Wednesday, January 22, 2020

Using the PDB in the College Classroom

The Protein Data Bank (PDB, was started in 1971 and now contains  almost 148,000 solved structures.  The Protein Structure Initiative (PSI) solved large numbers of protein structures between 2000 and 2015, whether a function was known for the protein or not.  This large pool of structures has deepened our understanding of structure/function relationships.  There are currently approximately 4500 proteins with solved structures but characterized as having “unknown function”.  Identifying functions for these proteins is the focus of the BASIL curriculum—see the BASIL curriculum links at the top of the page for more details.

The PDB can be used in many educational contexts.  In the January 2020 issue of the PDB Education Corner, I had the opportunity to highlight some of my own experiences using the PDB with students(  Those uses range from pre-nursing students in a General, Organic and Biochemistry (GOB) course to Biochemistry majors doing independent research projects.  Although I have become comfortable using the PDB with students, it was daunting the first time I had students use PyMOL to look at the details of a PDB file.  My graduate and post-doctoral work did not involve using the PDB, and I had no computational biochemistry experience.  The student worksheet/tutorial provided by Taylor et al. (Taylor, E.V., J.A. Fortune, and C.L. Drennan. “A Research-inspired Laboratory Sequence Investigating Acquired Drug Resistance.” Biochem. Mol. Biol. Educ. 2010. 38, 247-52. DOI:10.1002/bmb.20384) was immensely helpful for understanding how to access the rich detail present in each PDB file, and provided practical ways to engage students with structure/function relationships. 

The PDB itself now has its own excellent visualization tools (my current new favorite is the “Ligand View” in the “3D View” tab).  I find myself using the PDB more and more when teaching Biochemistry, even with non-majors.  I like that the PDB, and especially the Education Corner articles, push me to explore new proteins, new visualization tools, and new ways of interacting with structural information. 

Thursday, January 16, 2020

BASIL 2019 Year in Review

The Biochemistry Authentic Scientific Inquiry Lab (BASIL) team was hard at work in 2019.

  • Eleven BASIL modules with standardized pedagogy were published and are freely available at
  • Twelve institutions across the country and in Ireland carried out BASIL on their campuses.
  • Two papers published.
  • Development of Moltimate – a web application enzyme active site alignment tool.
  • BASIL became part of the CURENet collection (
  • One member carried out a BASIL-focused sabbatical.
  • A STEM for ALL BASIL video was viewed over 1300 times worldwide (
  • Workshops at Fayetteville State University and BCCE.
  • 7 presentations at national meetings.
  • BASIL members participated in the ACE-BIO network workshop on assessment.
  • One NSF supplement was funded.
  • One NSF-IUSE proposal was submitted.

2019 STEM for All Video Showcase: Innovations in STEM Education

The BASIL project is a combination of wet bench biochemistry experiments and bioinformatics exercises where students predict the function of a protein and then test their hypotheses. BASIL has been...(43 kB). Just in case the link above does not work, here is the full URL:

Friday, August 30, 2019

BASIL in Ireland, Part 2

BASIL Reflection by Geoff Morris

The task of optimising, purifying, and characterising the novel protein of 4DIU presented itself as a multi-faceted challenge, requiring an appreciation and understanding of numerous different branches of science to complete. Across the first semester of my final year, I took a novel protein of which I had no prior knowledge, and brought it from the initial glycerol stock containing a plasmid in a host cell, right through to a purified protein upon which I conducted characterisation tests and compared results achieved to sequence and structurally similar proteins.

The combination of research, laboratory testing and comparison of results to that of in silico matches provided a final year project which tested numerous skills developed in the three previous years of the course, coupled with the requirement to learn and apply new skills as they became required.

For me, the primary objective of completing the final year project was to gain as rounded an experience of experimental design and implementation as possible within the finite time allocated.

Initially, I chose the project title of “The optimisation, purification and characterisation of a novel protein”, based on little more than an inkling that protein research was to be my area of interest. Previous study of the macronutrients, compounded by biotechnology and biochemistry lectures had highlighted to me the huge potential of variation derived from simple structures of base pairs, leading to amino acids and on to form proteins with a hierarchy of structural confirmation.

