One of my favorite parts of doing our research involves "dissecting" bags of 4 cells on Petri dishes. They each started as a single diploid cell, underwent a form of cell division called meiosis (the same process that makes sperm and egg cells), resulting in 4 haploid cells. We use a microscope with a teeny needle controlled by a joystick to move individual cells to specific spots on a Petri dish so we can follow them individually. The different cells have different combinations of gene flavors, so we can then choose exactly which ones we need for our later experiments. It took a while to learn how to do it correctly and quickly! Once I did, I started enjoying the process.
The yeast we study have a mutation that makes them build up a red pigment. But let them grow a little extra and sometimes they'll end up changing color in parts of the colony! Mutations can build up really quickly, particularly if they're adaptive. Every time I see this happen on my Petri dishes, I'm amazed both at nature and at the people who still don't believe in evolution. Certainly, this is the micro-est of microevolution, but it happens in just a few weeks, under tightly controlled lab conditions. Seeing it on the small scale helps me relate a bit better to large-scale evolution, which is hard to conceptualize.
Life as a cell require mad resources! Living near others who are rapidly expanding can be detrimental to your own well-being (as true of yeast as it is of humans). To help the cells on my plate grow, I cut out the middle and stuck them back in their warm home to keep growing. By the next day, the colonies close to the middle will be much more similar in size to the lateral colonies.
Also fun: The two cut pieces of cell-y agar look like an antibody!
Love the Jurassic Park ride at Universal Studios! However, if we're considering scientific inaccuracies, I have a couple to point out in their Discovery Center:
1)To sequence DNA you have to extract it by breaking cells. Touching a hand to a sensor wouldn't be sufficient.
2) DNA has 4 base pairs (A,T,G,C) not a binary system as depicted. Although it's possible to represent the 4 bases in binary, it just isn't the way that most scientists work with DNA sequences.
I'm a big fan of openly discussing and accepting mistakes and failure (google "resume of failures" for some interesting ideas!). These tubes are an example of a mistake I made, as all 3 tubes were supposed to have 3mLs like the middle one). This mistake was no big deal and easily reversible. But like everyone else, I've made plenty of mistakes and had failures that have set me back much further. The PhD in Progress podcast calls failures "secret learning" and I love that! Let's embrace secret learning opportunities.
I've long been interested in a critical approach of "alternative medicine" products (check out What's the Harm or Science-Based Medicine for lots of great content on this topic)!
I saw this on a TV commercial. Not only is this product probably ineffective and/or unsafe, the drawing of DNA is inaccurate in at least 2 ways:
1) doesn't have major/minor grooves
2) incorrect number of base pairs per turn
Also, are they suggesting testosterone supplements affect your DNA? If so, that's another reason to avoid them!
I presented my thesis research at The Allied Genetics Conference in Orlando in July 2016. Because I love communicating science to people outside the field, I made a special section without jargon! (Parts of the poster are blurred because results are unpublished.)
Scientists often need to dilute our cells a lot to get a specific much smaller number. As my students can tell you, the calculations and number of tubes can get quite overwhelming. So I always write every step out and carefully label all tubes. My calculations are for each final tube to have just ~1000 cells! However, it's always an estimate, and we find out how many cells there actually are when we see how many colonies grow on our plates.
When we delete a gene from our yeast, we replace it with the ability to survive on a given poison (antibiotic). This process (plus some fabric pulled tight on a platform to stamp a pattern) makes it really easy to tell which cells have our gene deletion. In this case, all cells growing on the right plate aren't killed by the antibiotic natamycin because the enzyme I study has been replaced with natamycin resistance.
Funding to model organism databases (e.g. WormBase, FlyBase, and my beloved Saccharomyces Genome Database) is being threatened. In order to encourage scientists to be vocal about why funding to these databases is so vital, I created the #saveMODfunding campaign on Twitter. I started by passing on some helpful articles explaining the situation.
Funding to model organism databases (e.g. WormBase, FlyBase, and my beloved Saccharomyces Genome Database) is being threatened. In order to encourage scientists to be vocal about why funding to these databases is so vital, I created the #saveMODfunding campaign on Twitter. Here is my addition to the outreach booth at The Allied Genetics Conference (TAGC16) to make it easy for scientists to participate.
Funding to model organism databases (e.g. WormBase, FlyBase, and my beloved Saccharomyces Genome Database) is being threatened. In order to encourage scientists to be vocal about why funding to these databases is so vital, I created the #saveMODfunding campaign on Twitter. Here's my contribution.
