Summer research on using biologically-inspired models to fight water pollution

By Brian Tarnai ’20

The opportunity to participate in summer research as a freshman was incredible. This research gave me my first real glance into how the scientific community really works. In my project I was working with both Hampden-Sydney and Virginia Tech professors to create a bioinspired, 3D printed prototype that would collect trash in rivers.  The results of this work will be integrated into a National Science Foundation proposal that would enable undergraduates from across the nation to engage in projects that combine techniques in biology and engineering to ethically solve world challenges like water pollution.

3D-printed mangrove roots as a potential model for trapping and clearing of water waste

3D-printed mangrove roots as a potential model for trapping and clearing of water waste

During this project I stepped out of my comfort zone and developed valuable insight into many aspects of professional science that I was unaware of. I learned how to communicate with professors from different institutions to effectively accomplish a goal, write and submit research protocol, learn and master new technology,  obtain permission to use live animals in an experiment, and how to correctly address adversity in a professional manner. This research has taught me that I have the ability to think big and also possess the practical means that will allow me to reach any goal I set. The lessons and skills that I’ve developed this summer will be extraordinarily beneficial on my path to medical school and into the world beyond.

By testing biological models like this spider web at small scale, we can learn more about how effective they may be at fighting water pollution in a true environmental situation

By testing biological models like this spider web at small scale, we can learn more about how effective they may be at fighting water pollution in a true environmental situation

The author hard at work generating models from the 3D printer

The author hard at work generating models from the 3D printer

H-SC students present class-based research at national HHMI symposium

2017 marks the sixth year of Hampden-Sydney’s participation in the Howard Hughes Medical Institute’s (HHMI) Science Education Alliance-Phage Hunters Advancing Genomic and Evolutionary Sciences (SEA-PHAGES) program.  SEA-PHAGES is a national initiative in which undergraduates from roughly 100 institutions work to isolate and characterize bacteriophages, or viruses that infect bacteria, from the environment by molecular and bioinformatics methods.  Each year, students from Dr. Mike Wolyniak’s Molecular and Cellular Biology course work to isolate and analyze novel bacteriophages while Genomics and Bioinformatics students annotate and study the DNA genomic sequences of these bacteriophages.  Dakota Reinartz ’18 and Wood Morgan ’18 were members of both classes and recently presented some of the class’ work at the annual SEA-PHAGES symposium at HHMI’s Janelia Farm Research Campus in Ashburn, Virginia.

Dakota and Wood outside Janelia Farm

Dakota and Wood outside Janelia Farm

The HHMI Janelia Farm Research Campus

The HHMI Janelia Farm Research Campus

Dakota and Wood presented work on the class’ characterization of Thespis, a bacteriophage isolated previously by David Bushhouse ’19 that infects and destroys Mycobacterium smegmatis, a close relative of the bacteria responsible for tuberculosis.

Dakota presents the poster on Thespis characterization to a symposium guest

Dakota presents the poster on Thespis characterization to a symposium guest

Wood's turn

Wood’s turn

The data collected from SEA-PHAGES students can be examined at phagesdb.org and has led to several peer reviewed publications on the ways in which viruses evolve and adapt in different environmental conditions.  SEA-PHAGES is one of several opportunities Hampden-Sydney biology students get to interact with authentic research questions in their coursework.

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Wood, Dakota, and Professor Mike Wolyniak at the SEA-PHAGES Symposium

Student summer research on whale behavior and baleen dynamics

By Mark Mason ’18

For my summer research project I am working with Drs.  Alex Werth and Stan Cheyne from the Biology and Physics departments, respectively, to try and determine the factors that cause an unusual fish behavior. This behavior was first noticed when scientists observed humpback whales using bubbles to corral baitfish together near the surface, making them easier to catch, in a hunting strategy called bubble netting. Many studies have been done on the behavior of the whales and how they coordinate this unusual hunting strategy but there haven’t been any studies looking into why it works. This is why I will be using small fish and various tanks and aquarium bubblers to try and figure out why the fish don’t want to swim through the bubbles.

The author developing his model at small-scale

The author developing his model at small-scale using beads to simulate bubbles

Eventually I will use the five hundred gallon tank in the physics department that Dr. Cheyne uses for his bubble research to try and replicate this phenomena. Early results in small freshwater tanks using zebrafish, a small species of minnow like fish, are promising and have proven that this is something that can be replicated in the lab.

