I am thrilled to finally share this biofilm knit hat that I designed and knit last December! The pattern for this hat can be found here on Ravelry or directly here. I was excited to be asked if I could design a biofilm hat as I study bacterial biofilms at Stanford University. Click here for more about my research.
Bacteria are single cell organisms. The bacteria that I study, Bacillus subtilis is a soil-dwelling bacterium that is ~3-5 micrometers long. These bacteria can live on their own or they can "settle down" on a surface and form a biofilm. A biofilm is a group of cells that are held together by a substance that the cells produce and excrete. This substance (also known as slime) is a sticky substance that keeps the cells together. Once the cells are in a biofilm, they can adapt to take on different roles within the biofilm. For instance, the cells on the interior of the biofilm usually assume a more dormant role while the bacteria that are closer to nutrients and oxygen remain more metabolically active and can grow and divide. Biofilms are very important to study as several pathogenic bacteria can form biofilm infections in the body that are hard to treat. Bacillus subtilis, the strain that I study, is typically a soil-dwelling bacteria. However, the knowledge that I can gain through studying its biofilm formation can be applied to all types of biofilms including those that cause disease.
This hat is my version of a classical figure illustrating the developmental stages of a biofilm. This one represents a bacterial biofilm that forms on a surface in a liquid environment such as the bacteria Pseudomonas aeruginosa. Check out the movie I made below where I demonstrate how this knit hat illustrates biofilm development. If you want to learn more about biofilms, I'd recommend checking out the wikipedia page here.
Dr. Katharine Ng studies the bacteria in our gut (aka poop)
I was inspired to knit this #knityourPhD hat for Dr. Katharine Ng who got her PhD studying how bacteria that live in the intestines respond to antibiotic treatment.
In work published in Nature, Dr. Ng and colleagues found that some pathogens in the gut can gain an advantage by eating sugars from the host. In the gut, there are sugars present but tied up in the mucus that is made to line the gut. Some non-pathogenic ("good") bacteria cut some of the sugars off of the mucus molecules. After antibiotic treatment, two pathogenic (bad) bacteria, Clostridium difficile and Salmonella typhimurium, are able to gain a foothold in the gut by eating the sugars that the good bacteria had liberated from the mucus. Her work provides insights for developing therapeutic treatments to prevent the bad bacteria from taking hold during antibiotic treatments. Read more about her PhD work here.
To study the gut bacteria, Dr. Ng collected a LOT of mouse poop for analysis and sequencing before, during, and after antibiotic treatment. To honor all of the poop collected, I used the poop emoji as inspiration to design this hat with 6 poops around the hat. I added a pom pom on the top for some extra character. You can get the pattern here on Ravelry, on Craftsy here or directly here. Happy stitching!
"Scientists in Stitches" is a new series on my blog where I will interview scientists about their careers and the steps they have taken to get there. I have made each of these scientists a knit item that represents their PhD (#KnityourPhD) or career (#KnityourScience).
This post features Dr. Loren Cassin Sackett. Loren is an evolutionary biologist that does some amazing work studying natural resistance to pathogens using the prairie dog and the Hawaiian 'amakihi as model organisms.
What is your current job title and what do you do in your job?
I am an Assistant Professor in Integrative
Biology at the University of South Florida. I spend about half of my time on
research and half on teaching/mentoring activities (I teach both mammalogy and
evolution). My research is focused on evolutionary processes in wildlife,
including dynamics of small populations, adaptation to introduced diseases, and
the disruption of gene flow by habitat fragmentation. Given that much of my
research is on wildlife, I am in the enviable position of getting to do some
field work each year in amazing places like Colorado and Hawaii, although I
also do a lot of molecular lab work, data analysis and writing, and above all
mentor students in how to do those things.
What is a typical workday for you?
The first and most important part of my day is
making coffee. :) I bike to work, and then usually start my day by
writing something I'm working on (a paper, grant proposal, lecture,
etc.). I start this way because as soon as I open my email, chaos breaks
loose (I get about 100 emails a day during the middle of a semester). I
also have a lot of meetings with students. I teach two days a week and
spend those days planning activities, writing lectures, reading papers that are
relevant to the course, and grading. I try to infuse contemporary science
into the courses I teach, which benefits the students because they get an idea
of what scientists are actually doing in the field/lab, and
how they are generating knew knowledge. And it's good for me too, because
it keeps me abreast of the relevant literature. For me, this is one of
the things that I tend to let slide too much when I get busy, so it's nice to
have something that forces me to keep reading.
On the days that I don't teach, I try to pick
a specific project to work on so I can make noticeable progress on it.
