Now offered fall 2022!
Tuesdays and Thursdays 5:05 - 6:20 pm - Cox Science 217
Tuesdays and Thursdays 5:05 - 6:20 pm - Cox Science 217
Biology of Viruses featured in the College of Arts and Sciences news!
Viruses are the most abundant and diverse biological entities on the planet. Beyond causing devastating pandemics, they drive the evolution of their hosts and modulate nutrient cycles at planetary scales.
The Biology of Viruses is a 3-unit capstone course that explores the molecular biology, ecology, and clinical relevance of viruses through the discussion of scientific papers published in the most respected scientific journals in the last five years.
You will fully engage in active learning by developing an original research project using bioinformatics tools to analyze viral genomes and present your results in oral and written format (there are limited spots for writing credits with additional requirements).
The Biology of Viruses is a 3-unit capstone course that explores the molecular biology, ecology, and clinical relevance of viruses through the discussion of scientific papers published in the most respected scientific journals in the last five years.
You will fully engage in active learning by developing an original research project using bioinformatics tools to analyze viral genomes and present your results in oral and written format (there are limited spots for writing credits with additional requirements).
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Topics covered:
- Viral diversity, evolution and molecular biology - Lateral gene transfer and recombination - Viral ecology and viral spillovers - Viromics and bioinformatics - Impact of viruses in host evolution - Virus engineering and gene therapy - SARS-COV-2 pandemic |
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Syllabus
The Biology of Viruses – Fall 2022
Instructor:Dr. Cynthia Silveira (cynthiasilveira@miami.edu )
Office Hours:Thursdays after class until 5 pm in Cox 247.
Course background. Viruses are the most abundant and diverse biological entities in the planet. They drive the evolution of their cellular hosts and modulate carbon and nutrient cycles in the biosphere. Viruses are rising as promising tools against emerging multi-drug resistant bacteria and for gene therapy. The Biology of Viruses is a 3-unit capstone course for students in Biology and biomedical sciences. The course introduces the molecular biology, ecology, and clinical relevance of prokaryotic and eukaryotic viruses. The classes are designed to increase undergraduate interest on emerging topics in virus research, with a strong active learning component through project development. The course will also investigate viral spillovers – when viruses jump from one host species to another – using the 2019 coronavirus outbreak as a case study.
LEARNING OBJECTIVES
At the end of this class, students should be able to:
IMPORTANT ANNOUNCEMENTS
COVID-19 Announcement
Masks are strongly encouraged in the classroom and all indoor public and common spaces. Surgical masks or multi-layered, tightly woven cloth masks should be used. Single-layer cloth masks are not considered protective against the omicron variant and hence do not meet The University’s current standard for campus safety.
Students displaying any COVID-19 symptoms (https://www.cdc.gov/coronavirus/2019-ncov/symptoms-testing/symptoms.html) are must not come into the classroom and must immediately contact Student Health at 305-284-9100 (https://studenthealth.studentaffairs.miami.edu/health-education/health-topics/coronavirus/index.html).
Students are expressly prohibited from recording any part of this course. Any recordings made by the instructor will be available to students registered for this class through Blackboard. Students are expected to follow appropriate University policies and maintain the security of passwords used to access recorded lectures. Recordings may not be reproduced, shared with those not in the class, or uploaded to other online environments. If the instructor or a University of Miami office plans any other uses for the recordings, beyond this class, students identifiable in the recordings will be notified to request consent prior to such use according to FERPA policy.
Well-Being Resources and Support
As you complete your coursework, consider how you can 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 reach out to me or any of the 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 should 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.
SCHEDULE - TBA
GRADING
The final grade is calculated based on weekly reports of genome analyses (20%), a final paper reporting the results of the analyses (20%), a final oral presentation on the project (20%), a seminar discussing a published scientific paper (20%), and participation on weekly discussions of scientific papers throughout the term (20%). The paper and the final project presentation will be graded separately but will be part of the same project.
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 BIL675
The grading for graduate students will differ from that of undergraduates in two ways:
MATERIALS and TOOLS
All students will need a laptop computer during class for genome analysis practices. 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 project is to characterize the biology of an unknown virus using bioinformatics tools. Each student will receive a viral genome sequence at the beginning of the course, but this genome will not be labelled. 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, ecology and medical relevance. 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 propose strategies to further characterize this virus based on the scientific papers discussed throughout the course. 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.
Recommended Books
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
Bacterial and Viral Bioinformatics Resource Center | BV-BRC: https://www.bv-brc.org/
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
EVALUATION GUIDELINES AND RUBRICS
Oral presentation of published scientific papers
Participation points in discussions of scientific papers
Genome analysis report
As students make progress in the genome analyses that will be the basis for their final research paper, they will write short reports. There will be 6 reports (due dates on Schedule) that will contain each:
Final paper
The paper will contain:
APA format is recommended. Citations should follow author-date format and should be listed alphabetically at the end of the paper.
