Monday, June 7, 2010

Benchfly Helps Me Learn and LOL

Today I discovered Benchfly, a Web 2.0 science hub centered around instructional videos for scientists both in and out of the lab. Current protocols range from time-saving tips for minipreps (that eppi rack trick was news to me) to how to make an Old-Fashioned (I bet Dr. Becca will approve). The good folks at Benchfly also run a blog and, of course, Facebook and Twitter pages, so you can follow their musings about life as a lab rat.

But I have to say, what really won me over was how funny some of the videos are. This one, for example, speaks profoundly to anyone who's ever done immunofluorescent staining:

And this one really resonated with me, because four-letter words and violence are the best way to deal with equipment failure:

Benchfly seems to overlap a bit with the Journal of Visualized Experiments in the sense that both focus on video protocols. But, JoVE seems to be working under an older model of protocol sharing. According to my PI, who has been approached by JoVE in the past due to the "highly visual" nature of our research, JoVE can send a video crew to your lab to film experiments and help with all of the production work. The resulting videos aren't free, however -- you need a JoVE subscription to view most of their protocols. I don't know how many people/institutions do pay for a subscription, but I know Emory's library did not subscribe, last time I checked.

Benchfly, on the other hand, is crowd-sourced and free. Many of the video protocols are made by their staff, but other users are able to submit them as well. Not sure if they plan to implement a pay subscription later, but I hope not. I enjoy the humorous and informal nature of these video protocols. To me, the difference between JoVE and Benchfly feels like the difference between reading the Materials and Methods section of a journal article versus reading someone's lab notebook, complete with hand-written smiley faces and "WTF?!" notes.

Monday, May 17, 2010

Coffee and Cigarettes: Good for Your Brain?

ResearchBlogging.orgA recent paper by Kien Trinh et al. in the Journal of Neuroscience suggests that coffee and tobacco have a protective effect in two fruit fly models of Parkinson's disease. Surprisingly, these effects do not depend on the obvious "active ingredients" of these substances (i.e., caffeine and nicotine), but occur through some alternative mechanism.

The connection between coffee consumption and lower risk of Parkinson's disease has been known for a while. When I was applying for research assistant positions in 2006, one lab that interviewed me was studying the effects of caffeine in a mouse model of Parkinson's. Scientists began investigating this link after epidemiological studies based on large numbers of human patients showed that people who regularly consume coffee (and, to a lesser extent, other caffeinated beverages) are not diagnosed with Parkinson's disease as often as those who turn their noses up at the beverage of the gods (Elbaz et al., 2007). One interpretation of this trend is that something in coffee either ameliorates the symptoms of Parkinson's, or protects against the underlying cause of the disease -- death of the dopamine neurons in the substantia nigra of the brain. (The other possible interpretation is that some unknown factor, aka a "lurking variable," makes people both more likely to drink coffee and less likely to get Parkinson's.) Indeed, animal studies have already shown that giving mice caffeine and similar drugs protects against degeneration and death of their dopamine neurons in one model of Parkinson's disease (Kalda et al., 2006; Quik et al., 2008). Similar epidemiological studies indicate that tobacco users also have reduced risk of Parkinson's.

The authors of this paper wanted to test the effects of coffee and tobacco in another model organism, the fruit fly. For their study, they used two kinds of genetically-manipulated flies: one that overproduces the human alpha synuclein protein in dopamine neurons, and one with a mutation in the parkin gene. Alpha synuclein is the primary component of Lewy bodies, the abnormal protein aggregates seen in the neurons of Parkinson's patients. Mutations in the alpha synuclein gene (which is called SNCA) are known to cause some rare forms of familial Parkinson's disease. Similarly, mutations in parkin are linked to an inherited early-onset form of Parkinson's disease. Both types of flies exhibit degeneration and death of their dopamine neurons, making them a good model of the pathology of human Parkinson's disease. Additionally, parkin mutant flies exhibit abnormal climbing behavior and a reduced lifespan, similar to the movement disorders and other symptoms seen in human Parkinsonian patients.

Trinh et al. used lifespan, climbing behavior, and number of dopamine neurons in the brain as a measure of disease severity in mutant flies. The researchers wanted to test whether any of these characteristics were affected by exposure to coffee or tobacco.