By Shemar Blakeney ‘18

This summer, I am working with Professor Werth to examine the effects of oil on baleen plates. During these experiments, we will be analyzing the compression and tension of the baleen plates. Also, we will be using a flow tank to study the filtration system of baleen. With another version of the flow tank, we will test how the oil will affect the filtration system of the baleen plates. This research will benefit many baleen whales if an oil spill were to occur.

Baleen covered in oil for experimentation on its effect on water flow

Baleen covered in oil for experimentation on its effect on water flow

Shemar Blakeney '18 inserts baleen into the flow tank

Shemar Blakeney ’18 inserts baleen into the flow tank

This research will benefit me in the future because I plan on obtaining my Ph.D. in Marine Biology and becoming a cetologist to study killer whales. The research I am doing is priceless to me.

Baleen flow experiment in progress

Baleen flow experiment in progress

Summer research in protein biochemistry

By Jason D. Pough II ’19

This summer I am working with Professor Michael Wolyniak to create an experiment for a laboratory that will be part of the future Biochemistry classes. Moreover, we are working on creating and purifying the Myf-5 Myogenic Regulatory Factor protein to assist with Professor Kristin Fischer’s research in regenerative skeletal muscle tissue as a part of creating the lab. Myf-5 is one of several Myogenic Regulator Factors that is involved with differentiating and creating muscle cells during Myogenesis. For Professor Fischer’s research, we plan to take a plasmid containing Mus musculus DNA and mutate it using site-directed mutagenesis in order to create a mutant Myf-5 protein that hopefully will aid in skeletal muscle regeneration research in conjunction with Professor Fischer’s research.

The tools of the trade for site-directed mutagenesis

The tools of the trade for site-directed mutagenesis

The overall project will aid in creating a Biochemistry laboratory by familiarizing ourselves with the techniques and methods used to carry out the Myf-5 experiment, and we will create methods and procedures for future biochemistry students to follow. One instance is with the aforementioned site-directed mutagenesis where, much like Real Time PCR, one uses primers and enzymes, yet we mutate specific sections of DNA. The mutated DNA is then inserted into a host bacterium where it will clone into a plentiful amount of bacteria with the mutated plasmid. Another instance is with the MinION Sequencer, provided by Oxford Nanopore, which uses thousands of protein pores to read the nucleotide sequence of injected DNA. The MinION Sequencer will be used to determine if the plasmids actually mutated and thus create a mutated protein. We hope that the results will not only aid Professor Fischer’s research, but also be the roots of future biochemistry laboratories and aid prospective Biology and Biochemistry and Molecular Biology majors.

Bacterial colonies after selection against ampicillin. The plasmid DNA in these cells will be sequenced to see if the desired mutation was created.

Bacterial colonies after selection against ampicillin. The plasmid DNA in these cells will be sequenced to see if the desired mutation was created.

The author prepares DNA for analysis

The author prepares DNA for analysis

H-SC summer research: developing scaffolds for mammalian tissue engineering

By Tyler McGaughey ’18

This summer I am working with Dr. Kristin Fischer to develop a porous gelatin cross-linked hydrogel scaffold for skeletal muscle tissue engineering. Through my work as an Emergency Medical Technician, I have seen numerous patients that have lost major sections of tissue. These injuries result from things like major trauma such as a car accident, violent crimes or systemic burns. These injuries have either forcefully removed the tissue or damaged it beyond repair. There are several clinical options doctors may choose: amputation, skin grafting, transplantation, or, the most interesting option, tissue engineering which is growing a new section of tissue in vitro. The ability to grow tissues outside of the body then implant them in or on humans used to be science fiction, but it is happening this summer on “The Hill”.

Dr. Fischer and I are working to answer the question of what is the best way to use the tissue engineering approach. Currently we are working with a line of mouse muscle cells called C2C12.

C2C12 cells under 400x magnification

The cells grow well given the right environment in flat sheets. However, the problem stems from layering the cells vertically. The cells in the center of the mass begin to die off due to lack of nutrients and surface area for diffusion of waste products. I intend to solve this problem by developing a gelatin scaffold for the cells to grow in. This will allow for increased diffusion and hopefully increase cell longevity.

