Today (yes, October 12th!) at 4 PM, Dr. Heidi Andersen from Cincinnati Children’s Hospital Medical Center will be presenting her bioinformatics research. Computational genomics is a rapidly advancing field that uses and develops software to detect patterns in biomolecules like DNA, RNA, and proteins. Our guts host many different bacterial species, and Dr. Andersen pieces together their DNA sequences to determine which are present. She is especially interested in tracking the microbes that are multi-drug resistant (those that survive many of the antibiotics we throw at them) across pediatric patients in the hospital.
A quick brush up on some computational biology vocab before the presentation never hurts:
Metagenomics – the study of the many genomes present in a given environmental sample
Microbiome – the community of microbes in a given environment
Shotgun sequencing – a method of determining the order of nucleotides (A, C, T, G) in a given DNA sequence by breaking it into short fragments, sequencing these, then piecing them back together computationally
Contiguous sequence (“Contig”) – After sequencing the separate DNA fragments in shotgun sequencing, we need to assemble them back together for a longer, more complete sequence (a contig)
16S rRNA gene (“16S”) – a ribosomal RNA gene that is used to identify bacteria and archaea at the genus level
Extra credit – Understanding PCA
If you want to know all the gory details of Principal Component Analysis, a method you will see often in computational biology, check out this post here
This week, intro bio lab students geared up for their Manduca sexta dissection. These tobacco hornworms had grown significantly since students placed them in their plastic “bachelor pad” cages last week. While all hornworms at least doubled in size, the largest of the group were almost 100 times their weight from last week. Thank goodness that’s pretty impossible for humans to do or Kenyon would need to invest in a better health plan now that Marco’s Pizza accepts K-Cards.
Hornworm fact #1: Time to expand your insult dictionary – the genus Manduca literally means glutton. Try that one at Thanksgiving.
Hornworm fact #2: After a good chomp on a tobacco leaf, Manduca have “toxic halitosis” aka poisonous bad breath from the nicotine which deters spiders from eating them.
Hornworm fact #3: Adult Manduca hawkmoths can eavesdrop on the sonar clicks of bats and drop out of the air to avoid being bat food.
If you know the story of The Very Hungry Caterpillar by Eric Carle, the life of a Manduca is quite similar. Rather than eating sausages and ice cream turning into a beautiful butterfly, though, Manduca hornworms eat the leaves of tobacco, tomatoes and other members of the nightshade family (Solanaceae), then metamorphose into a hawkmoth that can hover like a hummingbird. Reared in the lab, however, the Manduca is a beloved model organism with ease of care, rapid growth rate, and accessible anatomy.
This year, the bio lab sections are testing the effect of diet nutrition on overall growth of the organism. Some Manduca will have less nutrition per bite in their food for 48 hours, perhaps affecting how much they eat, absorb nutrients, or grow in a 48 hour period. After this diet change, students hit the microscopes to investigate.
Spiracles and fat bodies
Malpighian tubules and midgut
Malpighian tubules and midgut
Malpighian tubules and midgut
Whether they named their Manduca after their TA (shoutout to Jeremy Moore ’19), took beautiful anatomical pictures under the microscope (see above), or made a video in their hornworm’s honor like Patrick Olmstead ’21 (below), students found a way to connect with their lab-reared pe(s)ts.
In Kenyon biology, students learn not only how to perform scientific inquiry but how to communicate their science clearly and effectively. Dr. Christopher Gillen has a passion for understanding how animals work, and his research specializes in salt and water balance physiology, most recently examining salt absorption and secretion in the Aedes aegypti mosquito. His course Biology 243: Animal Physiology is one of the most popular in the department, and students compare complex physiological processes across different organisms under Dr. Gillen’s enthusiastic instruction. In addition to his passion for understanding how animals work, Dr. Gillen is passionate about making scientific research understandable and enaging for all audiences and he is the faculty director of the Kenyon Institute in Biomedical and Scientific Writing. This semester, he launched Kenyon’s first science writing seminar course with Professor Sergei Lobanov-Rostovsky of the English department, where students read and discuss a wide variety of literature with a scientific focus, write voraciously on their own scientific fascinations, and experiment with the many techniques and nuances of the science writing genre.
Dr. Gillen stresses the importance of communicating science in all of his classes, particularly how to write about science for a variety of audiences:
“Pitching complicated research to a general audience is hard. Students must understand the science deeply and frame it with compelling writing and storytelling. And the skills they learn writing for a general audience transform them into better scientific writers.”
In Animal Physiology, students were asked to complete a News and Views assignment where they write two essays on the same scientific research article: one essay that makes an argument about the research to an audience of scientists and another essay that explains the research to a broader audience of non-scientists. Here is one such article for a general audience, written by junior neuroscience major John Wilhelm:
A beautiful birthday cake, courtesy of The 8 Sister’s Bakery
Every few weeks the biology department gathers in Fischman 103 for Biojournal club, an informal gathering of faculty and students. Student leaders mine recent journal publications for exciting research papers, and we carefully select an intriguing study to discuss as a department. We gather at 12 for pizza and beverages to accompany delving into deep scientific literature. At the small discussion tables, students and faculty alike delve into the texts of the papers, deciphering statistics, interpreting graphs, and raising questions about methods and conclusions. Every meeting yields a new discussion with topics ranging from plant physiology in seed dispersal mechanisms to rapid-scale bacterial evolution to editting the human genome.
In joint celebration of Charles Darwin’s 208th birthday and Valentines Day, our paper focused on sexual selection and the sex-driven ornamentation driving speciation of finches. Discussion was lively, and all involved felt the love for evolution, Darwin, and biology. The discussion ended with Dr. Slonczewski showing pictures from her trip to the Natural History Museum in London, England, which is proclaimed as a temple of sorts to Darwin and his revolutionary theories of evolution.
The paper discussion ended early so attendees could sing ‘happy birthday’ to our dear friend, Chucky D, and enjoy his delicious chocolate-vanilla layered birthday cake. We may have temporarily lowered our fitness by consuming all of this sugary cake, but rest assured that the long-term benefits of celebrating Darwin as a department outweighed any costs.