A Science Driven Life

An un-edited blog about science, discovery, technology, travel and the occasional whiskey

Optogenetics / Optophysiology References Page on SDL!

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Dear friends,

I am compiling optogenetics, optophysiology and advanced imaging references and will be organizing them by category/field.  I have launched the page and over the next week it will grow to contain all papers I can find in a given field.  Where possible I will post links to the articles for download and in some cases will post comments and footnotes on the research.

Science Publications / Reference Page

I will also have a page with references of the “Latest and Greatest” papers that I find interesting.  This will focus on “Advanced Online” publications and things that are hot off the press!

I’m very excited for this endeavor and am open to ideas and suggestions on how to improve the format and organizing.

I’m very behind on about 5-6 paper reviews I began writing, expect a lot of activity in the coming weeks!



Written by Michael Mohammadi

February 20, 2014 at 23:31

Science Driven Life (SDL) book club to begin February 2014

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Dear friends,

Just a one time notice that we’ll be starting a SDL book club in February 2014.  Details can be found here: https://sciencedrivenlife.wordpress.com/sdl-monthly-book-club/

February 2014:   A Universe from Nothing: Why There Is Something Rather than Nothing – Dr. Lawrence Krauss

If you’re interested in participating please comment or send me an email: michael dot mohammadi at gmail dot com!


Written by Michael Mohammadi

January 23, 2014 at 13:52

Posted in Book Club, Books, Physics

The Annual Meeting for the Society for Neuroscience – #SFN2013

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Screen Shot 2013-11-06 at 3.02.42 PMIt is that time of year again- the clocks have been set back, most deciduous trees in New England have shed their leaves, and my Siberian huskies their coats (mostly in the house), and autumn has brought us cool, crisp evenings signaling winters impending chill.

It’s also time for the annual meeting of the Society for Neuroscience, or SfN.

Read the rest of this entry »

Written by Michael Mohammadi

November 6, 2013 at 20:00

Quick Look: Another use for optogenetics and GPCR signaling

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Optogenetics is the rapidly emerging field in biotechnology and biological sciences that combines the genetic expression of light sensitive molecules and the delivery of light to control cells, populations of cells or animal behavior.  Often when we think of optogenetics, the first thought is back to the landmark papers where light was used to depolarize cells and cause action potentials (Zemelman et al. 2002, Boyden et al. 2005).  While these types of studies are highly prevalent in neuroscience today, a whole other branch of optogenetics exists that uses light sensitive molecules to modulate some biochemical or second messanger pathway.  One area, called OptoXRs, is of great interest as therapeautic targets for a variety of pharmaceutical products as a majority of these act through some type of g-protein coupled receptor (GPCR) pathway.


Screen Shot 2013-09-09 at 11.36.54 AM Read the rest of this entry »

Written by Michael Mohammadi

September 9, 2013 at 19:56

Science Technique: Making brains clear – bringing clarity to fluorescence imaging and CLARITY!

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Screen Shot 2013-04-11 at 12.32.23 AM

Image from Chung et al, 2013 – Nature

by Michael Mohammadi

Clear Lipid-echanged Acrylamide-hybridized (Anatomically) Rigid Imaging/Immunostaining/In situ hybridization-compatible Tissue-hYdrogel.

Or just CLARITY.  Whatever you call it, this newly published research technique from Karl Deisseroth and colleagues at Stanford University will allow scientists to image far deeper into fixed tissue than ever before.  The images are absolutely stunning.  A youtube video (below) of the data resulting from the first publicatoin on CLARITY went viral on the internet last week and a feature article appeared in the NY Times as well as a number of science sites and blogs.   The majority of these give a brief overview of CLARITY and the implications of the work.  Here I will focus on how scientists make things look colorful, why we do it, and what CLARITY has done to make some really cool and exciting pictures.  I hope to make scientific imaging as well as CLARITY approachable to the non-scientist. Read the rest of this entry »

C. Elegans, one of the most important organisms in science, “do the Harlem shake!”

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{{Description=en:category:Caenorhabditis elegans |Source=Originally from [http://en.wikipedia.org en.wikipedia]; description page is/was [http://en.wikipedia.org/w/index.php?title=Image%3AAdult_worm.jpg here]. (Original text : ''Don

Information| |Description = An adult hermaphrodite C. elegans worm |Author = Zeynep F. Altun, http://www.wormatlas.org

by Michael Mohammadi

I tend to not get caught up in viral video fads and am generally one of the last people I know to hear about them (case in point- my boss told me about Gangnam style in late November at a pub in Ireland).  That said, I’ll be the first to admit I tend to find them highly entertaining.  Such was the case the first video I saw of the Harlem shake– I spent an hour watching the many different renditions.  I still don’t know why I find them so hilarious, I guess I’m just easily amused.

A friend posted this today on Facebook- it’s of C. Elegans doing the Harlem shake.  How is a dish of worms dancing to a viral video relevant to a science blog?  Well, I guess it’s not that relevant…but let me try. Read the rest of this entry »

Written by Michael Mohammadi

April 13, 2013 at 22:01

Science in press: A look at two recent papers- Optogenetics to control GPCRs and optogenetics in monkeys!

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English: Based on PDB 1hzx and the Heller/Schaefer/Schulten lipid bilayer coordinates.

English: Based on PDB 1hzx and the Heller/Schaefer/Schulten lipid bilayer coordinates.

by Michael Mohammadi

Being free from the “chains” of academia I have been able to expand my scientific interests well beyond NMDA receptor signaling and short term memory.  I do miss actually producing research from time to time, but I now average 6 papers read in a week which is about double (or more) what I read in grad school so I’m still feel like I’m part of the process.  I do have the luxury of spending a lot of time in planes and on trains, both excellent venues for diving into a paper with few distractions (Bose noise canceling headphones are essential!).  I have found that it is liberating to be able to read articles from all different fields of science and not be limited to a very specific field or research question.  Exploring new research in neuroscience, physiology, physics, optics, imaging and more has really rejuvenated my spirit for science and discovery, a spirit that had faded over the long duration of wrapping up my dissertation.  Now that this curiosity and excitement is back and fully charged, I hope to share some of the cool papers I’m reading with you.  It is my goal with this “Science in press” series that I review a few papers that I have read in the last few weeks that really stood out.  These may be a bit more technical than my other articles, but I hope to keep it accessible to the mainstream reader.  As always, questions are encouraged.

For this first installment I tried to cover 5 papers I read recently, but I ended up a bit too excited and went into a lot of detail on paper one.  I’ll try to be more concise in the future if it’s more interesting to get into the details let me know, I would enjoy writing either way!  So I ended up giving overviews of two recent papers in Nature Neuroscience.

I welcome criticisms and feedback, suggestions on papers to read, as well as corrections to my interpretations or explanations of the experimental design, results or conclusions.  I accept I may get things wrong and hope to learn from my readers.  Without further ado…

1.  Optical control of metabotropic glutamate receptors. Levitz et al, 2013 Nature Neuroscience

I’ll start with a recent paper that employs optogenetics for something other than direct gating of ion channels!  Dr. Ehud Isacoff’s group at UC Berkely has been doing some amazing work in the field of molecular engineering with optical probes (among other things).  Previous work included a very cool probe called HyLighter (of which some data was acquired with the Mosaic) that is a light-activated glutamate channel that selectively gates K+.  In this most recent paper, Levitz et al describe a metabotropic glutamate receptor (mGluR) which is a specific type of G-Protein Coupled Receptor (GPCR; the most abundant receptor type in the body) that they have engineered to respond to specific wavelengths of light which results in a variety of downstream G-protein regulated outputs. Read the rest of this entry »