The Biology of Human Infectious Diseases, Fall 2023
Biology 418

Professor: Dr. Nita Bharti, contact in Canvas
Office hours: Catch me after class on Tuesday or contact me in Canvas to schedule any other with me.
LA: Sophia Vitolo, contact in Canvas
Office hours: after class Tuesday or 6 pm Wednesdays in 308 Boucke
(Boucke 214 on 9/20 and 9/27)

Course Description: 3 credits; prerequisites: Biol 110, Biol 220 Ecology/Evolution, Biol 230 Cellular/Molecular Biology.

Location: 106 Boucke Building.
Class time: Tuesday and Thursday 3:05-4:20

Required Materials: The Coming Plague by Laurie Garrett (1995 edition), all additional reading assignments available online at no cost on course site (some require PSU login for access through library), sites.psu.edu/humid/

Infectious diseases have been an important force in shaping human biology and are part of our daily lives. The complexities of health and disease continue to impact our populations, many of our behaviors, and much of our public health policy. The biology of infectious diseases is a fascinating topic and a critical component of biology and global health.

Course Goals: In this class, we take a careful look at diseases that impact human populations, disease management strategies, and their varying impact. This class includes case studies of diseases and disease control in recent history as well as current situations. Course materials highlight the integration of different subdisciplines of biology and complexities that drive disease dynamics and determine the efficacy of disease management strategies.

Course Objectives: We will cover the following topics in interesting and thoughtful ways. By the end of the semester, you will understand:

1. The epidemiologic triangle and the importance of the relationship between host, pathogen, and environment across different contexts.
2. Transmission and treatment thresholds, transmission types, and control options for various human infectious diseases.
3. The impact of human infectious diseases on populations across space and over time.
4. The links between sub-disciplines of biology in infectious disease dynamics and observed disease outcomes.
5. Major obstacles in human infectious disease control and how they have changed over time.
6. Changes in global health targets over time.

Participation: You must participate in this course to do well in it. This means you must be present and prepared to discuss the relevant material. You need to do the reading and engage with lecture content. You should take advantage of the ungraded quizzes during the weeks they are offered to help you assess your understanding of the material. The participation component of the course is worth 25% of your grade. Lack of preparation or participation will be reflected in your grade and may result in the replacement of ungraded quizzes with graded quizzes. Exams will include material presented in class and discussion content so show up and pay attention.

Exams: There are no make-up tests for this course. I take the highest scores from 2 of the 3 class tests given predictably throughout the semester (online this year). You have to be really unlucky for life’s catastrophes to get in your way more than once on an exam day. Each exam is worth 25% of your grade so do not miss a class test – your workload will only get harder, especially near the end of semester. Remember, ungraded quizzes will help you assess your comprehension of the material and prepare for exams.

Exams include content from assigned readings and any in-class lecture materials or discussions. Each exam is cumulative. Exams 1 and 2 are during our class period but in a computer lab location (check the syllabus). The third exam is given during the designated final exam period, it is worth the same number of points (25) as Exams 1 and 2. In accordance with university policy, if you have an official conflict for Exam 3, you must file for a final exam scheduling conflict (details at http://www.registrar.psu.edu). There are no other ways to handle this.

Due dates: Assignments, including reading, should be done before the class for which they are listed. Your Research Focus slides are due by 11:59 pm on the Friday due date. Due dates for readings and assignments as well as exam dates (except the final exam), are subject to change. Submit all materials in Canvas.

