awareness Week campaign. Her efforts have helped send practicing scientists (including me!) into hundreds of Atlanta-area public school classrooms to teach kids about neuroscience. Congratulations, Kim!

Thursday, October 15, 2009

SfN 2009!

I'm headed to Chicago tomorrow morning to attend the annual Society for Neuroscience meeting. This will be my first time attending, and I hope to blog and tweet about the experience throughout. That may be dependent on the quality of available wifi, though. If you're reading this, going to the meeting, and want to meet up for a talk or a beer, let me know! I don't have a poster this year, so I'll be free to just take it all in.

Saturday, October 10, 2009

Quote of the Day

"Our research shows that women who had children during graduate school or within five years afterward and continued in their careers had as high a success rate as women without children. Not taking a break proved to be a successful strategy. And, as we shall see, the increasing number of family accommodations at universities, corporations, and other institutions allow more mothers to continue their careers without a lengthy interruption or detour into a second tier." -- Mary Ann Mason and Eve Mason Ekman, Mothers on the Fast Track: How a New Generation Can Balance Family and Careers

It's nice to have your mission validated, isn't it, my GAWB friends? (Thanks to Teresa for loaning me this book. Full review to come when I finish!)

Wednesday, October 7, 2009

'Tis the Season for Supporting Public Schools

Those of you who get around the blogosphere may already be aware of the DonorsChoose Social Media Challenge. For those who haven't heard of it, I felt the need to write a post, because this fundraising effort is so awesome.

DonorsChoose is a charitable organization that works with public school teachers to fund educational projects. Teachers essentially write little grants, and DonorsChoose provides a platform through which those grants can be funded through individual donations from many different people. Projects raise money for field trips, microscopes, books, art supplies, games, and -- in some heartbreaking cases -- even paper, pencils, and food, for needy kids who can't get these things any other way. The folks at DonorsChoose also connect donors with the teachers they support, so that the teachers and students can provide thank-you notes. I have received these notes in the past. They are usually filled with adorable crayon drawings. Aww!

To drum up support for their estimable cause, DonorsChoose created the Social Media Challenge. During the month of October, bloggers and tweeters recruit their readers to donate through Giving Pages. When donations are made through these pages, they are tallied up for the blogger running the Giving Page, allowing social media users to compete in a "philanthropic throwdown."

Many science bloggers are participating in the challenge through the Seed Media ScienceBlogs Giving Page. Their combined efforts have raised over $9000 in the first week of October. You can check out the list of bloggers and see if there are any scientists who deserve your support in the challenge. Some are even offering offering tangible (e.g., t-shirts) and intangible (e.g., suggest a topic for a blog post) rewards to donors who support them.

And then there's Sarah Bunting. Through her blog, Tomato Nation, Sarah is attempting to raise $210,000 for DonorsChoose... this month. She and her readers have raised over $37,000, as of this post. In one week! To motivate donors, Sarah gathers fabulous prizes donated by fans of her work and gives them away to DonorsChoose supporters at the end of October. She also offers "mini-prizes" each day for funding a particular project. And if readers meet her fundraising goals, she does something silly to reward them (this year she promises to wear a tomato costume to Atlantic City casinos and videotape the ensuing hijinks).

But it isn't about the prizes. It's about coming together to do something great for kids. I've donated in support of several bloggers this month, but I'm really trying to support the school children who need our help. With that in mind, I donated a $50 Amazon.com gift certificate (thanks, credit card points!) to the Tomato Nation challenge as a prize for supporting this project. The teacher who submitted the project needs to raise a couple hundred dollars today (all projects on DonorsChoose have a deadline for funding; this one's is tomorrow) in order to purchase games for his high school dropout prevention program in Alabama. If you'd like to help, you can make a donation of any size through the link above. For a shot at the Amazon gift certificate, you must then forward your email receipt to Sarah (sars at tomatonation dot com), who will do a prize drawing later.

It's inspiring to see the donations piling up as October goes on. I know many readers of this blog are fellow poor graduate students, but if you can go without coffee and a bagel today and donate even $5 to one of these projects, you can make a difference. I hope you will.

Monday, September 28, 2009

Careers in Teaching

Today I went to a career seminar sponsored by the GDBBS on Careers in Teaching. The Division does a lot of these seminars, and I try to take advantage of them to help combat my natural tendency toward "career planning," which at this stage consists mainly of sticking my fingers in my ears and chanting, "I'm not listening, la la la!" Okay, maybe not that bad, but it is hard to think about where I'll be after getting my PhD, since I've only just started my dissertation research.

Anyway, the seminar featured several terrific speakers. I guess it's not surprising that people who've made a career out of their passion for educating others are engaging and energetic ambassadors for their jobs. It was a pleasure to hear them share their experiences and their enthusiasm.

The first speaker, Dr. Leah Anderson Roesch, is the director of Emory's SIRE program, which is focused on helping Emory undergraduates participate in research. This is something that I feel strongly about, since my own undergraduate research experience made a huge impact on my own decision to become a scientist. I'm really excited whenever the undergrads in my TA course come to me with questions about research opportunities and graduate school. This may partly come from the fact that their interest validates my own life choices, but I think there's more to it than that. Undergraduate research builds confidence, independence, and curiosity. Students who see what it's like to actually work in their chosen field (not just science -- SIRE encompasses every department at Emory, from social sciences to arts and humanities to public health) are more engaged with what they're learning in classes. I truly believe that participation in programs like SIRE can be crucial to a student's educational and personal development. So, basically, I'm a big SIRE cheerleader. (I also hope to apply for one of their Graduate Fellow positions later in my graduate career. So awesome!)

But, I had already known about SIRE before I came to today's seminar. The Fellowships in Research and Science Teaching (FIRST) program, however, was new to me. FIRST is Emory's version of the NIH/NIGMS's Institutional Research and Academic Career Development Awards (IRACDA) program. Two FIRST fellows, Dr. Brandi Brandon Knight and Dr. LaTonia Taliaferro-Smith, spoke about their experiences with the program. FIRST offers three-year postdoctoral fellowships (so, my own participation would have to wait until the distant postdoctoral future...) that combine traditional research with intensive pedagogical training, mentored teaching, and independent teaching at minority-serving institutions. FIRST's mission is focused on course development using current educational techniques (especially those incorporating new technologies) in an attempt to better engage undergraduates in their classes. The fact that these exceptional teachers go on to work with traditionally under-represented populations of students is especially inspiring. And, of course, FIRST graduates (and graduates from the other 12 IRACDA postdoctoral programs around the country) are well-prepared for teaching-intensive faculty positions at small liberal arts colleges. Plus they still participate in traditional postdoctoral research -- and publish papers -- under the supervision of a PI at their primary institution. Frankly, the whole thing sounds pretty cool, although I'm sure the workload is sizable.

It was great to walk out of an hour-long seminar feeling excited about all the possibilities that lie before me. I may change my mind about undergraduate education later (perhaps after I have to grade my first exams this week...), but in general I think it's great to have these moments of reflection. I'm getting a PhD in neuroscience because I think neuroscience is fascinating, but I also have this dream about making a difference, which sounds great but can be hard to actually spell out in a five-year plan. One way to make a difference is to discover some amazing new scientific truth, of course, and it thrills me each time I uncover a new result that no one has ever seen before. But we can also make a difference through our interactions with other people. Someday my dissertation will be moldering in the stacks of the university library, quaintly out-of-date in the wake of the ever-expanding scientific frontier. But, as the bumper-sticker says (echoed by the many teachers in my family), "to teach is to touch lives forever." A warm and fuzzy sentiment to save up for those lonely nights in the lab.

