The Lab Notebook

Bindi M. Doshi, PhD

Recent Posts

4 Cool Science Discoveries in 2016

Posted by Bindi M. Doshi, PhD on Dec 29, 2016 2:38:31 PM

As 2016 draws to a close, let’s look back on some significant advances made in science.

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Why Autophagy research won a Nobel Prize

Posted by Bindi M. Doshi, PhD on Nov 16, 2016 9:01:39 AM

The process of autophagy was first recognized in the late 1950s and it was thought of as bulk “junk” removal. Then, dedicated scientists did a little more digging and found there is an amazing methodology to the “junk” removal.  It was discovered that there is rhyme and reason for how a cell decides if and when its components should undergo degradation.  Autophagy is rather specific and aids in cell survival by making sure the cell has essential components during times of flux.  Autophagy can be selective (i.e. mitophagy) or non-selective (i.e. starvation-induced).  Using this method, the cell can have non-essential components recycled or send them to onto autophagolysosomes to be degraded.  It is more efficient for a cell to be able to recycle as much as it can, rather than to wait for new proteins to come into the picture.  Autophagy is also crucial for clearing out “junk” such as misfolded or aggregated proteins. Research in autophagy has helped provide a better understanding for how a cell is able to survive even under poor conditions.

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Topics: Autophagy

What does mitochondria have to do with mitophagy?

Posted by Bindi M. Doshi, PhD on Sep 20, 2016 11:42:36 AM

 What is mitophagy? It is when damaged mitochondria are removed from the cell by autophagy.  The damaged mitochondria end up in lysosomes for their final disposal.  This whole process is to maintain and assure proper cellular function.   The importance of this biological process is that it has been implicated in disease states such as cancer and Parkinson’s disease.

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Topics: mitophagy, Autophagy, mitochondria cell death, keima red

How to find and read a publication

Posted by Bindi M. Doshi, PhD on Jun 29, 2016 11:05:05 AM

When you start working in a new lab or working on a new research project, one of the first things to do is look up publications and learn about the field and what has been accomplished. This will help determine the experiments you will run.  It gives you a foundation to build on.  But how do you read a publication?  How do you know it’s worth your while to muster through?  Some publications are miles long with a million figures!  EEKS!  Don’t be frightened.  Keep reading to find out how to tackle a complicated publication and not go crazy.

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Who’s that on my mRNA?

Posted by Bindi M. Doshi, PhD on May 17, 2016 2:44:01 PM

You have an RNA of interest aka your favorite RNA. The question is: which RBPs interact with it? Who are these RBPs and what are their intentions with your precious RNA?

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Topics: RNA, Epigenetics, Gene Regulation, RiboTrap, RBP

Don’t rip your hair out- use our RIP certified antibodies!

Posted by Bindi M. Doshi, PhD on May 2, 2016 7:47:32 AM
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What are RBPs (RNA binding proteins)? Very briefly, they are proteins that bind to RNA. (You probably figured that out already.) More importantly, they have a role in regulating RNA as part of the ribonucleoprotein complex (RNP). They are involved in interactions that regulate posttranscriptional  gene regulation1. Not only are RBPs important because of their interactions, but also because it was found that mutations in RBPs can lead to disease formation 2, 3, 4. In order to investigate which RBPs bind with RNAs, a technique called RNP immunoprecipitation (RIP) can be used5.  And in order to have an amazing RIP experiment, one needs an equally amazing antibody.
 
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Topics: RIP Chip, RNA, Epigenetics, Gene Regulation

Don't FRET- You've got Fluoppi!

