Phage Safari Gives 1st Year Biology Students Practical Lab Experience while Participating in Annual Nation-wide DNA Sequencing Effort

By Dr. Julia Lee-Soety

Christina King-Smith helps a Biology student in the lab. In 2009, Dr. Christina King Smith and I applied and were chosen to participate in the Howard Hughes Medical Institute (HHMI)-sponsored SEA-PHAGES (Science Education Alliance – Phage Hunters Advancing Genomics and Evolutionary Science) program. This opened an opportunity for us to offer first-year students authentic research experiences and get them excited about doing science. SEA-PHAGES is now in its fifth year with 70 participating colleges and universities from around the country; Saint Joseph’s University has been a member since the second year.

Since the 2009-2010 academic year, four cohorts, each with 13 to 18 first-year Biology and Chemical-Biology students, have participated in Phage Safari. Students are selected to be a part of this two-semester lab experience in lieu of the traditional Cells and Genetics labs. In the fall semester, every student isolates viruses that have infected bacteria from a soil sample they have collected – from around campus, near their home, or at various animal enclosures at the Philadelphia Zoo. These viruses are officially known as mycobacteriphage or just simply phage. Each student would take ownership of his or her phage and even give it an official name. Nearing the end of the fall, the class agrees on one or two phages to be fully sequenced from all the phages the students had isolated.

Electron micrograph of a mycobacteriphage.Over Christmas break, DNA sequencing facilities off campus are hard at work mapping out the blueprints of the phages. Each phage has unique blueprints or DNA sequences that sets it apart from another phage even those that may appear almost identical. The sequences store information that builds up the components of the phage, dictates how it will infect a bacterial cell, and determine how it will multiply before leaving its host. When the DNA sequences are returned to us from the sequencing facilities, they are a long string of Gs, Cs, As, and Ts, representing the 4 nucleotides of DNA. Our job is to annotate it. If a DNA sequence from a phage genome is a continuous string of letters on a piece of paper, then annotating genes is analogous to identifying individual words and meaningful sentences. As each sentence has specific start and stop, each gene has the same.

Students have employed various software programs to help them do this. For the first two years, students worked on web-based workflow containing complex algorithms to identify consensus sequences frequently found at the start of each gene. To further validate the gene, students align each gene with genes of other known phages using BLAST tools; the Basic Local Alignment Search Tool is maintained by the US National Center for Biotechnology Information (NCBI) and has been the staple tool for molecular biologists globally. As freshman, the Phage students are learning and mastering complex bioinformatics tools for research that only a handful of upper level and graduate students routinely use.

In the most recent years, students have been using DNA Master, a specifically designed genome annotation and exploration tool designed and written by Dr. Jeffrey Lawrence of the University of Pittsburgh. This program combines the gene identification algorithms and the BLAST tools onto one single work space. When the software identifies multiple potential starts of a gene, the students must sort through each gene and authenticate it based on specific rules governing all phage genes. For example, one gene should not overlap too much with its adjacent genes. There also should not be large gaps between genes. There have been incidences that DNA Master missed a gene that should have been called. The students will use the BLAST tool within DNA Master and determine if a specific region of the DNA aligns with genes of other known phages. Working in groups of 2-3, students help each other, walk through these software programs, and discuss their decisions.

At the end of the semester, the students’ work is checked before submitting the final draft to the University of Pittsburgh Bacteriophage Institute for further quality control. The team at Pittsburgh formally submits all analyzed phage sequences to GenBank, a database of DNA and protein sequences that is curated by NCBI.

The first cohort (2009-2010) of students identified 102 genes in phage Daisy while the second cohort (2010-2011) identified 97 genes in phage BPBiebs31. The annotated genomes for these two phages are published in GenBank. The 2011-2012 Phage students annotated two phages, Flux and Winky. Using DNA Master, the students overcame several early glitches with the program and were able to map all of Flux’s 89 genes within four weeks. The draft annotations were submitted to Pittsburgh by mid-March. Within five weeks, the students identified 142 genes in Phage Winky. The draft annotations were completed and forwarded to Pittsburgh for formal GenBank submission. Flux was published in GenBank this past June but Winky still awaits quality control. This spring, Dr. King Smith is leading the fourth cohort of phage students to annotate phages DTDevon and Oaker, again using DNA Master.

