The 2012 Clinical Neuroscience Scholars from VBI have been named!
Evernote, how we love thee. Clip web notes, share notebooks and replace your hippocampus entirely with this great app. Oh, and did we mention its free?
Check out ongoing Clinical Research Trials at Vanderbilt HERE.
Asking timely topics and getting expert opinion on autism, the Marino Foundation has created Autube as an online dialogue for parents, professionals and media.
NEW!! Young Grasshoppers in need of advice on school, lab and science....check out our new ADVICE links next to the labbies to hear pearls of wisdom on pulling it all together.
Brain Facts - SfN Sponsored Information for Non Scientists about the Brain
Are you having a bad day, peanut? No worries. Just go here and it will be okay.
Streamlining Genius - Periodicals
Not a book, but a magazine everyone should get is Wired with cool science buzz, and techy information thats great.
Organization - Apps, Sites and Other Peripheral Brains
Is your email your go to source of what needs to get done? If so, FollowUpThen is your place to be. Send yourself a list or reminder at a the time of your choosing and link it right into your Gmail threat. Sweet!
Anatomy Structure and Function
Who doesn't love a bazillionaire who throws neuroscience the best tool in 20 years with The Allen Brain Atlas? Human brain, mouse brain, developing brain...name your protein and find where and when it's expressed. Snaps Paul Allen on philanthropy done right!
He also recommends gene expression omnibus a database of high throughput gene expression and hybridization arrays, chips and microarrays. From experience, this interface will require some tinkering or bribing a pro with a beer for a short tutorial as it's not the most intuitive for the newbies.
A little rusty on what projects where in the CNS? Hit USC's brain architure management site to see all your projections.
Lee Silver's landmark book on Mouse Genetics is free online and takes you through everything you could want to know. Find it here.
Heterozygote, haploinsufficient double mutant mice all explained by the fine folks at Jackson Laboratories. While there, check out their info on repositiories for aged animals, links to mutations for PD, spinal cord mutants and all manner of other great resources from Oak Ridge to Special Mouse Strains.
Once you get the critters, you'll want to make sure you are ubber nice to them so they can be happy and you can get reproducible results. DAC has great staff and resources to enrich enviroments, but we like this video on handling especially for newbies. Shout out to Tommy Saborito for finding it!
How to Use 'Em
Starter information on thinking about antibodies, fixation and protocols from immunohistochemistry world.
Abcam has a great starting site for how Westerns work here.
Pick your perfect gel percentage based on DNA, RNA or protein size with this snazzy chart from Clontech.
Find your 'hard to find' antibody here from the Antibody Resource Page.
And shout out to Cell Signaling for a positive control sheet from HEAVEN here and Journal of Comparative Neurology for their MONSTER database here of antibodies used in pubs. Dr. Cliff Saper was super grumpy as the EOC (Editor in Chief, people!) and killer piece on why antibodies aren't magic that should be required reading for everyone in the free world. Love you Cliff! H/T @bakermind Who has nothing to do with any of our snark but is a great wise Twitter overlord.
BioVu - Rocking the Personalized Medicine of it All
BioVu and The Synthetic Derivative are resources for Vanderbilt folks and the cool people who collaborate with us in which we can use deidentified patient records to look at numbers of patients we have seen and then link this data with genetic analysis. Erica Bowton, former VBI student, gave a great talk on this resource to the Clinical Neuroscience Scholars in February 2014 which you can find here
Why do it in vivo when you can grow it in a dish? We do love us some primary cultures and here is where we like to visit for fun.
Greg Brewer is a pioneer in making neurons grow like gangbusters. Check out his work in this online chapter laying the foundation of how to culture cells.
Giant props to Johannas Hell for calling manufacturers on the carpet for their unreliable supplements and making his own - NS21 is the way to go and Nature has a great story on why. And, because we are just that darn helpful, here's your handy protocol on how to make NS21.
We are big fans of Hibernate especially when you are making cultures from heterozygote matings and need to genotype fast before culturing. Keeps your brain bits alive for 24h until you can PCR.
