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Penn State Freshmen are making significant contributions to Science

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A contribution to Science.  What does that phrase convey?  What comes to mind when you hear it?  People often hear this phrase and immediately associate it to faculty or graduate students, because in order to make a contribution to science you have to have a Ph.D. or be close to earning one, right?  In the Biochemistry and Molecular Biology Department at Penn State, that is not the case.  The Freshman Research Experience I and II courses, BMB 398S & BMB 398D, are changing the way undergraduate students get involved and are introduced to science.

 

Dr. Greg Broussard

BMB 398S is a Course-Based Undergraduate Research Experience (CURE).  The course aimsto introduce incoming freshmen to research experiences from the start of their collegiate careers.  The course was created approximately two and a half years ago in the Summer of 2015 with the introduction of Dr. Gregory Broussard to the department.  At that time, the Dean’s Office was pushing for more freshmen research initiatives and Dr. Meredith Defelice, Associate Head of Undergraduate Affairs, was looking for a way to make this a reality.  Dr. Broussard proposed a CURE based on discovery of viruses that infect bacteria (phage) and was immediately asked by Dr. Defelice to design and facilitate the course.

 

The department found that it had research and classroom space, but very little opportunity for the two to overlap.  Students would go to their classes, often lecture-based and in non-laboratory spaces, and then some might make their way into a research lab.  The Phage CURE takes these two experiences and combines them.  Students have the opportunity to conduct real research that has the potential of contributing to science.

 

These freshmen, approximately 40 students divided over two sections, start in BMB 398S at Penn State in the summer.  Once they arrive, they are given their own research project.  Students are given oysters and are asked to open them to remove the virus that infects the bacteria that lives within the oyster.  The students then isolate the virus and then isolate the viruses genomic DNA.  Once the students have isolated the viruses genomic DNA they send it away for sequencing.  The students also perform electron microscopy.  Essentially the students use an electron microscope to get a picture of the virus.  All of this is done in a six week period of time.

FRI CURE Program photo 2 (2018)

The Phage CURE allows students to gain hands on research experience.  Many students find out how much they like research and are more enthusiastic about their science classes the following Fall semester.  Some find out they do not like research and decide afterwards that a career in research is not the career path they wish to take and look for other opportunities on campus to continue their studies.  For those that want to continue the experience, they can take BMB 398D in Fall and Spring.  Those who return to BMB 398D then have the opportunity to work with the sequenced genomes once returned to the lab.  Students are then asked to dig deeper and identify the genes within the genomes and identify what exactly each genes does.

 

The process is called “Annotation”.  Annotation is the identification of all the genes within a genome so that the genome itself can then be studied to determine its function and what it looks like.  The students in the course successfully annotated two full genomes and submitted the information to GenBank® (Accession No. MG649966 & MG649967).  GenBank® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences.  GenBank® is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Nucleotide Archive (ENA), and GenBank® at NCBI. These three organizations exchange data on a daily basis.  The two fully sequenced genomes were the first contributions the course had made.

 

FRI CURE Program photo 1 (2018)

The Phage CURE (BMB 398S & 398D) plans to annotate each fall and submit their research finding to GenBank®.  Prior to the recent contribution of two fully sequenced genomes, GenBank® had 60 other vibriofage genomes.  Dr. Broussard expects to have another 40 fully sequenced and assembled genomes at the end of Spring 2018 and 6 ready to submit to GenBank ® at the end of the Fall 2018 semester.

 

 

The Phage CURE has changed the timeline in which students were introduced to research opportunities and allows students to determine whether a career in research is right for them at a much earlier point in their collegiate career.  No matter which path the students in the program take they are then able to better plan for the rest of their time at Penn State.  Students who decide research is right for them and return to the program for the Spring semester are asked to submit a research proposal to Dr. Broussard for consideration.  Once the proposal has been approved the student goes into the lab and begins their own research project.  In many situations the Phage CURE has also helped students obtain internship opportunities, scholarships and positions in research labs at Penn State.