In one of the more whimsical Materials and Methods sections I've read, they explain:

Coffee extracts were prepared using Starbucks House blend (Starbucks Corporation) or Tully House blend (Tully Corporation) for regular coffee and Starbucks decaffeinated House blend for decaffeinated coffee (Starbucks Corporation). Tobacco extracts were made using Eve light (Liggett) or Skoal Smokeless tobacco (Skoal) for regular tobacco and Quest2 (Vector Tobacco) for nicotine-free tobacco. Extracts were prepared by adding 18.4 g of ground coffee and 50 mg of dried tobacco separately to 100 ml of water and boiling for 30 min. The extracts were ... added to standard cornmeal–molasses fly food at varying concentrations.

After feeding coffee and tobacco extracts to the mutant flies, Trinh and colleagues dissected their brains to count their dopamine neurons. These were compared to the brains of mutant flies that did not receive the extracts. They observed that both parkin and SNCA mutant flies given coffee or tobacco extracts had more dopamine neurons than those given regular fly food. These results were significantly different, although upon perusing the graphs I noted that untreated flies had about 8-9 dopamine neurons in the relevant brain region, while flies given tobacco or coffee had 9-10. We're talking about a difference of one cell, here. (Although, if you put it another way, it's a difference of 10-12%!)

The authors then repeated this experiment on other flies, but replaced the coffee or nicotine extracts in the fly food with pure caffeine or pure nicotine. This time, they could not detect a difference in the number of dopamine cells between untreated flies of either genotype and flies treated with caffeine or nicotine. Another experiment using extracts from decaffeinated coffee and nicotine-free tobacco did show a significant effect, however. This led Trinh et al. to deduce that the protective effect of coffee and tobacco on the flies' dopamine neurons was not due to the action of caffeine or nicotine.

The researchers tested the effects of coffee and tobacco on mutant flies with other methods, as well. They fed decaffeinated coffee and nicotine-free tobacco extracts to parkin mutant flies and measured their lifespan and climbing ability. The mutant flies given coffee and tobacco were better climbers than untreated mutant flies -- they were able to climb a distance of 10 cm within 30 seconds in about 50% of climbing trials, as compared to untreated flies, who only completed the climb about 40% of the time. The treated flies also lived longer: although most mutant flies (treated and untreated) died by the age of 40 days, a few coffee- and tobacco-treated flies survived to 50 and 55 days, while none of the untreated flies did.

Trinh et al. went on to verify that coffee and tobacco extracts (regular and caffeine-/nicotine-free) significantly reduced neuronal degeneration in a cell culture model. Neuron cultures from mutant flies that overproduce alpha synuclein do not have very many dopamine cells; the extracts significantly increased the number of dopamine cells seen in such cultures. In fact, based on the graphs, the alpha synuclein cultures treated with coffee or tobacco seemed to have more dopamine cells than neuron cultures from normal flies! The researchers didn't explicitly test the effects of coffee and tobacco on normal neurons, however, so I can't say whether this difference is significant.

Finally, the authors suggest a mechanism for how coffee and tobacco might protect against neuronal degeneration in Parkinson's disease. They suggest that compounds in coffee and tobacco (including a molecule called cafestol) act on a transcription factor called Nrf2. Nrf2 normally activates genes that lead to increased production of an antioxidant called glutathione. Trinh and colleagues treated mutant flies with cafestol and saw results reminiscent of coffee and tobacco extract treatment. They also showed that coffee and tobacco lose their neuroprotective effects in mutant flies if they block the action of Nrf2, suggesting that the extracts are indeed acting in an Nrf2-dependent manner.

This paper leaves us with several questions. Perhaps the most relevant one is, why does decaffeinated coffee improve dopamine neuron numbers, climbing behavior, and survival in mutant flies, when other studies in mice implicate caffeine as the factor responsible for coffee's neuroprotective effects? There are several important differences between the fly and mouse disease models to consider. Aside from the obvious fact that mice are not flies (and thus, the two species differ in many aspects of their brain chemistry), the Parkinsonian mice used to study the effects of caffeine were generated by giving genetically normal mice a toxin that kills dopamine neurons. The fly model used in this study, however, is based on genetic mutations. Therefore, it's possible that caffeine is useful for protecting dopamine neurons from toxins, whereas other compounds in coffee and tobacco (like cafestol) can correct intrinsic problems that arise from mutations in a dopamine cell. The obvious next step is to test the effects of caffeine and decaffeinated coffee on genetic mouse models of Parksinon's disease, to see if the fly results can be repeated in mammals.

