The 5 Stages of Failed Cloning Grief (and how to get back on track!)

Cloning is a fickle process that can make even the most seasoned bench scientists scream in frustration. By the time you perform a colony PCR and run the gel to check for your insert, you’ve invested several days in preparing these transformed cells. But then, the unthinkable happens. When you image your gel…the target band is missing.

This can trigger what’s known as “The 5 Stages of Failed Cloning Grief.” As you work through each stage at your own pace, just know that scientists all over the world feel your pain and can empathize with you in this difficult time. Continue reading

A Crash Course in Fighting Lab Contamination

When I first started in my undergraduate lab, one of the first things I learned was how to prepare agar plates for growing yeast. My supervisor, a grad student, looked over my shoulder as I added the yeast extract, bacto peptone, and other ingredients. I sealed the pitcher tightly with aluminum foil and autoclaved it until sterile. When I was ready to pour the plates, I carried the pitcher to the “plate-pouring” room, ripped the foil off, and started to pour an even layer of agar into each of the plastic dishes, leaving the lids off so they could cool. After I’d poured a dozen or so, my grad student supervisor burst into the room.

“What are you doing?” she demanded.

“I’m pouring plates,” I stammered back.

She took a deep breath and explained. By fully uncovering the pitcher and leaving my plates uncovered, I had left my precious media at high risk for contamination. The open containers were far too inviting for potential contaminants floating through the air. In the end, we ended up throwing away several of the plates that had been exposed the longest.

Now, I don’t share this story to demonstrate how clueless when I first started in the research lab as an undergrad. We all have those “uh-oh” moments when we realize for the first time that something that seemed so obvious was, in fact, more complicated than we’d expected. However, that day I learned how easily I could sabotage my own work by unwittingly inviting contaminants into my experiments.

Whether you work with yeast, bacteria, mammalian cells or anything else in a molecular biology lab, preventing contamination is crucial to getting desired results. Fortunately, minimizing your risk can be incredibly easy.

Let’s start with your lab bench. Everyone has their own organization system, but if yours is “out-of-control chaos,” you might want to reevaluate. Benchtop clutter makes it difficult to thoroughly clean the bench as often as needed. All those bottles of solutions, empty tip boxes, and wrinkled protocol sheets harbor dust and other unwelcome particles that you want to keep away from your cultures and reactions.

Once your benchtop is tidy (or at least somewhat tidy), make sure you keep the surface as clean as possible. Immediately clean up any spills or drips that happen while you’re working. Wiping your workspace with a 10% bleach solution will sterilize it, and following that up with 70% ethanol will dry it quickly. This wash should be performed at least once a day. Ideally you should also regularly remove everything from your workspace and perform a deeper cleaning of your benchtop, as well as any shelves and containers in your area.

Now that your bench is in good shape, it’s time to gear up . You should always follow standard safety procedures (lab coat and goggles, closed-toe shoes, hair tied back), but above all, make sure you never forget your gloves. Gloves protect you from harmful chemicals, but they also protect your experiments from anything that could be on your hands. Skin can carry reagents, bacteria, and enzymes that are good for your body but bad for your experiments. Change your gloves regularly to prevent potential carryover of reagents or samples between containers. A good rule is, “When in doubt, change your gloves.”

Finally, to guard against airborne contaminants, do your best to keep everything covered when you aren’t immdiately using it. I learned this rule the hard way when several of my yeast plates developed fuzzy patches of mold several days after I poured them. Bacteria and other undesirables floating through the air can affect stock solutions, cultures, plates, tubes, and basically anything else you rely on. Keep your lids on and cover open containers to minimize air exposure to reduce the chances of nefarious particles finding their way in.

There’s no way to guarantee you’ll never experience some form of contamination in your lab, but smart practices can help reduce your risk. Develop an anti-contamination routine that meets your needs and make sure you stick to it every day in the lab.

Working with RNA doesn’t have to be a nightmare

We’re all familiar with the Central Dogma of Molecular Biology: DNA is transcribed into RNA, which is translated into proteins. It’s drilled into our heads from the early days of biology classes, and it’s surprisingly useful when we start exploring in our own research projects. For example, if you’re interested in gene expression, you’ll most likely be working with RNA, specifically mRNA. Messenger RNA (mRNA) is transcribed from DNA and is used by ribosomes as a “template” for a specific protein. The total mRNA in a cell represents all of the genes that are actively being transcribed. So, if you want to know whether or not a gene is being transcribed, RNA purification is a great place to start.

When preparing your RNA samples for a downstream assay, there are several roadblocks and pitfalls that could give you quite a headache. Let’s tackle two of the most common.

Continue reading

Hello PhD + Promega: Partnering to Support Young Scientists

Hello PhD LogoThink back to your grad school days. Think about a time when you were struggling with challenges either inside or outside the lab. Maybe you dealt with failed experiments, a toxic lab culture or mental health problems. For graduate students, these have been real, everyday experiences for as long as anyone can remember. The Hello PhD podcast, hosted by Joshua Hall and Daniel Arneman, aims to address those problems. We’re excited to announce that beginning with Episode 94 (released June 11, 2018), we are now partnering with Hello PhD to promote their mission to support young scientists in training.