Schedule: Biology 418 Biology of Human Infectious Diseases Complete Assigned Reading before each class
	Week#	Topic and reading assignment	In class
	1	Intro: Epidemiology and Global health
22-Aug		Complete Tuesday reading assignment before class	1
24-Aug		Complete Thursday reading assignment before class	2
	Section 1	Directly transmitted, vaccine preventable diseases
	2	Orthopox viruses (Smallpox, Mpox) and Cholera
29-Aug		Reading before class Orthopox	1 Sophia lecture
31-Aug		Reading before class Orthopox/Cholera	2
	3	Smallpox debate, begin Measles
5-Sep		Reading before class debate Complete Canvas survey keep/destroy by Wednesday Anonymous quick assessment of your course experience	1 Class Debate: keep or destroy
7-Sep		Reading before class Measles Lecture Ungraded quiz #1	2
	4	Measles, Polio
12-Sep		Reading before class Measles in-class workshop	1 Case studies of 2019 outbreaks in different nations
14-Sep		Reading before class Polio Ungraded quiz #2	2
	5	Polio
19-Sep		Reading before class Polio	1
21-Sep		Exam 1 in 112 Boucke Bldg	2 Exam #1
	Section 2	Drug resistance and evolution
	6	Tuberculosis
26-Sep		Reading before class	1
28-Sep		Reading before class	2
	7	Malaria
3-Oct		Reading before class	1
5-Oct		Reading before class	2
	8	Dengue/West Nile Virus/Zika
10-Oct		Reading before class	1
12-Oct		Reading before class	2
		Research focus slides, abstract, outline due Oct 13 at 11:59 pm
	9	Influenza
17-Oct		Reading before class	1
19-Oct		Reading before class	2
	10	Research Ethics Debate/Discussion
24-Oct		Reading before class	1 Class Debate: DURC
26-Oct		Exam #2 in 112 Boucke Bldg	2 Exam #2
	Section 3	Spillover and complex ecology
	11	Ebola
31-Oct		Reading before class	1
2-Nov		Reading before class	2
	12	HIV/AIDS
7-Nov		Reading before class	1
9-Nov		Reading before class	2
	13	Coronaviruses (SARS-CoV-1 and 2/MERS)
14-Nov		Reading before class	1
16-Nov		Reading before class	2
	XX	University Break
	14	Research Focus presentations (daily topics subject to change)
28-Nov		Directly transmitted and/or vaccine preventable diseases	1 Class presentations
30-Dec		Directly transmitted and/or vaccine preventable diseases/Vector-borne diseases	2 Class presentations
	15
5-Dec		Vector-borne diseases	1 Class presentations
7-Dec		Complex ecology and spillover	2 Class presentations
	16	Exam #3 TBA – check final exam schedule
			Exam #3

 

Research Focus 25 points: 25% of class grade

Each student will research a human infectious disease that we do not cover in class. Choose a pathogen from my posted list, or suggest a topic (I must approve all suggestions). Students may not cover duplicate diseases; once a disease is chosen, it is no longer an option for anyone else. Choose wisely and sign up online early. This project requires the submission of 1) slides, abstract, and an outline mid-semester and 2) an oral presentation for the class at the end of the semester.

Research focus slides, abstract, and outline – 13 points Due Friday October 13 at 11:59 pm (week 8)

Content Think about the way we cover pathogens in class. Include the elements we discuss that are important for your pathogen (including, but not limited to burden, geographic distribution, epidemiological triangle, transmission model, control and management, global health funding, risk factors, co-infections, etc.). Be aware that the important elements will vary by pathogen and disease so include and eliminate content accordingly. Also consider contrasting/comparing your pathogen to pathogens that we cover in class, especially if you see any striking similarities or differences. Synthesize your thoughts clearly.

Preparing well-researched slides will help you prioritize and polish the content for your oral presentation at the end of the semester. We will cover the requirements for this in more detail as you start choosing topics and thinking about your research. Failure to submit slides, abstract, and outline disqualifies the student from the opportunity to give a presentation.

Tips for preparing slides
Focus on organization and clarity. Plan on a 7-10 minute presentation. It will help you write clearly if you:

• Start with an outline (submit this as a word document alongside your slides)
• Use your outline to organize broad topics in a way that makes sense to you. Organization is critical to lead your audience through a coherent story.
• Write a telescoping abstract to draw the audience in on your first slide – why should they be interested in this topic? An abstract should be ~200 words to help guide your story arc (submit this as a word document alongside your slides)
• Write your “script” in the notes section of each powerpoint slide or a separate document

Slide guidelines:

• Don’t include too much text on your slides. Instead, plan to guide the audience through what you will say, use the notes section of each slide to type out what you plan to say
• Figures, visual aids, and schematics can be really helpful ways to show complex ideas, tables can be helpful for comparisons
• Reference everything you use, including figures that are adapted from published figures
• Cite all your sources. Reference all your sources properly and include a references slide as your last slide. Use the AMA reference formatting style.
• Plan on using approximately 1 minute per slide (this means you would create about 10 slides for a 10 minute presentation)
• You have to do a lot of research to get ~7-10 minutes of high quality material for a presentation. You should complete and organize this research before your slides are due.
• Look into Nature Letters formatting guide for authors for help with organization and use examples of published Letters (accessible with PSU libraries login). These examples, particularly from review articles, should help guide your language (formal and scientific) and how to craft a story. Use our classroom discussions and lectures to guide your organization and main topics.

