Saturday, November 19, 2011

FoxP2 in the News

I wrote on Monday last week about Svante Pääbo's work with hominin lineage, and his recent findings with FoxP2 transgenic mice.  This morning, this article was printed in Nature News on FoxP2's spotlight moment.  The author highlights the work presented at SfN last week by Christiane Schreiweis, a colleague of Dr. Pääbo.

SfN Wednesday 2011: Second Wind

By the end of the conference, my eating schedule has not adapted to being on the east coast, but my body has.  Exhaustion kicks in like a toddler, and come Wednesday morning I feel like slithering through the grasping arms of Science and collapsing to the floor.  Of course, my poster is this morning.

In contrast to the anticipated slow puttering of folk on the final day of the meeting, area L10 boasted anywhere between 3-10 participants for the entire 4-hr block.  <thrillz>  In addition, several of teh femus peepl made appearances.  One hung out in the back of the crowd and chimed in when I referenced his work's influence on ours.  Another offered excellent discussion and announced that he had begun using the model that we developed last year (also employed in this year's work) <chillz>.  A third made offer of collaboration and (either partly or entirely in jest) a post doc position for five years from now when I potentially actually have a doctorate.  And a renowned woman for whom there is a special place in my heart offered suggestions for follow-up studies, collaboration, and an awkward scientist hug as she left. <second wind>

Also notably, there is good Phở in DC.  Following the rush of the poster session, Boss Man treated me to my second dose of Phở for the week, and it was grand.  The Super Shuttle that was then scheduled to escort me to my next 11 hours of travel failed to appear, and the taxi that rescued me from certain doom naturally forgot to tell me that his apparatus was broken and that he couldn't take my card, and naturally didn't have any change to break the $20 of which he only should have taken $14, and naturally had no means by which to provide me with a receipt for reimbursement.  This was not the first such incident during my week in DC.  <billz>

See you next year in New Orleans!

Friday, November 18, 2011

SfN Tuesday 2011: Winding

Tuesday morning: a slew of great posters and conversations.  I prefer poster sessions with fewer and more impactful scans, and was very impressed with the elegance of several presentations in this session.  I was also fascinated to see that several of the bigwigs whose work I have followed over the last four years are transitioning into more genetic/molecular and less neurotoxin-centric modeling systems.  This is a direction in which I may continue if planted in Dr. PDstemcell's lab next year, and wouldn't it be grand to already have some acquaintances in that new arena?