Friday, September 25, 2009

Third Culture Journal Club

Yesterday was the inaugural meeting of the Third Culture Journal Club, an organization for graduate students interested in interdisciplinary research. I felt like a bit of an impostor as I sat with a bunch of truly interdisciplinary students from Emory's Graduate Institute of Liberal Arts, but they assured me that they want to reach out to science students as well.

I enjoyed hearing what others had to say on this topic, and participating in the discussion. It was quite different from the sorts of journal clubs that I attend in the sciences -- we barely referred to the reading! Most science journal clubs engage in a figure-by-figure breakdown of the article, a lengthy critique of the methods, and an interpretation of the results in a broader context. Third Culture's discussion used the assigned articles mainly as a jumping-off point. Still, I found the reading helpful to put me in the right frame of mind. I'm not used to working with these nebulous terms, so the attempts at defining academic disciplines and inter/multidisciplinarity research were helpful to me. It was also refreshing to read a couple of non-science articles for 'school' -- imagine, spending less than an hour going over a five page document!

The group talked a bit about interdisciplinary initiatives at Emory. One student at the meeting helped form the Scholars Program in Interdisciplinary Neuroscience Research (so new it doesn't seem to have a website yet!). She talked about how different ideas of interdisciplinarity came up during the planning stages of the program, and how people had vastly different opinions on the matter: some feel the neurosciences are already interdisciplinary enough, while others feel that we should collaborate more with the social sciences and humanities. We decided that "interdisciplinarity" cannot be all things to all people, and that perhaps we should attempt to more specifically define our goals for a particular research initiative. We concluded that while certain questions are best addressed through interdisciplinary collaboration, one should not fall into the trap of slapping an "interdisciplinary" label on a project merely to generate buzz or funding, as not all work can be conducted this way. We also came up with the term "problem-based research" as an alternative to "interdisciplinary research." The distinction between the two will be a focus of next month's meeting.

One article from the assigned reading (Golde et al., 1999) used the Emory Graduate Division of Biological and Biomedical Sciences as an example of a successful interdisciplinary initiative. By putting all the life sciences under one "umbrella," Emory has freed graduate students from individual departments and thus allowed for more interdisciplinary research, or so the argument goes. In the ten years since the publication of this article, many other programs have followed in Emory's footsteps. In fact, all four of the graduate programs for which I interviewed had life science "umbrella" programs (in addition to the GDBBS at Emory, I visited the BBSP at UNC Chapel Hill, the IDP at UF, and the integrated PhD program at Albert Einstein College of Medicine).

As an insider in one such program, I'm not certain that they've achieved true interdisciplinary enlightenment. Each sub-program (there are eight of them in GDBBS) maintains its independence, setting its own standards for coursework, qualifying exams, and dissertation committees. Each has a Director of Graduate Studies, a Program Director, and other governing bodies. Outside of a first-year biochemistry course, students in different programs rarely interact. While we don't work for a specific "department," in many ways we might as well be separated along those lines, as the individual program boundaries have a similar effect. This was also true of most of the other "umbrella" programs I visited -- some of them had wildly different requirements for the different sub-programs, with variations in stipends, teaching responsibilities, and scholarship opportunities, among other things. Einstein was a notable objection, as their PhD program does not break itself down into smaller programs at all (though students become affiliated with a department once they join a lab).

There are some true benefits to the GDBBS, however. I do appreciate the fact that I work with students from the BCDB and GMB programs in my lab, even though it took me about a year to even learn what all the different program acronyms stand for (some of which seem a little redundant -- "Microbiology and Molecular Genetics" vs. "Genetics and Molecular Biology"?). My lab is in the Department of Human Genetics, and it wouldn't have occurred to me to apply to a genetics PhD program back when I was researching schools. Because I essentially have two 'departments' (Human Genetics and the Neuroscience Program), I'm exposed to a larger scientific network than I may have been with only one affiliation. The nature of GDBBS/Neuroscience at Emory meant that I could rotate in labs associated with many different departments (I also dabbled in Pharmacology and Neurology) before making up my mind about what I wanted to do. Still, if Emory had a Department of Neuroscience instead of a Neuroscience Program, I'm not sure that my rotation experience would have been noticeably different. So, while programs like GDBBS are a good start, there is more room for improvement.

In general, I support any effort to encourage graduate students to branch out from their tiny subfields into the broader academic world. I specifically chose a liberal arts university for my undergraduate training because I appreciated the opportunity to study things like Latin lyric and elegiac poetry alongside my neuroscience classes. While my own research isn't especially conducive to interdisciplinary exploration (not a lot of textual analysis can be done on the subject of neural tube development...), I'm glad that groups like Third Culture exist to help broaden my perspective. These conversations are worth having even if they don't fit into my dissertation.

Wednesday, September 16, 2009

PhD Diary, Year Two: September, 2009

I've been struggling to come up with blog-worthy material lately. My rotation diaries were fun and easy to write, but now that I'm not rotating anymore, I need some new impetus to keep writing. I figured more diary-style entries would be easier to generate than other content, and will hopefully help me stay in the habit of blogging. I really enjoy reading other blogs, and I love getting comments from you all, so I really ought to put in the effort to keep this going.

With the semester in full swing, I've found myself struggling to manage my time. I'm not even taking any 'real' classes (I'm required to attend a weekly department seminar and a weekly journal club style discussion with my classmates), yet each week seems packed to the brim.

My first TA assignment has proved both time-consuming and rewarding. I attend regular lectures on Tuesdays and Thursdays, where I help keep track of attendance (a non-trivial task in a class of 99 students). The four other TAs and I have a weekly meeting with the course instructor to make sure we're all on the same page. I also hold a weekly review session, which thus far has been attended by about a dozen students each week. Finally, I had the opportunity to give one lecture from the syllabus during regular class time, which was my first real experience with that kind of thing. I talked for an hour about nervous system development, axon guidance, and synapse formation. Unfortunately, the class is an hour and fifteen minutes long... but students rarely complain about finishing early. I wanted to leave ample time for mishaps and questions, but I should have had some back-up "optional" material to throw in if I didn't use all the allotted time. Live and learn! Other than that, I think things went well. I've had enough practice giving talks at lab meetings and in classes that I'm over my stage fright and fairly competent at public speaking; I just wanted to do a really good job for these students. I've found the undergraduates in this course to be excellent students overall, always prepared for review sessions with thoughtful questions, so I don't think they'll suffer much from having a newbie lecturer for a day.

I'm also working in the lab, of course. After I spent most of the summer struggling with a project, my adviser and I consulted with an expert in the department. He considered my findings and the relevant published data relating to the project and concluded that I was chasing a nonexistent gene product. D'oh. It does make me feel better about all those failed experiments, at least. Since then I've had some time to regroup and I'm working on a couple of things in parallel.