Applying eBook and Tablet Technology in a Laboratory Class Setting – Part I

by Dr. Jonathan Fingerut

Jonathan Fingerut, Saint Joseph's University, Biology DepartmentThe introduction of Apple’s free iBook Author software has made producing customized electronic texts and assessment tools easy and possibly more important, free. E-Books, of which the iBook format is just one type, provide the opportunity to embed engaging, interactive multimedia directly into texts. This can potentially increase student attention and comprehension as well as making it possible to illustrate subjects, techniques and other activities that would otherwise require moving from the text to a different platform (a computer or video screen). I use the term “potentially” because there exists little-to-no assessment of the efficacy of these new platforms in education. Anecdotal evidence seems to point towards students being more engaged by the format as it more closely resembles how this generation gets most of their other information (both educational and entertainment) but I know of no controlled studies that have proven or dis-proven this.

While E-books can be read on a variety of different platforms, including PC’s, phones, e-readers and tablets, it is the latter that appears to have the greatest potential for education. By pairing the iBook format with the iPad, it is possible to bring this tool into situations, such as wet labs, where texts and computers have previously been at a disadvantage due to the messiness that goes along with these activities. To test this combination I wrote a new dissection guide iBook for the upper division course Invertebrate Zoology.

The following video outlines that effort:

A New Dissection Guide iBook

Jonathan Fingerut demonstrates an interactive image in his iBook laboratory guide.One issue I faced was finding images and videos that could be used without licensing. I was able to produce some of the necessary material in-house with microscope-mounted cameras and cellphone video cameras, but I did not have enough time to produce all I needed, nor did I have access to all the specimens I wanted to include. Luckily a clearinghouse for creative-commons licensed multimedia is now available online at Through this site, multiple search engines (including Google Image Search) can be automatically set to only return Creative Commons-licensed material. Creative Commons is a widely used free-use licensing scheme. Combining the text and a mélange of material, I was able to fully populate dissection guides for 13 different species ranging from the simplest sponges to the most complex arthropods. Guides included slideshows of species diversity, full-color close-up images of anatomical features, videos of animal behavior (e.g. feeding, locomotion), and interactive images where students can select labeled parts of large image on which to zoom in.

Applying eBook and Tablet Technology in a Laboratory Class Setting – Part II

by Dr. Jonathan Fingerut

Apple iPad mounted in classroom laboratory.The ability to present and use these guides on the iPad is what really makes this a breakthrough product for use in labs where students’ hands are gloved, messy, wet and slippery. Viewing iBook format files is not currently possible on traditional computers but even if that changes, goopy gloved hands do not play well with keyboards and mice. For this lab, iPads were mounted on inexpensive (~$40) stands that placed the iPads at eye-level, up off the bench away from spills. The position of the tablet allowed students working in pairs to both navigate the guide without reaching across each other for mice and keyboards. Cheap ($1 per unit) plastic sleeves designed for using the iPad in the kitchen, were placed over the tablets allowing them to be used with gloved hands without fear of damage. The sleeves could be wiped down and lasted the entire semester.

Students responded well to the new guides and the iPad interface. While a true assessment of the project was not possible, (I did not have a comparable comparison group), students reported that they felt the guides allowed them to work independently. In my estimation this was true to a greater extent than when traditional paper-based guides were used in previous years. This provided me greater opportunity to move around the classroom asking questions, pointing out interesting features of the specimens and answering more sophisticated questions than the previously common “where is the ____” or “what is that blob?”. To facilitate studying of the material outside of class, PDF and iBook versions of the guide were made available via BB and iTunesU (necessary for dissemination of iBook files).

Jonathan Fingerut demonstrates an interactive quiz in his iBook laboratory guide.One additional useful feature is the iBook format’s ability to provide students with instant feedback on their mastery of the material through custom, auto-grading embedded quizzes. At the time of the guides’ production, question types were limited to multiple-choice, matching, and a format where labels must be correctly located on an image. New third party software now allows free answers, but they are not graded in real time as the simpler built-in choices are, and must be emailed to the professor from the tablet to be graded by hand. This may be very useful for other types of assessment, but for the purposes of an exit quiz or self-examination, it is less useful.