Sally Temple, the current director of the Neural Stem Cell Institute, gave an excellent talk later in the morning and into the afternoon.  Although my lunch rendezvous prevented my attending the full symposium, I was able to digest her historical overview.  Some key points of interest are below.  **If anyone was able to attend this full talk, please comment!**
  • In 1887, Wilhelm His identified 2 cell types: germinal cells as rounded cells nearest the lumen (neuronal precursors), and columnar spongioblasts (radial glia).
  • In 1987, Jack Price and colleagues were the first to monitor cellular development using retroviral lineage tracing with β-galactosidase.  The paper in PNAS is beautiful and succinct, and I highly recommend reviewing it for as an introduction to neural lineages.  Arnold Kreigstein's lab has also played a pivotal role in describing neural lineages, which Dr. Temple referred to briefly but I believe warrant more obvious credit in the evolution of this field.
  • The last piece I caught was in reference to recent software developed by Andy Cohen's lab: a program for tagging and following cell division in vitro via time-lapse microscopy, and easily translating these divisions into lineage trees.  To appreciate this fully, consider the giant leaps forward that technological development have allowed in the evolution of scientific industry.  The polymerase chain reaction (PCR) is so simple, and used so ubiquitously now that one has to imagine the grueling hours of restriction enzyme assays and semi-quantitative analyses that were necessary before its development in order to realize its gigantic contribution to throughput.  Andy Cohen's software is another such landmark in the progress of scientific industry.
I attended the Protein Synthesis and Axon Pathfinding in Regeneration minisymposia later in the afternoon.  Of note to your humble narrator was some research from Samie Jaffery's lab at Cornell U.  Dr. Jaffrey proposed a mechanism of axon guidance through nonsense-mediated decay (NMD), a process wherein mRNA is degraded following a "pioneer round" of transcription. 
  • Commissural neurons grow toward the midline and netrin-1 in the floor plate, then are repelled from the floor plate post-crossing.  A family of receptor proteins called Robos are key players in this mechanism.  Jaffrey's research indicates compartmental expression of Robo3.1 and Robo3.2 receptors in commissural neurons.  Robo3.1 suppresses other Robos so that the axon can grow toward the midline, after which point Robo3.2 expression enhances repulsion from the floor plate.  If ther eis no Robo3.1, axons don't cross the midline.  If there is no Robo3.2, axons cross and then turn backward and grow aberrantly.
  • Jaffrey's lab asked if the switch between Robo3.1 and Robo3.2 was temporally dependent, or in the determined in the floor plate.  They made open book explants of spinal cord with no floor plate, and observed protein expression at E10.  Although Robo3.2 expression was expected by this time point, only Robo3.1 was expressed.  When the floor plate was reintroduced, Robo3.2 expression was observed.  This indicated a floor plate mechanism as opposed to a temporal switch within the commissural neurons.
  • To confirm this suspicion, the spinal cord floor plate was cultured alone, and the resulting conditioned media was applied to the tips of axons in spinal cord explants without a floor plate.  With the floor plate media, the commissural axon tips expressed Robo3.2.
  • The next obvious question was what mediated this switch.  The group predicted a NMD switch based on indicative NMD sequence in the Robo3.2 gene not observe in the Robo3.1 gene.  When they expressed the dominant-negative form of NMD proteins, axons crossed the midline but then grew aberrantly.  If the NMD mechanism was blocked, more Robo3.2 was produced and there was increased repulsion to both the floor plate and midline.  Therefore, an NMD-dependent mechanism of axon guidance in developing commissural neurons was speculated, although the proteins involved in NMD activity in the floor plate is yet to be determined.
Tuesday evening was spent having a somewhat awkward but fun dinner with my former PI, and acting like a child with my fascinating and inspiring last-minute conference roommate.  The ideal way to wrap up a grueling SfN day as the conference approaches its final hours and inflicts an inescapable exhaustion/delirium.

Monday, November 14, 2011

SfN Monday 2011: Almost Femus

Saturday and Sunday were gargantuan days whose events were not ideal blog fodder (read: 5,000,203 posters).  Today's events, in contrast, are worth reporting.

This morning's poster session began with a very brief reunion with my most admired undergraduate professor, and ended with the development of a potential future collaboration to take place in the lab in which I have not yet even rotated (lolz...).

