Monday, April 27, 2009

Rotation #3 Diary: Week 6

This rotation is going by in a blur! I spent Week 6 working on more sub-cloning stuff. After sequencing some plasmids and deciding which ones we wanted to use, I grew some bacteria expressing those plasmids and made maxi preps to get more DNA. This week we'll be pasting these plasmids into vectors that will later be made into lentivirus for infecting neurons. It's been really interesting to go through all of these little steps -- some projects require a lot of work before you can actually do the cool experiment that will answer your research question. The work is going a little slower than usual because I'm new to these techniques, but the postdoc I'm working with has been very patient with me. He wants to make sure that I'll get to see the end result of the cool experiments, though. With only two weeks left in my rotation, I'm not sure we'll get there in time, but I am curious to see how things go, even if we don't get there until after my rotation has officially ended.

I also collected a lot of DNA samples from some mysteriously un-genotyped mice. For a while, no one was really maintaining this particular mouse line, so we're not sure if any of these animals have our mutation of interest. I'll be making lots of DNA preps and checking out their genotype, although I've been temporarily stymied by a bad batch of proteinase K (enzyme used to digest the tissue samples before I can extract DNA from them).

Outside of the lab, things are going well. I gave my poster presentation, and people seemed pretty happy with it. (Although, one professor suggested that I be "A little less Laura" in the future -- meaning that I should, for example, avoid using colorful slang terms when characterizing mutant phenotypes. It's hard for me to be "less Laura," but it's the more professional way to go.) Also, the poster was so shiny. It's amazing how impressive my work looks when blown up to gigantic size and printed on high-gloss paper.

I have a group project due for my grad seminar this week, and I'll be taking the final exam for my Cellular and Developmental Neuroscience class on Thursday evening. I'm pretty pleased with myself right now, as I reviewed about half of the material this weekend. I have relatively light lab duties for the next few days (today I will be setting up a couple of enzyme digests and then going home) so I ought to have plenty of time to study before Thursday. If I can be strong and avoid the siren song of daytime television, that is.

Wednesday, April 22, 2009

Guidelines for Scientist Blogging and Online Behavior

A Blog Around the Clock recently posted a draft of an institutional document governing employee blogging and social media use. This pseudonymous Big Research Institution is trying to establish guidelines about the information that its employees are allowed to share online. As someone who blogs under my own name about things that I do for a living, such policies would affect me if Emory decided to enact them. I'm posting the whole set of proposed rules in block quotes, with some of my own comments from a research blogger's perspective. I should note that this document did NOT come from Emory, and my response to it is purely hypothetical.

Social media guidelines for Big Research Institution (which I will abbreviate as BRI from here on out) staff

These guidelines are intended to cover blogs, where BRI staff discuss their projects or professional work, as well as BRI related pages set up by staff on social networking sites such as Flickr and Facebook. They do not cover any personal use of social media which is primarily about personal matters or hobbies.


I would consider my Facebook profile to be primarily centered around "personal matters or hobbies," but since it includes my university affiliation, it can be policed under this set of rules. Because nothing on the internet is anonymous, I am careful about the information that I share on Facebook, but I also get pretty personal there (sharing political links, making off-color jokes, posting pictures in which I am making a silly face, etc.). I'm completely aware of the fact that anyone can find my Facebook page and pass judgment on me because of it; what I'm not prepared to do is to act as though everything posted on my Facebook is directly linked to my job. Therefore, I would question any institutional policy that attempted to be so broad in its application to personal social networking sites like Facebook.

We have a long history of BRI staff actively contributing to public discussions. However there are a few simple guidelines for BRI staff to consider when setting up their personal blogs and wikis which are outlined under "Personal social media guidelines" at the end of this document.

Guidelines for a BRI context

BRI can clearly benefit from the use of social media to promote its activities, discuss projects and research, and increase its overall knowledge base. These guidelines are intended to ensure that BRI can have a strategic overview of how we are using social media, use it in an effective way to develop our vision, facilitate its development and cross promote where appropriate.

For the purposes of this document online social media activity by BRI staff and associates falls into two categories:

Public facing - Social media which directly relates to or discusses work or projects at BRI and has a general public audience.

Peer to peer - As above but where the blog, forum, wiki etc is used as a tool for scientists and others to communicate with their peers and is not intended for a general public audience. This includes both social media content hosted by BRI and collaborative projects.


Here again I would argue that some "public facing" content (like Facebook pages) does not directly relate to work or projects at the employee's institution, even if the employee happens to mention where he or she works.