Overall, the process of making the guides was fairly simple. The learning curve for using the software is not steep if you are already used to other WYSIWYG authoring software (PowerPoint, Page Mill, Desktop Publishing etc.) and the growing availability of CC-licensed content makes populating the files relatively easy as well. The question as to whether the new format makes a difference in terms of student learning has yet to be determined, but in this situation I saw students that were less stressed, more engaged, and overwhelmingly preferred the new format over previous traditional paper guides they had used in other courses. As the software and media resources mature, I envision that this technology can provide benefits to a range of educational situations and that more educators will feel comfortable producing their own content or using the eventual flood of commercially produced texts that are soon to follow.


Digital Recording Tools ~ Modern and Classical Languages

The Modern and Classical Languages department has various ways of assessment using different forms of technology.  The Language Specialist project developed by Professor Ewald requires students to interview a project partner who did not speak English before 18 years of age.   This exercise provides an opportunity to apply linguistic concepts and terms obtained from their course to analyze a specific language, and compare it with English. “The goal is to become more knowledgeable of a language system that is presently unfamiliar to the student.” (Ewald)  After the first interview the student writes a short report of the interview primarily on language-related issues. Throughout the course they have ongoing conversations and interviews with their project partner about his/her experiences learning English, and about various characteristics of this person’s own native language.” (Ewald)

Hand held recorders are an excellent tool for interviews because they give students the ability to review an interview multiple times, while compiling data for a report.  Recorders permit freedom from taking notes, so students can observe facial expressions, hand gestures and other visual elements within conversation.  As stated in the syllabus for the “Language Specialist Project” conducted and developed by Professor Jen Ewald “Do not write a “transcript” of this interview; rather, report on it and analyze it, incorporating examples of what your informant said to illustrate your analysis.”  (Ewald)

In the article “Digital Audio Recording and its Applications within the Foreign Language Classroom” Schwenkler writes:

If students have access to mini-disk recorders or stand-alone laptop computers with microphone hook-ups, they can interview their classmates or community members.  Students can record native speakers’ voices, to use in focusing on   their own pronunciation and how it can improve.  Students can interview native speakers about their opinions, experiences, or for information about their home countries.  This information can then be presented in a multimedia PowerPoint or Photo story presentation with visual images, maps and graphs to accompany the audio files. This is taking digital audio recording to another level in extending the interactive, communicative web and bringing more people into the learning community.  Students practice speaking with native speakers and interviewing others, key interpersonal skills in the target language. (Schwenkler, 2008)

Two other forms of digital recording applications utilized within MCL are Garage Band and Audacity.  At the beginning of the semester language professors give students a “Baseline Oral Evaluation” to assess their competency from the beginning of the semester until the end.  Students are presented with questions from either a PowerPoint or orally by their professors, students must respond by creating an audio recording for assessment. Students create audio clips using the applications Audacity or Garage band while wearing a headphone/microphone set.

As Schwenkler states:

Digital audio recording is a useful tool in foreign language classrooms where a primary goal is for students to practice speaking the target language, hear how they sound, and improve their speaking proficiency.  By recording themselves speaking with the software, students’ original language production is recorded, and students have the opportunity to go back and hear their selves speaking. Now students are able to reflect on their accent, grammar, fluency, intonation, etc. This tool can serve a variety of purposes, including self-assessment, group work, dialogues, links to culture, and teacher assessment.  (Schwenkler, 2008)

The Modern and Classical Languages department is developing their 21st Century skills by integrating various forms of technology into their classrooms.  These audio recording applications add a stronger component for assessment and review, both on the teacher and students side.  The MCL population also utilizes recording exercises through various online “Language Labs” even when technology glitches have created challenges.  Embracing the learning curve, MCL faculty has resolved to teach students in a 21st century fashion by creating a more engaging atmosphere, and thereby meeting students’ needs.

Works Cited

Ewald, D. (n.d.). Language Specialist Project Syllabus. PA.

