BioQuakes

AP Biology class blog for discussing current research in Biology

Author: cellmemmabrane

Diving Into the Life of Rene Francolini

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On March 7, 2021

In Student Post

Rene Francolini identifies as a proud bisexual, cisgendered female (she/her), who specializes in computational biology. Computational Biology combines her two greatest passions: marine biology and computer science.

Francolini discovered her love for computer science and marine biology in highschool, but was then introduced to the combination of those two topics by one of her highschool teachers. The rest is history. Francolini furthered her education in science and got her undergraduate and accelerated master’s degree at Carnegie Mellon University for Computational Biology. When she came right out of college, she worked as an oyster farmer for a few years before working at the Woods Hole Oceanographic Institute (WHOI). During the last two years spent there. Francolini spent her time in the environmental toxicology lab, collecting Environmental DNA (eDNA) from deep parts of the ocean, and the molecular ecology lab taking part in a larger project known as the Ocean Twilight Zone Project.

The Ocean Twilight Zone Project focuses on gathering research from a part of the ocean called the mesopelagic zone. It’s often referred to as the twilight zone, and is home to the greatest amount of fish in the sea. Often the fish we will find on our dinner plates like tuna and swordfish are coming from there. The twilight zone also takes part in removing some of the carbon in the atmosphere, which regulates our climate. In today’s world, we need to be careful in protecting it because it benefits not only the fish, but us too. This research will help advance ocean science; it will also give government officials insight on this zone, so hopefully they will try their best to protect it.

Francolini is currently getting her Marine Science PhD, while also taking part in the Maine-eDNA project as a Graduate Research Assistant. She’s specifically working on the Gulf of Maine’s kelp forests, and “how we anticipate climate change to alter the landscape and biodiversity of these vital ecosystems” (500 queer scientists). This project combines fieldwork, collecting samples, as well as computational and molecular work. This project showcases how versatile Francolini is as a biologist.

Franciolini loves that being a scientist means that you can share your passion with others, which even leads some to discover a love and interest in STEM and the environment around us. She is proud to be a part of the openly LGBTQ+ minority in STEM, as representation in this field encourages more young scientists that will be coming from our generation to outwardly be who they are without fear of not being accepted and/or respected.

Comparing Saliva Tests to Nasopharyngeal Swabs

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On January 10, 2021

In Student Post

Although many college campuses have closed within the past couple of weeks, for the few months they were in session, the general public was introduced to a new procedure for COVID-19 testing: Saliva tests. There are multiple reasons why a saliva test would be more ideal for campuses to use, and it’s not just because the nasopharyngeal swab testing is extremely uncomfortable.

A nasopharyngeal swab is basically a biological term for the COVID-19 test that goes all the way up your nose. News-Medical actually came out with an article going through the testing procedure, and how the SARS-CoV-2 is detected. The purpose of the swab test is to reach the nasopharynx, which is where nonpathogenic and pathogenic bacteria and viruses lie. It’s also used to test the flu and pneumonia. In fact, UC Davis published that they have just come up with a rapid test that could detect both the flu and COVID-19 in one nasopharyngeal test. This makes it the most convenient method, but it’s more expensive; making this harder to upscale for mass testing). It also requires more supplies, and puts health care workers in close contact with infected individuals. Saliva tests would be a lower cost, but there was uncertainty in its accuracy. The Scientist highlights three main experiments that help better our understanding of saliva testing.

The first experiment was led by Yale epidemiologist, Anne Wylie. Wylie and her colleagues tested the accuracy of swab testing using 70 suspected COVID-19 patients admitted to the Yale-New Haven Hospital. They found that saliva samples contained more copies of the SARS-CoV-2 than swabs. The group concluded by saying that they see potential in the saliva swab; however, this was only tested in one controlled area, and the patients at this point were showing symptoms.

The second experiment, led by Mathieu Natcher, took place throughout the French Guiana. There were 776 participants ranging from (wealthier) villages, forests, and more poor neighborhoods. Natcher discovered that the SARS-CoV-2 virus was still present within saliva for a long period of time, despite climbing temperatures, which makes this idea for situations where testing needs to happen in areas where temperature can’t be regulated. The one downside noticed during this experiment was that saliva testing was less sensitive than nasopharyngeal swabs, which means that it can be harder to pick up the bacteria, if there is less in their system. Therefore, saliva testing may not always be as efficient for asymptomatic carriers or people who just became infected.