Speak freely, but respect BRI's confidentiality and values

Whether social media content is public facing or peer to peer, the individual has a duty to:

* behave in a way that is consistent with BRI's values and policies

* respect the confidentiality of information as outlined in BRI's staff handbook

Unless there are specific concerns about the nature of the work, BRI staff are free to discuss work and research online. However, staff must not reveal any information which may be confidential. This might include aspects of research, BRI policy or details of internal discussions. Staff should check the BRI IP policy, the staff handbook and/or consult their manager if at all unclear about what might be confidential.


Before I can feel comfortable with these guidelines, I need to have "BRI's values and policies" defined. If I post pictures of myself holding a beer, or wearing a coconut bra and a grass skirt at a luau, am I somehow tarnishing the reputation of my university? If I flame someone for making a stupid post, am I considered to be doing so on behalf of my employer? If social networking sites like Facebook are to be held to these standards, do they also apply to personals like Match.com? If I were to write a lonely-hearts ad that mentioned both my employer and my participation in potentially shocking subcultures, for example, could my employer object? Those of us with any degree of internet prominence should carefully weigh the decision to make information about ourselves public, but we should do so using our own "values" as a yardstick, not a set of ambiguously-defined "values" from our employer.

I'm also uncomfortable with the idea that discussing my university's "policy" could be considered inappropriate. Shrouding institutional policy in secrecy does not bode well -- institutions with sound, sensible policies should be shouting them from the rooftops to try to attract the best employees. If my institution has a bad policy and I criticize it publicly, the proper response is not to censor me for talking about it. The response should be to improve the policy so that the institution is no longer ashamed of it.

I have no qualms about honoring confidentiality, however, or about keeping sensitive data out of the public eye. To me, that's just common sense, codified.

Editorial

The content of peer to peer pages or sites is the responsibility of the relevant department. The content should follow BRI editorial guidelines to ensure usability and accessibility. Content is the responsibility of the individual and their department and would not be edited by BRI editors. Moderation is the responsibility of the relevant department.

Public facing social media is covered by the general editorial guidelines, and should be written for the expected audience and have a moderation plan agreed with BRI.


This gives me pause. Because I have a blog that occasionally mentions my institution, I should have a "moderation plan" with them? And, what are the "general editorial guidelines" that I must follow? No blinking text? No curse words? I require more detailed information about the moderation and editorial policies in question before I would feel comfortable agreeing to anything like this. If such guidlines would entail much more than common sense policies covering confidentiality, I imagine I would find fault with them.

Intellectual property

All BRI social media output is the intellectual property of BRI.


Like heck it is. If I post one of my famously witty sonnets about DNA on my blog or my Facebook, the university doesn't get to slap it on a t-shirt and call it their own.

BRI will operate all of its social media under a creative commons license, which means that content such as images can be reused for educational purposes unless otherwise stated.

It is the responsibility of the author of any social media content to ensure that the copyright is cleared for any material published.


Ah, "for educational purposes." I don't have a problem with people sharing content from my blog -- after all, I make it freely available on the internet -- but I would like to at least be credited for creating it. It's unclear what sort of Creative Commons license is being proposed here, but I would be okay with this provided there is an attribution condition. For example, I wouldn't mind if my university linked to a post on my blog from their website, next to a picture of me, while crediting me for the writing. That does not make my blog their intellectual property, however.

Setting up of new social media and content pages

Whether you are setting up new BRI social media pages within the BRI website or on an existing social media site such as Flickr or Facebook, they need to follow the BRI interactive project process.

In the first instance please discuss with your manager. If they are in agreement then the next step is to complete and submit a concept brief for social media (link here) which outlines:

* the purpose

* the author

* the audience

* the contributors

* moderation plans

* expected duration

* how they fit with department/corporate plans

Concept brief forms are available from your manager.


This seems completely unfeasible. No one is going to consult with their manager and submit a "concept brief" before making a Flickr account. If I wanted to blog about details of experiments that were happening in my lab, I would consult with my PI before doing so. But if I just mention that I'm a graduate student in So-and-so's lab, I don't think my PI or university should have veto power over my blogging. Even if I removed all references to my PI and/or institution from this blog, any enterprising soul with access to Google could enter something like "Laura Mariani" + "neuroscience" and find references to me on my department's website. I see no need to pretend otherwise.

Existing blogs

Staff who already have a blog, wiki, forum etc. which is related to their work or BRI should discuss it with their manager and the BRI production editor. This will allow for a shared understanding of activity in this area and will help BRI promote and aggregate a body of BRI blogs in the future.