Schwenkler, C. (2008, October 19). Digital Audio Recording and its Applications within the Foreign Language Classroom. Retrieved October 24, 2012, from Connexions:

Bridging the Digital Divide — by Joanne Piombino

“Social Networking Sites (SNSs) such as Facebook are one of the latest examples of communication technologies that have been widely-adopted by students and, consequently, have the potential to become a valuable resource to support educational communications and collaborations with faculty.” (Roblyer, 2010)  Dr. Elaine Shenk noticed a reoccurring theme each semester when reviewing students’ feedback within her course evaluation forms. The majority of students were not fond of the discussion board section within their courses.  One of the major complaints students had was that they disliked having to navigate to the discussion board each day, to see if someone replied to their post. “Digital Natives are used to receiving information really fast. They function best when networked. They thrive on instant gratification and frequent rewards.” (Prensky, 2001) Communicating on Facebook eliminates this complaint because students receive notification of edits within their Facebook news feed, and within their email accounts.

Facebook Screenshot

The other major grievance students had was that the discussion board tool was boring.  Some students mentioned that they would rather lose points for an incomplete assignment, than use that tool.  Since Facebook is a tool students are already engaged in socially, I suggested tapping into that interest for schoolwork.  Because most students check their Facebook accounts multiple times a day, they will be informed of class activity within their news feed, eliminating the grievance of logging into Blackboard for updates.  “Today’s teachers have to learn to communicate in the language and style of their students. This doesn’t mean changing the meaning of what is important, or of good thinking skills. But it does mean going faster, less step-by step, more in parallel, with more random access, among other things.” (Prensky, 2001)

Facebook offers an engaging online alternative for classroom discussions facilitated by the instructor.  It also offers another form of assessment, demonstrating student comprehension of the language through monitoring their conversations. Dr. Shenk’s Facebook page “Composicion en espanol” permits an avenue for students to demonstrate their knowledge of the Spanish language in a less formal atmosphere, and it stimulates creativity due to the capability of sharing movies, photos, links etc… all within an environment students are proficiently comfortable with!

Please click on the image below, and become inspired:

Thumbnail image for Teaching In The 21st Century (Mathipedia 2010)

Teaching In The 21st Century (Mathipedia 2010)







Works Cited

Mathipedia. (2010). ASB Unplugged Conference in Mumbai, India . Retrieved October 23, 2012, from You Tube:

Prensky, M. (2001, October). Digital Natives Digital Immigrants. On The Horizon, 1-6.

Roblyer, R. D. (2010). Findings on Facebook in Higher Education: A Comparison of College Faculty and Student Uses and Perceptions of Social Networking Sites. Internet and Higher Education, 134-40.

New technology based science instructional laboratory in Connelly 130

By: Dr. Brian Forster

Bio Pac
In August 2012, Connelly 130 was redesigned and deployed as a science laboratory. Students working in this lab will have access to the same technology found in the other Connelly Hall science instructional laboratories. The software program that will be utilized extensively in Connelly 130 this year will be the Bio-Pac (Figs. A & B). Although I have previously mentioned Bio-Pacs, I wish to take this time and describe them in more detail and show how these devices help students in learning about how the human body functions (physiology).

Observations are a key feature to the nature of science. What we observe allows us as scientists to ask and answer questions. The invention of microscopes allowed scientists to open the door to the world of cells and microorganisms. Studying the physiology of an organism, most notably humans, can be difficult since we cannot easily visualize all the events occurring inside the body. The actions of the human body produce electricity. Different activities produce unique electrical signals. Bio-Pac uses special electrodes that can be connected to the body to detect these signals. These signals are transferred from the electrodes to a MP3X acquisition unit (Fig. A). The MP3X processes these signals and carries that information to the Bio-Pac Student Lab software that is installed on the computers in the Connelly Hall science instructional laboratories. According to the manufacturer, it takes 1/1000 of a second for a signal to be received and displayed on the computer (Bio-Pac Student Lab manual). The Bio-Pac software allows the student to not just visualize the signals, but allows the student to analyze the data and make specific measurements.

