A Science Driven Life

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

Archive for the ‘Science Techniques’ Category

What is the current technical limitation in your scientific field?

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Lavoisier conducting an experiment related combustion generated by amplified sun light.As a neuroscientist working for a technology company I spend a lot of time seeing new applications. These can range from new imaging probes, to new optogenetics tools or transgenic animals, all the way to new camera sensor technologies or super resolution algorithms. I spend a lot of time in labs seeing some really cool research, long before it’s published or presented at a conference. This is an aspect of my job I really love- getting to see where the fields of advanced imaging, electrophysiology, optophysiology, optogenetics, and neuroscience are headed.

The researchers we work with are constantly pushing the barriers of the latest and greatest in technology to better address increasingly complex questions in biology (side note: we also work with astronomers, physical science and chemistry, but I’m heavily focused on biological applications).

My question to my research friends and readers is simply this: what is the current technical limitation(s) in your field and if you could have one single new tool (either a new technology, new probe, new animal model, behavioral test, etc) what would you want?

I’m hoping to get a range of responses to open this up for a bigger question in how can we (academia and industry) work together to form open partnerships that are focused on advancing science. A lot of research money is wasted on overpriced, outdated, and often times the wrong technology for the research question at hand (I blame the sales rep as well as the researcher who doesn’t spend the time to educate her/himself) and an open discussion on how to save researchers time and (all of us taxpayers) money is long overdue.


Written by Michael Mohammadi

April 5, 2014 at 08:42

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 Techniques: What is optogenetics and why is it so trendy?

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by Michael Mohammadi

Screen Shot 2013-03-25 at 8.25.20 AM

Fun with an argon-ion and he-ne laser. |Source=[http://www.flickr.com/photos/28042570@N08/2648853050/ Beams in Fog + Car Windshield] * Uploaded by PDTillman

Pour a nice hot cup of your morning coffee and grab a recent issue of Nature, or Science, or Neuron and scan the table of contents.  I’ll bet you your next cup of Joe that at least one article in that issue (if not more) have some sort of optogenetic approach to address complicated questions in neuroscience and cell signaling.  “Optogenetics” is a very trendy term in science these days and for good reason.  It has been described as a way for researchers to take over your brain, provide bionic vision, possibly treat epilepsy, and for the founding researchers in the field, a way to cash in on big financial prizes.  With all the excitement, there is still some misunderstanding about how the technique works and exactly why it’s relevant.  I hope to answer both of these questions here without getting overly technical.

“Optogenetics” refers to a relatively new field that combines molecular biology with light stimulation to allow researchers (and someday clinicians) to have precise control over the behavior of a cell, populations of cells, or even a whole animal.

In this video we see a mouse that becomes hyperactive 
when blue light activates Channelrhodopsin-2 in its brain:  

Optogenetics: The basics

Read the rest of this entry »

Written by Michael Mohammadi

March 25, 2013 at 09:00