I ended Part 1 after the morning session on pushing the boundaries of imaging.
After the amazing talks on imaging, I browsed the halls, visited some exhibitors, sampled a couple of exhibitor tech-talks. I later went to a mycrosymposium (#2: signaling in health & disease). This was mainly to see how this ePoster thing works, but also I promised Qunxiang Ong – with whom I discussed optogenetics the day before – to be at his presentation. He used a light-induced dimerization of signaling proteins to study the effect on neurite growth. The nice thing in his system was that the cells were plated in wells which were partly dark – so light-induction cannot take place in these regions. This allowed for analysis of neurite growth in lit vs “light-protected” regions of the same cell.
After this session, I attended my first “discussion table”.
The idea is to have 8-10 people sit around a table and discuss all kinds of topics. My first experience was the international affairs committee roundtable. We’ve had a pleasant discussion, which revolved mostly on open-access, & the peer-review process as well as the problems with impact factor and academic career. One goal of the roundtable was to find new ways to increase scientific exchange and foster international collaboration. We came up with two suggestions: money and funds. Get funds from national organizations or other sources, and invest these funds in travel fellowships to ASCB meeting and/or for visits around the year to facilitate collaboration.
The next round-table I attended was titled “Quantitative cell biology and QCBNet”, which was led by Susanne Rafelski (University of California, Irvine and Allen institute). From the title, I was hoping to have a significant discussion on quantitative biology, because biological research should be quantitative. I envied Arjun Raj’s experience of “gene expression by the numbers” and hoped to replicate some of that in an hour’s discussion. Alas, most of the discussion was aimed at advertising QCBNet and the Allen institute. In essence, QCBNet is aimed in developing quantitative tools and organizing workshops, whereas the Allen inst. wants to create a complete quantitative model of the cell. Though it was nice to be informed about it, this is not what I was hoping for.
I dedicated the afternoon to tour the “Gas lamp quarter”. Not too much to look at. There’s a Chuck Jones art gallery, which was neat. And I found “Its sugar” store which was fun so much I later retuned twice to that store.
I also skipped Jonathan Weissman’s lecture in favor of going early to sleep (damn you, jet lag, still!).
Monday morning was dedicated to posters and exhibitors. It was interesting but exhausting walking in this huge exhibit hall. Two posters directly related to what we do in our lab was one on nuclear export in yeast by Azra Lari (I’ll get to that later) and on mRNA localization to mitochondria in yeast by Tatsuhisa Tsuboi from Susanne Rafelski’s lab. Tsuboi measured proximity and duration mRNAs stay near mito and is trying to correlate that with co-translational import; i.e. is the duration an mRNA stays in close proximity to mito enough to allow translation and import of the nascent protein? He has very pretty images.
A poster which has less immediate relevance, but was really interesting, showed that oxidized mRNA localizes to specific compartments in plant and human cells. Unlike oxidized DNA, which clearly leads to “damage” and therefore fosters numerous repair mechanisms, I never thought about the problems of oxidized RNA (8-oxo-G, to be exact). How does that affect translation? Localization? Folding? Is it “damaged” RNA? The poster (from the Zerges lab from Concordia university) didn’t discuss all that, only the compartmentalization issue, but it made me think and that is what matters…
In between, I also attended another roundtable discussion – this time about career. I first joined the “developing research teams & collaborations”. We were only 3 people & the host and I did not feel it benefited me alot other that to be careful when doing collaborations woh someone. I heards some horror stories there.
I then switched to “setting up your first lab” table. Again – only a couple of people there, and they already started their own lab. Which was good for me because they gave me several good advices:
1. During your last year as postdoc – make a list of ALL reagents, equipment, disposables – everything you use in your research. Make sure the list has vendor, cat number and when possible – costs. This will save you time when trying to compile such a list for your new lab.
2. Though it is good to try to get funding as soon as possible, one needs some preliminary results for the grant applications. Use the “starting money” you got when you started your lab to produce those results.
3. To produce preliminary results – don’t wait for students to join the lab and do the work. You are your own best postdoc. Do the benchwork yourself as much as you can.
4. To get students to join your lab, advertise your lab all around campus, other campuses, online through the university website, social networks, meetings.
5. There is no sure way to determine the quality of your students before accepting them. Try to get sutdents that you “click” with, and obviously those that have good background (lab experience, good grades).