Of course, neither animal model of Parkinson's disease (toxins or mutations) is perfect. The vast majority of human Parkinson's cases are idiopathic, meaning that we don't know what caused the disease in these patients. Their symptoms cannot currently be explained by exposure to toxins or inherited mutations in genes like SNCA and parkin. Therefore, it's not clear whether caffeine or Nrf2-related factors like cafestol are responsible for the epidemiological trends seen between coffee or tobacco consumption and Parkinson's disease. At this point, scientists are still searching for what factor(s) might be shared between idiopathic cases of Parkinson's disease, in order to develop effective methods for preventing and treating the disease in these cases. In the mean time, though, studies like this one continue to expose new molecular pathways that might be relevant in neurodegenerative disease. And, of course, this particular paper helps justify my coffee habit, for which I am grateful.


Elbaz A., & Tranchant C. (2007) Epidemiologic studies of environmental exposures in Parkinson's disease. Journal of the Neurological Sciences 262: 37–44 DOI:10.1016/j.jns.2007.06.024

Kalda A., Yua L., Oztas E., & Chen J.F. (2006) Novel neuroprotection by caffeine and adenosine A2A receptor antagonists in animal models of Parkinson's disease. Journal of the Neurological Sciences 248(1-2): 9–15 DOI:10.1016/j.jns.2006.05.003

Quik M., O'Leary K., & Tanner C.M. (2008) Nicotine and Parkinson's disease: implications for therapy. Movement Disorders 23: 1641–1652 DOI:10.1002/mds.21900

Trinh, K., Andrews, L., Krause, J., Hanak, T., Lee, D., Gelb, M., & Pallanck, L. (2010). Decaffeinated Coffee and Nicotine-Free Tobacco Provide Neuroprotection in Drosophila Models of Parkinson's Disease through an NRF2-Dependent Mechanism Journal of Neuroscience, 30 (16), 5525-5532 DOI: 10.1523/JNEUROSCI.4777-09.2010

Thursday, April 29, 2010

Using Mendeley for Long-Distance Mentoring

Last week I received an email from a student who's applying for one of Emory's undergraduate research programs. The SIRE Research Partner Program matches undergrads with faculty working in their areas of interest, teaches them research and communication skills through a series of educational workshops, and provides funding or class credit for their hours as a research assistant. This prospective SIRE trainee wants to work with my adviser. Once she joins the lab, I'll be training her in various laboratory techniques and providing some supervision for her day-to-day activities. I want to do more teaching and research mentoring, so I'm really looking forward to working with her.

In the meantime, she's asked me for a list of papers that she should read to help familiarize herself with the work we do in our lab. The simplest thing would be to email her some citations or PDFs, but I wanted a more interactive way to bring her up to speed. Papers are always easier to manage once you've talked them over at journal club, and it seems unrealistic to expect a rising college sophomore to understand all of the details in these papers without any help. Ideally, we'd get together regularly to discuss the papers and how they relate to her project, but that isn't possible while she's spending the summer with her family in another state.

So, I decided to create a shared collection with her on Mendeley. Using the free Mendeley Desktop software, I can add papers from my own reference library to a collection that I've named "Summer Reading." (This collection is not public; only the two of us have access to it.) My student can read the papers from home on her own copy of Mendeley, allowing her to familiarize herself with a reference manager (an important research skill!) and communicate with me about her reading list.

I attached PDFs to each reference in our shared collection. Then, I used Mendeley's annotation capabilities to highlight areas of particular interest for her project, and left a few comments in the "Tags & Notes" field to help her focus on the most important points in the paper. These annotations are shared along with the PDF, so my student can follow along easily while she's reading the paper at her computer. I've also encouraged her to add her own annotations as she goes along.