Scientists can link to their blogs from their CV's on the BRI website but it may also be appropriate to integrate it into other areas of the site and promote it more generally from BRI's website.


This seems reasonable. I think it would be cool to see a collection of blogs by Emory students, for example. Letting your supervisor know that your blog exists is one thing; making it their intellectual property or allowing them to censor what you post based on institutional "values" is another.

Personal use of social media by BRI staff

If within your blog, wiki or social media pages BRI or work at BRI is highlighted the content should comply with the Code of Conduct outlined in the staff handbook.

Additionally if a personal blog is clearly identifying the staff as a member of BRI it should have a simple and visible disclaimer such as 'The views expressed on this blog/website are mine alone and do not necessarily reflect the views of BRI.'

Personal social media pages or websites may link to BRI's website, but should not reproduce material that is available as a result of BRI employment, use any BRI branding, nor should the blog or website purport to represent BRI in any way.

If you wish to use BRI copyrighted material you need to obtain BRI's permission.


This isn't bad. As you can see, I've already included a disclaimer on my own blog stating that my opinions are my own, not Emory's, and that I don't officially represent my university. I'd be willing to maintain a reasonable Code of Conduct, but I'd have to see the handbook before deciding whether or not it was reasonable. And it's already against the rules to share confidential or privileged information that I have access to by way of my institutional login, whether through social media or some other avenue of distribution.

Social media

For the purposes of this document, the term Social Media includes:

* blogs

* forums

* networking sites such as Facebook, Bebo, Linked In

* photo sharing sites such as Flickr

* video sharing sites such as YouTube

* all other sites allowing publishing of opinion and comment where an individual might be viewed as representing BRI

Appendix: BRI's existing social networking rules

Social networking websites

We provide open access to the internet for business use. However, we do recognize that you might use the internet for personal purposes. This policy sets out your responsibilities in relation to using the internet to access social networking websites such as Facebook, MySpace, Bebo and Friendster.

Personal use of the internet

We allow you to access social networking websites on the internet for personal use during certain times. These times are:

* before and after work hours; and

* during the one-hour break at lunch.

We reserve the right to restrict access to these websites and to bar individuals who abuse our broad approach to open internet access.


Um... let's just say that I don't restrict my personal internet usage in this way. I get things done, but I also read a lot of blogs while samples are in the centrifuge. It's safe to say that rules such as the above do not apply to graduate students -- thank goodness.

Personal conduct

While we respect your right to a private life, we also have a general duty of care for the welfare of all our staff and also a responsibility to ensure that the reputation of BRI as an institution of world standing is protected. We therefore require employees using social networking websites to:

* refrain from identifying yourself as working for BRI;

* ensure that you do not conduct yourself in a way that could be perceived to be of detriment to BRI's reputation and its role as a public authority; and

* take care not to allow your interaction on these websites to damage working relationships between members of staff and clients of BRI.


Okay, this is awful. It's silly and unfeasible to require that employees never, ever mention who they work for. My neuroscience program uses Facebook groups for a lot of things, and participation requires joining the Emory Facebook network, so clearly they are not in agreement with such a policy. I think it's a bad policy for any institution. It's totally unenforceable for in-person "social networking" (i.e., going out to a bar and chatting with strangers), and it shouldn't matter for online networking, either. I'm also not a fan of "do not conduct yourself in a way that could be perceived to be of a detriment for BRI's reputation" -- what does that even mean? Rooting for BRI's rival at a football game? It's too nebulous to be useful, and just leaves the institution with an opening to reprimand employees for things they do on their own time that should be none of their employer's business.

Monitoring of internet access at work

We reserve the right to monitor internet usage, but will endeavor to inform you should your usage be under surveillance and the reasons for it. We consider that valid reasons for checking an individual's internet usage may include suspicions that you have

* been spending an excessive amount of time viewing websites that are not work-related; or

* acted in a way that damages the reputation of BRI and/or breaches commercial confidentiality.

We reserve the right to retain information that it has gathered on an individual's use of the internet for a period of 12 months.

Access to the web may be withdrawn in any case of misuse of this facility and may result in disciplinary action.


Again, I don't see this being an issue for me as a student. I'm against monitoring anyone's internet browsing habits unless there's probable cause to assume that they're doing something really bad -- and by that I mean illegal, not just unproductive. If someone's personal web browsing is keeping them from doing their job effectively, I can kind of see the argument for shutting off their access, but wouldn't it be better to just hire employees that you can trust? If it's a slow work day and someone reads the New York Times for two hours, I don't see that as a problem. Lazy people will find ways to be lazy that don't involve the internet if you take their internet access away, and people become less productive when they don't have access to useful tools, some of which are web-based.