Posted by Bindi M. Doshi, PhD on Sep 29, 2015 8:41:14 AM
Visualizing protein-protein interaction (PPI) is pretty neat. You are able to glimpse into a really unique aspect of nature that many people don’t get to see. It’s like watching lions and zebras interact but without the bloody violence.  However, anyone who has tried to visualize two proteins interacting can attest to how difficult it can be. It can involve long hours, uncertainty, and of course, photo bleaching. Blech! MBL’s new technology, Fluoppi, makes visualizing protein-protein interaction a little easier. This technology utilizes fluorescent tags that have a high signal:noise ratio. The only equipment you need is a microscope to observe fluorescence.
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Topics: Fluoppi, Fluorescent Proteins

Colorimetric?  Fluorometric?  How to choose the right platform for your ELISA

Posted by Bindi M. Doshi, PhD on Sep 21, 2015 11:41:52 AM

What happens when you use a black well plate for a fluorometric ELISA assay reading?  What happens when you use a clear well plate for a colorimetric ELISA assay reading?  Well the short answer is that you made the right plate decision!

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Topics: Kits and Assays

Autophagy Watch...What the Flux is that all about?

Posted by Bindi M. Doshi, PhD on Jul 21, 2015 1:49:00 PM

What does Autophagy Flux even mean?  It’s not in the Urban dictionary.  Dear reader, you have come to the right place to learn a little more about autophagy flux and how our Autophagy Watch kit can help you.

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Topics: Autophagy

Why Smart-IP is the smart way to IP

Posted by Bindi M. Doshi, PhD on May 28, 2015 10:49:05 AM

You have been given the mission to start a new project. A tiny tube is put in your hands and you’re told it contains a potentially interesting protein and your job is to characterize it. After you wipe nervous sweat from your brow, you get down to business. Step one- how to isolate your new buddy? Immunoprecipitation can help with this question! You determine which epitope tag is on your protein and go to mblintl.com to see what you can buy to help this new adventure. You see there are antibodies conjugated to magnetic beads, which help protein pull downs from cell lysates. It's easy, it's fast.  Hmmmm- promising.

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Topics: Epitope Tag

The ABC's of LC3

Posted by Bindi M. Doshi, PhD on Apr 14, 2015 12:22:39 PM

What are LC3 isoforms all about? What do they do?  How are they different?  How are they involved in autophagy?

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Topics: Autophagy

Investigating Parkinson's Disease Part III: The Role of PARK7/DJ-1

Posted by Bindi M. Doshi, PhD on Mar 17, 2015 7:00:00 AM
In the biomedical field, DJ-1 is a target of interest in a variety of disease states.  DJ-1 is considered a contender for a biomarker in the detection of early stage cerebral infraction since it’s concentration increases 3 hours after cerebral injury. When DJ-1 is expressed in excess, it can lead to cancer. For instance, breast cancer patients show increased levels of circulating DJ-1 and anti-DJ-1 antibodies. 3  However, a loss of function can lead to neuodegenerative diseases such autosomal early-onset Parkinson’s disease. 2  
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Topics: Neuroscience

Investigating Parkinson's Disease Part II: The Role of PARK5/UCHL1

Posted by Bindi M. Doshi, PhD on Mar 16, 2015 5:03:04 PM
PARK genes are associated with Parkinson's Disease. The cause of Parkinson's Disease is not currently known and the progression of the disease (on a molecular level) is not well established.  Human UCHL1 ELISA Kit  and Mouse UCHL1 ELISA Kit  has the ability to specifically detect UCHL1.
 
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Topics: Neuroscience

Why bother knowing if you are detecting Pro-IL18 or active IL-18?

Posted by Bindi M. Doshi, PhD on Mar 2, 2015 9:48:00 AM

il-18-01Antibodies are wonderful.  They can act as little detectives to help you determine if the protein you’re interested in is involved in a certain process or help characterize the function.  But what if your favorite protein has two forms?  Is your antibody sophisticated enough to be able to detect one form over the other?  Does this knowledge help you?  How?  IL-18 is one such protein that has two forms.  It is present when it is inactive and present when it is active.  So what is known about IL-18 and its function and the two forms it can exist in?

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Topics: Immunology, IL-18, Immune Response, Allergy