Lahore University of Management Sciences. BIO314 Virology and Microbiology (Spring 2015)

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1 BIO314 Virology and Microbiology (Spring 2015) Instructor Room. Office Hours Telephone Secretary/TA TA Office Hours Course URL (if any) Shaper Mirza and Sadia Hamera Course Basics Credit Hours 3 Lecture(s) Nbr of Lec(s) Per 2 Duration 75min each Recitation (per week) Nbr of Rec (s) Per - Duration - Lab (if any ) per week Nbr of Session(s) Per - Duration - Tutorial (per week) Nbr of Tut(s) Per Duration no Course Distribution Core Elective Elective Open for Student Category Juniors and Senior Year Students Closed for Student Category COURSE DESCRIPTION Lecture Series: The goal of this course is to provide a strong foundation for advanced microbiology course by familiarizing students with knowledge of bacteriology and virology. Microbiology is an exciting discipline with far-reaching impacts in human health and disease. This course will focus on the study of microbes in particular bacteria and viruses and their interrelationship with human disease. Understanding these relationships is essential in order to develop interventions to prevent infections in a community. The first quarter of the course will cover the basic principals of bacteriology including bacterial structure, growth, metabolism, genetics and general concepts of bacterial disease mechanisms. In the second quarter we will draw on the basic principals learned in the first quarter of the semester to understand bacteriology as it relates to human health and human disease. More precisely, the course will cover mechanism of disease and drug resistance and State-of-the-art technologies developed to understand pathogenesis. The next half of the course focus will be on viruses, another important pathogen that causes significant burden of disease every year. Globally viral infections kill approximately 2 million individuals every year. The higher burden of infections and fatalities caused by viruses are the result of their intrinsic diversity, which makes it difficult to treat and prevent viral infections. This part of the course will follow the same design as the part on bacteriology. However, in the next half the course will be focused on basic understanding of viral structures, assembly, replication, types of viruses, viral pathogenesis and finally vaccines. Laboratory component: Laboratory component is designed to provide an overview of procedures use to identify, isolate and correctly handle microorganism. Students will have the opportunity to learn basics of both light and fluorescent microscopic techniques and methods to for making medias for culturing and differentiating bacteria. The laboratory component will also, develop understanding of bacterial transmission and how to avoid it. Students will also learn basics of antimicrobial agents and antibiotics. Virology labs will be designed to give students background on basic cytopathic effects of viruses on human cell lines. Students will also learn to fluorescently label virus and visualize it in fluorescent microscope. COURSE PREREQUISITE(S)

2 BIO216 Microbiology and Virology COURSE OBJECTIVES Major objectives of the course are Develop a series of lectures to increase awareness and appreciation for microorganisms and their relationship to human health and disease Develop laboratory-based methods where student can apply basic microbiological techniques to identify, characterize and differentiate different lab strains and pathogens. Learning Outcomes Lectures: Students will be able to achieve the following from lectures Understand pathophysiology of viruses and bacteria important to human health Appreciate the diversity of host-pathogen interaction Distinguish between mechanism of pathogenesis caused by viruses and bacteria. Laboratory component: Students completing basic microbiology laboratory course, Will be able to use microscopic techniques, lab math, dilution series and bacterial enumeration Will gain awareness about the ubiquity and diversity of microbes Will explore a variety of microbiological techniques, skills and concepts. Will learn to generate, interpret and analyze data and design and conduct a small research project Grading Breakup and Policy Take Home Exam:20% (two take home exams will be posted one before mid term and one before finals) Midterm Examination:30% Lab project and Lab quiz: 20% Final Examination:30% Examination Detail Midterm Exam Yes/: Yes Combine Separate: Combine Duration: 2hours Preferred Date: Exam Specifications: Final Exam Yes/: yes Combine Separate: Combine Duration: 2 hours Exam Specifications: Lecture 1 Topics COURSE OVERVIEW Bacteriology and its importance in human health History Pathogenesis Epidemiology Instructor S.Mirza Recommended Readings Chapter 1-Todar s online text-book of bacteriology. Journal Articles. Objectives/ Application Introduction to Microbiology, what is Microbiology Why it matters.