Security and identity theft

You should be aware that social networking websites are a public forum, particularly if you are part of a 'network'. You should not assume that your entries on any website will remain private. You should never send abusive or defamatory messages.

Please be security conscious and take steps to protect yourself from identity theft, for example by restricting the amount of personal information that you reveal. Social networking websites allow people to post detailed personal information such as date of birth, place of birth and favorite team, which can form the basis of security questions and passwords. In addition, you should:

* ensure that no information is made available that could provide a person with unauthorized access to BRI and/or any confidential information; and

* refrain from recording any confidential information regarding BRI on any network


I agree with this 100%.

So concludes my fisking of BRI's proposed policy. Although I found fault with some of the items included here, I have to applaud the mysterious BRI for opening up their institutional guidelines to public discussion before setting anything in stone. It takes a certain humility for administrators to admit that their ideas might not be perfect, and I applaud them for seeking feedback from actual scientists and bloggers during the revision period.

If you have anything to add, please do so in the comments!

Tuesday, April 21, 2009

Bio-Tube

Sandra Porter at Discovering Biology in a Digital World posted this video (embedded below) made by one of her colleagues. It shows the whole process of preparing and running an agarose gel to resolve DNA samples. This is something that I've done about a million times in the lab, but I thought it was really cool to see it in a short video. I even learned a few things! (For example, because I am woefully ignorant of all things electronic, I never actually learned which electrode was positive or negative on a gel box. I just remember "black in the back / run to the red" to keep them straight!)



After watching this educational and oddly soothing video (I've repeated some protocols so many times that thinking about them is akin to a meditative mantra), I decided to see what else I could dig up on YouTube. I actually found a playlist of 15 different videos covering SDS-PAGE and Western blots! The videos brought back unpleasant memories of those darn BioRad plates (maybe I just don't know my own strength, but I broke a lot of those little glass plates at my old lab), but the time-lapse images of gels running are actually quite beautiful, and I learned a couple of new tricks. Plus, the last video, Demystifying SDS-PAGE, is adorable. It appears to be the work of two student instructors explaining this technique to a class of bio-newbies. I was immediately won over by their dorky enthusiasm, and by their chocolate cake analogy. It made me want to go teach undergraduate bio lab!

Anyway, I thought these videos would be entertaining for scientists and interested laypersons alike. If you want to know how I spend my time in the lab, these two techniques cover a lot it.

Saturday, April 18, 2009

Rotation #3 Diary: Week 5

I seem to have missed a few rotation diaries -- sorry about that! Things are getting more and more hectic as the semester winds down. I had a big exam at the end of March, I've got some projects in the works for my graduate seminar, and for the past week I've also been fighting a losing battle against housework while tending to my partner, who has come down with the flu. Even so, I had time to do some things for my rotation.

My latest project has been to assist a postdoc in the lab with some sub-cloning. This I would describe as the Legos of biology -- you have all these pieces that need to fit together to make the thing that you want, and a set of rules for how the pieces can be swapped out and combined with each other. Instead of plastic bricks, we use pieces of DNA, so the end result is harder to show off to people. I've still been showing off pictures of my gels, though.

We started with some DNA plasmids that the lab already had. The goal is to snip out some useful pieces of DNA and put them into other plasmids that will be used to make a lentivirus. Then we'll be able to infect cells with the virus and make them express the genes we're interested in. (One construct is a YFP-Cre, which will allow us to knock out a gene of interest in floxed mouse brain cells near the viral injection site through Cre-lox recombination, without messing with the rest of the brain. Nifty!)

To make these new constructs, I've had to digest the DNA with a bunch of different restriction enzymes, which cut DNA in predictable places. I've also been analyzing the sequences of the plasmids, to make sure that nothing funky happened to them when we grew them up in bacteria to get the quantity of DNA that we need. So far it's been pretty good, although I had a false start with my first digestion (I made a "transcription error" in copying the postdoc's instructions into my notebook, and left out an important reagent). I also got a much lower yield than I expected after I gel-purified my digested DNA. I don't know what happened, there, since I just used a commercial kit for that step, and those things are fairly idiot-proof. I may just be an unusually talented idiot.