In the late morning I attended the David Kopf Lecture on Neuroethics, given by Svante Pääbo of the Max Plank Institute of Evolutionary Anthropology in Germany (yes, I just Wiki-linked him).  The man's career is packed with astounding work, only a glimpse of which we were given today.  In brief, Dr. Pääbo's talk came down to three parts:
  • Although evolution has seen total replacement of mitochondrial DNA in modern humans such that none of us share mitochondrial DNA with Neadertals, 2.5% of our nuclear genome derives from Neandertal lineage.
  • Analysis of a newly unearthed finger tip fossil reveals a hitherto unknown line of hominin that Pääbo's group called Denisovans, who share Neandertal DNA back to 650,000 years, and with modern humans back to 800,000 years.  From genome comparisons, Pääbo elucidated the geographical interbreeding patterns of these three lines.  Matching between modern humans and  Denisovans was 90K in a French subject, 70K in an African subject, and 86K in a New Guinean subject (*approximations).  Which... if you've ever read [and loved] Richard Dawkins' The Ancestor's Tale, Pääbo's work will blow your mind.
  • Finally (and my favorite part, as a basal ganglia fanatic), Pääbo et al have utilized the divergence of Neandertal, Denisovan and modern human to identify genomic regions positively selected in human evolution.  He elaborates on one such candidate, the FoxP2 gene, which is involved in speech and language development.  In a transgenic mouse, the expression of human FoxP2 produces 323 phenotypes.  One of these phenotypes is elongation of dendritic trees in the striatum.  Another is an overall decrease in whole brain dopamine levels, and finally altered vocalization patterns.  I'll reiterate: a human gene positively selected by evolution to help humans develop language is capable of altering the morphology of a mouse brain region involved in spatial learning and attention, and altering the way mice "speak".  (scencegasm)
Elated by Pääbo's lecture, which has nothing to do with what I'm researching currently (or in the forseeable future), I re-entered the massive dungeon hall of posters and ran into my current rotation PI as well as a crew of several of his past students and post docs.  What fantastic people they were, and how enamored they were of Dr. Spinal Cord Repairman, and how encouraging they were that I continue in his lab!  At what a time, too, when I am frustrated by my lack of productivity this term and the general disorganization of the lab atmosphere.  Perhaps these are things which are worth taking with a grain of salt after all.  I was even more encouraged when I happened upon [read: hunted down] a collaborator of Dr. Spinal Cord Repairman's who is mucho femus.  This is a man with whom I have exchanged all of two emails discussing the direction of the project I'm currently working on which happens to be a collaborative one, and who remembered my name.  (flutter)

Tonight: tour of the sites, BANTER.

Sunday, November 13, 2011

SfN Sunday 2011: Ms. Raga goes to Washington

The great and consuming thing about the Society for Neuroscience meeting is that even veterans can be noobs.

Last year, I approached SfN as somewhat of an expert in my niche of the Parkinson's field, seeking out renowned folks whose work had inspired my own and carrying meaningful scientific conversations with poster and talk presenters as if it were casual chatter.

This year, I find myself engaging in so many unfamiliar arenas that I have retired a whole 2 hours early to the comfort of my snazzy hotel room to put my feet up and compile/further research the whirlwind of fascinating information gleaned today.

Today was poster intensive, to put it lightly, so tomorrow will include some symposia.  Just to mix it up.

Second lesson learned: Neurotypical? is as fantastic IRL as in the blogosphere.

Tuesday, November 8, 2011

SfN Survival Guide 2011

This is my second year attending SfN.  Last year, I managed to pull off a pretty successful run.  However, SfN is such a vast meeting that the experience you have there is redefined every year you go, depending on where you are in your career.

This year, I am a first year grad student and will be scoping out roughly 3x the content (catering to rotations) as when I was a research assistant last year.  This means that burn-out is 3x as likely, but I have planned my schedule with two things in mind:

1)  I will not get to everything that I have put on my itinerary.
2)  The goal is to get an introduction to the most exciting recent activity in the 3 areas encompassing my rotation projects, and not to get bogged down by exciting developments in these entire fields.  I have some people to meet, some "old" acquaintances to schmooze, and some free mugs to acquire.  Should be baller.

I was going to write a First Year Graduate Student's Survival Guide to SfN, but found that Dr Becca has beaten me to it: SfN Survival 101.  Check out her stellar overview of things to keep in mind while planning your SfN experience.  Seriously, she hits everything.

As for yours truly, although I am not an official Neuroblogger this year, I will be reporting regularly.  And I will be seeing some of y'all at BANTER...

Friday, April 15, 2011

are exosomes the Priuses of RNAi transport?

Knocking out insidious genes using RNA-interference (RNAi) has been massively pursued as a therapeutic technique since its discovery.  Specifically, methods of delivering RNAi through the blood stream to target tissues have been of great interest.  Scientists have successfully packaged and delivered RNAi in  lentiviruses, micelles and other nanoparticles.  However, the search for cost-effectiveness, efficiency and target accuracy never sleeps (insert wise crack about the tendency of their funding to hibernate).

