Syllabus for BIL354 and BIL 644
The Biology of Viruses
Instructor:
Dr. Cynthia Silveira ([email protected] )
Lectures:
Tuesdays and Thursdays: 3:30 pm—4:45 pm, Cox 122
Office Hours:
Thursdays at 2PM in Cox 248D.
Course background. Viruses are the most abundant and diverse biological entities on the planet. They drive the evolution of their cellular hosts and modulate carbon and nutrient cycles in the biosphere. Viruses are also important biotechnology tools against emerging multi-drug resistant bacteria and for gene therapy. The Biology of Viruses is a 3-unit capstone course for Biology and biomedical sciences students. The course introduces the molecular biology, evolution, and epidemiology of prokaryotic and eukaryotic viruses. The classes are designed to increase undergraduate interest in emerging topics in virus research, with a strong active learning component through project development. The course also explores viral spillovers – when viruses jump from one host species to another – using the 2019 coronavirus outbreak as a case study.
Topics covered
Molecular Biology
Viral nucleic acids, replication cycles, capsid structures
Genomics
Lateral gene transfer, recombination, diversity-generating retroelements, genomic modularity
Evolution
Origins and evolutionary relationships of viral lineages, molecular taxonomic classification, virus and host genome coevolution
Ecology
Modulation of biocheochemical cycles and biomass turnover, predation and mutualistic relationships, quantitative viral ecology, virophages, archaeal viruses
Pathogens
Transfer of virulence genes and toxins, the emergence of pathogens, epidemiology of human viruses, phage therapy, and gene therapy
LEARNING OBJECTIVES
At the end of this class, students should be able to:
● Characterize viral diversity and types of replication.
● Describe the relationships between viral structures and modes of replication.
● Apply the properties of viral genome organization to infer replication strategies and interactions with hosts.
● Determine the types of ecological interactions between viruses and bacterial hosts.
● Interpret patterns of environmental distribution of viruses and their roles in biogeochemical cycles.
● Associate viral genomic features with clinical microbiology, including the transfer of toxin genes and phage therapy.
● Analyze viral genomic data using basic bioinformatics tools to make predictions on viral ecological roles and clinical relevance.
Note: Students are prohibited from recording any part of this course.
Well-Being Resources and Support
As you complete your coursework, consider how to maintain your health and well-being as a top priority. To help you become familiar with the many programs and services available on campus, review the information collected on the Division of Student Affairs Student Well-Being and Resiliency website available at miami.edu/well-being. Please contact me or any resources listed on the site if you need assistance or support throughout the semester.
Academic Integrity Policy
All students must comply with the University of Miami Academic Integrity Policy. The University of Miami community recognizes integrity as a core institutional value. The responsibility to uphold the University Honor Code and high academic standards is a shared value between faculty, students, and administrators. It is each community member’s responsibility to ensure that academic integrity is upheld. Faculty, in particular, have a vital role to play in this regard and are expected to be diligent in reporting violations. This policy acknowledges that the norms and the responsibility of academic integrity are to be jointly upheld by the faculty and student members of the University community.
MATERIALS and TOOLS
All students will need a laptop computer during class for genome analyses. If you do not have a laptop computer, contact the instructor as soon as possible.
Scientific publications discussed in the course will be provided by the instructor through Blackboard as pdf files.
PROJECT
The goal of the genome project is to characterize the biology of an unknown virus using bioinformatics tools to extract information from its genome. Each student pair will receive a viral genome sequence at the beginning of the course. The instructor will create groups on Blackboard where students can interact with each other and upload papers and reports. Each week, the students will learn how to use a different bioinformatics tool available in public databases and servers to identify the virus, annotate the coding regions, predict the structure of the capsid, and infer their evolution and host interactions. Some of these tools and databases include the NCBI, EMBL, JGI Global Virome Database, Chimera, Viral Zone, PATRIC, BLAST, iTOL, etc). The students will describe the results they obtain each week in a final paper, where they will also discuss any ecologically and/or clinically relevant features of each virus (host, genome architecture, presence of auxiliary metabolic genes, virulence genes, etc). On the paper, the students will also contextualize their findings with the current literature using the scientific papers discussed throughout the course and propose strategies to further characterize this virus. The students’ projects will be presented orally at the end of the semester. Upon course completion, each student will have a deep understanding of virus biology and will have developed basic bioinformatics skills.
