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.
I designed this hat to feature Dr. Deborah Gordon's work with harvester ants. To see a synopsis of her work and Dr. Gordon modeling the hat herself, check out my blog post here. This hat features two pairs of harvester ants that are interacting through their antennae. Dr. Gordon provided a lot of help with the design, insuring that the ants would be interacting through their antennae, just like they do in the environment. The pattern for this knit hat is available here on Ravelry or can be purchased directly here.
Harvester ants interact with each other by briefly touching antennae
This "Scientists in Stitches" post features Dr. Deborah Gordon, a professor at Stanford in the Department of Biology. Dr. Gordon studies the collective behavior of biological systems using harvester ant colonies. Ants are social insects that operate without central control. This means that there are not 'boss' ants to direct the behavior of underling ants. Harvester ants gather seeds from the environment. They leave their protected colony and enter harsh desert conditions in search of scattered seeds. Once an ant finds a seed, it returns to the colony. As the ant returns to the colony, it will briefly touch antennae with another ant and that ant will go foraging. In particular, Dr. Gordon investigates how harvester ants use these interactions to regulate behavior and how these small local interactions direct the dynamics of the entire colony. Ants use these interactions as a proxy for how much food is available. If there are a lot of seeds near the colony, ants will find seeds and return more frequently, thus sending more ants out to collect all the seeds. When there are fewer seeds, the ants meander longer and cover the area more thoroughly before they find a seed and return, reducing rate of ants leaving the nest. Dr. Gordon's work is relevant to studying other networks without central control such as other biological systems and, perhaps even networks such as the internet. To learn more about Dr. Gordon's work, check out her lab's website here, her TED talks in 2003 and 2014, and her article in Scientific American. If you would like to see more photos of the hat and get a link to the pattern, check out this blog post.
Dr. Gordon showing off some of her ant paraphernalia while wearing
her hat that features ants interacting
One of my New Year's goals is to do more science communication on social media and here on my website. I am off to a good start with the Swimming Bacteria Knit Hat post that explains bacterial swimming that I published last weekend.
As part of my motivation, I took to Instagram and searched through #scicomm posts to find new accounts to follow. Here are a few that stuck out to me. If you have an Instagram account where you share science outreach posts or if you follow any awesome science communicators, please leave the information in a comment below! I'd love to feature more in the future.
Here are a few science communicators to follow on Instagram:
1) Sunburnedscientist - I love the conversational style and questions posed by @thesunburtscientist. Follow this UC Santa Barbara PhD student for some provocative questions and insights into everyday scientific experiments.
2) Mouse_kween - She only has two posts so far, but I hope to see more from her in the future. She promises to deliver science communication that millenials can relate to.
3) travelingcassin - stories from nature, traveling, research, and life (full disclaimer, Loren is a close friend and my first featured "Scientist in stitches"). I love Loren's nature pictures and accompanying explanations to the underlying science.
4) Katcholamine - Kat has been designing these awesome science "stickers" and animations. If you are a scientist, you will love Kat's interpretation of lab wins and fails. (Full disclosure: Kat is also a friend of mine! I made her this poop hat to celebrate her thesis as one of my #knityourPhD projects.
5) Craftimism! Yup, that's me! I could not resist some shameless self-promotion and as I am gearing up for even more science outreach as well as knitting and craftivism in the new year, you should most definitely follow me on Instagram!
My latest science knit shows rod shaped bacteria swimming around the brim of the hat. The pattern for this hat can be found here on Ravelry or purchased directly here. These bacteria could be
Escherichia coli or Bacillus subtilis or any other rod-shaped bacteria that have flagella over their body.
Flagella behavior during tumbling and swimming
The flagella on these bacteria are peritrichous, which mean they
surround the cell. The flagella are controlled by a molecular motor and the
motor can either spin clockwise or counterclockwise. When all of the flagella
on the cell spin counterclockwise, the flagella can propel the cell, as shown on this hat.
When the flagella spin clockwise, they spread out and thus have no net force so cannot
propel the cell anywhere. Instead of going in a direction, these cells “tumble”
and basically somersault in the same place to change direction so when the flagella spin the other way again, they can
set out in a different direction. These periods of “running and tumbling” allow
the bacterium to explore its environment. During this exploration, when a
bacterium is swimming toward nutrients, it can adjust the durations of running
and tumbling so it is running for longer periods and tumbling less, thus
biasing the movement toward the nutrients, in a process that is called
“chemotaxis.” The bacteria on my hat are all swimming, although I considered making a version of the hat with tumbling cells as well. See the movie below for a video that I took of my favorite bacterium Bacillus subtilis. Some cells are stationary as they are stuck between an agar pad and a glass coverslip while others are in an area that is a bit wetter and they can swim around. This is best viewed fullscreen to better see the little organisms. It is a very short video, so you may have to hit replay to catch the action.
Full disclosure: this video was the result of an experiment that did not work. I didn't let the microscope slide dry enough before imaging and my bacteria were still swimming around. I made the most of the situation and filmed my swimming bacteria for this blog post (and I repeated the experiment to get the information I was looking for). Experiments often do not work or give inconclusive results - we as researchers learn to deal with failure very well and just keep plugging along and listening to the data to learn about the world around us. It is fascinating!
I designed this Shark Knit hat pattern for a friend of a friend who really loves sharks.
As a backstory, the friend (who did not know how to knit at the time) paid for a ridiculously difficult shark sock knitting pattern. He learned that I knit and showed the pattern to me. After laughing and saying I would never make those socks, I said that instead I would design a shark knit hat - as that is more of my thing. I have since taught this friend how to knit. We will see if he ever decides to tackle those socks!
Thus, this pattern was born. You can get it here on Ravelry, here on Craftsy, or buy it directly here. Enjoy!
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!
Y'all, I am so excited to see the solar eclipse tomorrow! I extended a trip to visit my family for a few days so that I could swing back through St. Louis first just so I could witness my first ever total solar eclipse. I designed this knit hat to mark the occasion. The hat features the path of the moon as it covers the sun. I even embroidered on the corona of the sun onto the hat. If only the solar eclipse was during the winter! Unfortunately, I'll only be wearing this when I am in air conditioned places on Monday, but it is awesome anyways.
You can get the hat here on Ravelry or purchase directly here. It will be free up until the eclipse with the promotion code "Eclipse2017".
Here are some interesting facts I have learned about the eclipse:
1) It is only safe to look at the sun when the eclipse is in totality. It is never safe to look at the sun, but it is even more dangerous during the eclipse because the decrease in ambient light will make your pupils dilate and expose more of the retina. Bottom line: DON'T LOOK DIRECTLY AT THE SUN UNTIL TOTALITY! If you are not lucky enough to be in the path of totality, DON'T LOOK DIRECTLY AT THE SUN!
2) Safe ways to view the sun include special approved solar glasses (my rad ones complement my knit hat perfectly), pinhole camera obscura viewing boxes that project an image of the sun onto the inside of the box, and even using binoculars to direct an image of the sun onto a screen and focus on it. Find instructions for 6 safe ways to view the eclipse here.
3) Some animals will begin their nighttime behavior during totality even though it is in the middle of the day. I am particularly excited to witness this occurring.
4) Many people will be participating in citizen science efforts by using apps on their smart phones to record observations during the eclipse. In particular, one project by NASA will be monitoring temperature before, during, and after the eclipse (more information here) and another project from the California Academy of Sciences will record plants and animal behavior during the eclipse (more information here).
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.
