The Disadvantage of Long-Distance Relationships

Despite advanced communication technologies that enable distance collaboration, working side-by-side can generate true synergy – an extra bounce that carries a project beyond the initial design, says Dr. Mei Zhen, Senior Investigator at Lunenfeld-Tanenbaum Research Institute.

Dr. Zhen returned in early August from working with her collaborators at Harvard University on their comprehensive neuronal map of the juvenile C. elegans, the pin-head sized nematode worm. “When we started working face-to-face, we realized that we had underappreciated both capacity and challenges on each side. The project turns out to be much harder than we had envisioned. By working together on-site we not only solved existing problems, but – also unexpectedly – took the project design to the next level,” she says. She extended her stay at Harvard from nine months to almost a year.

Her collaborator Dr. Aravi Samuel adds, “There’s a reason that no one has tried to reconstruct whole worms at electron-microscope resolution in almost 30 years: It’s the Mount Everest of structural neurobiology. Only with worms can we dream of using large numbers of connectomes of worms that have key differences, whether caused by development, genetics, or even learning, to uncover how circuits encode behavior.”

Read more…

August 27, 2014 at 2:18 pm Leave a comment

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

August 26, 2014 at 7:12 am Leave a comment

Skip RNA Purification and Still Receive Awesome RT-qPCR Results

Bio-Rad Laboratories announced the launch of new rapid cell lysis kits that allow researchers to obtain reverse transcription quantitative PCR (RT-qPCR) data directly from cultured cells without the need for a separate RNA purification step. Bio-Rad’s SingleShot™ family of cell lysis RT-qPCR kits provide high-quality gene expression results in less than two hours.

Available column isolation methods for purifying RNA are time-consuming and laborious while other methods that enable RT-qPCR directly from cell lysates can damage the RNA and result in poor genomic DNA clearance. However, Bio-Rad’s SingleShot Kits eliminate those challenges and offer superior reproducibility and accuracy of gene expression results. In addition, minimal setup and pipetting steps create an automation-friendly workflow and, unlike other similar methods, Bio-Rad’s kits do not require an additional pipetting step to stop the cell lysis reaction.

 

The SingleShot Kit removed genomic DNA (Cq > 40) while another available kit resulted in poor genomic DNA clearance.

The SingleShot Kit removed genomic DNA (Cq > 40) while another available kit resulted in poor genomic DNA clearance.

 

“The SingleShot Kits are ideally suited for high-throughput laboratories with large-volume workloads and for researchers who are faced with a limited number of cells and require extreme accuracy in each analysis,” said Paul Streng, senior product manager in the Gene Expression Division of Bio-Rad’s Life Science Group.

Bio-Rad’s SingleShot Kits are the only available kits that include an RNA control template and qPCR assay to help researchers determine optimal cell number and lysate inputs for their RT-qPCR reactions.

SingleShot Kits are validated for use with a wide variety of adherent and suspension cell lines and are offered in multiple formats, including one-step RT-qPCR and two-step RT-qPCR kits that are compatible with either SYBR® Green or probe-based assays. SingleShot Kits are available as a stand-alone cell lysis kit. All SingleShot Kits are validated for use with PrimePCR™ Assays and Panels.

August 20, 2014 at 2:40 pm Leave a comment

Animations Help Scientists Test Hypothesis

August 19, 2014 at 4:35 pm Leave a comment

Could Probiotics Be the Next Big Thing in Parenting?

New University of British Columbia research found that receiving antibiotic treatments early in life can increase susceptibility to specific diseases later on.

Most bacteria living in the gut play a positive role in promoting a healthy immune system, but antibiotic treatments often do not discriminate between good and bad bacteria. The study published today in Journal of Allergy and Clinical Immunology helps scientists understand how different antibiotics affect good bacteria.
“This is the first step to understanding which bacteria are absolutely necessary to develop a healthy immune system later in life,” says Kelly McNagny, a professor in the Dept. of Medical Genetics who led the research along with UBC microbiologist Brett Finlay.

The researchers tested the impact of two antibiotics, vancomycin and streptomycin, on newborn mice. They found that streptomycin increased susceptibility to a disease known as hypersensitivity pneumonitis later in life, but vancomycin had no effect. The difference in each antibiotic’s long-term effects can be attributed to how they changed the bacterial ecosystem in the gut. Hypersensitivity pneumonitis is an allergic disease found in people with occupations such as farming, sausage-making, and cleaning hot tubs.