Currently scrambling to finish a poster for grad seminar (needs to be sent to the printer's on Monday; I finally gave a draft to my professor this afternoon...). It's my first scientific poster (not counting elementary school creations that featured a lot of construction paper), and I'm amazed at how time-consuming it can be to take things that you already have or know and put them into a new format. I spent forever tinkering with background colors and fonts and things, seeking clarity. Hopefully it'll come out all right. I put off working on it for much longer than I should have (partly my own procrastination, partly the unpredictability of life), so my goal at this point is to get it done rather than make it perfect.

Saturday, April 11, 2009

First Transgenic Dog: Adorable Puppy Glows in the Dark

ResearchBlogging.orgA post on Reporter Gene describes how a team of Korean researchers has created the first transgenic dog. She expresses red fluorescent protein (RFP) in all of her cells, causing her to glow quite nicely under normal light, and even more strongly under the wavelength of light that excites RFP. The researchers named her "Ruppy," a contraction of "ruby puppy." And, I must say, she's adorable.



Above: Ruppy, the first transgenic dog. In panels b and c, Ruppy's paw is compared to the paw of a dog that does not express RFP.

"Transgenic" simply means expressing a "transgene," or a gene normally found in another organism. Transgenic mice are commonly used to study human genes in a model organism, because mice are small, easy to work with, and their genome has been well-characterized over the years. Not many other transgenic species are available. Transgenic rats are in the works in many places -- helpful because although rats may look like they're just big mice, they're actually more intelligent than their smaller rodent cousins. Transgenic rats allow us to combine powerful genetic manipulations with a wider variety of behavioral assays. Finally, some scientists at Emory have created transgenic monkeys to use in the study of neurodegenerative disease. Non-human primates may be the best way to model the human brain, and some rodent models of neurodegenerative disease don't produce the same symptoms as in humans. One reason might be that the human symptoms take many years to accumulate, and mice only have about a two-year lifespan. Transgenic monkeys may help us better understand the diseases than a rat or mouse would.

As someone who has kept dogs as pets, it's hard for me to think about using them as research animals. Beagles like Ruppy (and like my beloved pet, Teddy) are a common breed used for research because of their small size and gentle temperament (terriers are also small, for example, but they are more aggressive). While I recognize the importance of research that's been conducted in dogs, I'm not sure that I could personally work in a lab that studies them, due to my emotional involvement with the species. Happily, the use of dogs and cats in research has been declining (down by over 50% since 1979, according to the CDC), as scientists have found ways to conduct their experiments in rodents or in non-animal models. The smaller number of dogs still used for research are kept by thoughtful scientists who attempt to minimize their stress and provide them with a comfortable environment. Transgenic dogs like Ruppy will help those who still must use companion animals for their experiments develop less invasive techniques for studying these model organisms.

Hong, S., Kim, M., Jang, G., Oh, H., Park, J., Kang, J., Koo, O., Kim, T., Kwon, M., Koo, B., Ra, J., Kim, D., Ko, C., & Lee, B. (2009). Generation of red fluorescent protein transgenic dogs. Genesis DOI: 10.1002/dvg.20504

Tuesday, April 7, 2009

Combating Obesity with the Anti-Munchies: Are CB1 Inhibitors Any Good?

ResearchBlogging.orgIn a nice bit of synchronicity, I just found a study by Dr. John McPartland in PLoS ONE examining conflicts of interest in academic medicine with respect to the cannabinoid (CB1) receptor antagonist, rimonabant (aka Acomplia). We actually discussed this drug in my Cellular and Developmental Neuroscience class yesterday, as we've been learning about long-term potentiation, long-term depression, and other forms of synaptic plasticity that can be mediated by endogenous cannabinoids. I've also been hearing a lot about conflicts of interest lately as I move through the coursework in scientific ethics that I'm required to complete. (And, of course, Emory has gotten some press about an academic physician's major conflicts of interest recently. The university is making a substantial effort to ensure that things like this don't happen again, but it's a big deal.) So, this paper seemed like a good one for me to blog about.

First, a little background on endogenous cannabinoids, or endocannabinoids. You're probably all familiar with an exogenous cannabinoid -- that is, cannabis/marijuana. More specifically, the THC found within cannabis is an agonist for the CB1 receptor, which is responsible for the majority of the drug's effects. In addition to exogenous ligands like THC, there are endogenous ligands for CB receptors found naturally in your brain, including anandamide and 2-AG.

