Following the people and events that make up the research community at Duke

Author: Nidhi Srivaths

Quorum Sensing: The Social Network of Bacteria

Dr. Bonnie L. Bassler, the Chair of Molecular Biology at Princeton University, is an advocate for diversity in science.

Bonnie Bassler of Princeton University

Throughout her presentation of the Ingrid Daubechies Lecture on Jan. 31 during Research Week, she emphasized that the diversity of her scientific team allowed every lab member to contribute to different steps of the process of studying quorum sensing, a form of microbial communication. (Watch her talk.)

Bacteria are everywhere. They’re sitting at the tables you sit at, burrowing in the clothes you wear and unfortunately, also crawling around on your skin. For a long time, they’ve had a pretty bad reputation, and for good reason! They have caused plagues that have wiped out masses across the globe, driven up breath mint sales by thriving in your mouth and mutated into every biologist’s Boogeyman when you try to kill them with antibiotics – super bugs!

However, the bacterial redemption arc is also quite compelling. “Good guy” bacteria in the gut help us break down food, produce essential vitamins and also sometimes fight off their evil siblings.

So, good or bad, the impact of bacteria in our daily lives is undeniable. But how does a microscopic little being have the capacity to influence the macroscopic world so greatly?

It doesn’t. At least, not by itself.

Lactococcus lactis is one of the starter bacteria in a cheese culture!

A bacterium never works alone because its strength lies in its numbers! Groupwork and communication (as any Pratt star going through recruiting season will swear to their interviewers) are what make bacteria so powerful. A bacterium by its lonesome will act differently than a bacterium surrounded by its daughters, sisters and cousins (bacterial family tree dynamics can get a little unusual).

Knowing that bacteria optimize their behaviors to work efficiently in a group answers the question of how they are so powerful, but it raises another.

How do bacteria know when they have company?

In a world where social media helps us stay connected, it is easy to take rapid status updates for granted. But for tech-deprived microbial colony, how does one member gauge the population of their surroundings? This question is one that Bassler’s lab answered: with a special chemical compound called autoinducers.

Autoinducers are little chemical signaling molecules that each bacterium sends out into its immediate environment. These molecules allow for quorum sensing, or cell-to-cell communication, to take place among bacteria.

Basic quorum sensing: How bacteria know who’s around them. (Nidhi Srivaths)

Every bacterium senses changes in the concentration of these autoinducers in their surroundings. Sensing a sudden increase in autoinducer concentration will change a bacterium’s gene expression, protein synthesis, and consequently, behavior. It will adapt to group behavior, while a bacterium that senses a drop in autoinducers will adapt to individual behavior.

Bacteria not only sense how many others are around them but also who their neighbors are. Autoinducers are universal to both Gram positive and negative bacteria and are unique to the type of bacteria that produce them.

This provides the bacterium with qualitative information on the population of its surroundings. Are they friends or foes?

Quorum sensing also includes nametags so bacteria can tell friend from foe. (Nidhi Srivaths)

In marine vibrio (a genus of Gram-negative bacteria), Bassler’s lab found that quorum sensing could perform intra-species, intra-genus and inter-species identification. This additional information helps the microbes adjust their behavior – from being friendly and supportive towards their relatives to being aggressive and competitive with their enemies.

Bassler provided a real-world perspective on quorum sensing. One species of the vibrio genus, Vibrio cholerae, is responsible for causing Cholera a deadly food and water-borne disease that has plagued low- and middle-income countries for centuries.

When the cholera bacteria enter the host, they are highly virulent and create a sticky biofilm around themselves that helps them clump into aggregates. Their cell density increases with bacterial division until the bacteria sense a certain concentration of autoinducers. Then their gene expression is modified to reduce virulence and biofilm production and the bacterial gene expression patterns shift to escape mechanisms. The bacteria soon break out in large numbers in search of a new host. (Their human host has voluminous, watery diarrhea in response and that becomes the vector for infecting new hosts.)