GRADING
The final grade is calculated based on the following:
1. Participation in weekly discussions of scientific papers throughout the term (20%)
2. A seminar discussing a published scientific paper (20%)
3. Five reports on the genome analyses of your assigned virus (20%)
4. A final paper reporting the results of the genome analyses (20%)
5. A final oral presentation on the genome analysis project (20%)
The paper and the final project presentation will be graded separately but will be part of the same project.
Items 2-5 can be done in pairs (see below exception for BIL644).
Missed class policy
A second chance will be given to students that missed in-class discussions for medical reasons covered by UM’s Class Excuse Policy. The student can communicate their medical issue with Student Health Services, which will send a notice directly to the instructor, or with the instructor directly. Private health information will never be disclosed by Student Health Service, nor will information be shared with the instructor until the student provides Student Health Service with authorization to disclose dates that a student is excused from attending in-person classes.
Final Grade
The final course grade will be the percentage of the total possible points you receive during the semester. The grade ranges are as follows:
A = 90 - 100%
B+ = 88 - 89.9%
B = 80 – 87.9%
C+ = 78 – 79.9%
C = 65 – 77.9%
D = 55 – 64.9%
F = below 55%
Graduate students taking BIL644
The grading for graduate students will differ from that of undergraduates in two ways:
Students taking Writing in Biology BIL 380-SIL
The grading for students seeking writing credit will differ from that of undergraduates in two ways:
EVALUATION GUIDELINES
Oral presentation of published scientific papers
• Pairs of students will choose a news article about their virus and identify what is the primary literature publication behind that news article.
• The students will read the news and primary literature article and prepare a presentation that covers both. The presentation should address the following:
• What does the news article say about this virus? What was the motivation for the research described in the primary literature? How about the approach and results? Do the conclusions of the paper substantiate the claims made in the news?
• The articles (news and academic) should be shared with the class at least of one week ahead of each presentation (uploaded to the group journal page on BB).
• The remaining students in the class must read the paper before class and ask questions that will spark discussion.
• Additional scientific literature that any student would like to discuss is welcome and encouraged.
Participation points in discussions of scientific papers
All students must participate with questions and/or comments on 6 of the 8 papers that will be discussed in class. Students will be given participation points. Your questions/comments will not be graded for correctness.
Genome analysis reports
As students progress in the genome analyses that will be the basis for their final research paper, they will write short reports. There will be 5 reports that will contain each:
Final paper
The paper will contain:
1) Introduction (300-400 words)
a) Relevant scientific literature that gives context to your analyses, which you will encounter as you progress through your research.
a) Description of each tool used, including its theoretical basis. This is not a description of how you upload the sequences and download outputs, but rather an “under the hood” description of the method.
3) Results (500 – 600 words)
a) A detailed description of your results with figures
4) Discussion and future perspectives (300-400 words)
Put your results in the context of the recent scientific literature and discuss the implications of your findings. Throughout the semester, you will encounter these scientific papers during your searches through the NCBI, ViralZone, PDB, and JGI. Propose future research.
APA format is recommended. Citations should follow author-date format and should be listed alphabetically at the end of the paper.
Final presentation
Each student pair will prepare a 10-minute presentation describing their final project to their colleagues. The presentation should contain an introduction explaining the significance and motivation of the research, a brief overview of the methods applied (no details here; this should focus on the reason for choosing the methods and should not take more than one minute), and a careful description of their results and conclusions. Students are expected to explain the figures containing results.
Students should prepare a PowerPoint file to accompany their presentation. This ppt should be rich in images with very little text. The presenting students should also include one to two questions for their audience in the presentation.
Recommended Books (not required)
A planet of viruses (2nd edition). Carl Zimmer. University of Chicago Press, 2015.
Spillover: Animal infections and the next human pandemic. David Quammen. WW Norton & Company, 2012.
Life in our phage world: a centennial field guide to the Earth's most diverse inhabitants. Rohwer, F, et al. Wholon, 2014.
Thinking like a phage: The genius of the viruses that infect bacteria and archaea. Youle, Merry. Wholon, 2017.
Online Resources
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science). https://seaphages.org/
Year of the phage. http://2015phage.org/
National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/
European Nucleotide Archive. https://www.ebi.ac.uk/ena
Pathosystems Resource Integration Center. https://patricbrc.org/
Tara Oceans Viromes. http://ocean-microbiome.embl.de/companion.html
Rapid Annotation using Subsystems Technology. http://rast.theseed.org/FIG/rast.cgi
SCHEDULE
The schedule will be posted at the beginning of each term.
APPENDIX A.