After she's had a chance to read, highlight, and add notes to a paper, she can sync Mendeley Desktop and upload the annotations that she made. They'll show up on my computer the next time I sync my reference library. I encouraged her to include any questions that she has about the papers in these annotations. I think the "sticky notes" will be especially useful for this -- instead of having to quote a paper at length, or refer to "page 7, paragraph 2" in a message, she can stick a digital note right next to the relevant portion of the text. I can continue editing the PDF to respond to her questions, and we can go back and forth as needed.

I did have a little trouble while I was setting this up. This is my first time using shared collections on Mendeley, and some of the documentation on their FAQ is a bit sparse, so I had to go by trial and error. The most important point: In order to collaboratively annotate PDFs, all members of a shared collection must open the collection in Mendeley Desktop, click the "Edit Settings" button, and check the boxes for "Upload attached files to shared collection" and "Download attached files from shared collection." Otherwise, PDFs attached to the references won't show up, and annotations made to those PDFs won't be shared with other members of the collection. These are turned off by default, and until I stumbled onto the relevant menu options, I had no idea how to make attached files show up in the collection. I made one of my labmates join a shared collection with me, then ran back and forth between our two computers a few times until I got it working. It seems obvious now, but I thought I'd mention the solution in case other people who want to try this are as clueless as I am.

We'll see how this works over the summer. If written communication proves insufficient for our needs, I may suggest a few Skype chats to talk things over in real time. Anyone else have suggestions for long-distance collaboration / educational tools?

Sunday, April 18, 2010

Troubleshooting Gateway Cloning

After struggling with a particularly annoying problem in the lab, I finally got my experiment to work this weekend! When I crowed about this to my partner, he told me that whenever he figures out the solution to a tricky problem in his line of work, he blogs about it, for the sake of others who might have the same issue. I did my share of Googling while troubleshooting my experiments and didn't find a solution, so I thought this was worth blogging about. The following will make very little sense if you don't do molecular cloning.

I spent almost three months trying to clone my DNA sequence of interest into a mammalian expression vector using Invitrogen's Gateway Cloning system. Things were going smoothly for a while -- I made a pENTR entry clone, chose a pDEST destination vector, did the LR clonase reaction according to the instructions in the kit, did a diagnostic restriction digest to confirm that my plasmid had the expected sequence, and then... I couldn't maxi-prep the plasmid. This was my first time using the Gateway system, so I expected to hit some bumps in the protocol, but I've been doing maxi preps (with Qiagen kits -- regular and the HiSpeed) for years. So, I felt pretty stupid when my experiment broke down at that point. I got my plasmid out of a mini prep, but failed to recover the plasmid after inoculating a maxi-sized culture with the same exact construct in the same exact competent cells. What the hell?

As I grew increasingly frustrated, my adviser had the outlandish idea to repeat the experiment with good controls. So I did. I used every control I could think of. I transformed, mini-prepped, and maxi-prepped: my entry vector, a known entry vector with a similar sequence that we had lying around the lab, my expression vector, a similar expression vector from the lab, and the empty entry vector. I also repeated the LR clonase reaction with my plasmids and with other Gateway plasmids we had on hand.

I could get maxi prep DNA from everything except LR reaction products (i.e., any sequence of interest flipped from pENTR into pDEST through attR/attL recombination). For some reason, the expression clones would grow in mini preps, and some sort of antibiotic-resistant bacteria would still grow in my maxi cultures, but I would get abysmal plasmid DNA yield from the maxi preps. I tried growing my bacteria at a lower temperature over a longer amount of time, which sometimes helps bacteria keep larger plasmids (my plasmid of interest was about 9 Kb), but that didn't help. I bought fresh new LR clonase enzyme, but that didn't help either.

Eventually, senior lab members remembered someone having a similar problem a few years ago. They thought that the issue was finally resolved by making fresh pDEST vector by culturing bacteria containing the empty vector from the original glycerol stock. I thought that made no sense, but it was easy enough to dig the glycerol stocks out of the freezer, grow up some cells, and prep the DNA. So I did. I then used the newly made pDEST DNA to repeat the LR clonase reaction with my entry clones, transformed the LR product, and grew up some bacteria for a maxi prep.