CB1 receptors help regulate signaling in the brain. In the traditional model of synaptic transmission, the presynaptic neuron releases a neurotransmitter, which binds to a receptor in the postsynaptic neuron. Messages are sent from cell to cell, allowing for the operation of the complex network that is your nervous system. Endocannabinoids play a somewhat unusual role in this process by generating a retrograde signal -- sent from the postsynaptic cell back to the presynaptic cell. Neurotransmission causes the postsynaptic cell to produce endocannabinoids, which are released back into the synapse and bind to CB1 receptors on the presynaptic cell. CB1 activation then attenuates subsequent neurotransmitter release by the presynaptic cell (or by other cells that just happen to be in the neighborhood, if they express CB1 receptors), which decreases the strength of the synapse. This feedback balances other forms of synaptic plasticity like short-term facilitation and long-term potentiation. The endocannabinoid mechanism is also important for long-term depression (LTD), a form of synaptic plasticity that can play a role in the extinction of old memories. Some believe that this explains anecdotal accounts of short-term memory disruption after cannabis use, as overactivation of CB1 receptors by the agonist THC could detrimentally dampen synaptic strength.

Endocannabinoids

The figure above shows a simplified version of the endocannabinoid system, in which glutamate neurotransmission from a presynaptic cell (top) leads to endocannabinoid synthesis by the postsynaptic cell (bottom), release of endocannabinoids into the synapse, and subsequent inhibition of further glutamate release by the presynaptic cell. Figure stolen from Prof. Randy Hall, who used it in his lecture yesterday.

Of course, LTD isn't the only mechanism of action for cannabinoids. THC is a popular recreational drug because it induces many other effects, including euphoria, relief of pain and nausea, and reduction of anxiety. It also, as any liberal arts graduate can attest, gives people the munchies. For this reason, the endocannabinoid system is a potential target for many avenues of drug development[1], but for now we'll focus on appetite suppressants.

Hunger and feeding behavior are controlled by a variety of molecules produced peripherally (for example, insulin made by the pancreas and leptin made by fat cells) and centrally (such as neuropeptide Y). Most biological functions related to feeding are centrally controlled by the hypothalamus, the brain's main neuroendocrine center. Hypothalamic cells are capable of sensing both circulating hormones and neuropeptides, allowing them to balance signals from the brain and the periphery. The endocannabinoid system plays a role in controlling hunger and feeding behavior via the hypothalamus, as described in this review by Di Marzo & Matias[2]:

[T]he brain endocannabinoid system controls food intake at two levels. First, it tonically reinforces the motivation to find and consume foods with a high incentive value, possibly by interacting with the mesolimbic pathways involved in reward mechanisms. Second, it is activated 'on demand' in the hypothalamus after short-term food deprivation and then transiently regulates the levels and/or action of other orexigenic and anorectic mediators to induce appetite.

In other words, stimulation of CB1 receptors causes animals to eat more food, and to seek out more rewarding foots (sweet or fatty) than they otherwise word. Inhibiting the action of endocannabinoids removes the preference for rewarding foods and can prevent an animal from eating, even if it has been deprived of food for some time. Other research indicates that the hormone ghrelin, which induces feeding behavior, increases endocannabinoids in the hypothalamus, and that CB1 receptor knockout mice don't have a normal appetitive response after receiving a dose of ghrelin[3].

Because of the crucial role that endocannabinoids play in hunger and eating, they're a potential target for appetite suppressant drugs. Rimonabant, which was commercially marketed as Acomplia, acts as a CB1 antagonist. This straightforward mechanism decreases appetite by interfering with endocannabinoids and their hypothalamic effects. In other words, this drug gives people the anti-munchies. But, given the broad spectrum of endocannabinoid-mediated effects in the brain, does a CB1 antagonist have other, less desirable effects? This is why we do experiments before making a new drug publicly available.

Any effective weight loss drug is a potential goldmine, and drug makers know this. Acomplia was developed by the pharmaceutical company Sanofi-Aventis and sold on the European market. During that time, Acomplia was also undergoing clinical trials in the US in an attempt to achieve FDA approval. It seems that despite some potential drawbacks to the drug, it was promoted heavily by academic physicans, many of whom did not disclose the fact that they were being paid by Sanofi-Aventis (indeed, some flat-out denied any conflict of interest when prompted) or the fact that articles being ascribed to them were probably ghostwritten by the pharmaceutical company. Dr. McPartland notes these facts in his study[4] of literature published on Acomplia during the pre-approval period.