One project involves growing cells in culture for many days, and the cells need attention even on the weekends. I don't mind Saturday morning jaunts to the lab, but because the bus I take to campus doesn't run on weekends, and my partner and I share a single car, I have run into some logistical issues. This weekend my partner will take the car to visit his parents in Florida, and thus I am unable to start a new experiment until next week. A labmate did volunteer to help me out, but I told her not to bother with my experiment unless she has other reasons to come in on Saturday and/or Sunday. In the meantime, I have other stuff I can work on.

Finally, I've become fairly involved with some student groups on campus, and the fall semester has brought lots of meetings and other events. The Third Culture interdisciplinary journal club has its first meeting next week (complete with complimentary coffee and bagels!). We'll be discussing interdisciplinarity in research and reviewing some articles on the subject. Subsequent meetings will focus on more specific topics that have interdisciplinary appeal. I've been thinking about history of science and similar subjects, but could use some ideas if you've got 'em.

I'm also really excited about the work I'm doing with Graduate Advocates for Work-Life Balance. The senior students who founded the group have already done a lot to explore issues of work-life balance for graduate students at Emory, but they've allowed me to share my opinions with them. Our eventual goal is to implement more progressive policies for parental leave, child care, elder care, and similar issues that affect the graduate student body. Some administrators have expressed interest in our projects, and we'll be speaking at the next meeting of the Graduate Student Council, so we're pretty psyched. We have a long way to go, but we're making some promising first steps, and meeting with the other students in the group is a continuing source of inspiration for me.

So, that's what I'm up to. I really want to get a new Research Blogging post out in the near future -- I'm presenting a critique of a Journal of Neuroscience paper for my journal club / seminar, so I have some material ready. It's just a matter of finding the time to type it up... always a challenge.

Wednesday, September 2, 2009

Qualification

I have updated my Blogger profile to say "second-year neuroscience PhD student," for two reasons. First, the semester has officially begun and the new first-year students are on campus. Second, and perhaps more important, I passed my written qualifying exam! (I will also have an oral exam at the beginning of my third year, which I must pass to achieve candidacy.)

Monday, August 10, 2009

Audio Entertainment

Sorry for the lack of blogging. (I'm starting to sound like The Least Interesting Man in the World!) I've been ramping up for my qualifying exam, which occurs this Thursday. After that I've got an intensive TA prep course and our program retreat to deal with, not to mention classes, teaching, working in the lab, and participating in a few student organization... but I do hope to step up the blogging as well.

In the meantime, I thought I'd share a few of my favorite science podcasts. Scientists spend many not-so-glamorous hours on boring, repetitive tasks. Whether you're photographing things with a microscope, quantifying cells, sectioning tissue, or just pipetting the same solutions into a hundred little tubes, it helps to have an mp3 player handy. When I tire of listening to "The Rise and Fall of Ziggy Stardust and The Spiders From Mars" (okay, I never tire of it...), I put on some science talk. Then listening to my iPod becomes work-related, and I'm less tempted to yell "Wham, bam, thank you ma'am!" in the middle of the lab.

Many of your favorite science journals have podcasts nowadays. Nature Podcast summarizes top stories from the journal each week and offers other specialized audio programming as well (including my favorite, NeuroPod). Not to be outdone by Nature, Science has a weekly podcast of its own. Cell rounds out the big three, although those slackers only produce a new podcast once a month.

Science podcasts targeted to the general public include NPR's Science Friday and NPR: On Science podcasts. The Naked Scientists also covers a broad range of topics, including science experiments you can do at home, and answers to listeners' science questions.

For more neuroscience-specific discussion, I really love All in the Mind by Australia's ABC Radio National. They bring a human angle to stories about mental health, psychology, and neurology, often interviewing patients and their families as well as scientific experts. Finally, I recently discovered the Brain Science Podcast, which recently featured an hour-long interview with my first scientific mentor, Dr. Eve Marder. I've only listened to a few podcasts so far, but the host, Dr. Ginger Campbell, is great at getting the scientists she meets to talk about their lives and careers as well as the details of their research. For example, I really enjoyed hearing Eve discuss what it was like to be a female graduate student during the Vietnam War era (when the number of American women in science jumped suddenly, as men stopped being able to defer the draft for graduate school).

Once you download some of these great science podcasts, you probably won't even miss my lackluster blogging! I hope you enjoy them as much as I do, and I'll see you on the other side of this crazy August.

Wednesday, July 15, 2009

Emory Blog Update

It looks like Emory has called off its dogs with respect to Dr. Doug Bremner and his blog. I'm relieved to hear that the whole thing was a "misunderstanding."

Hat-tip to Abel Pharmboy for bringing this to my attention.

Tuesday, July 14, 2009

Supporting Women in Science

During my blog hiatus, I was nominated for my program's Institutional Predoctoral Training Grant. Six students from the neuroscience program are nominated each year (as long as NIGMS keeps renewing our grant!). The funds provided by this grant will support me for the next academic year, providing my stipend (taking the financial burden off Emory) and fees (taking the financial burden off me) as well as funds for travel, research equipment, and hosting a guest speaker.

I'm thrilled to have been nominated for this grant, and I look forward to all of the exciting opportunities it has created for me. With these travel funds and my NextBio travel grant, along with support from my mentor, I will be attending the annual Society for Neuroscience meeting in the fall. Some classmates and I are registering for the conference and booking our hotel rooms today. We're psyched!

I've also been searching for a guest speaker to invite to our program seminar. My mentor made some suggestions based on people whose research would interest the department and who are known for giving engaging talks. I looked up the people on her list and did some searching on my own to narrow things down to a few candidates. And, during the course of my search, I decided that I want to invite a female speaker.

My graduate program, like most in the life sciences, has a predominantly female student body. It also has noticeably fewer female faculty (again, like most life science programs). While our seminar series has done a good job of bringing diverse guest speakers to Emory in the past, I felt that this was a rare opportunity for me to have direct influence on the gender balance of faculty who will interact with our students. Numerous research studies have shown that even people who strive for fairness when selecting candidates from a mixed gender pool will often bias themselves toward men. (See Prof. Virginia Valian's excellent slideshow tutorial on gender schemas, especially the bit in Tutorial #1 on gender bias in peer review, which begins at slide 15.) This is true whether men or women are evaluating the candidates.

To avoid this pitfall, I made a conscious effort to create a pool consisting entirely of female candidates. I joked about my "blatant sexism" with my adviser, but it's something that I take seriously. It did feel a bit strange and arbitrary to me as I removed speakers from my list simply because they are male, but I don't think a single missed opportunity to speak at our seminar series will have a large impact on their professional success. (All of the male speakers I was considering have already achieved professional success in the form of full professorship, selection by HHMI or NAS, etc.) I'm also sure that some other students on the training grant will end up inviting male speakers. But choosing to bring a female professor into my program for a talk could have a significant benefit, especially if students and postdocs who attend the talk are seeking a mentor for the next stage of their scientific training. Female role models in the sciences can be few and far between, so I think it's worth something to expose my classmates to more of them.

This is, ultimately, a small thing. But many small efforts can add up to larger achievements. When I was elected to a position within my program's executive committee, a classmate emailed to congratulate me. She also wrote, "I hope you plan on using your feminist powers for good." When I made this decision, I was thinking of her, and of the other amazing female graduate students who make my program great. (Our male graduate students are also great, I should add, but they don't often engage me about my feminist powers.) I'm doing what I can.