We have tried every lipid, salt and voodoo method to transfect primary neuronal cultures and the reigning champ is Amaxa. Dissociate, zap and enjoy 30-40% efficiency.
And a final shout out to Sciencell who can do custom media for your faster and cheaper than Gibco.
Cell Culture Boogers
Find out what's wrong with your cells with this handy guide for beginners and pros. Provided by our buddies at Corning. Download it here. Then memorize it.
Is it the 12 beers to celebrate your first paper or is it delerium? Find out on the Delerium diagnosis and research page. (BTW, it's the beers)
Clinical Neuroscience Certificate Program
We are proud to be spearheading an initiative to facilitate translational neuroscience research by addition of the Clinical Neuroscience Scholars program. Predoctoral applications are due April 23, 2012 as a single PDF. Information about the program can be found here. The slides for the informational program on March 28, 2012 can be found here.
Descum your PC with ccleaner. Its free, its awesome.
Save up to 5G of your data online for free using iDrive.
PC users....figure out why it takes a year for your computer to boot and what crashed it using Soluto for free.
Oh, and for those pesky shortcuts to make science symbols, use this site.
Bottoms up....learn how to cast, run and analyze your agarose gels here.
Got your gene but need to sub clone the sucker? Here's our favorite site to cut and paste in an easy to use platform from Cyagen. Clean graphics and easy for your newbies to understand. We also have come to like Vector Builder in 2013.
A public repository for plasmids saves you the hassle of mailing them out. Simply turn your DNA over to Addgene and let them do all that pesky 'communicating' stuff we don't like as left brained folks. Site has lots of cool DNA constructs and manipulation tools and links to boot.
For those who want their cytometry basics visit this free site to analyze, plot and replot your data.
You can also check out Geeka's special version of snark and science at her blog.
Freeing Your Radicals
Reactive oxygen species....oh, we could go on and on about how much we love (hate?) thee. But be sure to check out the following sites for background, discussion, meetings and protocols.
Die Dyes: Have you ever read a clever flyer from a company telling you that they can measure free radicals with a fluorescent dye? They are dirty, dirty liars. Before you waste your bosses money and this happens to you, you should read this masterful work by people who might review our grants and we love, love, love them. Its a great overview on limitations of fluorescent dyes for ROS, RNS and whatnots.
Any part of this website that gave you the impression any way of measuring ROS damage to cells that isn't as fabulous as lipid injury with isoprostanes is totally misleading. Use isoprostanes people. Biomarkers of Oxidative Stress Studies already said they are the bomb. Talk to Ginger at the Vanderbilt Core. We love Ginger.
New but intriguing is the Society for Free Radical Medicine and Biology's new online forum. The Boss is grumpy that it is member only and thinks they are really missing the boat in appealing to a broad audience though. Our buddy and superhero debunker of bad science Paul Brookes agreed on the MitoList Serve saying that "The first two talks every morning at their annual conference are "Free Radical School" didactic lectures, aimed at providing a strong framework for the day's plenary sessions....The great thing is that all the lectures get archived on their website - there are over 100 up there, including downloadable powerpoint slides on a range of topics."
Radical Update 2012
The good people at Free Radical Biology and Medicine have put together a handy guide on what your dyes are and aren't measuring when you use them to measure ROS. Find it here if you want to publish with them.
Protocols online is a great clearinghouse for information and bench protocols.
Cold Spring Harbor is the mac-daddy of published and online protocols. Love their peer reviewed works....just hope your university has access to it.
Nature Protocols is rocking in print....not a huge fan of their online site as advice is sketchy and it is hard to navigate in its current format.
BitesizeBio falls into so many domains on education, protocols and networking I feel bad about 'just' putting it here, but if you're a Twitter person, they have a great feed.
Benchfly I guess if you are picking between being a lab rat or a bench fly, you will get more information at the Benchfly site where they have video protocols and great information for lab newbies.
OpenWetWare is a unique high potential site which combines lab protocols and notebook features online. McLaughlinites don't believe in trusting some company to preserve our notebooks for us so we are hard copy, but it's highly functional and a great concept.