Statement on Diversity and Inclusion
Every student in this class, regardless of background, sex, gender, race, ethnicity, class, political affiliation, physical or mental ability or any identity category, is a valued and equal member of the group. We all bring different experiences to this class and no one experience has more value or import than another. In fact, it is our different experiences that will enrich the course content. I encourage every student to share their own experiences as they are relevant to the course, but I also stress that no student is ever presumed to speak for anything or anyone more than their own experience or point of view.
If there are aspects of the instruction of this course that result in barriers to your inclusion or a sense of alienation from the course content, please contact me privately without fear of reprisal. If you feel uncomfortable contacting me, please contact the Office of the Dean of Students.
I will not tolerate disruptive or insulting remarks, gender or racial slurs, or other forms of
bullying, intimidation or hate speech in classroom or any of the communication channels we use, including Top Hat and Slate. Publication of the remarks or questions or work of any
classmate - in any form, written or recorded - without clear consent will be regarded as a
violation of academic integrity and treated as such. I expect you to act with respect for this
space, this subject, our process and each other.
APPENDIX B.
A Note on Sexual Misconduct
The University of Miami is committed to fostering a safe, productive learning environment. Title IX and our school policy prohibits discrimination on the basis of sex. Sexual misconduct — including harassment, domestic and dating violence, sexual assault, and stalking — is also prohibited at our school.
The University of Miami encourages anyone experiencing sexual misconduct to talk to someone about what happened, so they can get the support they need, and our school can respond appropriately.
If you wish to speak confidentially about an incident of sexual misconduct, want more information about filing a report, or have questions about school policies and procedures, please contact our Title IX Coordinator, which can be found on our school's website: https://titleix.miami.edu/
The University of Miami is legally obligated to investigate reports of sexual misconduct, and therefore it cannot guarantee the confidentiality of a report, but it will consider a request for confidentiality and respect it to the extent possible.
As an instructor, I am also required by our university to report incidents of sexual misconduct and thus cannot guarantee confidentiality. I must provide our Title IX coordinator with relevant details such as the names of those involved in the incident.
The Biology of Viruses
Instructor:
Dr. Cynthia Silveira ([email protected] )
Lectures:
Tuesdays and Thursdays: 3:30 pm—4:45 pm, Cox 122
Office Hours:
Thursdays at 2PM in Cox 248D.
Course background. Viruses are the most abundant and diverse biological entities on the planet. They drive the evolution of their cellular hosts and modulate carbon and nutrient cycles in the biosphere. Viruses are also important biotechnology tools against emerging multi-drug resistant bacteria and for gene therapy. The Biology of Viruses is a 3-unit capstone course for Biology and biomedical sciences students. The course introduces the molecular biology, evolution, and epidemiology of prokaryotic and eukaryotic viruses. The classes are designed to increase undergraduate interest in emerging topics in virus research, with a strong active learning component through project development. The course also explores viral spillovers – when viruses jump from one host species to another – using the 2019 coronavirus outbreak as a case study.
Topics covered
Molecular Biology
Viral nucleic acids, replication cycles, capsid structures
Genomics
Lateral gene transfer, recombination, diversity-generating retroelements, genomic modularity
Evolution
Origins and evolutionary relationships of viral lineages, molecular taxonomic classification, virus and host genome coevolution
Ecology
Modulation of biocheochemical cycles and biomass turnover, predation and mutualistic relationships, quantitative viral ecology, virophages, archaeal viruses
Pathogens
Transfer of virulence genes and toxins, the emergence of pathogens, epidemiology of human viruses, phage therapy, and gene therapy
LEARNING OBJECTIVES
At the end of this class, students should be able to:
● Characterize viral diversity and types of replication.
● Describe the relationships between viral structures and modes of replication.
● Apply the properties of viral genome organization to infer replication strategies and interactions with hosts.
● Determine the types of ecological interactions between viruses and bacterial hosts.
● Interpret patterns of environmental distribution of viruses and their roles in biogeochemical cycles.
● Associate viral genomic features with clinical microbiology, including the transfer of toxin genes and phage therapy.
● Analyze viral genomic data using basic bioinformatics tools to make predictions on viral ecological roles and clinical relevance.
Note: Students are prohibited from recording any part of this course.
Well-Being Resources and Support
As you complete your coursework, consider how to maintain your health and well-being as a top priority. To help you become familiar with the many programs and services available on campus, review the information collected on the Division of Student Affairs Student Well-Being and Resiliency website available at miami.edu/well-being. Please contact me or any resources listed on the site if you need assistance or support throughout the semester.
