MCB3020 Lecture 1 Ch01 PDF

Introduction Instructors Bobrovskyy Lab Dr. Maksym Bobrovskyy Richard Agyen Assistant Professor Koushik Majumder Department of Molecular Biosciences...

Introduction Instructors Bobrovskyy Lab Dr. Maksym Bobrovskyy Richard Agyen Assistant Professor Koushik Majumder Department of Molecular Biosciences Isabelle Powell ISA6209 Mon. 3:30-4:30pm Alberta Bossi [email protected] Beatriz Araujo Dr. Fatema Moni Chowdhury Assistant Professor of Instruction Department of Molecular Biosciences ISA1051 Thur. 4-5pm [email protected] Mr. Amiratabak Rajaei (TA) Graduate Student Department of Molecular Biosciences BSF 221, Fri. 8-9am [email protected]  Course Information ▪ Book Microbiology: An Evolving Science by Joan L. Slonczewski, John W. Foster, and Erik R. Zinser (6th edition), 2020 by W.W. Norton & Company. ISBN: 978-1324-033523 ▪ All the lectures and course materials will be posted in Canvas ▪ Course related updates and announcements will be made via Canvas Course Information ▪ Four Modules Cell structure and function Genetics Microbial growth and control Infectious diseases ▪ Assignments Exams (75%): 4 exams, in-person, lowest score can be dropped Quizzes (10%): 4 quizzes, online, due on Friday prior to the exam Assignments (7.5%): 4 assignments, completed at home, submitted on Canvas Participation (7.5%): concept check questions completed during lecture only on Canvas Questions and Office Hours ▪ If you have questions or need help: Please use Canvas for communications Post to Q&A DISCUSSION FORUM on Canvas Contact Mr. Rajaei; expected response time is 5 business days Dr. Bobrovskyy in-person office hours on Mon. 3:30-4:30pm ISA6209 ▪ If you need to meet via MS Teams or at different time, contact me to schedule  LECTURE 1 Microbial Life: Origin and Discovery  OVERVIEW 1.1 WHAT IS A MICROBE? 1.2 IMPACT OF MICROBES ON HUMAN HISTORY 1.3 ORIGINS OF MEDICAL MICROBIOLOGY 1.4 MICROBIAL ECOLOGY AND ENVIRONMENT 1.5 THE MICROBIAL FAMILY TREE 1.6 CELL BIOLOGY AND THE AMAZING DNA REVOLUTION What is a Microorganism or Microbe? ▪ A Microbe is a microscopic organism that cannot be seen with an unaided eye Microbial cells range in size from millimeters (mm) to 0.2 micrometer (µm) Viruses may be 10x smaller ▪ Some microbes consist of a single cell ▪ Contains capacity to reproduce its own kind within its genome  Incredible Numbers of Microbes 1024 stars in the visible universe 1012 species of microbes (only 0.1-1% have been identified) 1030 individual bacteria on Earth 1031 individual viruses on Earth Microbes in all Domains of Life ▪ Microbes include members of the three domains of life Great Variety of Microbes Outliers Challenging the Microbe Definition ▪ Giant microbial cells Thiomargarita namibiensis ▪ Microbial communities Biofilms ▪ Viruses Pandoravirus  Microbial Genomes are Sequenced ▪ A genome is the total genetic information contained in an organism’s chromosomal DNA ▪ The first method of DNA sequencing fast enough to sequence large genomes was developed by Fred Sanger - He shared the 1980 Nobel Prize in chemistry ▪ The collection of sequences taken directly from the environment is called a metagenome First Sequenced Microbial Genome ▪ By 1976, first complete viral genome of bacteriophage MS2 was sequenced ▪ In 1995, enabled by Sanger sequencing, scientists completed the first genome sequence of a cellular microbe, the bacterium Haemophilus influenzae  OVERVIEW 1.1 WHAT IS A MICROBE? 