The researchers stress that infants should be treated with antibiotics when needed, but they hope these results will help pinpoint which bacteria make us less susceptible to disease. This could open up the possibility of boosting helpful bacteria through the use of probiotics.

“Probiotics could be the next big trend in parenting because once you know which bacteria prevent disease, you can make sure that children get inoculated with those bacteria,” says McNagny.

Thanks to the University of British Columbia for contributing this story.

August 18, 2014 at 2:21 pm Leave a comment

What Does the Plant Say?

August 13, 2014 at 3:52 pm Leave a comment

Do YOU Know What Daily Lab Life is Really Like?

The Canadian Foundation for Innovation (CFI) recently posted an article (adapted from a publication at the University of Toronto), entitled “A Day in the Life of a Lab.” The article touched upon six points that, according to the author, “you” don’t know about life in the lab. Without copy-pasting the article, (you should read it for yourself), here are the 6 points in brief:

  1. Students make up the bulk of the laboratory workforce
  2. Running the lab is like running a small business
  3. Lab research is a form of teaching
  4. It’s not about a breakthrough
  5. There is no rest…cell culture doesn’t take a vacation
  6. It’s fun…lab members get together every evening to discuss science

OK. Where shall we begin? While I agree with the majority of what is written in the article, there are a couple of points that I take issue with. Let’s start with the points of agreement and move on from there.

I give the article credit for recognizing the role of students in scientific research and scientific progress. Without graduate students, NOTHING in the lab would get done! Students are the heart and soul of the lab and so it is refreshing to hear someone give them the acknowledgement that they deserve.

Point number one fits very well with point number three. It is due to the fact that students make up the bulk of the lab workforce that has enabled lab research to become a form of teaching. Where there are students, there must be teachers. And who are the teachers? None other than the students themselves! While the PI is there to give overall guidance and direction, she is largely relegated to fundraising (i.e. grant writing), networking and publishing papers. The real education happens at the hands of other students. Post-docs teach grad students and second year students teach the newbies. It is a refreshing system of paying it forward.

I also applaud point number 4. Despite what has been portrayed in pop culture, working at the bench is not about coming up with a scientific breakthrough or earning the next Nobel Prize (although that would be nice). Bench work is about slogging it out day after day, making small changes to experimental conditions in order to come up with something that will hopefully be a small piece in the larger scientific puzzle. Although it is often hard to see the forest for the trees, without these every day baby steps, the bigger picture would never appear. There is no glory in daily bench work. It is tough. That is why point number 5 is so hard to swallow.

In point number five, the author correctly points out that there is no rest for the bench scientist. Whether you are working with animals that need to be fed daily, or performing crazy dose response curves, you need to make sure that someone is always there to keep things running smoothly. Lab work is not even close to your neighbor’s desk job. Your vacation schedule revolves around your samples and your experiments. If your cells need to be passaged at 90% confluence, you better be around to do the passaging or your entire experiment may go down the drain.

Until now, I have discussed the points that I agree with in the article. Now for the other side.

Since the CFI is the largest scientific research funding organization in Canada, I would imagine that the majority of its visitors are indeed scientists. If that is the case, then I doubt that the “you” the author is referring to is indeed in the dark about life in the lab. After all, who would know more about life in the lab than those of us who have dedicated our lives to laboratory research?

In point number two, the author states that “running the lab is like running a small business.” While on the surface that may seem logical, (after all a PI has to worry about expenses such as equipment, consumables and staffing), businesses and scientific research are on the opposite ends of the funding spectrum. While businesses consume products in order to grow their bank accounts, scientists consume their grant funding in order to produce scientific output. In other words, businesses are about making money while science is about spending money (albeit in order to produce results).

With regards to the final point in the article, lab members do indeed have fun after work, however, portraying scientists as having a one-track mind, (science, science, science), feeds into the negative stereotype that all scientists are boring nerds. Scientists come from many different backgrounds and have a myriad of interests…just like the general population. I believe that it is up to us, the scientific community, to get the word out there that scientists are people too!

That’s all for now. What do you have to say?

August 12, 2014 at 2:56 pm Leave a comment

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