Hello PhD will be celebrating its third anniversary in July 2018, and in the past three years they’ve covered topics from grad school admissions to choosing a career path, and everything in between. They’ve interviewed post-docs, science communicators and students with interesting experiences to share. Their most popular episode ever, “When Research Sucks,” discusses what to do when research starts to drag you down. After 94 episodes, they still haven’t lost sight of their mission to make the grad school experience better for both current and future students. Continue reading

When School is just a Memory: Science after Graduation

Happy graduation! Whether you graduated last week or twenty years ago, the experience is roughly the same. As soon as you arrive on the far side of the stage, empty diploma folder under your arm, hand still sticky from the Dean’s sweaty handshake, the reality of post-academic life sets in. Perhaps grad school is on the horizon for some and others might be busy prepping for med school. For some of us, though, our years of formal education end after four and we run off to rejoice in our newfound freedom. No more exams, group projects, late nights writing papers, disapproving professors, supervisors and mentors – done with that life forever! We didn’t even bother with the GRE, MCAT, LSAT or a single “Why [insert school]” essay. Now it’s off to enjoy the Real World, which will definitely be better than college.

I’ve found, in my one year of post-college life, that sometimes you can miss academic life. You’ll occasionally look back and think, “I didn’t know how good I had it.” In particular, those of us with a pure love of learning can find ourselves unsatisfied with our prospective learning opportunities or lack thereof. We spent college soaking up mountains of knowledge–and not just from textbooks. University life gives you access to free talks from eminent thought leaders, unrestricted access to myriad scientific journals, and plenty of people around who are eager to argue about that day’s lecture in Cell Biology or Neuroscience. After college, it’s tough to fill that void.

I work at Promega (obviously), a biotech company, so I still have access to journals and there are plenty of brilliant scientists around me. However, I’m still looking for more opportunities to learn and grow. I may be out of school, but the love of science never goes away. Here are a few of my tips for everyone receiving their hard-earned science degree this spring.

Continue reading

From Antarctica to Mars: Growing Food in Extreme Conditions

Even those of us with the greenest thumbs are baffled by the idea of growing food in Antarctica. From my tiny desk plant to my neighbor’s cabbage patch, plants generally have the same requirements: soil, sun and water. At the southern end of the planet, however, those are all scarce commodities. Nonetheless, on April 5, 2018, the team managing the EDEN-ISS greenhouse at Neumayer III announced that they had harvested 8 pounds of salad greens, 18 cucumbers and 70 radishes. This project has implications beyond just Antarctica, from moderate climates on Earth to future Mars missions. Continue reading

The Intersection of Poetry and Science

March 21, 2018 is World Poetry Day, we’re getting into the spirit with some scientific poetry. Science and poetry overlap more than many diehards in either camp would like to admit. History is filled with poets who dabbled in science, as well as scientists who dabbled in poetry. In honor of World Poetry Day, I’ve pulled out some of my favorites. Continue reading

The Free Scientific Resource: Evaluating the Accuracy of Wikipedia

Several weeks ago, I came across an article on ScienceNews.org about how Wikipedia is becoming a scientific resource, whether we like it or not. Scientists are reading Wikipedia, the article said, and it’s affecting how they write. The article cited a study by researchers from MIT and Pitt that found statistical evidence of language in peer-reviewed articles being influenced by Wikipedia articles relevant to the topic. They concluded that journal articles referenced in Wikipedia are subsequently cited more than other similar articles, and that on a semantic level, Wikipedia is influencing the language of scientific journal articles at an astounding rate.

I was intrigued by the idea that reading Wikipedia affects how we later write about a subject. When I start writing about a new topic, the first thing I do is head to Wikipedia to gather a basic understanding before I dive into journal articles. I’ll skim through the overview and most relevant subsections, then check out the references to see what I should continue reading. However, the findings of the study imply that even though I don’t directly use information or language from Wikipedia in my work, it’s still subtly influencing how I write. Continue reading

The Making of a Vaccine: Preparation for Flu Season

At the time that I’m writing this, I still haven’t succumbed to the “yuck” that’s been knocking out my co-workers one-by-one since November. Those of us who are still healthy were discussing how we fortify our immune systems in preparation for the flu season. All of the suggestions were pretty typical—orange juice, Vitamin C supplements, and of course, the the annual flu shot.

For all of the agencies responsible for the production of the seasonal influenza vaccine, preparation for flu season begins long before the rest of us are stocking up on Emergen-C. Continue reading

Promega Partnering with UC-Davis Drought-Resistant Rice Project

The Foundation for Food and Agriculture Research (FFAR) announced on November 30 that they are awarding $1M to a project based at the University of California, Davis, to study protein kinases of rice plants. The team is led by Dr. Pamela Ronald, a leading expert in plant genetics who has engineered disease- and flood-resistant rice. This project aims to address the growing agricultural problem of water scarcity by gaining a better understanding of the role kinases play in enabling drought-resistance. Promega will be supporting this research by providing NanoBRET™ products to help characterize kinase inhibitors.

Principal Investigator Pamela Ronald, Ph.D. Photo Credit: Deanne Fitzmaurice

The research team will begin by screening over 1,000 human kinase inhibitors to determine which ones do interact with the plant kinome and, if applicable, which kinase(s) they inhibit. Once the compound library has been established, the team will assess the inhibitors’ phenotypic effects on rice to identify kinases that, when inhibited, positively impact root growth and development. The long-term goal is to use these findings to engineer drought-resistant rice.

Continue reading