Sunday, July 12, 2009

I've Been Away

It seems that this blog has been on the back burner for over a month. Sorry about that! It's been a busy time for me -- I finished my last rotation, visited friends and relatives out of state, moved to a new apartment, and joined the lab where I will conduct my dissertation research. Things are going well for me, but I haven't had much time for blogging.

Also during my blogging hiatus, this happened. I find it worrisome, to say the least, and I've been thinking a lot about my decision to write under my real name without hiding my university affiliation. Perhaps it would be wiser to avoid the hornet's nest of new media at my university for the time being. But that doesn't feel right to me. If someone from my institution has a problem with what I write, they are free to contact me to discuss it. If I'm ordered to obscure my school's name (which doesn't really accomplish anything, given that interested parties are free to Google me...) I will comply. Until then, I will continue writing about my experiences practicing the science that I love, and hope that my university comes to a more sensible position on honest, open lines of communication between researchers and the blog-reading public.

Friday, May 29, 2009

More Travel Grants Available!

As some of you may know, I recently received a $500 travel grant from NextBio, makers of a free web-based "curated, correlated database of public data, integrated literature, clinical trials, and scientific news." The grant can be used to attend the scientific conference of my choice, which is awesome.

Well, they're at it again! If you're a graduate student or medical student interested in applying for a travel grant, check out the NextBio grants website. To apply, you must submit a one-page essay describing how you've used NextBio tools in your research. The deadline for applications is June 30, 2009, and recipients of the award will be notified by July 15. It looks like the company has decided to award grants like this on a continuing basis, which is great news for poor grad students everywhere.

TRP Channel Variations Determine What's "Too Cold"

ResearchBlogging.org In the fairy tale of Goldilocks and the Three Bears, Goldilocks encounters three bowls of porridge in the bear household. Papa Bear's porridge is too hot; Mama Bear's porridge is too cold; Baby Bear's porridge is just right. Why would Papa Bear and Mama Bear choose to heat their porridge to non-optimal temperatures? A new study by Benjamin Myers et al. published in PLoS ONE suggests that their perception of "just right" depends on their TRP channels.

Okay, it's unlikely that three members of an anthropomorphic bear family would possess significantly different temperature-sensitive ion channels. But the paper shows that warm- and cold-blooded species living in different environments have evolved ion channels with different temperature thresholds to help them maintain a body temperature that is "just right."

Transient receptor potential (TRP) ion channels are responsible for many different sensory functions. The first TRP channel was discovered in the fruit fly, where it plays a role in visual signaling. Many other TRP channels have since been found. Though these channels share a similar structure, they contribute to many different sensory systems, including touch, pain, taste, and smell. A class of TRP channels also responds specifically to temperature, allowing nerve endings in the skin to sense heat and cold. Interestingly, the channels also detect certain chemicals that create a hot or cool sensation even without a change in temperature. In 1997, we learned that the heat-sensitive TRPV1 channel also responds to capsaicin, the molecule that makes chili peppers taste "hot" (Caterina et al.). In 2002, other research showed that TRPM8, a cold-sensing ion channel, can be activated by the minty freshness of menthol (McKemy et al.; Peier et al.). But although we have learned a lot about the function of temperature-sensitive channels in mammals, not much work has been done in other model organisms.

Myers et al. examined the TRPM8 channel in a commonly used cold-blooded model organism, the South African clawed frog (Xenopus laevis). They wanted to see whether this species, with a core body temperature and preferred environmental temperature much lower than that of mammals, would have a different range of temperature sensitivity in its TRPM8 channels. They hypothesized that these animals would have channels tuned to temperatures appropriate for their ecological niche, meaning that they would require a colder temperature to become active than the TRPM8 channels of a warm-blooded mammal or bird.

To test this theory, the researchers dissected out the dorsal root ganglia (DRG) of several frogs and used calcium imaging to measure the cells' responses to different temperatures. The DRG is the portion of the spinal cord that contains the cell bodies of sensory neurons, including the cells that produce temperature-sensitive nerve fibers. Thus, the cold-sensitive cells in the DRG express the TRPM8 channel. Calcium imaging involves use of a fluorescent dye that produces light when exposed to calcium inside a neuron. Because calcium influx is related to neuronal activity, we can use the fluorescent intensity to determine which neurons respond, and how strongly, to a given stimulus.

About 23.7% of the X. laevis DRG neurons responded to menthol, the chemical activator of TRPM8. Similar percentages of menthol-sensitive neurons are seen in mammalian sensory ganglia. Frog neurons differ from those of mammals, however, when the neurons are stimulated with cold temperatures instead of menthol. While rat neurons have a thermal activation threshold of 25.4°C, frog neurons have a much colder threshold of 9.6°C. Thus, a frog TRPM8-positive sensory neuron requires a much colder temperature to become active and produce a "cold" sensation.

Myers et al. wanted to be sure that this change in temperature threshold was caused by differences in the TRPM8 channel and not some other difference between rat and frog sensory neurons. Therefore, they expressed frog, chicken, and rat TRPM8 in oocytes (egg cells which do not normally express any ion channels; this is a common experiment used for studying ion channel physiology in an isolated system). Voltage-clamp recordings were used to measure the changes in oocyte membrane potential caused by activation and opening of the TRPM8 channels. The oocytes expressing X. laevis TRPM8, as well as TRPM8 from the related frog species X. tropicalis, displayed a much lower activation temperature than the oocytes expressing chicken or rat TRPM8. This experiment also showed a slightly higher activation temperature for chicken TRPM8 than rat TRPM8, which is consistent with the elevated body temperature of birds compared to mammals.

The differences in the temperature-sensitive properties of TRPM8 channels between species occur because of slight changes in the ion channel's structure through evolution. X. laevis TRPM8 differs from rat TRPM8 in about 25% of its amino acids. The differences in protein structure allow the ion channels to exhibit slightly different responses to temperature, even though they are similar enough to retain their general TRP structure and cold sensitivity.

The researchers summarize their findings as follows:
Within visual and chemosensory systems, stimulus detectors (receptors) undergo great functional diversification as organisms evolve to inhabit a wide range of ecological niches. Our findings demonstrate that genes encoding somatosensory receptors display the same capacity for adaptation to species' environmental conditions. Specifically, we have shown that a cold receptor can be tuned to respond within a temperature range most relevant to the normal resting temperature of the primary afferent nerve terminal, whether determined by an internally regulated core body temperature or the environmental milieu.

They go on to add that it is not clear whether the X. laevis and X. tropicalis TRPM8 channels are specifically tuned to the niches of these two species, or whether they represent a universal amphibian cold-sensitive channel that does not vary between frogs inhabiting different environments. As we sequence the complete genomes of more organisms, it will become possible to search for genes homologous to TRPM8 in other cold-blooded species and compare them to these frog channels. The authors add, "It may also be interesting to examine species that experience substantial variations (short- or long-term) in environmental temperature, as there may be corresponding changes in TRPM8 expression and/or function that allow for optimal temperature detection under such circumstances." Some cold-blooded species become dormant during the winter months, and it would be informative to see whether their temperature-sensitive neurons exhibit different properties during dormant and active seasons.