And... it worked!

I don't know why it worked. I guess somehow, after being stored in the freezer for a while and going through enough freeze-thaw cycles, the pDEST DNA that we had stockpiled went bad. It worked well enough to take up the insert from my pENTR clones and grow in competent cells in a 2 mL culture, but then it petered out when I tried to grow a 150 mL culture of the same cells. So, if you are having a similar problem, I say to you: find your old glycerol stocks. My labmates say that the last time they had this problem, transforming the plasmid back into some ccdB-tolerant cells (the pDEST vector we used contains the ccdB suicide gene) and re-prepping from them also worked, but I can't verify that.

Next up: transfecting my expression vector into some mammalian cells to see what happens! (Also known as: the experiment that I actually care about, which I was sure I would have gotten to by now...!)

Tuesday, March 30, 2010

Rebecca Skloot's Visit a Success!

After many months of planning and 197 event-related emails (according to a quick search of my inbox this morning), Emory welcomed Rebecca Skloot to our campus yesterday. Our plans for her visit came together almost perfectly. There were about 50 people at our student seminar on The Immortal Life of Henrietta Lacks, and about 200 in the audience at Rebecca's talk in Cannon Chapel. Many participants took the time to tell me how much they enjoyed reading the book, discussing the story, and listening to Rebecca speak. I'm glad to know that others found the events to be as rewarding as I did.

When I originally invited Rebecca to come to Emory, I imagined a reading and book signing similar to the ones I've attended in the past (at lovely shops like Brookline Booksmith and Back Pages Books). This event surpassed my expectations. The Immortal Life of Henrietta Lacks connects with people on an intimate, emotional level, and inspires readers to ask themselves hard questions about life and death, love and loss, right and wrong. Rebecca presents years of meticulous research with an engaging writing style to educate her audience without patronizing or preaching. She describes the members of the Lacks family, their history, and her own relationships with them in a way that reminds us that these characters are not just characters, but real people with complex personalities and tragically human problems. After a reflective introduction by Emory's Senior Vice Provost, Ozzie Harris, Rebecca's straightforward narrative left the large crowd completely rapt at her reading.

We were also incredibly fortunate to have Dr. Roland Pattillo (if you've read the book, you may recognize the name) in attendance last night, as well as two relatives of the Lacks family: Jessica Holmes, a doctoral candidate at Emory's Woodruff School of Nursing, and her mother, Imogene. Several other members of the audience had roots in Clover, VA (the home town of the Lacks family) or at Johns Hopkins University (where Henrietta Lacks was treated for her cancer, and where the HeLa cell line originated). For me, meeting all of these wonderful people in person brought the story of HeLa and the Lacks family home for me in a powerful way that is hard to describe. After Rebecca's talk, some of the event organizers chatted with these special guests next to the bookseller's table until the long line of autograph-seekers had gone by. Hugs were exchanged.

As a scientist, I've known about HeLa for a long time, and I was even told a brief version of the Henrietta Lacks story in my college biology lab, but I'd never felt personally connected to this chapter of scientific history. Reading The Immortal Life of Henrietta Lacks made me imagine how I'd feel if I learned that part of my father, who died of cancer when I was 17, was alive in a lab somewhere. It made me look up the origins of other immortalized cell lines that I have used, like SH-SY5Y cells. (Those cells were derived from a bone marrow sample from an anonymous four-year-old girl with metastatic neuroblastoma -- "After progressive debilitation and continued growth of tumor, the patient died in January 1971.") It made me re-evaluate every sarcastic conversation I've had with my fellow grad students about our required ethics training seminars. (Suggestion to ethics seminar organizers: Put this book on the syllabus.)