Final paper
Project presentation
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 – Fall 2022
Instructor:Dr. Cynthia Silveira (cynthiasilveira@miami.edu )
Office Hours:Thursdays after class until 5 pm in Cox 247.
Course background. Viruses are the most abundant and diverse biological entities in the planet. They drive the evolution of their cellular hosts and modulate carbon and nutrient cycles in the biosphere. Viruses are rising as promising tools against emerging multi-drug resistant bacteria and for gene therapy. The Biology of Viruses is a 3-unit capstone course for students in Biology and biomedical sciences. The course introduces the molecular biology, ecology, and clinical relevance of prokaryotic and eukaryotic viruses. The classes are designed to increase undergraduate interest on emerging topics in virus research, with a strong active learning component through project development. The course will also investigate viral spillovers – when viruses jump from one host species to another – using the 2019 coronavirus outbreak as a case study.
LEARNING OBJECTIVES
At the end of this class, students should be able to:
- Characterize viral diversity and types of replication.
- Describe the relationships between capsid structures and modes of replication.
- Apply the properties of viral genome organization to infer replication strategies.
- 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.
IMPORTANT ANNOUNCEMENTS
COVID-19 Announcement
Masks are strongly encouraged in the classroom and all indoor public and common spaces. Surgical masks or multi-layered, tightly woven cloth masks should be used. Single-layer cloth masks are not considered protective against the omicron variant and hence do not meet The University’s current standard for campus safety.
Students displaying any COVID-19 symptoms (https://www.cdc.gov/coronavirus/2019-ncov/symptoms-testing/symptoms.html) are must not come into the classroom and must immediately contact Student Health at 305-284-9100 (https://studenthealth.studentaffairs.miami.edu/health-education/health-topics/coronavirus/index.html).
Students are expressly prohibited from recording any part of this course. Any recordings made by the instructor will be available to students registered for this class through Blackboard. Students are expected to follow appropriate University policies and maintain the security of passwords used to access recorded lectures. Recordings may not be reproduced, shared with those not in the class, or uploaded to other online environments. If the instructor or a University of Miami office plans any other uses for the recordings, beyond this class, students identifiable in the recordings will be notified to request consent prior to such use according to FERPA policy.
Well-Being Resources and Support
As you complete your coursework, consider how you can 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 reach out to me or any of the 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 should 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.
SCHEDULE - TBA
GRADING
The final grade is calculated based on weekly reports of genome analyses (20%), a final paper reporting the results of the analyses (20%), a final oral presentation on the project (20%), a seminar discussing a published scientific paper (20%), and participation on weekly discussions of scientific papers throughout the term (20%). The paper and the final project presentation will be graded separately but will be part of the same project.
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 BIL675
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
MATERIALS and TOOLS
All students will need a laptop computer during class for genome analysis practices. 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 project is to characterize the biology of an unknown virus using bioinformatics tools. Each student will receive a viral genome sequence at the beginning of the course, but this genome will not be labelled. 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, ecology and medical relevance. 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 propose strategies to further characterize this virus based on the scientific papers discussed throughout the course. 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.
Recommended Books
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
Bacterial and Viral Bioinformatics Resource Center | BV-BRC: https://www.bv-brc.org/
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
EVALUATION GUIDELINES AND RUBRICS
Oral presentation of published scientific papers
- Groups of three of students will be assigned a highly impactful scientific paper (see schedule) on the first day of class. The pdf file of the paper will be available on Blackboard.
- The students will read and prepare a presentation that includes background information, methods, and results from the paper.
- Make sure not to split the presentation in the middle (i.e., one student only talks about introduction, the other methods, and the other the rest – mix it up!)
- 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 are required to participate with questions and/or comments on 8 of the 10 papers discussed in class.
- The participation can be through one of each:
- Posting at least one question on Blackboard discussion board before class.
- Asking at least one question during the live presentation in the classroom.
- Students will be given participation points. Your questions/comments will not be graded for correctness.
Genome analysis report
As students make progress in the genome analyses that will be the basis for their final research paper, they will write short reports. There will be 6 reports (due dates on Schedule) that will contain each:
- Brief description of the bioinformatics tool or approach being used (50-100 words).
- Description of the results (50-100 words) including one figure.
- Brief discussion of the significance of the findings in the context of papers discussed in class, or connections with previous/future analyses.
Final paper
The paper will contain:
- Introduction (300-400 words)
- Relevant scientific literature giving context to your analyses
- Question (This should come at the end of the introduction, within that word limit):
- What is not well-known about this virus that you can investigate with the methods you learned in the course?
- Methods (500-600 words)
- Description of each tool used, including its theoretical basis. This is not a description of how you upload the sequences and get outputs, but rather an “under the hood” description of the method.
- Results (500 – 600 words)
- A detailed description of your results with figures
- Discussion and future perspectives (300-400 words)
APA format is recommended. Citations should follow author-date format and should be listed alphabetically at the end of the paper.
Final paper
Project presentation
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.