Side view of gelatin scaffold to show thickness

Side view of gelatin scaffold to show thickness

I plan to increase diffusion to the gel by introducing pores in varying configurations. Over the last two weeks, I have tried varying number of pins per scaffold from 0-12 pins per scaffold. I have also experimented with different shapes like diagonal lines, squares, and triangles. I have concluded that the triangle formation is most likely the best formation for diffusion. I am currently attempting to print these pore inducing structures using HSC’s newest 3D printer.

3D printing a pore-inducing disk

3D printing a pore-inducing disk

The cross-linking helps the gelatin maintain its 3D structure. Cross-linking is the binding of gelatin molecules together by an enzyme called microbial transglutaminase. I have also been experimenting with different levels of microbial transglutaminase in the gelatin. More cross-linking makes the gels stiffer. There is a fine line between too much microbial transglutaminase causing the gels to rip under tension and too little microbial transglutaminase causing the gelatin to degrade too quickly.

Hydrogels with varying degrees of cross-linking in a 6-well plate

Hydrogels with varying degrees of cross-linking in a 6-well plate

In the body, muscle cells fuse together and work as one. This fusion is caused by the natural tension our muscle cells are under. In addition to introducing pores into the gel, I intend to apply a slight tension to the gels. This tension causes the muscle cells to fuse and mature in one direction as if they were in the body.

Hopefully this summer I am able to design a gelatin scaffold that helps muscle cells grow rapidly and mature.

The author working on cell culture technique in a laminar flow hood

The author working on cell culture technique in a laminar flow hood

3D Printing comes to H-SC Biology

As part of a seed grant project between Hampden-Sydney and Virginia Tech for the development of research opportunities in bioengineering, the Biology Department has received a 3D printer for classroom and research purposes.  As the summer research season kicks off at the College, the timing of this new acquisition could not be better:

Tyler McGaughey '19, Jason Pough '19, and Brian Tarnai '20 install and set up the new printer

Tyler McGaughey ’18, Jason Pough ’19, and Brian Tarnai ’20 install and set up the new printer

The first student project that will take place using the printer will be the construction of filter structures that can be used to clean local streams and lakes.  The project is well-positioned for both undergraduate research and extension to the Department’s ongoing high school outreach program.

This lawn gnome is the first creation of the new H-SC Biology 3D printer

This lawn gnome is the first creation of the new H-SC Biology 3D printer

Congratulations to the Biology Class of 2017!

The Biology Class of 2017 has achieved great things in their four years at the College, and we will miss their presence in Gilmer Hall.  Best of luck to all of our graduates!

DJ Bines                                         Fletcher Borum

Brant Boucher                                Blake Brown

Robbie Bugbee                              Josh Chamberlin

Alex Crabtree                                 Tazewell DelDonna

William Echols                                Gannon Griffin

Treavor Hartwell                             Ryan Kluk

James Lau                                     Zach Martin

Traylor Nichols                               Tyler Reekes

Reuben Retnam                             Zach Tabrani

Harris Thomas                               Mitchell Thomas

Joey Tyler                                      Thomas Vinyard

Dustin Wiles                                  Michael Willis

A.J. Willy                                       John Zohab

 

Biology students honored at Hampden-Sydney Final Convocation

The Hampden-Sydney Biology Department was well represented at the College’s Final Convocation, an award ceremony recognizing outstanding academic achievement during the 2016-17 year.

The James R.T. Hewett Biology in recognition of outstanding achievement in the Biology Department was given to James Lau ’17.  James graduated as the Valedictorian of the Class of 2017 and will be attending Eastern Virginia Medical School in the fall.

James Lau '17 receives the Hewett Biology award from Chair of Biology Alex Werth

James Lau ’17 receives the Hewett Biology award from Chair of Biology Alex Werth

The H.B. Overcash Prize for outstanding achievement among pre-health junior students was awarded to Nicholas Chase ’18.

Dr. Werth enthusiastically awards the Overcash Prize to Nicholas Chase

Dr. Werth enthusiastically awards the Overcash Prize to Nicholas Chase

The two Sophomore Academic Excellence Awards for highest GPA in the sophomore class were both given to biologists.  First awarded was Biochemistry and Molecular Biology major Blake Martin ’19.