A MEDLINE search was performed for rimonabant review articles, limited to articles authored by USA physicians who served as consultants for the company that manufactures rimonabant. Extracted articles were examined for industry-friendly bias ... Eight review articles were identified, but only three disclosed authors' financial conflicts of interest, despite easily accessible information to the contrary. The Takhar CME bias instrument demonstrated statistically significant bias in all the review articles. Biased statements that were nearly identical reappeared in the articles, including disease mongering, exaggerating rimonabant's efficacy and safety, lack of criticisms regarding rimonabant clinical trials, and speculations about surrogate markers stated as facts. Distinctive and identical misrepresentations regarding the endocannabinoid system also reappeared in articles by different authors.

To see Dr. McPartland really lay the smack down on the biased reviewers, please read his article. It goes into plenty of detail about "publication bias, which arises when pharmaceutical corporations choose not to publish unfavorable studies. ... [T]he use of unvalidated or disputed surrogate endpoints, favorable claims not supported by trial data, overstated treatment efficacy, downplayed adverse effects, lack of internal validity and external validity or generalizability, and failure to disclose financially-conflicted interests" in the Sanofi-Aventis-funded studies of Acomplia. Perhaps most damning: "[Evidence-based medicine] relies upon meta-analyses of [randomized clinical trials]. A meta-analysis of the [trials] concluded that rimonabant was safe and effective. The meta-analysis was funded by Sanofi-Aventis. ... four independent meta-analyses of the trials have questioned rimonabant's efficacy and potential for adverse effects."

Since Dr. McPartland completed his analysis of Acomplia studies, Acomplia has been taken off the European market, and the FDA rejected the drug "after data submitted by Sanofi-Aventis revealed adverse effects in RIO trials that went unreported in RIO publications, including one death in a rimonabant-treated subject (ruled a suicide by the FDA) that did not appear in the pertinent publication." It seems that chronic CB1 inhibition is not a good thing, which makes a kind of intuitive sense -- if CB1 agonists like THC make you "high," it's likely that CB1 antagonists could make you "low" (even suicidally so, if you believe the FDA's ruling). Anecdotal reports from Acomplia users in Europe suggest that while the drug effectively suppresses appetite, it also noticeably increases feelings of anxiety and unease.

Despite taking Sanofi-Aventis to task rather brutally for misrepresenting data in an attempt to sell their skinny pills, Dr. McPartland suggests that CB1 antagonists may be useful for acute conditions mediated by the endocannabinoid system, even if they are not appropriate for chronic administration. He also makes sure to declare his own potential conflict of interest: "The author previously received research and/or salary support from the Cannabinoid Research Institute, a research division of GW Pharmaceuticals."

References

1. Pacher, P.; Bátkai, S.; Kunos, G. (2006) The Endocannabinoid System as an Emerging Target of Pharmacotherapy. Pharmacological Reviews 58:389-462. DOI: 10.1124/pr.58.3.2

2. Di Marzo, V.; Matias, I. (2005) Endocannabinoid Control of Food Intake and Energy Balance. Nature Neuroscience 8:585 - 589. DOI: 10.1038/nn1457

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4. McPartland, J. (2009) Obesity, the Endocannabinoid System, and Bias Arising from Pharmaceutical Sponsorship. PLoS ONE 4(3) DOI: 10.1371/journal.pone.0005092

Sunday, April 5, 2009

Let There Be Light: Paramecia Communicate With Photons

ResearchBlogging.orgAn article in last week's PLoS ONE kind of blew my mind. I'm far from a microbiologist, but I was fascinated to read about this study on Paramecium caudatum and its ability to communicate with other members of its species by emitting photons. Even though Paramecia have no nervous systems, and are thus somewhat outside the scope of a neuroscience blog, I decided to post about this study because that's just so cool. The article, by Daniel Fels of the Swiss Tropical Institute in Basel, Switzerland, highlights previous work on so-called biophotons and establishes a protocol for testing the effect of biophoton emission in cultured single-celled organisms. Please forgive me if I muddle up the review, as this stuff is far outside my area of expertise!

So, apparently all sorts of cells can produce "ultra-weak" photons, in species ranging from plants to human beings. References in the Fels article indicate that this has been known since the 1980's, which leaves me feeling somewhat indignant that I never learned about biophotons in any of my classes. I'm going to quote the paper because it has a nice summary of previous biphoton studies (click the link to the article if you'd like to see all of the citations -- PLoS ONE is open access, so I know everyone can see the Fels paper, but reading the other references might be difficult if you don't have institutional subscriptions to their sources):

Although biophotons may carry biologically relevant information [12], [13], [22], only very little is known about whether individuals indeed use them for sending and receiving information. A few studies (with populations separated from each other molecularly but not electromagnetically) strongly suggest biophotons as transmitters of information: e.g., onion roots influence mitosis positively in neighbouring onion roots (supposedly due to so-called mitogenetic radiation [23], being probably effective in the UV-range [24]); yeast cells, which emit biophotons in the UV- and the visible range [25], affect growth in other yeast cells positively [26]; tissue cells arrange themselves in a non-random manner according to the pattern of tissue cells on the opposite side of a glass slide [27]; and germinating Fucus-zygotes probably sense biophotons emitted by their living substrate to which they direct their growth [28].