While the sequence of events that occurred in a cholera infection was known, the discovery of quorum sensing in V. cholerae opens doors for possible treatments, Bassler said. As bacterial communication sets the cycle of infection and division in motion, interfering with the autoinducers produced or disrupting bacteria’s ability to sense them sets the stage for innovative therapies for several infectious diseases.

Quorum sensing is another step towards understanding the world of the tiny microorganisms that influence our world and Bassler and her team are another example of the incredible research that can come from diverse teams in science.

Post by Nidhi Srivaths, Class of 2024

A Puzzling Saga – Meet Duke Math’s Breakout Star!

When I think of crosswords, I think of young and old alike gathered around a couch, scribbling away on a freshly arrived newspaper on a clear Sunday morning. When I think of math, I think of passionate professors covered in chalk dust from a hard day’s work of etching out complicated Greek symbols and numbers on a huge blackboard. These two visions had always been comfortably separate from each other (disjoint sets, if you will) – until I met Dr. Adam Levine.

Meet Duke’s Adam Simon Levine – who shares his name with a pop star, and is a math and crossword rockstar in his own right.

Levine is an Associate Professor in the Department of Mathematics at Duke who studies low-dimensional topology, surfaces, knots and manifolds, using something called Heegaard Floer homology. But apart, from his incredible passion for his field, numerous grants and tongue-twister-esque research interests, Levine has one accomplishment that sets him apart.

He published a crossword puzzle in the New York Times on Sept. 25!

In our Zoom conversation, Levine was bright, chirpy and incredibly excited to talk about his unique love for crosswords and how he’s kept his hobby alive even under the pressures of academic life. As a teenager he loved working on puzzles like Scrabble, playing around with words and etymology, and of course, crosswords. As he grew older, he continued to be fascinated by words.

As an undergrad taking a History of Life class at Harvard, Levine learned about the the impact site of the asteroid that wiped out the dinosaurs, the Chicxulub crater. His first thought was, “That’s a fantastic word– that would make the perfect crossword entry!” His fascination with the word would stay alive for years, until it became the seed entry (the word that anchors the puzzle) for his first crossword to be published in the Times. His love for wordplay through the years is clear, from a self-composed song on Heegaard Floer homology, to a sonnet summary of his PhD thesis.

Watch Levine’s self-composed song here.

Levine continued to solve puzzles as he earned his multiple graduate degrees in mathematics, and began publishing his own puzzles a few years on his aptly named blog – Knotty Grids. Crosswords have been a fun and necessary hobby for him – a way to de-stress or take his mind off his academic work. He thinks it is an important example to set for undergraduate students hoping to pursue a career in math – to show them that it is possible to be “full human beings” and have diverse and unique hobbies, interests and a life outside of your research.

Levine often intertwines his puzzles with his primary interest. Some of his puzzles are “themed” – with “Tying Up Loose Ends” built around topological concepts, and the math-y “Indivisible” which was published in The Mathematical Intelligencer. His personal favorites, however, delve into the meta-puzzle genre with “The Queen’s Gambit” and “A Series of Unfortunate Events.”

Levine’s crossword grids are very literally inspired by his daily work with knots.

When I talked to him shortly after the NYT puzzle appeared, Levine was still visibly excited. He compared the puzzle-publishing journey to that of submitting his mathematical research to academic journals – tedious, long and not very fast-moving. Having submitted the crossword to the newspaper more than a year ago, he heard back from them early this year, at which point they began editing and working on the final publication.

As Levine spoke about the editing process, he brought up an issue that has been important to him – diversity in the puzzle world. Because most crosswords have been written by white men, clues and answers are often tilted towards what that demographic considers common knowledge, and minority and female creators have remained a very small voice. Erasure of their identities is common, and  Levine related a firsthand experience. His clue for “ROBIN” was “the first Black woman to host Jeopardy.” But it was initially edited to be a reference to the bird.

Levine says he pushed back on the parts of the puzzle that were important to him, and was glad with the final published result.