Molecular Station has some depth in odd areas for biochemistry and reagent prep, but its spotty in lots of places, but worth a look.
Elabprotocols is not the biggest, but it has a great interactive component and clear protocols.
Biowww.net is a mix of protocols and products with some depth in transfection and siRNA. Jeannette likes it, so that's good enough for us.
Andrew Kropinski has done an amazing job of cultivating a great collection of protocols on everything from DNA to lipds and his site is a continously updating and great resource.
Oh, did you want to BUY that reagent? Yeah, you're gonna need some cash for that.
For Vandy-ites, we recommend you check our in house well currated list of opportunities.
Anyone who is not subscribing to DrugMonkey's Blog on grants is missing out on some powerful gens of knowledge. Also, so very serious snark. The advice is good. The choice of shoe apparel is entirely sketchy.
For those who can never QUITE get the right colors, we love Kuler - upload your image and get a full range of matching colors. Excellent for graphics and posters. ColorSuckr (yes, it's spelled right smarty pants) is another great nature inspired palette generator.
Also, if you aren't using Picasa for saving photos and playing with cool filters you are missing the boat. Tons of free storage and the ability to download your photos in their original high resolution format.
If the 50 fonts available in Microsoft aren't enough, check out Google Web Fonts.
Can't quite figure out your lasso tools, layers and other Photoshop mayhem, well You Suck at Photoshop. Oh and there's a website for that which is AWE-some. Say it right. Aweeee (pause) some. Now go there.
And your posters aren't as amazing as you think or your mom reassures you they are. Fix them using pointers from The Scientist.
The Mac-Daddy site for all things cellular is The Cell: An Image Library. So many awesome pictures, so little time to drool. EMs, fluorescent staining, live cell imaging of all kinds of biological processes and organelles...its all there!
Using a fluorophore that might be bleeding into your other signals? Check it here at Omega Filters.
Make up your data and save time! Err, we mean virtually stain your cells and see how they would look at this ubber creepy and equally cool Molecular Probes Site.
We buy our 'scopes from Zeiss, but have to give snaps to Nikon's Microscopy U for excellent intro materials on imaging for folks at all levels from phase bright to confocal and FRET.
Mitochondria - Our Favorite Organelle!
Mitosciences has a great newsletter and some cool technologies to look at expression of components of the electron transport chain etc.
Seahorse Biosciences....when we finally win some big bucks with our well planned scratching lottery ticket strategy, we are SO getting one of these. In the meantime, be sure to check out their killer webinar series.
Be sure you are on the email for the mitochondrial interest group out of NIH. Great user forum and lots of the big guns actively participate and Mitopedia is shaping up to be a great resource for mitochondrial information and cool current reading.
Papers, References - Controlling the Chaos
The lab is sharply divided on this section with some 'old schooling' it sticking to Endnote until they get it right (2020 perhaps?) while others enjoy the following electronic resources.
Mac Folks, it goes without saying you are going to want Papers from the genius' at mekentosj.
Our new favorite site is LabGuru. it lets you follow your minions on what they are doing electronic notebook style. You can share jobs, results and attachments online as well as incorporate information on your DNA/Protein/Cells of interest, do some inventory control and develop protocols. Our go to app for giant shareable notebooks is Evernote which is getting increasingly integrated with helpful 'clip from PDF' options, to do lists and ease in crossing from your PC to phone.
For those that haven't turned their lives over to Steve Jobs, may we recommend Jake's favorite reference manager Zotero to take notes, make a library, share it with your peeps and assemble a publication quality paper from all of it (actually it only does 3 of those things). Great for most things, but still not an 'import style' for many journals and runs as a Firefox extension which isn't for everyone (like those who love Chrome for instance).
Mendeley trumps Zotero in finding similar papers to what you are reading, ranking their impact but is missing the ability to take notes from a webpage. Our friend Mr. Gunn loves it, so we give it a shout out.
Finally, check this handy resource for figuring out if you are submitting to a high impact journal if you are into that kind of thing.
Primer Blast is the oldest of the search tools from NCBI allowing you to integrate Primer 3.0 design with Blast to limit overlap with other genes.