Grading rubric for slides, abstract, and outline:

13 points total:
Organization: 3 points
Accuracy and critical content: 4 points
Clarity: 2 points
Grammar, writing, aesthetics (proofread, don’t use too much text on slides): 3 points
Proper referencing (formatting and completeness): 1 point

Presentations – 12 points (10 points for your presentation + 2 points for attendance and participation for your classmates’ presentations)

During the last two weeks of the semester, each student will give a presentation (~7-9 minutes, depending on the total number of eligible students), plus 2 minutes of answering questions from your classmates. You should have a solid understanding of the important material based on how we cover diseases in class and your research focus paper. If there are some characteristics of a pathogen or a disease that we always cover that are relevant to your pathogen, you should cover them, too.

Time slots for presentations are assigned and posted. 

You will be graded on the content of your presentation, your delivery of the material, your ability to stick to the time allotted (presentations that are too short or too long will be penalized). A good presentation will have strong organization, clarity, and it will be succinct. Avoid rambling. Practice for a friendly audience at least a few times (dog, campus squirrel, roommate, etc.). Don’t be nervous and remember that you’re the class expert on the subject.

10 points total:
Organization: 3 points
Accuracy and critical content: 2 points
Clarity: 2 points
Delivery and timing: 2 points
Creativity and originality: 1 point

After you’ve delivered your presentation, your classmates will ask you questions on the topic, which you should be able to answer. If you can’t answer a question, try to build on what you know to say something relevant but don’t make stuff up. Questions should be reasonable and respectful. The professor will police this as necessary.

This means you must also ask questions following your classmates’ talks. ATTEND ALL PRESENTATIONS. This is an important part of your grade (participation + asking questions = 2 pts). Questions that are insightful and non-repetitive will earn points.

Presentations will take place during weeks 14 and 15, the last two weeks of class. Material from student presentations will be included on the final exam. You must post your slides in our class OneDrive folder before your presentation.

 

Class Grade Breakdown: 100 points total
25 points: Participation – these points are earned throughout the semester, not lost. You do not start the semester with 25 points and lose points for lack of participation, you start with 0 points and earn points for participation. To earn these points, you must 1) be active during class discussions, 2) ask and answer questions during lectures, and 3) be prepared for class each day by completing the reading assignment before class begins.

25 points: Research Focus – slides and presentation; failure to submit slides, outline, and abstract disqualifies the student from the opportunity to give a presentation. This would result in the loss of all 25 research focus points.

50 points: Exams – 25 points each, the lowest score of 3 exams is dropped

 

Extra credit: While you should focus the majority of your efforts on ‘regular’ credit, you can earn up to 5 points of extra credit in this course in any of the following ways. Note that extra credit maxes out at 5 points per student but there are often more than 5 points in extra credit opportunities in the semester listed below so play to your strengths.

(1) Write an essay about your course experience, up to 2 points. Write an essay about how this class has impacted your understanding of global health, human health, or infectious diseases. Be specific and technical. Your essay must be submitted no later than Week 13 of the class (before Thanksgiving break), but can be completed anytime during the semester. Thoughtful, well-written essays will receive up to 2 points in extra credit. Essays that do not meet class standards will not be awarded points. This essay is not supposed to be a review of the course or an endorsement, it is supposed to highlight a learning experience you had through the course. Remember, this is an advanced course and I expect advanced work. I will not accept revisions, resubmissions, or late essays. If you have questions, contact me.