In a study recently published in Nature Biotechnology, exosomes are suggested to be a significant improvement over other vehicles.  The scientists used dendritic cells -- derived from bone marrow progenitor cells, and not to be confused with neural somas -- and proceeded to test the efficiency and accuracy of their RNAi packaging and delivery.  They purified the exosomes, tagged them with muscle or brain targeting peptides, loaded them with exogenous cargo (siRNA for GADPH, a housekeeping gene), and tested their delivery both in vitro and in vivo.

Alvarez-Erviti and colleagues achieved a marked knockdown of GADPH in vitro, and an even more impressive knockdown in several peripheral organ and brain region tissues in vivo, suggesting an improved blood brain barrier-transcending capacity compared to other methods.  The exosome delivery method was accurate, and achieved a 60% knockdown of mRNA and a 62% knockdown of protein expression using, allegedly, 10% of the siRNA cargo that other methods have used.

62% efficiency is generally accepted as a pretty high yield in the biomedical sciences.  Whether this exosomal packing and delivery system can be optimized to better penetrate the blood brain barrier remains to be seen.  However, with its cost-effective, accurate and non-invasive methods, the exosome may be the Prius of siRNA delivery.
Alvarez-Erviti L, Seow Y, Yin H, Betts C, Lakhal S, & Wood MJ (2011). Delivery of siRNA to the mouse brain by systemic injection of targeted exosomes. Nature biotechnology, 29 (4), 341-5 PMID: 21423189

Thursday, April 14, 2011

Saccharomyces boulardii improves migration of new epithelial cells

The lifespan of healthy intestinal epithelia is generally accepted to be about 5 days.  These cells, once departed and sloughed off into the fecal stream, are replaced by newer, younger, healthier cells which proceed through the same life-cycle.  In the case of inflammatory bowel diseases (IBDs), in addition to inflammation/ulceration/tissue injury, the migration process of these new epithelial cells is stunted.  Since the replacement cells have trouble reaching their destination, damage to the intestinal lining is exacerbated.

A recent study -- published in PLoS ONE and open access if anyone wants to take a peek -- investigated the capacity of a nonpathogenic yeast to alleviate this stunted migration of new epithelial cells to the tips of intestinal villi (the fingers of tissue that protrude from the intestinal wall to create surface area for absorption).  Saccharomyces boulardii (Sb) is typically used to treat issues such as diarrhea, the idea being that it stimulates growth factors that help restore homeostasis to the gut.

This nigh-rockstar study strikes me because it is targeting a curative mechanism as opposed to a squelching of symptoms.  To achieve actual remission in IBDs, one has to pwn both inflammatory and repair dysfunctions.  The inflammatory component is predominantly targeted by the entourage of immuno-suppressants with which Crohns are so familiar.  Repair is seldom highlighted as it should be -- excepting methods of balancing gut flora.

The team of scientists in France, lead by one Frederic Andre, looked at the beneficial effects of Sb in both mice and an in vitro wound model (this is a strain of cultured epithelial cells which are attacked gently with a toothpick... rather cute).

The first major finding was that mice who were fed Sb for one week doubled new epithelial cell migration.  Only one downer for me in this study was that the mice were all healthy, with no in vivo IBD model for comparison.  Nonetheless quite encouraging, no?

The second conclusion was that the wounded cell line closed its wound (or, repaired its injury) by roughly 70%.  Their video supplement to this end is quite something.

The scientists conclude that Sb improves new epithelial migration both in vivo and in vitro.  Interestingly, the study suggests that increased migration is due to increased motility of cells and not to increased proliferation (the generation of new cells).  Sb may be stimulating this activity by secreting factors that stimulate  a target signaling pathway FAX/paxillin, which leads to several physiological changes in the intestinal epithelial lining that enable motility of new epithelial cells.