Jacquelynn claims that this video on PCR is 'good nerdy fun' and a great primer on primers. (Get it, you need primers for PCR and it is a primer on the content). Whatevs, don't be a hater just check here
No one has made the Periodic Table more interesting than the University of Nottingham. Check 'er out (thanks Scott Palubinsky!)
Proteins - one on one
Structural Biology Knowledgebase, More of a specialists database than they probably intended this site contains information from the Protein Structure Initiative containing structure function info and help developing methods.
Protein Databank, THE repository of protein structure coordinate with useful tools for quick looks at structures and ligands.
Chimera, free for us academics a great molecular visualization program even for the wee babies of science.
The EBI Toolbox, tools for analyzing and aligning protein and gene sequences.
Check your ammonium sulfate protein precipitation calculations here.
Calculate what your protein Pi should be using this snazzy site.
Scripps site will give you all kinds of basic and higher order information about your protein here.
If cicular dichromism is your problem (and really - when isn't it!) check out this friendly site.
Proteins - Networks
Science Magazines database of cell signaling is the mac-daddy of who your protein is and who they like to play with. High quality. Lovely pictures. Clearly written by a woman. :-)
Check out the good folks at the Badger Lab for assembling proprietary and open code resources for analyzing protein networks, predicting gene function....all kinds of great information.
Tired of doing all that pesky 'research' to give a talk? Check out Vadlo's site for other scientists background talks as well as some protocols. You can also check out TalkMiner which is home to our favorite slide show on CNS vascularization. And snaps to Cozette for finding this online textbook on Cell and Molecular Neuroscience
Also, mad, mad love to Khan Academy purveyer of all things from biology to physics in digestible nuggets for little tater tots to big kids too. Also, huge fans of Science Friday's Educator forum for videos and mini experiments for the minis in your life.
Loving 2014's breakout publication Fronteirs for Young Minds. Papers written, reviewed and edited for 4-8th graders. So. Much. Fun!
Society for Neuroscience's NERVE site has pretty graphic and digestible science nuggets for all.
SNPs (If you know this is pronounced 'snips', you're a geek
Single nucleotide polymorphisms, or SNPs, they are what make all of us so very special and unique. Some folks more special while some are decidedly less special. If you are wondering if the protein you are working on has polymorphisms in the general public, you can use Exome Variant Server to enter your Entrez number and, easy peazy, you're good to go. SNPs are not disease linked, but at least you can say 'my conserved Serine is mutated in 2% of the public' and then Voila! Your research is translational. Snaps, not snips, to our buddy Nick Campbell for helping us with our SNPs.
Stats and Programming
When your good old t-test won't do...check out @nparmalee's buddies at R-project to enjoy data handling at its finest.
Someone pesky send you something where you need to know Unix and you don't. No worries (okay, worry because they should know you don't know!) but catch up fast with help from the Korf lab.
It comes in all forms...wearing the right clothes, checking weather and knowing your risk in when Zombie Apocalypse hits. Check your safety here. You're welcome.
Oh, and for life's minor emergencies, enter your cell phone number and Zip code with Umbrella Today and they will send you a text everyday there's rain forecast in your area.
Fractions...they are more than your simple numerators and denominators. They are ways to seperate your biological samples into organelles, cytosol and all kinds of other cool things to do biochemistry on. We use Amy's awesome subcellular fractionation protocols.
You can isolate mitochondria from liver, mitochondria from primary neuronal cultures, nuclei from HT22 cell lines, and all kinds of cool things from bioenergetics to transcriptional activity. Be sure you check out ProteinTech's eight pointers on doing isolations for some thoughtful backgrounds about proteins.
Brain on a Chip Funded!
The McLaughlin lab joins Vanderbilt colleagues in creating a one of a kind biofluidics platform for drug discovery. Find out more here
Tennesseans - Demand your children get taught science and not religion, in science class. Read Roger Cone's OpEd here.
Bonnaroo June 7-10, 2012 line up being continually updated. Find out more here!
Vanderbilt voted one of The Top 10 Places to Do a Post Doctoral Fellowship. Find out more here