Commencing the project, I did not have the slightest idea of the layers of work, or multitude of steps and procedures that were required to complete the thesis. Here is where the BASIL modules slotted in appropriately to fill a void in my knowledge. The breakdown of aspects into background knowledge, objectives, techniques, supplies, sample procedure and theory provided a solid foundation of information, from which I was able to build a greater and more specific understanding of the scientific aspects to suit my particular novel protein. As I’m sure everyone has experienced when attempting a new subject or topic, starting is the most difficult part. This holds particular truth when there is no prior experience or understanding of a procedure. The BASIL modules provided a baseline of understanding which I had found difficult to achieve when attempting to comprehend a topic purely from the work of other research papers.

The modules are unlike research papers in that there is no requirement to navigate around the results of the research paper and their (often very different) procedures. The modules outline the rationale of the procedure as a whole, with the intended end-goal while also including the highly beneficial section of “Experimental Design Considerations”, in which possible considerations are highlighted, allowing the user to effectively think through the process prior to commencing, and therefore avoiding the issue of completing a step, only to realise particular considerations were not made, negatively impacting upon results and requiring repetition.
Having now completed the final year project, I have developed an appreciation of the numerous disciplines required to investigate a novel protein. Additionally, I have found a great interest in the stages of optimisation, purification and characterisation of proteins, which have influenced my desire to complete a post graduate degree in MSc Bioprocess Engineering, within Dublin City University. The understanding and skills I have developed throughout the final year project will be utilized and added to through additional lectures and a bioprocessing design project, ultimately allowing me to progress my education and build a career with the potential to work in several industries including biotechnology, pharmaceutical and food.

Geoff Morris completed this work with Dr. Barry Ryan at the University of Dublin in Dublin, Ireland. 

Monday, August 12, 2019

BASIL in Ireland, Part 1

BASIL Reflection by Claire Reynolds

For my final year dissertation, I selected a challenging project which involved optimizing, purifying and characterising an unknown novel protein known as 3H04. This project presented a complex challenge which required adverse scientific knowledge and a strong understanding of scientific laboratory techniques. The project title “Novel Recombinant Protein Production, Optimization, Purification and Characterisation” appealed to me due to my keen interest in the development of novel proteins. Personally, the main objective of this project was to gain additional skills and further develop my laboratory techniques which I have gained over the past three years in my Nutraceutical course. After studying several subjects including biotechnology, biochemistry and microbiology, I have developed an in-depth understanding of the structure and function of proteins and gained insight into the expanding market of novel proteins which offer potentially new innovative treatments, functional foods and areas in the animal, plant and medical sector.
For this project to be sufficiently completed, the BASIL modules were utilised and followed to successfully achieve a final outcome. The in silico analysis tools provided by the BASIL website were primarily used at the beginning of the task to determine previous studies on the 3H04 enzyme and its predicted protein sequence, structure and function. The novel 3H04 enzyme was characterised as an alpha/ beta hydrolase by the protein data bank. This enzyme was derived from the organism Staphylococcus aureus strain Mu50 and expressed in E. coli BL21 (DE3) cells in a pMCSG19 cloning vector.

The production and optimization stages were quite tedious as optimum conditions including optimum time, temperature, optical density and Isopropyl β-D-1-thiogalactopyranoside (IPTG) concentrations were essential for optimal growth. Optimization proved to be successful when recombinant protein cells were grown to an optical density of 0.4, induced with a final IPTG concentration of 1mM and shaken at 220rpm for 24 hours at 37°C. The enzyme was extremely difficult to purify and thus proved to be the most time-consuming step out of the whole project. Purification was carried out using His-Tag affinity chromatography. This step was carried out in conjunction with another final year student who was also attempting to purify a novel enzyme. After several weeks of troubleshooting the failed purification, the target protein was eluted with 50mM imidazole concentration. Sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) was carried out to identify the molecular weight of the protein. However, this proved to be unsuccessful as only a small concentration of protein was purified. A non-reducing SDS-PAGE was then carried out and a band was visible under ultraviolet light at the 31kDa mark. This successful purification step then allowed me to move on to the final characterisation process. Throughout this process, I worked collaboratively with another final year student who was characterising his novel enzyme. Characterisation was conducted by determining the proteins optimum temperature, activity loss, solvent tolerance and pH profile. The novel protein proved to have an optimum temperature of 40°C, optimum pH 7, and could tolerate polar solvents better than non-polar solvents. A substrate specificity assay also clarified the proteins binding specificity to short chain fatty acids (p-NP acetate).