Academic Integrity Policy
All students must comply with the University of Miami Academic Integrity Policy. The University of Miami community recognizes integrity as a core institutional value. The responsibility to uphold the University Honor Code and high academic standards is a shared value between faculty, students, and administrators. It is each community member’s responsibility to ensure that academic integrity is upheld. Faculty, in particular, have a vital role to play in this regard and are expected to be diligent in reporting violations. This policy acknowledges that the norms and the responsibility of academic integrity are to be jointly upheld by the faculty and student members of the University community.
MATERIALS and TOOLS
All students will need a laptop computer during class for genome analyses. If you do not have a laptop computer, contact the instructor as soon as possible.
Scientific publications discussed in the course will be provided by the instructor through Blackboard as pdf files.
PROJECT
The goal of the genome project is to characterize the biology of an unknown virus using bioinformatics tools to extract information from its genome. Each student pair will receive a viral genome sequence at the beginning of the course. The instructor will create groups on Blackboard where students can interact with each other and upload papers and reports. Each week, the students will learn how to use a different bioinformatics tool available in public databases and servers to identify the virus, annotate the coding regions, predict the structure of the capsid, and infer their evolution and host interactions. Some of these tools and databases include the NCBI, EMBL, JGI Global Virome Database, Chimera, Viral Zone, PATRIC, BLAST, iTOL, etc). The students will describe the results they obtain each week in a final paper, where they will also discuss any ecologically and/or clinically relevant features of each virus (host, genome architecture, presence of auxiliary metabolic genes, virulence genes, etc). On the paper, the students will also contextualize their findings with the current literature using the scientific papers discussed throughout the course and propose strategies to further characterize this virus. The students’ projects will be presented orally at the end of the semester. Upon course completion, each student will have a deep understanding of virus biology and will have developed basic bioinformatics skills.
GRADING
The final grade is calculated based on the following:
1. Participation in weekly discussions of scientific papers throughout the term (20%)
2. A seminar discussing a published scientific paper (20%)
3. Five reports on the genome analyses of your assigned virus (20%)
4. A final paper reporting the results of the genome analyses (20%)
5. A final oral presentation on the genome analysis project (20%)
The paper and the final project presentation will be graded separately but will be part of the same project.
Items 2-5 can be done in pairs (see below exception for BIL644).
Missed class policy
A second chance will be given to students that missed in-class discussions for medical reasons covered by UM’s Class Excuse Policy. The student can communicate their medical issue with Student Health Services, which will send a notice directly to the instructor, or with the instructor directly. Private health information will never be disclosed by Student Health Service, nor will information be shared with the instructor until the student provides Student Health Service with authorization to disclose dates that a student is excused from attending in-person classes.
Final Grade
The final course grade will be the percentage of the total possible points you receive during the semester. The grade ranges are as follows:
A = 90 - 100%
B+ = 88 - 89.9%
B = 80 – 87.9%
C+ = 78 – 79.9%
C = 65 – 77.9%
D = 55 – 64.9%
F = below 55%
Graduate students taking BIL644
The grading for graduate students will differ from that of undergraduates in two ways:
- Graduate students will lead the discussion of a scientific paper individually
- Graduate students will develop their projects and present their final paper and seminar individually
Students taking Writing in Biology BIL 380-SIL
The grading for students seeking writing credit will differ from that of undergraduates in two ways:
- Students will write their final paper individually
- Students will turn in the first version of the paper one month before the due date for the rest of the class for instructor feedback
EVALUATION GUIDELINES
Oral presentation of published scientific papers
• Pairs of students will choose a news article about their virus and identify what is the primary literature publication behind that news article.
• The students will read the news and primary literature article and prepare a presentation that covers both. The presentation should address the following:
• What does the news article say about this virus? What was the motivation for the research described in the primary literature? How about the approach and results? Do the conclusions of the paper substantiate the claims made in the news?
• The articles (news and academic) should be shared with the class at least of one week ahead of each presentation (uploaded to the group journal page on BB).
• The remaining students in the class must read the paper before class and ask questions that will spark discussion.
• Additional scientific literature that any student would like to discuss is welcome and encouraged.
Participation points in discussions of scientific papers
All students must participate with questions and/or comments on 6 of the 8 papers that will be discussed in class. Students will be given participation points. Your questions/comments will not be graded for correctness.
Genome analysis reports
As students progress in the genome analyses that will be the basis for their final research paper, they will write short reports. There will be 5 reports that will contain each:
- A brief description of the tool or approach used (50-100 words).