This research further elucidates how evolution has shaped individual species to thrive in different environments, down to the smallest molecular details. Frogs, rats, and chickens, like Goldilocks, sense heat and cold while searching for a temperature that is "just right." But what's good for one species might not suit another. Their specialized ion channels allow them to appropriately respond to thermal stimuli -- even the ones that don't like porridge.

References

Caterina M.J., Schumacher M.A., Tominaga M., Rosen T.A., Levine J.D., et al. (1997) The capsaicin receptor: a heat-activated ion channel in the pain pathway. Nature 389 (6653): 816–24

McKemy D.D., Neuhausser W.M., Julius D. (2002) Identification of a cold receptor reveals a general role for TRP channels in thermosensation. Nature 416: 52–58.

Myers, B., Sigal, Y., & Julius, D. (2009) Evolution of Thermal Response Properties in a Cold-Activated TRP Channel PLoS ONE, 4 (5) DOI: 10.1371/journal.pone.0005741

Peier A.M., Moqrich A., Hergarden A.C., Reeve A.J., Andersson D.A., et al. (2002) A TRP channel that senses cold stimuli and menthol. Cell 108: 705–715.

Wednesday, May 27, 2009

Synaptic Vesicles Are Not All Created Equal

ResearchBlogging.orgA pair of articles in Nature Neuroscience this month provide new insights into the mechanisms underlying spontaneous and evoked release of synaptic vesicles. Spontaneous release of a single vesicle (a "mini" release event) at a synaptic site was first observed over 50 years ago. A mini is considered to represent a single "quantum" of neurotransmitter, therefore the quantal theory of neurotransmitter release states that all synaptic responses will reflect some multiple of the response to a mini (depending on the number of neurotransmitter vesicles released). This provides a convenient way to study neurotransmitter release, and many experiments have been conducted under the assumption that minis are a reliable shorthand for evoked synaptic responses. Scientists have debated the mechanism behind spontaneous release, however. Are minis produced by the same vesicles as those that produce evoked neurotransmission (that is, release of neurotransmitter in response to an action potential)? A paper by Naila Ben Fredj and Juan Burrone address this question, showing that two non-overlapping pools of synaptic vesicles exist in rat hippocampal neurons for spontaneous and evoked release. Are minis truly random, or are they responding to signals that we don't fully understand? Jun Xu et al. show that the same calcium-sensing molecule, synaptotagmin-1 (Syt1), is responsible for regulating spontaneous and evoked release of synaptic vesicles, and that Syt1 further regulates some yet-unknown sensor responsible for other mini release events. Both of these papers reveal new complexities behind spontaneous vesicle release that challenge some of our fundamental assumptions.

Synaptic vesicle release depends upon molecules called SNAREs, which are present on the vesicle (v-SNAREs) and the target membrane (t-SNAREs). Complementary SNAREs allow vesicles to fuse with the target membrane and release their contents (neurotransmitters) into the synaptic space. The prevailing theory of release states that these fusion events occur spontaneously at a very low rate, producing minis. An action potential causes an influx of calcium into the presynaptic cell, which activates a calcium sensor and greatly increases the probability of vesicle fusion, creating a large, synchronized release of neurotransmitter from many vesicles.

The first paper I will discuss, by Fredj and Burrone, addresses the assumption that spontaneously-released vesicles are the same as evoked vesicles. If minis are caused by the random fusion of synaptic vesicles with the cell membrane, then we would expect spontaneously-released vesicles to resemble all other vesicles, with the only difference being that they accidentally fused without receiving a calcium signal. Previous experiments have indicated that this is probably not the case (Sara et. al, 2005), but Ben Fredj and Burrone developed a new technique for labeling presynaptic vesicles that supports the notion of a separate pool of spontaneously-released vesicles. Vesicles that have released their contents are recycled by the cell, allowing them to be refilled with neurotransmitter and used again later.

The researchers created a tagged version of an internal vesicle protein called VAMP2, which they called biosyn. Fluorescently-labeled streptavidin will permanently bind to biosyn. If streptavidin is present in the synaptic space, it will label the biosyn that is exposed when vesicles fuse to the cell membrane. This allowed the researchers to visualize active, fused vesicles in a living synapse under different conditions. After verifying that biosyn is a reliable measure of spontaneous and evoked fusion events, and that the tagged protein does not interfere with normal synaptic processes, they went on to test whether spontaneous and evoked release events use the same populations of vesicles.

After testing biosyn labeling of spontaneous and evoked vesicle release, Fredj and Burron noticed that they saw only about half as much biosyn signal when examining spontaneous release, compared to evoked release. This occurred even though the vesicle populations appeared to be saturated (that is, the biosyn signal reached a maximum level after a sustained period of release, indicating that all of the available vesicles had already fused and been labeled with fluorescent streptavidin). This could mean that spontaneously-released vesicles represent a sub-population of vesicles that can undergo evoked release, or it could mean that the two types of release draw from distinct vesicle pools, with fewer spontaneous vesicle than evoked vesicles.

To distinguish between these two possible explanations, the scientists sequentially labeled evoked and spontaneous vesicles within the same cell using two different colors of fluorescent streptavidin. They describe that experiment as follows:
Synapses were first stimulated with a saturating stimulus of two 90-s depolarizations in the presence of strep488 [green streptavidin], which strongly labeled the entire recycling pool. A further depolarizing stimulus in strep594 [red streptatividin] resulted in no further labeling (or very small amounts of labeling), as all biosyn binding sites were occupied by strep488, confirming that our depolarizing stimulus mobilized all possible vesicles. On the other hand, after labeling the recycling pool with strep488, a further 15-min exposure to strep594 in conditions that would only allow spontaneous fusion events resulted in a substantial amount of labeling.

The data show that two different populations of vesicles are exposed to the fluorescent streptavidin probes under different release conditions. This prompted them to ask, "If the recycling pool of vesicles cannot account for spontaneous release, then where do these vesicles come from?" They propose that the spontaneous vesicles may come from the so-called "resting" pool. This is the name given to a previously-identified pool of vesicles that are not mobilized by neuronal activity. Further experiments by Fredj and Burrone provide evidence that this resting pool does provide the vesicles for spontaneous release.

A News and Views summary of the paper gives us more to think about:
The big question now becomes what other differences might exist between these vesicles besides the pools that they come from. Are they released from different locations in the presynaptic terminal, as suggested by a recent study? Does their protein and/or lipid composition differ? We can take some comfort in Fredj and Burrone's observation that the sizes of the evoked and spontaneous pools were highly correlated in individual axon terminals, consistent with previous studies. Further experiments will be required to identify all of the similarities and differences between these two forms of vesicle fusion and validate the continued use of spontaneous release to characterize evoked transmission.

Another paper from the same issue of the journal, by Jun Xu et al., indicates that while spontaneously-released vesicles may be drawn from a separate pool, they are using the same calcium sensor as evoked release (contrary to the belief that minis are, by definition, calcium-insensitive). They studied spontaneous (mini) and evoked inhibitory post-synaptic currents in cultured cortical neurons. While removing extracellular calcium from the culture medium depressed evoked currents more strongly than minis, the application of the membrane-permeable calcium chelator BAPTA blocked over 95% of minis. Meanwhile, applying caffeine (which increases intracellular calcium availability) increased the number of minis observed. This implies that while evoked vesicle release depends strongly on extracellular calcium influx, even minis are not calcium-independent -- some calcium must be present to trigger a spontaneous release event.

