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.
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
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!
"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!
Today I would like to showcase a fundraiser that is ongoing through the end of August at Cafe Zoë, my local cafe.
Cafe Zoë regularly runs fundraisers to provide Willow Oaks Elementary with needed items. Willow Oaks is part of the Ravenswood School District, which, from what I can gather, was the victim of some unfortunate rezoning over 25 years ago after the completion of Highway 101. It appears that some of the more middle class neighborhoods "opted" to join the Menlo Park City School Disctrict (source). Willow Oaks Elementary in particular, was pretty much abandoned by the neighboring communities, whose members must send their kids to schools that are farther away than the elementary school nestled in their neighborhood.
Cafe Zoë is a neighborhood cafe run by Kathleen Daly and it's my regular blogging and knitting pattern writing hangout. Daly has a huge heart and has, along with the patrons of her cafe, adopted Willow Oaks to raise money for items the school needs. In the past, the successful fundraising campaigns have purchased spare school uniforms and choral risers for the children. The current fundraiser is providing art tables to the school. Daly says some of the students are rewarded for good behavior by being able to make artistic creations on posterboard. Currently, the art teacher must push together small desks to make do as the school does not have art tables.
A map showing the communities that "opted" out of the Ravenswood school district (source)
Daly's daughter, Zoë Sharkey, who manages events took the lead on this fundraiser and recruited local artists (including myself) to donate items to the fundraiser. The artists are displaying their art in the cafe through the end of August and a portion of any art sold will be donated to Willow Oaks. The artworks can be viewed in an album here. If anyone would like to help out with the fundraiser or purchase art, they can contact Cafe Zoë directly here. Cafe Zoë is almost halfway to its goal for the fundraiser and hopes to purchase four art tables for the school.
Craftimism's "Politiknits" items for sale at the Cafe Zoë fundraiser - earrings, pins/magnets, and coffee sleeves
I am a microbiologist and a knitter. As a microbiologist, I have access to some fancy lab equipment. As a knitter, I have A LOT of yarn (seriously, my one of my kitchen cabinets is chock full with yarn as I have more yarn than kitchen items).
Last week, I decided to look at yarn under the microscope. Enjoy these photos of yarn up close!
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.