It's hard for me to multi-task different projects on the same day, so I try to
generate some momentum to carry them forward separately. I still have to
answer emails these days, but I spend more time reading abstracts and papers,
writing, and planning research projects. Those things pretty much eat up 8
hours in what feels like no time! I am currently developing a new class,
so unfortunately my workday does not end after 8 hours, but I try to minimize
the amount of time I spend at home working (work-life balance and all that).
:)
It had to be my mom and my grandpa, who encouraged me to constantly ask questions about the world around me, and to try to understand the patterns I saw. I did not recognize this as an interest in science until much later -- in fact, I rebelled against my mother in high school be deciding that I would study psychology. I obviously did not know exactly what science was! I think I was probably subject to many subconscious ideas that science was performed by old white-haired men in lab coats in dark windowless labs, and my understanding of science was limited to what I had done in high school courses, so I thought it consisted of essentially doing 30-minute experiments that had no purpose because we already knew what the outcome was supposed to be. I had no concept that a scientist designed her own experiments to answer her own questions about the mysteries of the world, or that those experiments could lead to fascinating new questions. But when I finally figured out that research was a career--that a person could get paid to seek knowledge--I knew right away that that was what I wanted to do for the rest of my life. My mom and my grandpa probably wondered what took me so long.
I think I was probably subject to many subconscious ideas that science was performed by old white-haired men in lab coats in dark windowless labs ... I had no concept that a scientist designed her own experiments to answer her own questions about the mysteries of the world, or that those experiments could lead to fascinating new questions.
What training/education did you do to get to where you are now?
I took kind of a circuitous path to get
here. I was always passionate about conservation, but I never really knew
what types of careers could be associated with conservation work, except some
that did not appeal to me (like fundraising from private donors, which is
essential work but is better suited to extroverts). I was fascinated by a lot
of scientific fields and ended up studying psychology in college, even though I
didn't want to be a practitioner. It was through participating in
psychology research that I learned research could be a
career. By this time, I had discovered conservation genetics,
and immediately after I graduated, I enrolled in undergraduate
courses in biology to get the prerequisites for graduate school (but I never
actually got a bachelor's in biology). I received my PhD in Ecology and
Evolutionary Biology at the University of Colorado, and I was lucky to have
received really solid training in both ecology and evolution from a fantastic
department. And thanks to the patience of my PhD advisor, I took a lot of
opportunities to receive specialty training elsewhere: I took 2 short
courses in Costa Rica through the Organization for Tropical Studies, and I took
a leave of absence from CU for personal reasons and audited Alan Templeton's
population genetics class at Washington University in St. Louis. I think
it was really useful to gain intellectual perspectives from a lot of very
diverse-thinking scientists. Eventually (!) I finished my PhD and secured
a postdoctoral fellowship at the Smithsonian Institution, which is really the
dream for a conservation biologist. One of the things that was important
to me in a postdoc was to work in a different system and learn a new skill
set. Not everyone chooses this strategy, because it does take a lot of
time to shift systems and techniques, and many postdoc terms are not really
long enough for this. I was fortunate that my PI and I were able to
secure funding to keep me there for 3 years, and I learned a lot of genomics
tools--which is becoming essential for biologists today.
What was your best day in science?
Wow, that's a really tough question. I
haven't had a Nature paper or anything prize-worthy, but I appreciate the
little victories (like an editor choosing my paper to feature on the journal's
website) and I love fieldwork. Last year I got to backpack into a field
site on Kauai with a 40-lb pack that kept hitting trees above my head level,
and army-crawl under fallen logs to get to one of the most pristine places on
Hawaii (except for the tourist helicopters flying overhead). And catching
elusive species (like the Kauai amakihi, which we caught only three of in a
week) is really satisfying. When the animals make us really work hard for
it, the feeling of success is greater.
And actually, I really like the day-to-day
work in almost all respects. I love having students get excited about
projects, and getting grants funded is an awesome feeling.
A post shared by Loren Cassin Sackett (@travelingcassin) on
What was your worst day in science?
Well, some of the same days. Before we
caught that Kauai amakihi, it felt like a huge failure and a waste of money to
be spending all this time not catching anything. It is always really
frustrating having dozens of traps set at a prairie dog colony with dozens of
prairie dogs and not having ANY of them go into the traps. The days when you
realize rodents are outsmarting you really start to make you question your
sanity.
Bad days are also the ones when I get rejected
from something. There's a lot of rejection in science -- rejection from
jobs, rejection from grant proposals, rejection of papers. I try to just
assume everything will get rejected, and then I'm not too disappointed when it
happens, and if it doesn't, then it's especially exciting. And I remind
myself that everyone gets rejected and not to take it personally.
There's a lot of rejection in science -- rejection from jobs, rejection from grant proposals, rejection of papers.
What do you do in your free time?