Thus, it seems that many simple cells are about to "see" photons emitted by their neighbors, and respond to these electromagnetic signals through changes in their growth patterns.

With this background, Fels decided to test the effect of putative biophotonic communication in the single-celled organism Paramecium caudatum. The experiment was simple: he cultured the Paramecia in glass and quartz containers called cuvettes -- an outer cuvette containing one culture, with a smaller cuvette placed inside it that contained another culture. The different cuvette materials allowed different wavelengths of light to pass between the cultures. He placed the cuvettes into a dark box to control for the effect of other light sources in the environment. After giving the Paramecia some time to grow, he then observed the effects of one culture on its neighbor, to see if the organisms were able to transmit information between cuvettes even though no molecular signals were able to diffuse across the barriers. Cell growth and cell division (measured by counting the total number of Paramecia in each culture at the end of the experiment) and feeding (measured by vacuole formation) were quantified, to see if electromagnetic signals between cultures could influence these simple behaviors. The study found that:

[P]opulation growth and the feeding rate of Paramecium caudatum depended significantly on (i) the presence or absence of a neighbouring population, (ii) the number of cells in the neighbouring population and (iii) the material (glass or quartz) separating these populations. The results strongly support the existence of a non-molecular information-carrying system that is based on photons.


In other words, the culture adjacent to the one being measured has an effect on the growth and feeding behavior of a group of Paramecia, and this effect is dependent on the material that separates the two cultures. Specifically, when analyzing growth, Fels saw that "large populations grew significantly better (than controls) when separated with glass from the small neighbour populations, but they grew as well as the controls when separated with quartz from the smaller neighbour populations." For feeding behavior, he reports: "When separated by quartz from a few neighbouring cells (15–20), vacuole formation was higher than for the glass units, but when separated from many neighbours (300–400 cells) it was the lowest of all treatments. The opposite effect was found for populations separated by glass." This suggests that the effects on growth were largely explained by feeding behavior -- the populations that exhibited increased growth also seemed to have a higher rate of feeding.

Are we sure that this effect is due to biophoton transmission? Not exactly. However, the differences observed between populations separated by glass and those separated by quartz would seem to indicate that at least some of the effect can be explained by the different wavelengths transmitted through those materials (glass serves as a filter for some wavelengths of UV light; quartz allows them to pass). This seems to rule out other possible mechanisms for information transfer, such as a gaseous molecular signal that diffused into the air around the cultures, or an infrared (heat) effect, as it's not likely that these would be dependent on the filtering effects of the separating material.

Interestingly, Fels reports a difference in cell growth based not only on the material separating the two cultures, but on the outer material. Glass and quartz were used to form both the inner and outer cuvettes, yet only the inner cuvette should have had an effect on electromagnetic transmission between the two cultures (the outer cuvette's job was just to keep Paramecia from spilling everywhere). The article claims that the nature of this effect is outside the scope of this study, which is a reasonable position to take, but if the cultures are interacting with the material that houses them in a way that doesn't involve biophotonic communication, this presents a potential confound for the results.

Of course, under natural conditions, single-celled organisms or cells within a single organism are not separated from each other by glass/quartz, and use a variety of molecular signals for communication. Even if biophotons play a role in cellular communication, their effects may be modulated by molecular signals (or vice versa). It would be interesting to figure out the mechanism by which biophotons are generated or received and to selectively disrupt it in Paramecia, to see if that had an effect on growth and feeding behavior between populations separated by glass/quartz or by a more permeable barrier. This would allow us to further dissect the effects of electromagnetic signaling in the presence or absence of molecular signaling, and to better understand what those crazy biophotons are really doing.

Fels, D. (2009). Cellular Communication through Light PLoS ONE, 4 (4) DOI: 10.1371/journal.pone.0005086

Friday, April 3, 2009

Yeast Geneticists, Beware

...we will soon have robots to replace you.

From the video at New Scientist:

This work is normally carried out by human graduate students, but Adam has shown that robots can be just as effective researchers.


I'm getting a bit nervous.