(2) Attend pre-approved out-of-class events, up to 2 points, worth ½ point each (the number of eligible events will vary by semester). Periodically, opportunities will arise throughout the semester to attend seminars given by visiting speakers, participate in science outreach, or be involved in something that I consider important to the fabric of humanity. I’ll bring your attention to events that are eligible for extra credit, virtual or in person. To receive extra credit, you must provide a photo of you at in-person events (this must be indisputable, try to get the speaker or their title slide in the background, feel free to do this for virtual events if you’d like) and a written reflection of what you learned from the event (this should be about one page of well-written text). Materials must be submitted via Canvas (in an ‘extra credit’ assignment) within one week of the event occurring. (Note that if you attend an event during the last week of classes, you must submit your reflection on the last day of classes.) If your submission clearly demonstrates that you attended the event and what you learned from it, you will get ½ a point of extra credit. These points are added to your point total for the class. I cannot give you points if your photo doesn’t definitively place you at the in-person event or if you forget to take a photo. Late or insufficient submissions will not receive points and are not eligible for resubmission and regrading. You should also bring my attention to events that you think would be relevant to our interests – some may be eligible for extra credit if they are announced to the class in advance of the event and some may just be interesting to share.

Grading Scale
Final grades will be assigned based on the following percentages. These categories correctly indicate that I will round final grades from the second decimal place.

A       94.0-100%

A-      90-93.9%

B+     87-89.9%

B       83-86.9%

B-      80-82.9%

C+     77-79.9%

C       70-76.9%

D       60-69.9%

Fail   <60

 

Guidelines for grade disputes or regrade requests

Exams: regrade requests
If you assess your exam was graded incorrectly and you did not receive points for an answer that you think was correct, you may submit via Canvas message, a written point by point justification for each question where you feel an error was made. The entire exam will be regraded, with a focus on the issues raised in the written request. You must submit your request within one week of receiving your returned, graded exam. Do not take this lightly, as the entire exam will be regraded and may result in a loss of points.

Assignments: regrade requests
If you assess that an assignment was graded incorrectly and you did not receive points you think you earned, you may submit, in writing, a point by point justification for each point where you feel an error was made. The entire assignment will be regraded, with a focus on the issues raised in the written request. You must submit your request within one week of receiving your assignment grade. These requests should be messaged to the professor within Canvas. Again, do not take this lightly, as the entire assignment will be regraded and may result in a loss of points.

 

Additional Info

Academic Calendar
Refer to the registrar’s academic calendar for important dates this semester. A few are highlighted in this syllabus but you are responsible for being aware of all of them, including the late drop deadline.

Academic Integrity
Unless specifically directed otherwise, all assignments must be completed without assistance from others, except for guidance from Dr. Bharti and/or guest instructors. You must submit and present your own work. By enrolling in this course, you are acknowledging that you have read and accepted PSU’s Academic Integrity Policy and The Eberly College“Code of Mutual Respect and Cooperation”.

PSU Disabilities Statement
Penn State welcomes students with disabilities into the University’s educational programs. Every Penn State campus has an office for students with disabilities. The Student Disability Resources (SDR) website provides contact and procedural information for Penn State students.

In order to receive consideration for reasonable accommodations, you must follow their guidelines. If the documentation supports your request for reasonable accommodations, your campus disability services office will provide you with an accommodation letter. Please share this letter with your instructors and discuss the accommodations with them as early as possible.

PSU Educational Equity/Report Bias Statement
Consistent with University Policy AD29, students who believe they have experienced or observed a hate crime, an act of intolerance, discrimination, or harassment that occurs at Penn State are urged to report these incidents as outlined on the University’s Report Bias webpage. Similarly, hate or disrespect will not be tolerated in the classroom.

PSU Counseling and Psychological Services Statement
Many students at Penn State face personal challenges or have psychological needs that may interfere with interfere with their academic progress, social development, or emotional wellbeing.  The university offers a variety of confidential services to help you through difficult times, including individual and group counseling, crisis intervention, consultations, online chats, and mental health screenings.  These services are provided by staff who welcome all students and embrace a philosophy respectful of clients’ cultural and religious backgrounds, and sensitive to differences in race, ability, gender identity and sexual orientation.

Counseling and Psychological Services at University Park  (CAPS): 814-863-0395
Penn State Crisis Line (24 hours/7 days/week): 877-229-6400
Crisis Text Line (24 hours/7 days/week): Text LIONS to 741741

COVID-19 Guidelines
You must follow all university policies regarding COVID-19. These may change during the semester and it is your responsibility to stay updated on current policies. Failure to comply with the university’s policy will result in your removal from class.

For student support, visit this website: https://keeplearning.psu.edu/student-support/
For general university COVID-19 info, visit this website: https://virusinfo.psu.edu