I try to stay active and keep my body healthy
as a balance to working my brain all day. I love being outside. Biking
makes me feel completely liberated, like I am capable of anything (it's a nice
illusion). Biking--mostly commuting rather than going on long weekend
rides right now--is the main thing that keeps me sane. And I like hiking,
rollerblading along the water, running, etc. I read, but never
enough!
What are your hobbies?
I dabble in photography. Nothing
fancy--mostly pictures from my travels. I really love traveling.
Well, it's more than love: it's more like an insatiable desire to explore every
corner of the planet. When I see a dirt road winding around a bend, I
have to take it. It's not even a choice, it's an urge I can't
control. I love meeting people from all over the world and seeing the
day-to-day life in other countries, and I really appreciate the perspective it
gives me on the world.
7 of Loren's travel photos, 1 from each continent
If you could send a letter back to your 18-year-old self, what advice would you give yourself?
Ha! So many things: Listen to your
mother. Practice your Spanish with your classmates. Science is fun,
and you can be good at it.
Now it is your time to participate:
If you have any questions for Dr. Cassin Sackett, leave them in the comments below. If there is enough interest, I'll gladly publish a follow-up with Loren so she can answer your questions!
I'd like to welcome the newest addition to my #KnitYourPhD line of #ScienceKnits: this amazing uterus patterned knit hat. One of the things I love about making PhD-related items is the chance to explain the awesome research of my friends on this blog. This hat was designed for Dr. Erin Reinl, my amazing friend who just earned her PhD at Washington University in St. Louis. During her PhD, Erin studied the uterus. In particular, she investigated the function of an ion channel that was involved in uterine contractions during labor. She found that this ion channel was important for successful labor and her work contributes to a broader understanding of uterine contractibility and dysfunctional labor. Isn't that cool!
To design Erin's hat, I took some inspiration from the cake at her celebration party after she defended her thesis. The "You do You(terus)" theme was awesome and I could not wait to put uteri on a knit hat. This is even better than that time I put sperm on a hat. I may have to start a new line of "ReproductionKnits." The pattern for the hat can be found here on Ravelry, here on Craftsy, or purchased directly here.
Thanks to Kat Ng for taking the photos of me in the Uterus Hat.
Woohoo, I am very excited to finally share my latest "knityourphd" hat! This hat was designed for my friend Jeff, who recently defended his thesis in the physics department at Washington University in St. Louis. Jeff had a super cool thesis project that involved, among other things, determining what areas of the brain responded to different patterns and types of light presented the visual field. Jeff studied this using the red eared slider turtle as a model organism and uncovered several interesting insights about how the brain processes visual cues.
Photo credit: Pablo Tsukayama
I designed this hat with red eared sliders walking along the brim. The pattern can be found here on Ravelry, here on Craftsy or purchased directly here.
Congratulations on your PhD, Jeff! I hope you enjoy the hat!
Today is a big day for me as my very first first-author paper is published online today in Current Biology. Non-scientists can check out the press release here. I would like to celebrate by sharing my own #knityourthesis project - these bacterial cell cycle fingerless mittens.
Our lab cartoon detailing the bacterial cell cycle.
DNA is blue and the cell divsion protein FtsZ is in red.
My thesis research in the Levin Lab focused mainly on identifying how the bacterial cell cycle is regulated. In particular, I studied what happens to bacterial cells when you block them from dividing, as would be the case when you treat them with antibiotics that block the cell cycle. As outlined in my paper, I uncovered some previously unidentified regulatory mechanisms that ensure proper cell cycle progression, which is very important for maintaining bacterial cell populations. I also discovered that cells blocked for division enter a zombie-like state where they remain alive but can no longer reproduce.
I originally designed these cell division mitts as a present for my boss, Petra Levin upon my graduation. I based the design on a cartoon detailing the bacterial cell cycle that appears in almost all of the presentations by our lab. I liked the mitts so much that I am now making a pair for myself. I also am making a hat that details the bacterial cell cycle that I am sure will be featured in a future blog post.
The bacterial cell cycle begins with a newborn daughter cell (top left). The DNA (blue) replicates and the cell division ring (red) forms at midcell (bottom left). The ring serves as the site for new cell wall construction that septates the two new daughter cells (right - top is a cell about to divide, the bottom is the result).
Meet Kelsey Tinkum, the inspiration for another biology themed knit item. Kelsey recently received her PhD from Washington University where, as one facet of her PhD work, she studied the adverse side effects of chemotherapy using mice as a model organism. She also developed new tools to study the cell cycle and identified a novel mechanism of how one cell cycle gene is regulated. To see more of Kelsey's prolific PhD work, click here.