He says he was amazed by the outpouring of support and congratulations he received after the crossword came out. His parents were “really pumped,” family excited, and colleagues incredibly surprised to see his name in print (on a non-academic paper). Unfortunately, the weekend that the crossword was published, his undergraduate students were cramming for a midterm scheduled that Monday, which Levine figures might be the reason some of his crossword-fanatic students seem to have missed his big moment of glory.

In the following week, I spoke to one of Levine’s academic advisees and other Duke students passionate about puzzles, who shared an initial shock and an immediate subsequent joy in the Blue Devil puzzle representation that this publication debuted.

 While Levine has no imminent plans of writing another NYT puzzle, he continues to write for his personal blog. Hopefully, his unique journey inspires students and faculty from different fields and of varied backgrounds to contribute, create and participate, helping make his dream of a diverse puzzle world a reality.

Post by Nidhi Srivaths, Class of 2024

New Blogger Nidhi Srivaths: Attracted by Words

Before I moved to the U.S, the concept of a “Starbucks name” was foreign to me, but after six cups of coffee that read everything from “Nemo” to just an unintelligible scrawl, I understood the need for it. Back home in India, my name was quite common, but having to repeat myself multiple times only to still be misheard made suddenly made feel unusually unique.

Speech can often be tricky, and growing up in a family that speaks four languages interchangeably, I’ve always been acutely aware of that. Missing a tongue roll on the word for “tell” in Kannada makes it dinner-table inappropriate, and a small vowel slip in Telugu can completely alter conversational context. I lived in India’s objectively best city, Hyderabad, that has its special version of Hindi, which was unacceptable in conversation with my mother’s own dialect. Language was thus the most unique part of my upbringing, and the unconventionally twisted sentences that combined the vocabulary of two languages and the grammar of another are characteristic of my childhood.

Raised amidst the chaotic storm of my family’s polyglotism, I found my shelter under the pages of books. Writing soon became a beautiful structure of stability for me, and the decisiveness of ink on paper drew me to it. At first, I began to read simply because I loved dragging my finger across the smooth finish of my brother’s gigantic encyclopedia but soon my childish captivation with the book turned to fascination with its contents. I loved hunting for and sounding out difficult words, and my favorite ones would always be the scientific terms.

So, the world of science was the logical next destination.

My strange love for the word “bioluminescence” led me to the ocean, and for months, I dreamed of glowing plankton and starfish. When “constellation” caught my fancy, I spent years imagining myself flying through the vast expanse of outer space, journeying to the very ends of the universe as an astronaut. From the cozy confines of my bedroom, I traversed through Egyptian ruins with “pharaoh”, Norse myths with “valkyrie” and dinosaur dig sites with “paleontology.” Finally, it was an anatomy book that bound me to the world of healthcare and the human body, and my brother’s weekly technology magazine that pulled me towards automation, before I settled on the middle ground I now love – biomedical engineering. Now a sophomore majoring in BME and ECE, I learn new words every day!

Scientific innovations and advancements are often looked at as difficult to understand, discouraging many from learning more about them. But science is embedded in every facet of our daily lives, and I believe it is essential (now, more than ever!) that its literature and progress become more accessible and understandable. As a child, it was the simple, clear and concise language of informal blogs and books that convinced me that I belonged in the fields I read about, and as a blogger, I want to convince many more that the world of science is well within their reach! Fancy terms like glycolysis may seem daunting, but everything can be broken down and made simpler (in this case, quite literally!). Blogging for Duke Research, I hope to meet trailblazers, learn and write about research that fascinates me, and make it accessible to more people. Along the way, I want to introduce the next inquisitive little girl to the exotic word that feeds her imagination, propelling her into the world of science!

However, beyond my selfless mission of spreading the good word of science and technology far and wide, I recently found a new, far more relatable reason to love writing – I don’t need a Starbucks name! It’s a lot easier to just tell you my name is Nidhi.

Post by Nidhi Srivaths, Class of 2024

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