Droplet Digital™ PCR Tips & Tricks: ddPCR™ Assay Design

 :: Posted by American Biotechnologist on 09-16-2014

Admitting My Darkest Secret

 :: Posted by American Biotechnologist on 09-15-2014

OK…this might sound a little childish, but I bet that many of you have felt the same way at one time or another. Sometimes, when I’m alone in the lab, I pretend that my pipette is a weapon and I wield my pipette like John Wayne at the OK Corral. Am I alone? I think not!

Stressed Out Cells Shut Off Protein Production

 :: Posted by American Biotechnologist on 09-12-2014

Living cells are like miniature factories, responsible for the production of more than 25,000 different proteins with very specific 3-D shapes. And just as an overwhelmed assembly line can begin making mistakes, a stressed cell can end up producing misshapen proteins that are unfolded or misfolded.

Now Duke University researchers in North Carolina and Singapore have shown that the cell recognizes the buildup of these misfolded proteins and responds by reshuffling its workload, much like a stressed out employee might temporarily move papers from an overflowing inbox into a junk drawer.

The study, which appears Sept. 11, 2014 in Cell, could lend insight into diseases that result from misfolded proteins piling up, such as Alzheimer’s disease, ALS, Huntington’s disease, Parkinson’s disease, and type 2 diabetes.

“We have identified an entirely new mechanism for how the cell responds to stress,” said Christopher V. Nicchitta, Ph.D., a professor of cell biology at Duke University School of Medicine. “Essentially, the cell remodels the organization of its protein production machinery in order to compartmentalize the tasks at hand.”

The general architecture and workflow of these cellular factories has been understood for decades. First, DNA’s master blueprint, which is locked tightly in the nucleus of each cell, is transcribed into messenger RNA or mRNA. Then this working copy travels to the ribosomes standing on the surface of a larger accordion-shaped structure called the endoplasmic reticulum (ER). The ribosomes on the ER are tiny assembly lines that translate the mRNAs into proteins.

When a cell gets stressed, either by overheating or starvation, its proteins no longer fold properly. These unfolded proteins can set off an alarm — called the unfolded protein response or UPR – to slow down the assembly line and clean up the improperly folded products. Nicchitta wondered if the stress response might also employ other tactics to deal with the problem.

In this study, Nicchitta and his colleagues treated tissue culture cells with a stress-inducing agent called thapsigargin. They then separated the cells into two groups — those containing mRNAs associated with ribosomes on the endoplasmic reticulum, and those containing mRNAs associated with free-floating ribosomes in the neighboring fluid-filled space known as the cytosol.

The researchers found that when the cells were stressed, they quickly moved mRNAs from the endoplasmic reticulum to the cytosol. Once the stress was resolved, the mRNAs went back to their spots on the production floor of the endoplasmic reticulum.

“You can slow down protein production, but sometimes slowing down the workflow is not enough,” Nicchitta said. “You can activate genes to help chew up the misfolded proteins, but sometimes they are accumulating too quickly. Here we have discovered a mechanism that does one better — it effectively puts everything on hold. Once things get back to normal, the mRNAs are released from the holding pattern.”

Interestingly, the researchers found that shuttling ribosomes between the ER and the cytoplasm during stress only affected the subset of mRNAs that would give rise to secreted proteins like hormones or membrane proteins like growth factor receptors — the types of proteins that set off the stress response if they’re misfolded. They aren’t sure yet what this means.

Nicchitta is currently searching for the factors that ultimately determine which mechanisms cells employ during the stress response. He has already pinpointed one promising candidate, and is looking to see how cells respond to stress when that factor is manipulated.

Thanks to Duke University for contributing this story.

More Deadly Biohazards Found at the NIH!

 :: Posted by American Biotechnologist on 09-10-2014

So what can you get while working at the NIH? In the past we told you about your risk of exposure to Anthrax, Smallpox, and the Avian Flu Virus. Well, now you can add ricin and Burkholderia pseudomallei, two well-recognized biological weapons, to your shopping list!

The Washington Post is reporting that during a beefed up safety inspection, NIH employees unexpectedly found these and several other deadly biological agents improperly stored among old and long-forgotten stockpiles, some dating back over 60 years.

I must admit that, unfortunately, I have found the news much less shocking this time around than in the past. In fact, I believe that I have now gone through several of the classical stages of grief:

  • Denial (it can’t be that the most respected scientific agency in the United States would irresponsibly allow the dangerous transfer of Anthrax to a low level bio-hazard lab)
  • Anger (what the heck is wrong with the scientist that left Smallpox at the back of the freezer?
  • Depression (we are all going to die from the Avian Flu virus)
  • Acceptance (ricin, staphylococcal enterotoxin, Melioidosis…these are just some of the things you should expect to find at an unsecured government research facility)

There really isn’t much more to say. I applaud the fact that the NIH are trying to introduce measure to more strictly control these substances, but I am not sure that the system will ever be 100% foolproof. There are probably tens, if not hundreds, of dangerous materials floating around labs all over the US, (not to mention the rest of the world). Is this a reason to be scared? I think so. What about you?

Why We Should Trust Scientists

 :: Posted by American Biotechnologist on 09-09-2014