In the afternoon, I joined another “round table” to discuss science communication with Ron Vale, founder of iBiology. It was a nice discussion revolving about scientific publication and less about other science comm avenues (e.g. journalism, blogging). Vale advocated pre-print publication and the ASAPbio meeting that he is organizing to promote that (Feb 16-17, live video streaming). [Read Vale’s article at PNAS “Accelerating scientific publication in biology”].
I came in late to the minisymposium on nuclear mechanics and transport, but I was glad I came – these were four excellent talks.
Azra Lari from the Monpetit lab (U. Alberta) talked about mRNA export. Earlier, I visited her poster, which featured single molecule dynamic of mRNA export in yeast. She labeled an mRNA with PP7 and followed its movement around the nucleus, through the nuclear pore complex into the cytoplasm. First she calculated how long it takes an mRNA to exit the nucleus. On average, it takes 200ms. However she noticed that the mRNA typically lingers close to the nuclear lamina after export. It may be due to association with the rough ER, but this needs to be further tested. But now she has an assay to examine mutants that are defective in export. Indeed, the mutant she tested, mex67-5, showed much prolonged time for association with the nuclear envelope and for export, as expected. A very exciting observation is that on some occasions in the mutant strain, an mRNA returns to the nucleus – retrograde transport of the mRNA. The paper was just published at JCB.
Next came Dave Nellis, from Gene Yeo lab at UCSD, who developed, in collaboration with Doudna lab, RCas9. RCas9 is a system, based on the CRISPR/Cas9 technology, but for RNA instead of DNA. The idea here is to use a nuclease-dead Cas9 that will recognize and be targeted to the RNA. The trick here is that together with the sgRNA, they add a second RNA called PAMmer. This sequence is also hybridizing to the RNA, creating the double helix with the PAM motif (an NGG tri-nucleotide) required for Cas9 binding. And it works. He used that to visualize mRNA in live cells, using a CAS9-GFP fusion protein. It is still not single molecule, but we’ll get there. The work isn’t published yet, but he published a theoretical paper in Bioessays.
Amir Mor from Fontoura lab (U. Texas) provided visual data on flu virus RNA splicing, using smFISH. He found a pathway of several proteins, viral and cellular, that are required for localizing the unspliced RNA into specific nuclear compartments, where the RNA is being spliced. Deciphering this mechanism could lead to drug discovery against flu.
Last was the amazing talk by karsten Weis. He was looking at the diffusion rate of different objects in yeast cells upon glucose starvation. He looked at gene loci (using LacO-LacI system), at mRNA (using PP7), and at other cellular components. He noticed something strange: the diffusion of everything was slowed down. What could explain that? Well, starvation may lead to ATP shortage. So he depleted ATP but that did not give the full phenotype. It is known that under glucose starvation conditions, yeast cytoplasm acidifies. So he used several techniques to acidify the cytoplasm. Again, only partial recapitulated the initial observation. In fact, he found that the cells loose volume, the cell becomes denser, almost solid (glass-like state). In fact, this is not unique to budding yeast. It happens in other yeast species. It also happens in bacteria. What does this mean? Why would starvation elicit such a unique stress response? And what is the mechanism? This is still to be discovered.
The day ended with a symposium on mitochondria and cancer biology. Susane Rafelski (again!) showed great images and movies of mitochondria. Unfortunately, I can’t recall the details of her talk. I was too tired and I left right after her talk.
To be coninued….
(Happy new year!)
Smith C, Lari A, Derrer CP, Ouwehand A, Rossouw A, Huisman M, Dange T, Hopman M, Joseph A, Zenklusen D, Weis K, Grunwald D, & Montpetit B (2015). In vivo single-particle imaging of nuclear mRNA export in budding yeast demonstrates an essential role for Mex67p. The Journal of cell biology, 211 (6), 1121-30 PMID: 26694837
Nelles DA, Fang MY, Aigner S, & Yeo GW (2015). Applications of Cas9 as an RNA-programmed RNA-binding protein. BioEssays : news and reviews in molecular, cellular and developmental biology, 37 (7), 732-9 PMID: 25880497
Vale RD (2015). Accelerating scientific publication in biology. Proceedings of the National Academy of Sciences of the United States of America, 112 (44), 13439-46 PMID: 26508643