The thing about supplement studies such as this one is that they make me want to stop by the grocery and pick some up on my way home...
Canonici A, Siret C, Pellegrino E, Pontier-Bres R, Pouyet L, Montero MP, Colin C, Czerucka D, Rigot V, & André F (2011). Saccharomyces boulardii Improves Intestinal Cell Restitution through Activation of the α2β1 Integrin Collagen Receptor. PloS one, 6 (3) PMID: 21483797

Wednesday, January 12, 2011

increasing women in neuroscience

The Department Chair Training to Increase Women in Neuroscience (IWiN) is scheduled to meetin in Tucson, at the University of Arizona this April.  The workshop, funded by the National Science Foundation's ADVANCE program, is a three-year program aiming to increase the number of women on neurosciences faculty.  The participants of these workshops expect to leave them with tools to implement recruitment and advancement plans for women within their universities, and to disseminate the information they have gained in "echo" workshops at their institutions.

The IWiN workshops will be hosted in 2011 and 2012 at two of the graduate schools at which I may be a [woman] student at the time... depending on how interviews go at the end of this month.  Three of my four choice graduate schools are already participants of the ADVANCE program, which is not too shabby except that the missing institution has a ratio of approximately 1:3 women to men and does not facilitate an equity program in research.

I mention the IWiN workshops in response to a recent article in the New York Times discussing a nice array of statistics about the paucity of tenured female faculty, and women in the upper administrative echelons of science in general.  This was summarizing a study based out of UC Berkley.  The statistic that I thought was deserving of further attention in the New York Times report was this one:
"Tenured male scientists are considerably more likely to be married with children than tenured female scientists — 73 percent for men versus 53 percent for women. The report noted that among tenured science professors, women are nearly three times more likely to be single without children than men — 25 percent to 9 percent."
 The Berkeley article itself furthers this discussion beautifully, and as a woman weighing the possibilities of children and eventual faculty tenure (albeit, we're talking about ten years down the line), I highly recommend a read and consideration of the original research article:
Mary Ann Mason, Marc Goulden, Karie Frasch (2010). Keeping Women in the Science Pipeline Focus on Workplace Flexibility

Tuesday, January 11, 2011

in indirect support of the hygiene hypothesis

A recent study out of the University of Michigan Medical School suggests that the stomach bacterium Helicobacter pylori protects against inflammation caused by Salmonella in a mouse model of Inflammatory Bowel Disease (IBD).

This is surprising for two reasons: 1) IBDs occur primarily in the colon while H. pylori is active in the stomach, and 2) the H. pylori bacterium is regarded as dangerous gut flora and typically treated with antibiotics to avoid the development of stomach ulcers.

The findings of Higgins et al are equally unsurprising given the light that has been shed on helpful bacterial/parasitic gut balance by the Hygiene Hypothesis.  The Hygiene Hypothesis suggests that a modest intestinal hookworm population may stave off the excessive inflammatory response inherent to Crohn's disease, Lyme disease, asthma, rheumatoid arthritis and other conditions.  If this parasite whose reputation is built from its roles in epidemic illnesses in countries where sanitation is poor can, in small doses, help defend inflammatory diseases, then why couldn't the H. pylori bacterium as well?

There are currently no reports of an additive or destructive effect of both H. pylori and hookworm on gastrointestinal inflammation in humans, although it would be quite telling to see the results of their coincidence.  Patients from many H. pylori studies have been excluded from reports because they also shown signs of hookworm-related anemia (Vijayan et al 2007, as an example).  But this scientists wonders, because humans evolved almost symbiotically with both of these flora, if all of our immune systems would be better balanced were we not to wipe them both out completely.

A few thoughts from Dr. Higgins, one of the Salmonella study's researchers, can be found in an interview here.
Higgins PD, Johnson LA, Luther J, Zhang M, Sauder KL, Blanco LP, & Kao JY (2010). Prior Helicobacter pylori infection ameliorates Salmonella typhimurium-induced colitis: Mucosal crosstalk between stomach and distal intestine. Inflammatory bowel diseases PMID: 20976712