Biofilm Knit Hat

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.

Ant Knit Hat

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  

Scientists in Stitches - Dr. Deborah Gordon

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 

5 science communication instagram accounts to follow in 2018

Follow me on instagram for more science outreach posts in 2018

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.

Electricity is weird. Can you define it? If I were to try, I’d say it’s the result of a special kind of force that both originates from & acts upon a charged object. • I bring this up because it’s (1) just fun to think about something so abstract yet actually physical and (2) it’s a totally appropriate topic for this image of an electrocuvette. • • • When electric charges move, they form what is called a current. Think: electrons. Why would they move? Well, in my definition of electricity, there’s some force acting on them. Indeed, electricity is the attractive or repulsive effect of a charge on a neighboring charge. But electricity cannot propagate through a vacuum (which here means a space devoid of atoms). Electricity needs a conduit. You know all those warnings on your hair drier, telling you to keep it out of water? Turns out all the dissolved ions found in water (=salt) can conduct charge quite well. That’s because the ions are also charged, meaning they have lonely electrons which are free to move about. The push or pull of an electric field moves these electrons through the material their parent atom is found in... resulting in propagation of the electric field. Thus, electricity is the movement of electrons through a medium of charged atoms. • • Water isn’t the best electrical conduit, though. The best material for conducting an electric current is actually metal. EVERY atom that forms a conducting metal has electrons that can move about, meaning that the entire object is dense with “conductable” material (in contrast the variable number of salt ions in liquid water). Indeed, electricity can be propagated near the speed of light in metal lattices. • • • By now you might have noticed that the cuvette shown above appears optimized for conducting electric currents (you’d be correct). To use this thing, the cuvette chamber is filled with bacteria and an electric field is applied, which opens up the cell membranes and also creates an ionic driving force (the electric field). If we add DNA to the culture prior to applying the current, we can force the cells to uptake that new DNA. Pretty cool, right? 🤙 #Physics + #Biology 😁

A post shared by .tiff (@sunburnedscientist) on Dec 31, 2017 at 7:54am PST

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.

Hello 2018, I’m your girl mouse kweeeeeeeen! One of my New Years resolutions is to spread my science knowledge to all you millennials out there who still aren’t sure what the difference between DNA and RNA is, kind of like what’s the difference between the iPhone 7 and iPhone 8. Follow here for your weekly dose of science talk from a real scientist who still enjoys her Starbucks venti lattes and rose gold accessories. I’m bringing science to you, in your terms—think Bill Nye meets Beyoncé (I wish). . . . . . . . . #scicomm #womeninSTEM #womeninscience #science #scienceedu #research #researchlife #millenials #sciencetalk #scienceinsta #resolutions #newyearresolutions #2018 #realtalk #talknerdytome #millenialpink #rosegold #educate

A post shared by Mouse Kween 🐭👑 (@mouse_kween) on Jan 4, 2018 at 3:24pm PST

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.

Stapelia gigantea, aka carrion flower—so named because its flowers smell like rotting flesh (experimentally confirmed by me). This weird adaptation attracts flies that the plant needs to pollinate its flowers. These flowers can be up to 25 cm (10 in) in diameter, and there are competing hypotheses about why the flowers are so large. Most people think that the large flowers emit more scent and better mimic a decaying corpse (thereby better attracting pollinators), but others suggest a heat-regulation role. #weirdplants #nature #evolution

A post shared by Loren Cassin Sackett (@travelingcassin) on Jan 4, 2018 at 9:46am PST

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.

Day 15/100: Mold contamination in the media Have you ever set up cultures and then picked up the bottle and seen a floaty reflection where there shouldn't be? It's beautiful and puffy like a dandelion. But much like a dandelion, it will contaminate your whole yard. Time to bleach that bottle and start over. :( #100daychallenge #100daysofdrawing #achievementunlocked #illustrator #sciencefail #sciencewins #lablife #lb #contamination #media #mold #moldbrokethemwhentheymadeit

A post shared by Kat Ng (@katecholamine) on Oct 12, 2017 at 10:00am PDT

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!

After pic of one of my bacterial growth curve experiments (swipe left to see the before and a side-by-side shot). . I put a small amount of bacteria into some clear media (media = food for bacteria, see second photo). There are so few, you can't even see them and the media is very clear. As the bacteria grow and divide, the media starts to get cloudy (seen in first photo). This cloudiness can be measured with a machine that measures how much light can make it through the solution. For a clear solution, almost all light can go through, but in one with a lot of bacteria, much of the light will be blocked, resulting in a higher density measurement. By taking measurements periodically while the bacteria grow, I can tell how well my bacteria are growing! Fun, right! Look/listen to yesterday's post to see/hear the plate readers in action! ... Each well in this plate has a different bacterial mutant, so I can compare the growth of each mutant to find ones that look different, and then I can look at the mutation to see why they might grow differently. Plus, I am measuring 8 plates at a time to see growth in different media and with dyes to see cell death and energetics. Fun! I'm excited to process the data next week! #scienceoutreach #womeninscience #womeninstem #steminist #scicomm #microbiology #heidithebiologist #biologist #microbiologist #growthcurves #lifeofapostdoc #postdoclife #bacteria #experimenting #experiment #biologist #sciencecommunication #talknerdytome

A post shared by Heidi (@craftimism) on Jan 4, 2018 at 5:18pm PST

Swimming Bacteria Knit Hat

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!

Poop Emoji Inspired Knit Hat

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!