The electrical activity that the Bio-Pac system measures allows our students to visualize skeletal muscle activity (electromyography), brain activity (electroencephalography), heart activity (electrocardiography) (Fig. B) and eye activity (electroculogram). Other aspects of human physiology the Bio-Pac system can measure include blood pressure, respiration and the human body’s response to relaxing and stressful conditions. Given the proper electrodes, numerous aspects of human physiology can be explored. There is even a prepared lab on using the Bio-Pac as a polygraph machine! Students can see firsthand what happens physiologically when someone tells their professor that the dog ate the assignment! Currently, the biology lab courses that use Bio-Pacs include Bio 165 (Exploring the Living World), Bio 201 (Bio III: Organismic Biology), Bio 260/261 (Anatomy and Physiology) and Bio 417 (Systemic Physiology).

Since several of our students are pre-health students, they also gain practice in using more common equipment to look at human physiology. Stethoscopes and sphygmomanometers (blood pressure cuffs) are provided for students to measure heart rate and blood pressure, respectively without the aid of the computer. The students are then provided the opportunity to compare their own measurements to the measurements calculated by Bio-Pac.

To learn more about the Connelly Hall science instructional laboratories and their technology, please contact Dr. Brian Forster (

Learning about the Physical Principles Behind Weather through Technology

By Dr. Brian Forster


In January 2012, I wrote an entry for the CAS Technology blog entitled “Technology in the General Education Program Natural Science Laboratories.” In that article, I discussed the technology used in the GEP lab-based natural science courses designed for students who are not majoring in science. This semester, a third course was introduced “Exploring the Physical World” (Phy113) taught by Drs. Douglas Kurtze and Brian Forster. During lecture, students learn about the weather while in the laboratory, they analyze current weather conditions and learn the physics behind these weather patterns.

St. Joseph’s University has purchased access for Phy113 students to obtain current and past weather data from the American Meteorological Society. Student computer stations throughout the lab allow students a look at our weather in relation to the topic being discussed during lecture (Figure A). A goal for our course is that by the end of the semester, students could simply look at weather conditions and be able to make their own forecasts instead of relying on the weatherman!

As with our other lab-based courses, Phy 113 utilizes Xplorer GLX readers for a wide variety of experiments. These readers have been extremely useful in not only the GEP lab-based courses, but in other science courses too. These courses include Drs. Jonathan Fingerut and Piotr Habdas’ Biomechanics course as well as Dr. Catalina Arango’s Environmental Microbiology course.

The attachment probes we use in conjugation with the Xplorer GLX for Phy 113 are the ideal gas law chamber (Figure B) and the solar panel (Figure C). In the gas law chamber, a syringe controls the volume of gas inside the tube. Pressure and Temperature probes are connected to both the chamber and the Xplorer. As students manipulate the volume of the gas, they are able to see the relationship between the pressure, volume, temperature and density of a gas. As the students perform more experiments, they are challenged to refine their ideas for the relationships between these properties of a gas.

A solar panel allows our students to learn about solar altitude, or how far above the horizon the sun is in the sky. The solar panel has a temperature sensor that can plug into the Xplorer GLX. A halogen bulb lamp serves as our sun. Using this experimental design, students can learn the relationship between temperature, solar altitude and our seasons. The solar panel also allows students to model the greenhouse effect. If it is a clear day outside, these panels can be used “in the field” (aka outside the laboratory) to calculate solar altitude as well.

The Xplorer also serves an important pedagogical function. For our students who are less experienced in the technique of graphing, they can see how the data is plotted out to assist them in properly preparing, graphing and analyzing their data.

In addition to this technology, several of the physics experiments that our students carry out use common household items. In a recent lab for example, students learned about angular momentum. This concept is used by figure skaters who spread their arms out when they wish to slow down their rotation. We used common household supplies to illustrate this physical principle.

We hope this emphasizes to our students that many concepts in science can be seen and performed in their everyday lives. You just need to stop, look around, observe and wonder!
To learn more about these labs and their technology, please contact Dr. Brian Forster (

Using iPad for OnLine Grading by Dr. Vincent McCarthy


I received the iPad on its first day in 2010 and have been a fan since (and upgraded to the iPad 3 in March). I immediately recognized its potential for instructional use, particularly in the OnLine philosophy courses that I pioneered at SJU. Students typically write two papers a week and send them as email attachments. I quickly realized that, if I could grade them OnLine and return them, it would facilitate the courses and might even help in getting students to read the comments.