- Results (50-100 words), including one figure.
- A brief discussion of the significance of the findings based on papers discussed in class or connections with previous analyses and additional links encountered through the research.
Final paper
The paper will contain:
1) Introduction (300-400 words)
a) Relevant scientific literature that gives context to your analyses, which you will encounter as you progress through your research.
- Question (This should come at the end of the introduction, within that word limit):
- What is unknown about this virus that you will investigate with the methods you learned in the course?
a) Description of each tool used, including its theoretical basis. This is not a description of how you upload the sequences and download outputs, but rather an “under the hood” description of the method.
3) Results (500 – 600 words)
a) A detailed description of your results with figures
4) Discussion and future perspectives (300-400 words)
Put your results in the context of the recent scientific literature and discuss the implications of your findings. Throughout the semester, you will encounter these scientific papers during your searches through the NCBI, ViralZone, PDB, and JGI. Propose future research.
APA format is recommended. Citations should follow author-date format and should be listed alphabetically at the end of the paper.
Final presentation
Each student pair will prepare a 10-minute presentation describing their final project to their colleagues. The presentation should contain an introduction explaining the significance and motivation of the research, a brief overview of the methods applied (no details here; this should focus on the reason for choosing the methods and should not take more than one minute), and a careful description of their results and conclusions. Students are expected to explain the figures containing results.
Students should prepare a PowerPoint file to accompany their presentation. This ppt should be rich in images with very little text. The presenting students should also include one to two questions for their audience in the presentation.
Recommended Books (not required)
A planet of viruses (2nd edition). Carl Zimmer. University of Chicago Press, 2015.
Spillover: Animal infections and the next human pandemic. David Quammen. WW Norton & Company, 2012.
Life in our phage world: a centennial field guide to the Earth's most diverse inhabitants. Rohwer, F, et al. Wholon, 2014.
Thinking like a phage: The genius of the viruses that infect bacteria and archaea. Youle, Merry. Wholon, 2017.
Online Resources
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science). https://seaphages.org/
Year of the phage. http://2015phage.org/
National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/
European Nucleotide Archive. https://www.ebi.ac.uk/ena
Pathosystems Resource Integration Center. https://patricbrc.org/
Tara Oceans Viromes. http://ocean-microbiome.embl.de/companion.html
Rapid Annotation using Subsystems Technology. http://rast.theseed.org/FIG/rast.cgi
SCHEDULE
The schedule will be posted at the beginning of each term.
APPENDIX A.
Statement on Diversity and Inclusion
Every student in this class, regardless of background, sex, gender, race, ethnicity, class, political affiliation, physical or mental ability or any identity category, is a valued and equal member of the group. We all bring different experiences to this class and no one experience has more value or import than another. In fact, it is our different experiences that will enrich the course content. I encourage every student to share their own experiences as they are relevant to the course, but I also stress that no student is ever presumed to speak for anything or anyone more than their own experience or point of view.
If there are aspects of the instruction of this course that result in barriers to your inclusion or a sense of alienation from the course content, please contact me privately without fear of reprisal. If you feel uncomfortable contacting me, please contact the Office of the Dean of Students.
I will not tolerate disruptive or insulting remarks, gender or racial slurs, or other forms of
bullying, intimidation or hate speech in classroom or any of the communication channels we use, including Top Hat and Slate. Publication of the remarks or questions or work of any
classmate - in any form, written or recorded - without clear consent will be regarded as a
violation of academic integrity and treated as such. I expect you to act with respect for this
space, this subject, our process and each other.
APPENDIX B.
A Note on Sexual Misconduct
The University of Miami is committed to fostering a safe, productive learning environment. Title IX and our school policy prohibits discrimination on the basis of sex. Sexual misconduct — including harassment, domestic and dating violence, sexual assault, and stalking — is also prohibited at our school.
The University of Miami encourages anyone experiencing sexual misconduct to talk to someone about what happened, so they can get the support they need, and our school can respond appropriately.
If you wish to speak confidentially about an incident of sexual misconduct, want more information about filing a report, or have questions about school policies and procedures, please contact our Title IX Coordinator, which can be found on our school's website: https://titleix.miami.edu/
The University of Miami is legally obligated to investigate reports of sexual misconduct, and therefore it cannot guarantee the confidentiality of a report, but it will consider a request for confidentiality and respect it to the extent possible.
As an instructor, I am also required by our university to report incidents of sexual misconduct and thus cannot guarantee confidentiality. I must provide our Title IX coordinator with relevant details such as the names of those involved in the incident.