Evoked neurotransmitter release is known to be regulated by the calcium sensor synaptotagmin. Somewhat paradoxically, genetic deletion of synaptotagmin-1 (Syt1) causes an increase in the number of minis, leading to the theory that this protein both allows evoked release and prevents spontaneous release through some sort of clamping mechanism. But as the authors note, "The clamping hypothesis ... argues against the notion that spontaneous release may be biologically meaningful, as it is difficult to imagine how an accidental byproduct of evoked release could control a physiological process. Moreover, the clamping hypothesis fails to explain why at least some mini release is Ca2+ dependent."

Xu et al. decided to better elucidate the role of Syt1 in spontaneous vesicle release. By studying minis in neurons lacking Syt1, they found that the upregulated minis in those cells were still calcium-dependent (they, too, could be blocked by BAPTA). They showed that the synapses with no Syt1 seemed to exhibit greater calcium affinity than wild-type synapses. This indicates that Syt1 is not acting merely as a clamp to block spontaneous release in normal cells, but that some other, more sensitive calcium sensor is able to produce spontaneous -- but not evoked -- vesicle release in the absence of Syt1. This was true for both excitatory and inhibitory synapses.

One explanation for this result would be that Syt1 serves as the primary calcium sensor for spontaneous release, but that an unknown sensor, normally clamped by Syt1, can lead to spontaneous release in Syt1's absence. To test this, Xu et al. generated neurons expressing mutant varieties of Syt1 with different calcium affinities. If Syt1 is indeed responsible for both evoked and spontaneous release, one would predict that changing the calcium affinity of Syt1 would create a commensurate change in the magnitude of both spontaneous and evoked release. Indeed, this is what they found. The result held true when they tested the different Syt1 mutations in brain slices as well as in cultured neurons.

The authors leave us with this conclusion:
Evoked and spontaneous neurotransmitter release are generally considered to represent distinct types of release that are differentially regulated. Their distinct natures are evidenced by the fact that spontaneous release is maintained in the presence of the sodium-channel inhibitor TTX, which abolishes action potentials and evoked release. We found, however, that despite their differential regulation, these two types of release are mechanistically identical in that they both are triggered by Ca2+ binding to Syt1. The major evidence for this conclusion rests on the three Syt1 knockin mutations that we used. We previously demonstrated that these mutations either increase Ca2+-dependent binding of Syt1 to SNARE complexes or decrease the apparent Ca2+ affinity of Syt1 binding to phospholipids. In a direct comparison of all three knockin mutations, we found that they cause a corresponding change in evoked release and a precisely equivalent change in spontaneous release. ... Moreover, our results support previous suggestions that spontaneous release is physiologically important. Ca2+ regulation generally implies a physiologically controlled function; thus, the finding that spontaneous release is controlled by Ca2+ binding to Syt1 implies a physiological role... Many neurotransmitters and neuromodulators act by increasing or decreasing presynaptical Ca2+ concentrations, suggesting that these agents may control synaptic circuits, at least in part, by regulating Syt1-dependent spontaneous release without triggering action potentials.

Of course, this article also leaves us with some burning questions. What is this second calcium sensor that is clamped by Syt1? Why is it so sensitive? What important physiological roles are being played by these highly-regulated mini release events? Clearly, more research is needed into these areas.

In conclusion, we've learned from this month's Nature Neuroscience that spontaneous release events are not the same as evoked neurotransmitter release. Although these two types of synaptic vesicles use the same major calcium sensor (and are both calcium-dependent, contrary to popular belief!), there exist separate pools of spontaneous and evoked vesicles that respond differently to intracellular calcium fluctuations, and never the twain shall meet. It will be interesting to see where we go from here, teasing apart the distinct roles that these two types of vesicles play in neurotransmission.

References


Fredj, N., & Burrone, J. (2009). A resting pool of vesicles is responsible for spontaneous vesicle fusion at the synapse Nature Neuroscience, 12 (6), 751-758 DOI: 10.1038/nn.2317


Xu, J., Pang, Z., Shin, O., & Südhof, T. (2009). Synaptotagmin-1 functions as a Ca2+ sensor for spontaneous release Nature Neuroscience, 12 (6), 759-766 DOI: 10.1038/nn.2320

Sara, Y., Virmani, T., Deák, F., Liu, X., & Kavalali, E. (2005) An isolated pool of vesicles recycles at rest and drives spontaneous neurotransmission. Neuron, 45 (4), 563-573 DOI: 10.1016/j.neuron.2004.12.056

Tuesday, May 26, 2009

Scientiae: Moving Forward

How are you moving forward in life? Are you close to your degree, tenure, sabbatical, or summer holiday? Is that paper almost ready to go out the door? Is your baby almost potty trained or are you training for a marathon? What keeps you moving forward in your science, work, and life? Is it the drive to cure a disease, make the world a more sustainable piece, or discover something that no one else knows? Is it the promise of exciting data at the end of a long assay? Is it the thought of people calling you Dr.? Is it your daughter's smile when she wakes up in the morning, or the enthusiastic tail wagging of your dog? When things get tough, how do you motivate yourself to move forward?


The "moving forward" theme is an appropriate one for this time of year. After a two-year break while working as a research assistant, I once again find myself in step with the academic calendar, when May marks the end of the year. It's a bit unsettling to think that school has been the major focus of my life for so many years. When I was working full time, I felt a bit of resentment when I didn't get a summer vacation -- but then, I didn't really take summer vacations in college (I spent each summer taking classes, doing research, or both), and I'm not getting too much of a break this year, either.

Even so, I've finished the first year of my PhD work. That is such an exciting accomplishment. I haven't taken my written qual yet, but based on my grades in my classes I'd say I'm doing well. For someone who spent many years as a squeaking-by slacker, and made some rather embarrassing grades in college, this is a big deal. I spent much of my academic career feeling smart, but not particularly successful. Now I'm actually feeling a little hint of pride in my accomplishments, which is a good feeling, although I worry about things going to my head. When I receive independent confirmation of my success, like an A in a course or some praise from a professor, my self-esteem actually seems grounded in reality.

Related to that self-esteem is the idea that I might actually be of use to other people. In the lab, I'm starting to come up with my own ideas for experiments. In other academic settings, I've been elected as a student representative on my program's executive committee, I'm working with a cool group of students from other departments on an interdisciplinary journal club, and I'm looking forward to TAing my first class in the fall. All of these things make me feel like I'm part of a team, doing important work that might even have some impact on the outside world. My ideas might contribute to a publication, a policy, an inspiration. And, in my personal life, I recently heard from my aunt that my teenaged cousin declared a science "major" (her high school has students on different themed academic tracks). I'm sure I can't claim to be the sole determining factor in that choice, but I like to think that I've been a good role model for her, and that I can be there to offer her advice as she continues her education.

Overall, I'm in a good place right now. I have new challenges to face in the next year, and I continue to fret over failed experiments, family crises, and the legions of bugs that have settled in my kitchen, but I draw strength from some great support systems. Quals and roaches had better watch their backs.