But, all that is just my opinion. What made yesterday so rewarding was hearing that others have responded to Rebecca's book in similar ways, and in different, equally important ways. Our "book club" seminar yesterday afternoon included faculty from four disciplines (Dr. Michelle Lampl from Anthropology, Dr. Ora Strickland from the School of Nursing, Dr. Paula Vertino from the Winship Cancer Institute, and Dr. Dorothy Roberts, visiting Emory from Northwestern University's School of Law) sharing their expert knowledge and helping us examine the story of Henrietta Lacks from multiple perspectives. We also invited undergraduates, medical students, nursing students, law students, business students, theology students, and graduate students from Anthropology, Biological and Biomedical Sciences, Comparative Literature, Educational Studies, the Institute of Liberal Arts, Sociology, and Women's Studies to join the conversation, each with their own unique point of view and response to the story. The Immortal Life of Henrietta Lacks is a truly interdisciplinary work that inspired us to reach out to our colleagues in different corners of the academy, to learn from each other. Several people said that this seminar was the most truly interdisciplinary event they'd attended since coming to Emory, and that they would love more opportunities to have these kinds of discussions. (In response to these comments, we informed people about other interdisciplinary activities on campus -- though most of them don't give away free books.)

In summation, I'm very proud to say that I was a part of the events that took place here yesterday. With the support of dozens of Emory faculty, administrators, staff, and students, my colleagues and I were able to do something that I feel is supremely important: We opened minds. We brought people together. We affirmed essential human principles. Based on the emails I've gotten today, we changed at least a few lives.

Thanks for reading, for listening, and for helping.

Tuesday, March 16, 2010

Rebecca Skloot at Emory on March 29!

I have some exciting news to report today. After months of planning, I am pleased to announce that Rebecca Skloot will be visiting Emory on Monday, March 29, to discuss her bestselling book The Immortal Life of Henrietta Lacks. She'll be speaking at Emory's Cannon Chapel at 7:00 PM, with a book-signing to follow. This event is free and open to the public. We hope to draw a large crowd, so come on down!

I've had a lot of help putting this event together. Rebecca and her publicist have been great about dealing with the unique demands of a grass-roots book tour, and I appreciate their patience as I've flailed around trying to set this up. I'm also forever indebted to a fellow graduate student, David Ritchie, and to the Assistant Dean of Student Progress and Special Programs at Emory's Laney Graduate School, Dr. Virginia Shadron. VA and Dave stepped up when I came to a Graduate Student Council meeting begging for money and assistance, and they really came through for me. Also, Quinn Eastman, a science writer at Emory, tracked me down via this blog and helped organize and promote Rebecca's talk.

We're fortunate enough to have received financial and administrative support from twelve different offices and departments across the university (so far!), proving that if everyone chips in a little bit, you can make something awesome happen.

Finally, this event would not have come to be without the science blogosphere. I found out about Rebecca's book tour through her blog, and left a comment expressing interest in bringing her to Emory way back in the day. Since then, The Immortal Life... has been featured on the cover of Publisher's Weekly and praised by the likes of NPR, the New York Times, ABC World News, Oprah Magazine, and many others. It's currently #5 on the New York Times Hard Cover Best Seller list for hardcover nonfiction (and has gone as high as #2 in recent weeks!). So, I'm glad I got in on the ground floor of this tour, because the hype has totally exploded! To me, this is one more example of how web-based media provide unique communication and networking opportunities for scientists and science enthusiasts. That's something I hope to explore further in the future (I'm applying for a teaching fellowship to do this with Emory undergrads... stay tuned for an update on that later!).

Saturday, February 27, 2010

Mendeley: My New Favorite Reference Manager

This semester, I'm writing my first grant. My graduate program includes a course called Hypothesis Design and Scientific Writing, in which students work with faculty and peers to prepare an application for an NIH National Research Service Award (NRSA). My grant is coming along, but I still have lots of work to do. My goal is to submit the final product to the NIH sometime this summer. If I'm lucky, they'll decide to fund my proposal, and I'll receive additional support for my dissertation research. (Emory Neuroscience students have about a 60% success rate at getting their NRSAs funded, so I have high hopes!)

This grant has required a lot of background reading. I spend my free time in the lab scouring PubMed for relevant articles that will support my hypothesis. I've therefore been required to come up with a system for keeping track of all these papers. After trying several options, I've found Mendeley to be the most useful.

Mendeley shares features with other research bibliography tools like Papers, Zotero, and Quosa, but in general I find it to be more suited to my needs. The Mendeley Desktop program works "like iTunes for research papers." It keeps track of citation information and allows users to sort their references by category. Mendeley stands out, however, by linking the desktop client to web-based services that make my life much easier.