Director of the Office of Academic Success Lisa Burns presents Blake Martin '19 with his award.

Director of the Office of Academic Success Lisa Burns presents Blake Martin ’19 with his award.

Next awarded was Biology major Coleman Johnson ’19.

Coleman Johnson '19 with Director Burns

Coleman Johnson ’19 with Director Burns

Finally, to show that Biology majors appreciate the full gamut of the liberal arts, Biology major David Bushhouse ’19 received the Sallie Wright Harrison award from the Department of English for his poem which considered the origins of his last name.

Dr. Steele Nowlin, Chair of the Department of English, and David Bushhouse '19

Dr. Steele Nowlin, Chair of the Department of English, and David Bushhouse ’19

H-SC Biology research presented at international Biochemistry and Molecular Biology meeting

This year, Hampden-Sydney sent two of its students, Brant Boucher ’17 and Jason Halmo ’17, accompanied Associate Professor of Biology Mike Wolyniak to the Annual Meeting of the American Society for Biochemistry and Molecular Biology  (ASBMB) in Chicago.  Part of the Experimental Biology federation of 6 biology professional societies, ASBMB is an international gathering of scientists and one of the premiere opportunities to explore the frontiers of biochemistry and molecular biology.

Jason Halmo and Brant Boucher at the meeting

Jason Halmo and Brant Boucher at the meeting

Both Jason and Brant presented work done as part of their work done jointly between the Biology and Chemistry departments.  The work was presented both at an undergraduate-only session as well as the general session for the entire meeting.  Jason presented his work on the characterization of chemical and genetic differences in hopped meads done between Dr. Wolyniak and Associate Professor of Chemistry Paul Mueller.

Halmo presents his work to fellow undergraduates.

Halmo presents his work to fellow undergraduates.

Halmo also coordinated an outreach initiative, the Prince Edward County Environmental Molecular Biology Institute (PECEMBI) with Dr. Wolyniak.  Funded in part by a grant from the ASBMB, PECEMBI brought a long-term research project to the students of Prince Edward County High School with outreach support from Hampden-Sydney students and faculty.  Both Halmo and Wolyniak presented a poster on PECEMBI at the meeting.

Presenting at the Public Outreach Poster Session

Presenting at the Public Outreach Poster Session

Boucher’s work was jointly done by Dr. Wolyniak, Associate Professor of Biology Kristian Hargadon, and Visiting Assistant Professor of Chemistry Rupak Due and focused on the development of bacterial biofilms on titanium bone replacement implants.

Brant Boucher presents his work

Brant Boucher presents his work

ASBMB is one of several national and international meetings that are regularly attended by Hampden-Sydney undergraduates as a culmination of their research work at the College.

H-SC biology student research presented at the Virginia House of Delegates

Two Hampden-Sydney students, Brant Boucher ’17 and Jason Halmo ’17, recently presented their ongoing research work at the Virginia House of Delegates in conjunction with the Student Research Showcase at the Capitol event put on each January by the Virginia Academy of Science.  The event is designed to highlight undergraduate student research in the STEM fields to the state legislature and allow legislators to interact with students from across the Commonwealth who are actively working on projects.  Brant and Jason represented 2 of 19 total projects that were presented at the event.  The projects represented all varieties of undergraduate institutions in Virginia, including public and private schools as well as 2-year and 4-year institutions.

Brant presented his work done with Dr. Hargadon on the characterization of methods to combat melanoma.

Brant presenting his research poster

Brant presenting his research poster

Jason’s presentation focused on work being done in conjunction between the Biology and Chemistry departments on the characterization of yeasts used in the production of different types of meads.

Jason listening to questions on his project

Jason listening to questions on his project

Jason and Brant accompanied Biology professor Dr. Mike Wolyniak to the event.  Dr. Wolyniak is the Science Education chair for the Academy and helped to coordinate the event.

Group picture of all student participants

Group picture of all student participants

Brant and Jason valiantly transport the easels and poster backings to Dr. Wolyniak's car in a driving rainstorm

Brant and Jason valiantly transport the easels and poster backings to Dr. Wolyniak’s car in a driving rainstorm