3 2 Microbes and environment Bacterial physiology and anatomy Difference between a prokaryotic and eukaryotic cell Cell wall Extracellular proteins Intracellular proteins Other cellular organelles Bacterial growth and Metabolism (Part I) Differences between aerobic and anaerobic growth Respiratory chain Bacterial Metabolism (Part II) Energy generating pathways Diversity in Pathways The bacterial Chromosome DNA structure, Replication Segregation Bacterial Gene Expression Trancription Translation Post translational modification (N-terminal signal sequences) Genetic transfer of information in bacteria Conjugation Transformation Transduction Gene Regulation in bacteria Stress response Response to nutrients in media (catabolite responsive elements) Regulation of virulence Chapter 2 Todar s online text-book of bacteriology Journal Articles Chapter 2 Medical Microbiology 4 th edition Chapter 4 Todar s Online Bacteriology Chapter 4 Medical Microbiology 4 th edition Chapter 4 Medical Microbiology 4 th Chapter 1 Molecular Chapter 2 Molecular First exam from first 7 lectures Chapter 5,6,7 Molecular Genetics of Bacterial Snyder Chapter 13 Molecualr Chapter 14 Bacterial Understand the complex association of bacterial with environment. Difference between bacteria good for health and harmful for health. To understand the architecture of bacteria To understand how bacteria acquire nutrients How bacteria metabolize nutrients Appreciate the diversity in metabolic processes between different bacteria Understanding bacterial genome To understand how proteins and other virulence factors are expressed in bacteria. Just like host, genetic information is transferred from one bacterial cell to another. The mechanisms involved in transfer of information are complex and precise. Lectures in this class will be focused on understanding the flow of information in bacteria and different mechanisms that are used to transfer the information from one cell to another. Bacteria responses to the microenvironment of the niche that it occupies by differential expression of genes. The lecture will present mechanisms by which bacteria respond to different extracellular environment, which include nutrient deprivation and presence of chemical mediators such as host cytokines, enzymes and reactive oxygen species. 10 Genetic determinants of bacterial pathogenecity Bacterial virulence factors Toxins Proteases Chapter 12 Bacterial Bacteria posses a whole array of extracellular and intracellular proteins that it uses as an arsenal against its host. These lectures will describe in detail some of the toxins and other virulence proteins from common pathogens and their mechanism of action. 11 Delivery of virulence factors into host Bacterial secretion systems Secretion systems specific for Gram negative bacteria Chapter 13 Bacterial To cause infections bacteria is required to transfer its virulence proteins into host. Bacteria possess several mechanisms from injecting host cells with toxins and other virulence proteins. This section will highlight

4 12 Secretion systems specific for Gram positive bacteria Host response to bacterial infections Host Immune system Mechanism of protection against bacterial infections Innate Immunity Adaptive Immunity 13 Antibacterial agents different mechanisms of delivery of virulence factors. Familiarize students with basic immune mechanisms applied by host to prevent infections. This lecture will highlight methods used in everyday life to prevent infections 14 Antibacterial resistance in bacteria History of viral pathogenesis Viral Pathogenesis Virulence Epidemiology Introduction to Viruses and viral classification Genome Capsid Envelop Mechanism of drug resistance is an important area of bacterial pathogenesis. This lecture will briefly describe common mechanisms of drug resistance in bacteria. Second Exam from lectures 8-14 provided Understanding fundamentals of virology. Provide insight into Types of viruses. Basic structure of viruses Icosahedral symmetry Helical viruses Virus Genome Animal viruses Human viruses Identification of viruses in cell cultures Virus Entry Into Cell Attachment and entry Virus Replication Stages of viral replication in the cell Nucleic Acid synthesis RNA synthesis Making viral RNA Making viral DNA Genome Replication of DNA viruses Transcription Reverse Transcription Transcription and RNA processing Translation (Protein Synthesis) Mechanisms of viral entry into host cells. As viruses can have either DNA or RNA and in nucleic acids viruses can either have a positive or a negative strand, this lecture will provide background into how viruses synthesize their nucleic acids. DNA viruses transcribe themselves by first synthesizing a mrna by a process called as transcription. Process of transcription in bacteria and virus is different. While focusing on viral transcription, this lecture will explain differences between viral transcription and bacterial transcription Genome Packaging/Viral entry Mechanism of entry of nonenvelop viruses Mechanism of entry of envelop viruses Viral Assembly Assembly of Icosahedral Viruses Assembly of Helical Viruses The most important step in a viral life cycle is the packaging of the genome into its capsid. Once the capsid is packaged virus is ready for assembly and release. This lecture will focus on mechanisms of genome packaging of envelop and non-enveloped viruses Exam III Lectures Finally this series of lecture will be concluded by viral assembly and release 22 Infections caused by negative strand Some infections of human importance caused by negative

5 viruses strand viruses will be discussed Infections caused by positive strand viruses Recurring viral infections and antigenic variations Viral Immunology Host response to viral infections 26 Antivirals 27 Vaccines Infections of public health relevance caused by positive strand virus will be discussed This lecture will focus partly on viral evolution, antigenic variation and its role in recurrent viral infections Host response to viruses will be discussed and difference between host response to virus and bacteria will be highlighted Commonly used antivirals and their mode of action will be discussed. Additionally effect of Tami-Flu on reemergence of H1N1 viral flu will be discussed Prevention of viral and bacterial infections by vaccines, logic, logistics, and legends. Final Exam Textbook(s)/Supplementary Readings 1. Molecular Genetics of Bacteria L Snyder and W Champness 3 rd. 2. Todar s Online Bacteriology: toc.html. 3. Bacterial 4. Medical Microbiology Edited by Samuel Baron 4 th 5. Reading material for all lectures on viruses will be provided by the instructor. 6. Principals of virology S.J Flint, Facaniello III