Strawberry DNA necklace! The white stuff is DNA, the rest is purple glitter glue :D my students came through in helping me troubleshoot (it didn't work last time)! I used a different protocol, suggested by one of my students! :) all you need is dish soap, salt, a coffee filter, and rubbing alcohol.
One of the most common tasks we have is to separate different components in a tube. Centrifuges are incredibly useful for this! But that can be rough, and sometimes cells have to be treated extra gently, such as these cells whose next step is to be deprived of an important nutrient. So we let gravity and time do the work for us. It takes about 45 minutes for these cells (which are much heavier than the solution they're in) to settle to the bottom.
Sometimes my annotations betray my excitement :) This sequencing shows I successfully made a specific mutation in a gene I study in my yeast. It's taken a few months and several attempts to get this to work. Now I can look at the effect that messing with the gene at this spot has on how the cells function!
Ours is an eco-friendly lab, so we often try to salvage what we can when there's contamination on part of a plate. I cut out the growth on this plate a few days ago and left it out. Alas, it grew back! Good thing I didn't use this plate for any precious cells, or I might have lost them to contamination. Upside to contamination issues: you get to see a huge variety of cool organisms growing!
Isolating DNA is a frequent requirement of working in my lab. We do it by messing up the cell membrane so it comes apart, getting rid of proteins and RNA, and using salts and alcohol to pull the DNA out of solution. It's amazing to be able to see DNA with your own eyes! First time I saw it I got tears in my eyes. Usually it's white (left), though some of our yeast are pink, which can end up staining the DNA pink during the process of extracting it (middle). What's also amazing is that sometimes it looks like you isolated no DNA (right), but there is often enough DNA there for our uses even though you can't see it, because in many cases even teeny amounts of DNA can be enough!
Controls are important in planning experiments. I was happy to see cells had grown in the top half of this plate until I saw that one of the negative control cells (bottom left) had also grown. Doh! I realized I had to change the plan. Luckily I work with yeast so I ended up only about 3 days behind :)
In my lab we manipulate genes and look at how different combinations of mutations affect yeast growth, with different environmental stresses. We use these data to draw conclusions about the purpose of the genes. The missing cells in the third row confirm an exciting result I found! It means that a very specific spot on a protein I study has a yet-unknown function that I'm going to spend the next few years figuring out!
"Slim but significant margin" makes sense to people who understand statistics, but what percent of Time readers have a strong background in stats? Translation: Scientists found that religious and non-religious people had different divorce rates but that that difference was tiny. I think the word "significant" should be completely avoided when communicating to the public, because scientists are using a different definition of the word than people expect!
I conducted an experiment to figure out what factors are important for an effective strawberry DNA extraction.
Variable 1: how much the strawberries are crushed
Variable 2: whether the strawberry mixture is filtered
What do you hypothesize made for the best extraction?
It's important that we start with single colonies for our experiments, so that the cells within the cultures that grow from them are as similar as possible. (Note: colony=group of cells that grew up from a single cell.) This helps keep our results more consistent and makes it easier to track problems when they arise. Drawn above is the pattern I use, with a fresh toothpick for each stroke. Everyone has their own style, and I think sometimes that these streaking styles are like handwriting!
In order to insert various genes into our yeast cells, we let them sit all day in a solution that encourages them to take in foreign DNA. But if we kept them in this solution after putting them on a Petri dish plate to grow, the process would actually be inhibited. The centrifuge is very convenient to separate cells from the solution so we can then put the cells in a new solution (sorbitol) which will help relieve some of their stresses as they grow. After just a few days, you get colonies that grow up from cells that took up the pieces of DNA.
Major contamination! (left=bottom view, right=top) Luckily I was able to get the cells I needed from this plate before it got this bad. I see this contamination relatively often and always think the bottom view would make a cool clothes button :)
My Klipsch earbuds (which cost about $100!) have broken at least 8 times since I got them. The company now says it's my fault. Here's the problem: if you're going to draw conclusions about causal factors, you have to mix up your variables. Earbuds 1-8: all Klipsch brand, all owned by me. How do you conclude it's my fault? For the record, I'm extremely careful with my earbuds. Guess I need to find a new earbud brand.
We got some weird contamination that is super visible in the bottle (left one), but somehow isn't visible under the microscope (top right pic). Bottom right is the pretty colors you get when you disinfect with bleach!
It never reached 100C, even in the parts boiling the hardest. Faulty thermometer or some function of the ingredients in the broth? Salt and oil are both supposed to raise the boiling temp, not lower it. Science or cooking knowledge, anyone?