The Mendeley web importer is absolutely dreamy. If I'm looking at an article on Pubmed or on a journal website, I can use the "Import to Mendeley" bookmarklet in Firefox or Safari to automatically add the citation to my Mendeley database. Doing this prompts the user to enter tags and notes about the article right in the browser, which will be carried over to the desktop client as well. This is similar to Zotero's browser-centric approach to reference management, but I prefer Mendeley's approach. The Mendeley bookmarklet is unobtrusive -- it opens a small pop-up window or a new tab every time I add a reference. When I tried Zotero, I didn't like the way that it generated weird browser panes at the bottom of whatever page I was reading when I added a new reference. Adding tags to a Mendeley citation takes just a few seconds and doesn't interrupt my browsing experience -- I just close the tab/pop-up when I'm done. When I want to pore through my references in more detail, I use Mendeley Desktop, which as a dedicated application feels 'separate' from my browser, and makes it easier for me to focus on the articles. I find the interplay between Mendeley Desktop and the web importer to be just right -- this comes in contrast to Quosa, for example, which tries to integrate web-based search into the reference manager, but feels clunky and awkward. I already know how to use PubMed in my browser; I don't want my citation manager to make me learn a different way to search (even though Quosa's automated searches are pretty nifty).

Mendeley also automatically backs up all of my citation information to the cloud. I can log into my Mendeley account from any computer, and if that computer has Mendeley Desktop installed, I can sync the desktop client to my web account by entering my email address and password. The Mendeley account preserves all of a user's citations, as well as custom user-generated notes and tags. So, I can easily access all of my references and notes from home, even if I originally found all of the articles at lab. This is both convenient and smart -- in addition to making my life easier when I need to take a project home with me, this automatically creates two backups of my reference database: one at home, one in the cloud. If my lab computer dies (unlikely for now, since my PI just bought me a shiny new iMac, but it's always a risk), I won't lose my precious papers.

One aspect of Mendeley that doesn't thrill me is the social networking component. My Mendeley account includes a user profile, and I've been encouraged to add 'contacts' who also use Mendeley. I can see how this might be useful for sharing papers between lab members or collaborators, but I don't find it necessary. When my PI wants to send me a paper or an EndNote library, she can just email me the files. And I have some concerns about security -- sharing Mendeley databases with the wrong person might reveal too much about a sensitive line of research. I favor a more open-source approach to science, but many scientists are terrified of being scooped, and would prefer to guard their lab secrets more stringently. Even so, it's quite possible to use Mendeley's other services without creating a list of contacts. And Mendeley uses personalized account info to do a few nifty tricks, like displaying the most popular papers for Biological Sciences, based on which citations were imported by the most Biological Sciences users on a given day. Users can also add papers to the "My Publications" category in their profile, and track the popularity of their own articles on Mendeley.

The web-based features are my primary reason for preferring Mendeley over other options, but I also like Mendeley Desktop a lot. I can attach a PDF to a Mendeley citation, making it easy to browse full-length articles as well as my notes. The desktop client can open tabs containing multiple PDFs and allows highlighting and Post-It style notes right on the article (although for now, these annotations are not kept in the cloud, so I can't highlight a paper at lab and retrieve the same highlighting when I sync Mendeley Desktop at home). I can sort my citations by title, author, publication date, date added to Mendeley, or by my custom tags. Mendeley is also smart enough to show me articles related to a tag even if I didn't tag them that way -- an article that I tagged "review" will come up when I select the "motor neurons" tag, if it talks a lot about motor neurons, even if I didn't add that tag myself.

Mendeley is compatible with EndNote (select any number of citations in Mendeley, export them as an EndNote XML file, and Cite While You Write to your heart's content) and with several word processing programs (obviating the need for EndNote), although it doesn't yet work with Microsoft Word on Macs. I've had no issue using EndNote as a middleman, however. Mendeley can also import citation information from EndNote, Zotero, CiteULike, and RefWorks, making it easy to transition from another reference management system (have not yet tried this myself, since I haven't been working on this project long enough to generate a huge reference database in another system). It's also free! If you're intrigued but not completely sold, check out some other reviews, or just download it and see for yourself.