Pharmacologist at the University of South Carolina helped develop the school’s saliva test, and reported her findings after school came back in session. She noticed that although saliva may be less sensitive, the repetition of testing these students makes it more possible to catch the infection shortly after it comes. She also ran an experiment on two students living together: one of which had a confirmed COVID-19 diagnosis, and the other was at risk. Both students got tested daily using the nasopharyngeal and saliva swabs for the two weeks. She found that the amount of the virus detected in both tests for the positive patient were the same, leading her to conclude that saliva and nasopharyngeal tests both have the same sensitivity. Banister also explained that not the lower sensitivity coming from the saliva test in comparison to the nasopharyngeal test could be due to the fact that saliva turns over quickly in the mouth, while the nasal cavity and lungs hold the virus for longer. Banister also said because of this saliva tests might be a more accurate depiction of who is actually infectious, because the virus stays in the lungs even after the patient is no longer infectious.

We have come a long way since this article was initially posted, and saliva tests have been released to more of the public for a longer period of time. It is interesting to see how these preliminary tests played a role in whether or not to further release saliva tests.

A Sweet Post About Sourdough!

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On October 25, 2020

In Student Post

When Covid-19 hit the US, some of the biggest quarantine coping mechanisms all revolved around a fan favorite carbohydrate: bread. With the copious amount of time on people’s hands, baking sourdough bread was the perfect activity.

Unlike any other bread, it’s hard to get the perfect tasting sourdough. Research has found that there are biological reasons behind sourdough bread and its taste, but before doing so, it’s important to learn what sourdough bread is made up of, and how it’s made. To help learn more about the process of making sourdough bread from scratch, I got a mini crash course from Little Spoon Farm. The starter (initial mixture) contains flour and water and sometimes salt, which will eventually grow into a diverse selection of microbes (these are tiny living organisms, which in this case are bacteria). The starter has to sit for 7-14 days, and within that time, the starter grows through the flour by eating the sugars within itself. With that growth comes bacteria/microbes and lactic acid, which eventually will allow the bread to be able to leaven in the oven.

Recent studies have shown that each starter is made up of different microbes. One study had 18 professional bakers from all around the globe make their sourdough, and send it to a lab in Belgium, where DNA sequencing was used to identify the microbes in the different starters. Although there were common yeasts and acids found like Saccharomyces cerevisiae and Lactobacillus, the strands and amount of each differed according to the starter. Another study done by Elizabeth Landis, at Tufts University, looked at 560 different starters submitted from all around the world. Through doing so, she found recurring microbe groups within these different sequences. There is still no definitive reason behind the microbe groupings, and why exactly they differ for each starter, but Landis mentioned that certain yeasts “specialize in feeding on distinct sugars,” due to the fact that they are made of different sugar mixtures. Some yeast also lack certain enzymes, which as we learned in class, help break down molecules. In this specific situation, the enzymes within different yeasts feed on and break down sugars. Differing yeasts could also be a reason why sourdough bread has different flavors. (Keep in mind that Landis’ findings are still under review, so there are still limited details on this experiment and not definitive reasoning).

Microbial ecologist, Erin McKenny, further elaborates on how “each microbial community can produce its own unique flavor profile.” For example, when more acetic acid is present in the starter, the bread will have a more sharp and vinegary taste. When the starter produces more lactic acid, it has a more sour and yogurt like taste. Metabolic byproducts within the starter could also potentially add to the complexity of the sourdoughs’ taste. In addition to each microbial community, scientists have identified other features that influence the taste of the bread like temperature. When lactic acid ferments in a warmer area, the bread has a more sour taste, and when it ferments in a colder area, the bread has a more fruity taste.

After looking at multiple articles showing how bakers get their sourdough to have a certain taste, I have learned how important the specifics are when it comes down to making sourdough. One article that gave tips on how to manipulate the taste of sourdough reinforces everything that the main article helped explain, and talks about the importance of keeping a warmer, dry climate to ensure that the bread tastes sour. It turns out that a quarantine treat may be a bit more complex than it appears. It’s interesting to see how biology plays a key role in one of the most prominent foods, and next time you consider making sourdough or get a bread basket from the Cheesecake Factory, you’ll now know the biology behind it.

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