Written for .

Monday, May 11, 2009

Rotation #3 Diary: Week 8

I'm now in the last week of my third rotation. Soon I will be choosing the lab where I'll spend the rest of my graduate school career. Thankfully, I'm in the happy position of choosing between several good labs. I haven't completely made up my mind, but I am leaning in one direction. I hope to sort everything out and join a lab by the beginning of June. If any former or current grad students would care to offer me some advice on making this decision, I'd be happy to get your input!

Last week I presented my rotation work at lab meeting. I made a little PowerPoint presentation that went over my progress on a couple of projects, complete with cute cartoon mice and screenshots from the gene sequencing software I've been using. Then, much to my horror, I deleted the entire thing 30 minutes before the meeting. I know I should have backed it up, and I had intended to. My original plan was to fine-tune the presentation the night before, which would have involved transferring it from my laptop to my desktop either by email or by flash drive. Unfortunately, I spent the night before the meeting at the emergency room, being treated for a bad allergic reaction to a bee sting. (It really wasn't my week...) So, I got no work done, and never transferred the file between computers, and thus had only one copy. Which I deleted. As Charlie Brown would say, "AAUGH!"

Fortunately, my PI and labmates were understanding of the mishap, although they did scold me for not making a backup copy. (I know. I know!) I gave lab meeting as a "chalk talk" instead, drawing diagrams on the board when I needed to, but mostly just talking and glancing at some hastily-scribbled notes to remind me of the details. Despite the awkwardness, this forced me to really explain the reasoning behind what I did and summarize the relevant results, rather than being like, "Look! I ran a gel! And here it is!" Hopefully the lab doesn't think I'm too much of an airhead, despite my technical difficulties.

More lab foibles: We transformed some bacteria last week. After spending a while cloning and sub-cloning, we finally had some DNA plasmids that we wanted to make in large quantities. This is done by tricking bacteria into taking up the DNA, i.e. transforming them, and then growing cultures of the bacteria so we can extract plasmid DNA from them once they've been fruitful and multiplied. I'd done transformations before using heat shock (putting the bacteria into a hot water bath for a minute or two), but this protocol called for electroporation (zapping the bacteria with electricity). No one in the lab had used the electroporation machine before, and our first run did not go too well. In fact, a very impressive spark was produced, along with a crackling sound and a strong aroma of barbecued competent cells. After daring everyone in the lab to smell the tube, we adjusted the settings on the machine and it seemed to be okay after that. No more fireworks occurred, and my transformed bacteria grew on some ampicillin plates, so it worked for at least some of them. (The plasmid we put into the bacteria contains an ampicillin resistance gene, so we know that successfully transformed bacteria will grow even when treated with that antibiotic. The untransformed bacteria die when you put them in ampicillin.) Now I've selected transformed bacterial colonies and grown enough of them to make DNA preps. We'll have to do some more analysis to see which colonies have the plasmids we want -- some of them might have recombined in weird ways, which isn't desirable. Progress marches on, with tiny little steps. Someday we'll make these into a lentivirus, honest.

I also had my last class of the semester last week. (We had our final session of my graduate seminar at a pub. It was quite grueling.) This August, I'll be taking my written qualifying exam. Until I pass that, I don't want to jinx myself by updating my Blogger profile from "first-year" to "second-year." But, I am very happy to be one year closer to a PhD. Next year I'll be working on dissertation research, TA assignments, grant-writing, and serving as a student committee representative for the Graduates in Neuroscience organization. I'm excited!

Vaccine Dinner Club: Simultaneous Administration of Vaccines

Wednesday night, I attended a meeting of the Vaccine Dinner Club at the Emory University School of Medicine. This group of clinicians, researchers, policy makers, and other interested parties meets monthly in Atlanta to discuss issues related to vaccines. This is sort of tangential to my own research, but the May meeting theme (Simultaneous Administration of Vaccines: How Many is Too Many?) is a hot topic right now, so I was interested in hearing what the speakers had to say. Plus, they serve food and drinks. If you're in Atlanta and think this sounds like a good deal, I encourage you to click the link and learn more about the club -- it's free to join and to attend the nosh-filled meetings.

I must admit that I am a bit hesitant to make this post, because so many people have such strong opinions about immunizations these days, but I think it's important to share the kinds of things that experts talk about when they get together. This contributes to public education on the subject of vaccines, and it also lets people know that their concerns are being heard, and that medical professionals are trying to understand and alleviate them.

This month we heard from Andrew Kroger, MD, MPH, and Melinda Wharton, MD, MPH, both from the Center for Disease Control's National Center for Immunization and Respiratory Diseases. I did my best to takes notes during both talks, and I'll try to hit the key points in this post, but you should know that I'm not a doctor or a vaccine expert, so my interpretation of these lectures may be inaccurate. If I write something in error, please blame me and not Dr. Kroger or Dr. Wharton.

Dr. Kroger, a medical health educator, gave the first talk. He discussed the current vaccination recommendations established by the CDC, which cover a total of 17 different vaccines administered to children, adolescents, and adults. Because we now have the ability to protect against more diseases with vaccinations, people are getting more shots. Simultaneous administration of vaccines (which is defined as getting two or more shots during the same doctor's visit; not to be confused with combination vaccines, which consist of multiple antigens in a single syringe) is a strategy used by health care providers to ensure that people receive all of the recommended immunizations within the appropriate time frame. Dr. Kroger cited several studies indicating that giving two vaccines in one office visit is just as effective as giving them separately. In fact, it can sometimes be more effective. If vaccines are not administered simultaneously, they should be spaced out by at least one month. Giving two vaccines within the same month can lead to reduced efficacy of the second vaccine. Giving both shots at once, however, induces an immune response that is just as effective as the response to individual vaccines that have been spaced further apart. The only vaccines for which simultaneous administration is not recommended are varicella and smallpox. This is because doctors need to be able differentiate between the two diseases in the event of an adverse reaction. That is, if the shot gives you the pox (this is extremely uncommon, but possible), doctors want to be sure they know which pox you have, so they can treat it properly.

The CDC has been recommending simultaneous administration of vaccines for many years, but has added eight new vaccines to the recommended schedule since 1994. Dr. Kroger investigated simultaneous administration of these newer vaccines to see whether the historical data held true for them as well. You can find a wealth of information on this subject at the FDA's vaccine website. Dr. Kroger spent quite a while summarizing studies on new vaccines, and concluded that while we haven't rigorously tested every possible combination of shots (there are a lot of them), none of the studies conducted thus far present a contraindication for simultaneous administration.

Dr. Kroger went on to a bit of basic immunology, explaining why it's possible for our immune system to handle simultaneous vaccines. It comes down to a bit of math. Seroprotection (the goal of vaccination) is defined by antibody levels of 10 ng/mL of blood. To achieve this within a week of vaccination, only one B cell clone is needed per immune epitope for each mL of blood in the body. A typical vaccine contains about 100 epitopes for each disease that it protects against, so we need 100 B cells/mL of blood to achieve seroprotection for a disease within one week of vaccination. One mL of blood normally contains about 10 million B cells, so a healthy immune system should easily be able to handle several vaccines at once while still responding to other antigens that the body encounters.