Within a few weeks, iAnnotate PDF appeared and, for the price of $9.95 (out of my own pocket of course!), it was exactly what I was looking for. As a result, I was able to write onscreen comments, usually in red, as well as add typed longer comments, and to return the papers immediately. This was satisfying to both students and to instructor.

iAnnotate PDF has improved in various upgrades, and I have occasionally used it to grade and return term papers and exams, also while traveling by plane or rail.

In short, the combination of iPad and iAnnotate PDF has been an excellent tool for OnLine grading.

2012 Senior Art Show by Jeanne Bracy, Assistant Gallery Director

The 2012 Senior Art majors are very excited to present their theses that they have been working on since September. This year there are three photography majors, Laura Colussi, Evan DiPaola, and Cara Howell. Laura is using her own Nikon D5000 digital SLR camera to shoot landscape photographs which she is presenting in varied sizes 8” x 10” and smaller. Evan uses his own Nikon D7000 digital SLR camera to take portrait photographs which are all framed to 13” x 19.” And finally, Cara uses her own Nikon D90 digital SLR camera to shoot urban storefronts which are framed to 11”x 14.” All three photographers are using Adobe Photoshop CS5 software system to manipulate their images before printing them on the Epson Stylus Pro 4880 printer all in our iMac editing lab in Boland Hall.

The exhibit will also include ceramic work from fellow senior art majors, Maegan Arthurs, Angela Bennie, Darby Cotter and Tina Eccleston, and paintings by Kaitlin Ammirati, Megan Brady, Holly Colaguori and Martina Tagher. The exhibit will open on April 13th and run through May 31, 2012. All are welcome to the opening reception on April 13th from 5-9 PM.

iPad as a Tool for Science Education

by Drs. Jonathan Fingerut and Piotr Habdas

Much ado has been made recently regarding the iPad’s potential to revolutionize the realm of education through its use as a reader for e-textbooks. New software makes publishing your own textbooks as easy as making your PowerPoints, and a new marketplace for those textbooks has been created. Most importantly the price-point for those textbooks has been set an order-of-magnitude lower than most of our current texts. At $15 a piece, a student could recoup the cost of a new iPad in one semester. However, until the texts available for the iPad increase in number and quality, as much as many of us would like to save our students money, the use of the iPad in the science classroom remains limited in its scope.

There are, however, examples of how this simple, intuitive device can earn its keep until the eBook revolution occurs. In particular, boutique software that takes advantage of the iPad’s unique combination of power and intuitive input mode. In the course Biomechanics, offered jointly by the Biology and Physics Departments, as part of two different labs covering drag in fluid flow, students were given the opportunity to use a program called Windtunnel HD. This App visualizes and quantifies the flow of fluids over, around, and through objects that the students draw on the screen. This $6 download is the best fluid-dynamics software outside of expensive ($>1,000) mathematical modeling packages, and far and away the most user friendly. Instead of learning software syntax, coding rules, and complicated datasets, the students’ time can be spent manipulating the objects by dragging and rotating them with multi-touch motions, changing fluid properties using on-screen sliders and varying the data output with simple radio buttons. The students in the course were familiar with manipulating objects and settings this way, and were very engaged by the software.

Students had previously experimentally measured drag forces on objects dragged through oil with relatively inexpensive equipment (<$1000 per station). However, that approach, which is excellent for a number of pedagogical reasons, is limited in the situations it can replicate. This new software allowed students to concentrate on their predictions, testing and analyzing data without worrying about the limitations of the experimental setup. Further, its drawing features allowed students to rapidly design and test different object shapes to develop the most hydrodyanamically efficient form possible. While this could have been done empirically, the ability to try, modify and test multiple forms in a matter of minutes allowed students to be more creative before making their physical model.

This is just one small example of how the iPad can play a role in scientific education, but it is one that is uniquely suited to the interface the iPad provides. No other device combines such ease of use, input and processing power. It is likely, as more and more students have iPads, the development of such specialty software will become more financially attractive and move beyond the current hobbyist realm. One could foresee interactive software in molecular biology, mechanics, and any other field in which the easy manipulation of objects can tear down barriers to student learning and bring subjects into a medium through which they have become accustomed to interacting with their environment.


Fig 1. Examples of the types of analysis and outputs available in Windtunnel HD to visualize flow fields, turbulence structures and lift forces (left to right respectively).