Overall, the BASIL modules collectively allowed me to successfully characterise the novel enzyme as an alpha/ beta hydrolase. I found this project challenging yet extremely rewarding when the results came together and allowed me to progress further onto each step until characterisation was finally completed. I feel the BASIL website is extremely useful and user friendly which is essential when trying to optimize, purify and characterise a novel enzyme. Now that the 3H04 enzyme has been characterised as a hydrolase, one could apply the hydrolase to a chemical reaction to determine its effects and identify if the reaction may be reversible. Having completed my dissertation, I now feel I have gained valuable experience in the biotechnology industry allowing me to pursue a career in the biotechnology, pharmaceutical industry and food sector.

Claire Reynolds completed this work as a final year project with Dr. Barry Ryan at The University of Dublin in Dublin, Ireland. Dr. Ryan became interested in BASIL after meeting Dr. Julia Koeppe from SUNY Oswego at a biophysics meeting.

Wednesday, July 10, 2019

BASIL Update from Ursinus

Image Preview
Ursinus students in Rebecca Roberts's lab perform interdisciplinary research outlined in the BASIL curriculum, which is being adopted in science classrooms around the world.

Here is a link to a great article on the Ursinus College web site. I have pasted in the image and content as best I could.

Ursinus-led BASIL Curriculum Takes Root in Science Classrooms
July 10, 2019

Ursinus College is one of eight institutions that have collaborated on an inventive new biochemistry curriculum designed for lab courses at the high school, undergraduate and graduate levels.

After a number of years of development, the BASIL (Biochemistry Authentic Scientific Inquiry Lab) curriculum, developed in part by Rebecca Roberts, an associate professor of biology at Ursinus, has been published and is publicly accessible online for any institution to incorporate into their science lab classrooms.

It is an effort funded by a grant from the National Science Foundation and developed in tandem with California Polytechnic State University, San Luis Obispo; Hope College; Oral Roberts University; Purdue University; Rochester Institute of Technology; St. Mary’s University; and SUNY Oswego.

“The idea is that anyone can utilize it,” says Roberts, who is lead author on a forthcoming article about the curriculum in Biochemistry and Molecular Biology Education, a leading international journal.

In BASIL, students predict the function of a protein and then study that protein in the lab. The curriculum is flexible and can be adapted to match the available facilities, the strengths of the instructor and the learning goals of an institution, Roberts says.

At Ursinus, it’s part of two Ursinus courses: Structural Biology and Biochemistry II. The structural biology students use computational tools to investigate protein structure and deduce a possible function. Then, biochemistry students express and purify the protein and, informed by the insights of their structural biology peers, assay the protein for the proposed function.

The curriculum aims to get students to work across disciplines and transition from thinking like students to thinking like scientists, Roberts says.

In addition to the development group of institutions, the curriculum has already been adopted by one high school in Massachusetts and a college in Great Britain.

“Graduate students have also picked up on it and so have independent researchers,” Roberts says. “We’re starting to think about how to expand BASIL even more beyond the initial development team and that’s exciting.”

The BASIL initiative, she says, provides broader course-based research experiences for students.

“It’s allowing these students to have a scientific inquiry-based experience,” Roberts says. “They’re learning cutting-edge bioinformatics skills and it gets them to think cooperatively and as part of an interdisciplinary team. That’s how science works now.”

Wednesday, May 15, 2019

BASIL Starter Pack

If you are interested in trying the BASIL curriculum on your campus, you can now order a "BASIL Starter Pack" for just $25 from DNASu, thanks to our own Mike Pikaart. The kit was designed to include ten plasmids that have performed well in our undergraduate teaching labs.

Saturday, May 11, 2019

BASIL Manual

The complete BASIL student manual is now online at the following URL:, thanks to contributions from many of our members, especially to everyone who spend two very fruitful and productive writing days in Rochester in March. A special thanks to Ashley Ringer MacDonald, who build the Github site that supports the manual. Additional information is available to registered university faculty. To register, contact us from your university email address and include your name university affiliation, and the courses where you are considering using the BASIL curriculum. Please use the subject line BASIL Registration in your email.