To celebrate Kelsey's thesis defense and thank her for taking the time to read and provide insight to an early version of my own manuscript, I made her these mouse fingerless mittens to keep her hands warm when typing up her next paper. The pattern for these fingerless mittens can be found here on Ravelry and here on Craftsy.
Photo credit: Pablo Tsukayama (the first 3, the 2 not as good photos were my own:))
This post features the eyeball hat I made for the one and only Nick Tran. If you follow my blog, you may recall I made another mario-themed hat for Nick a while back (seen here and pictured to the right). For his PhD work, Nick studied a collection of diseases that result in vision loss. The diseases he studied resulted from degeneration of the retina, which is the primary neuronal tissue in the eye supporting vision. The retina is composed of photoreceptors called rods and cones which detect light and additional neurons that process and send light information to the brain. To see more of Nick's work, click here.
To celebrate Nick's accomplishments, I made him this eyeball hat. I considered making Nick a rod and cone patterned hat, but decided an actual eyeball hat would be much cooler. I began by knitting a white hat for the base. Then I crocheted the pupil (black) and iris (brown) in a flat circle using this tutorial. When transitioning from the black to the brown, I simply switched colors. My flat circles usually end up like shallow bowls which was perfect for this hat. When I was satisfied with the size of the pupil and iris, I tied off the end and used a yarn needle to sew the crocheted piece to the top of the hat. I then added the "gleam" with white yarn and the blood vessels with red yarn. Nick asked for lots of blood vessels which gives the hat a rather creepy (but very cool and nerdy) appearance.
So I have another science-themed knit item to add to my collection. I knit these brain slippers for my friend Elizabeth who got her PhD by studying the genetic determinants of brain folding. Her work was even featured in this article in the Huffington Post.
I originally was going to make her a brain hat such as this one, but she actually got a similar hat at her defense party. So I used my brain and thought of a different brain-themed project.
To make these slippers, I began with my favorite slipper pattern. Then I knit a super long I-cord (using this tutorial). For my I-cord, I used the 2 double pointed needle method with 5 stitches and size 6 needles. Then I sewed the I-cords on the slipper to resemble a wrinkly brain. As the wrinkles increase the surface area of the brain, it took a lot of yarn and I ended up going through all the pink yarn in my stash (3 different colors of pink). To make the slippers more durable and last longer, I cut pieces of suede fabric and sewed them to the soles of the slippers.
Meet my friend Beth! She is a super talented high school biology teacher. While she enjoys all aspects of Biology, she especially loves neurobiology. Her previous research experience was in the field of neurobiology, in particular how cell signaling in neurons works. Therefore, to continue in my science-themed hats, I designed a neuron hat, complete with dendrites, a cell body, an axon, and synaptic terminals. I even included some signaling molecules for good measure.
The pattern can be found here at Ravelry (buy directly here) and here at Craftsy. I have included an easier chart that eliminates most of the long carries in the pattern as well as a chart for the pictured hat.
Erica's microscope image of sperm fertilizing an egg.
The first chromosome division is shown in the upper portion of the egg (DNA is stained blue).
Erica posing with our
kickball championship trophy.
We are ballers!
This is the second hat in my thesis-themed hat series. I made it for my good friend Erica who is an amazing scientist. She defended her thesis today and I am so proud of her! I am going to miss her so much when she moves to her post-doctoral position in San Diego.
For her thesis project, Erica studied diabetes and how it affects fertility. Specifically, she studied how diabetes affects sperm development and function using mouse models of diabetes. She investigated the role of insulin in sperm and how other hormones were altered in diabetes. Her work is extremely cool, novel and very fun.
Here are some pictures of me modeling Erica's hat. Unfortunately, I do not have any pictures of her in the hat, but I hope to change that soon. I topped off the hat with a sperm pom pom. I am working on typing up the pattern and will post it online if you are dying to make this hat for your sperm loving friends.
My friends Erica (left), Beth (right), and myself (middle)
posing at a friend's wedding
Bacteria are single cell organisms. The bacteria that I study, Bacillus subtilis is a soil-dwelling bacterium that is ~3-5 micrometers long. These bacteria can live on their own or they can "settle down" on a surface and form a biofilm. A biofilm is a group of cells that are held together by a substance that the cells produce and excrete. This substance (also known as slime) is a sticky substance that keeps the cells together. Once the cells are in a biofilm, they can adapt to take on different roles within the biofilm. For instance, the cells on the interior of the biofilm usually assume a more dormant role while the bacteria that are closer to nutrients and oxygen remain more metabolically active and can grow and divide. Biofilms are very important to study as several pathogenic bacteria can form biofilm infections in the body that are hard to treat. Bacillus subtilis, the strain that I study, is typically a soil-dwelling bacteria. However, the knowledge that I can gain through studying its biofilm formation can be applied to all types of biofilms including those that cause disease.
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