These data left me convinced that simultaneous vaccines are effective. But are they safe? Fewer studies have been done on safety than efficacy, and there are data that indicate certain vaccine combinations can lead to a higher risk of side effects than individual administrations. Dr. Wharton, the second speaker, discussed these issues during her talk. While Googling for some of the studies she mentioned, I found this PowerPoint presentation, which is similar to the one she gave at the Vaccine Dinner Club. I suggest downloading it and looking through the slides if you're interested in this subject, as she covers more material relevant to common concerns about vaccine safety than I could possibly summarize here. The take-home message seems to be that while simultaneous vaccines may increase the incidence of side effects, these side effects are already rare, such that any additional risk caused by simultaneous administration doesn't make a huge difference. (Studies cited in Dr. Wharton's talk involved the combination of MMR and varicella vaccines. One study tracked over 531,000 children, divided into cohorts who received single, simultaneous, or combination vaccines. Only about 1% of the children across all groups were brought back to their doctor for fever symptoms after vaccination. The incidence of more severe complications, like febrile seizures, was much lower -- about 0.1%, with similar rates for sequential and simultaneous vaccines.) Parents who wish to take every possible precaution can ask their pediatrician about spacing vaccines out over several months, but this can present practical concerns for people who must take time off from work, arrange care for other children, and pay office fees during each trip to the doctor. If these issues create enough of a stumbling block, children might not be brought back for subsequent vaccines in a timely manner. And it's crucial to have children vaccinated within the recommended age range to protect them as early as possible from potentially fatal diseases. Delaying vaccination over concerns about simultaneous administration also delays protection against those diseases, so the relative risks must be balanced. While it is important to acknowledge that some children suffer unpredictable complications from vaccines, the optimal way to understand and prevent those complications is to come up with better screens for risk factors, not to simply stop vaccinating.

I thought Dr. Wharton brought up some excellent points during her discussion of risk communication with patients and parents on the subject of vaccines. Concerned parents will often reject expert opinions in favor of advice from individuals that they feel to be more caring and compassionate, even if that advice is misguided or inaccurate. It's important for healthcare providers to communicate effectively with parents, letting them know that not only do scientific studies support the importance, efficacy, and safety of vaccines for all children, but that adhering to a vaccination schedule is the best way for them to protect their child. Doctors with children of their own should be candid about their decision to vaccinate, and all physicians should make it clear that providing preventative medical care is the role of every loving mother or father. One survey of parents found that the most common concern with simultaneous vaccination comes not from spurious connections drawn between vaccines and conditions like autism, but from the additional pain and stress that children experience when receiving multiple shots. A kinder bedside manner can help with this problem, although it may be impossible to keep a child completely calm when he sees a needle coming.

The internet is teeming with discussions of vaccine safety and the dangers of the anti-vaccination movement, of course. For further reading on the subject, you can check out this article in the New England Journal of Medicine on vaccine refusal, Chris Mooney's summary of the vaccine/autism controversy in the June issue of Discover Magazine, and med student blogger Whitecoat Tales' Hard Conversations: Vaccines and Autism series.


Saturday, May 2, 2009

Rotation #3 Diary: Week 7

I think I lost count of rotation weeks somewhere back there... for consistency, I'll call this Week 7, but I actually have two more weeks left. Admission to PhD program in neuroscience? Check. Counting to single-digit numbers? Fail.

The sub-cloning project continues. I had one restriction enzyme digest that didn't work, so we chose a new enzyme for those samples and seemed to get it on the second try. I cut and blunted and cut and gel-purified, in between studying for my final exam and finishing my group project. These experiments lend themselves well to a crazed finals week, as I could set up a lot of reactions in an hour of lab time and just let them go overnight. Running the gels takes a while, though, as I'm working with some pretty big chunks of DNA and they are slow to separate, even on a low-density agarose gel. Outside the lab, I was proud of myself for coming up with a study schedule and sticking to it. I outlined all of the lectures, made flash cards, and got together with classmates to review material, without last-minute cramming. After taking the test on Thursday, I felt pretty good about it (although one professor did ask some really picky questions... we'll see).

I'm still waiting on the sequencing results from the mystery mice. Actually, I haven't even sent the samples to the sequencing facility yet. For some reason it's taking a long time to get purchases approved by the person managing the grant that funds these experiments, so every time I want to get something sequenced, there's a turnaround time of sometimes three days before I get the purchase order. By the time we got the funds approved for this batch, it was Friday, and no one at the sequencing facility would be there to receive our samples on Saturday, so they'll sit in the freezer this weekend and go out on Monday. One solution to this issue would be to put in a request for a really huge purchase order and reuse it many times over a couple of months, but you're technically not supposed to do this. You're just supposed to wait. Red tape is everywhere, even in the lab. Oh well.

Practiced some more stereotaxic surgeries this week. The concept seems pretty simple: anesthetize the animal, stabilize the head in the stereotax, do the procedure (in this case, we expose the skull, drill a tiny hole in it, and insert a needle into the brain to deliver our treatment), close the animal up, and let it recover (including medication for any post-operative pain). In practice, it's hard to get the head position right and adjust the arm that holds the needle/syringe into the right spot. I was constantly worried that I would do something wrong and hurt the mouse, although it was under anesthesia and felt no pain. We didn't do any survival surgeries; we sacrificed the animals immediately after injection and dissected them to check that the injection site was in the right place. Although this doesn't seem very nice to the mice, it's important to optimize the procedure before conducting the real experiments, to ensure consistent and meaningful results. This cuts down on animal use, overall. The dissection looked pretty good, so this weekend a postdoc from the lab will be doing the real experiment with some Cre virus. Once the animals recover and the virus has a chance to do its thing, we could see some interesting results. Probably this will take more time than I have left in my rotation, but I feel invested enough in it that I want to know what happens.

Although I'm just a trainee, I felt useful this week. A labmate presented some data a while ago and mentioned a weird result that might indicate a flaw with either the transgenic mouse line or with the fundamental assumption behind the experiment. When this happens, we tend to assume a technical problem first -- the mouse isn't what you think he is. Checking on this is difficult, though, because we don't have good antibodies for the protein this mouse is supposed to lack, and it's a conditional knockout, so some of its cells do have the gene and some don't (making it hard to just isolate mRNA and look for gene expression at that level). In situ hybridizations to look at the gene expression would work, but it can be hard to look at individual cells this way. Anyway, I read some papers for my last rotation where a group used laser microdissection to isolate individual cells from a brain slice, purified RNA, and then did RT-PCR to figure out if the cells were expressing certain genes of interest. I looked around and saw that Emory has a core facility that will do laser microdissection for a reasonable rate, or train lab members in the technique so they can do it themselves. We can already do RT-PCR in the lab, too. So I suggested that we try that, rather than in situs, and my labmate seemed really into the idea. I think he was already exploring this possibility with our PI, but they didn't know about the core facility. So I felt all smart and helpful for mentioning it. It's been cool to realize just how much I'm learning in grad school, and that I'm coming up with good ideas for experiments on my own. My education is working!

Now that finals are done, I have a lot of free time in my schedule for these last few rotation weeks. Then I'll be presenting my results in lab meeting, writing up a report, and choosing which lab I want to join. I might take a little summer vacation first, though...