1.2 IMPACT OF MICROBES ON HUMAN HISTORY 1.3 ORIGINS OF MEDICAL MICROBIOLOGY 1.4 MICROBIAL ECOLOGY AND ENVIRONMENT 1.5 THE MICROBIAL FAMILY TREE 1.6 CELL BIOLOGY AND THE AMAZING DNA REVOLUTION  Microbes Shape Human History ▪ Microbes shaped human culture since the dawn of civilizations Yeasts used in bread making or production of beer (10,000 BCE) Fungi and bacteria in making of cheese Bacteria used in fermentation of Sauerkraut and Kimchi, yogurt and sour cream “Rock eating” lithotrophic bacteria enable extraction of metals from ore in mining Photograph: Horizons WWP/TRVL/Alamy industry, or breakdown of ancient Belgian monk brewing beer monuments Microbes Shape Human History  Microbial Disease Devastates Human Population ▪ Throughout history, microbial diseases have profoundly affected human demographics and cultural practices - Plague of Justinian (6th century) and Black Death (14th) century bubonic plague epidemics caused by Yersinia pestis, killed 30-60% of European population - Spanish flu (1918-1920) flu epidemic caused by Influenza A (H1N1) killed 20-100 million people and majorly The Triumph of Death by Pieter Bruegel depicting contributed to death during World social upheaval and terror that followed the plague War I in Medieval Europe  Epidemics of the Current Day ▪ Microbial infections affecting changing our world today - Acquired immunodeficiency syndrome (AIDS) caused by the human immunodeficiency virus (HIV) have claimed 43 million lives since 1981 - COVID-19 pandemic caused by SARS-CoV-2 virus reported to have killed ~ 7 million, but estimated 18-33 million people worldwide since 2019 Quilts representing individuals who died of AIDS were displayed before the Washington Monument in 1992  Florence Nightingale (1820–1910) ▪ Throughout history, more soldiers have died of microbial infections than of wounds in battle ▪ The significance of disease in warfare was first recognized during the Crimean War by the British nurse Florence Nightingale (1820–1910) - Founder of professional nursing and the science of medical statistics - devised the “polar area chart” to represent deaths of soldiers due to various causes  Microscopes Reveal the Microbial World ▪ Robert Hooke (1635–1703) - Mentored by Robert Boyle and Thomas Willis at Oxford - Curator for the Royal Society - Built the first compound microscope - Published Micrographia in 1665, the first manuscript illustrating microbes - Coined the term “cell”  Microscopes Reveal the Microbial World ▪ Antonie van Leeuwenhoek (1632-1723) - Worked as a cloth draper (tailor) in Dutch city of Delft - Built single-lens magnifiers, complete with sample holder and focus adjustment - First to observe single-celled microbes (or extravagantly moving small living Animals) Microscopes Reveal the Microbial World ▪ van Leeuwenhoek’s observations published by the Royal Society in more than 150 letters and in “Animalcules” ▪ Established microbiology as a discipline (Animalcules late 1600s) Origin of Microbes: Spontaneous Generation ▪ Spontaneous generation is a theory that microbes could arise spontaneously, without parental organism ▪ Jan Baptist van Helmont proposed a recipe for spontaneous generation of mice The Vegetable Lamb growing from the earth like a melon from a seed Origin of Microbes: Spontaneous Generation ▪ Francesco Redi (1626-1697) - Italian, priest, physician and natural historian - showed that maggots in decaying meat were the offspring of flies ▪ Lazzaro Spallanzani (1729-1799) - Italian priest - showed that a sealed flask of meat broth sterilized by boiling failed to grow microbes Amitchell125, Wikimedia Commons  Origin of Microbes ▪ Louis Pasteur (1822-1895) - French chemist, microbiologist and immunologist - discovered the microbial basis of fermentation - Performed the famous swan-neck flask experiment - Process of pasteurization is named after him  OVERVIEW 1.1 WHAT IS A MICROBE? 1.2 IMPACT OF MICROBES ON HUMAN HISTORY 1.3 ORIGINS OF MEDICAL MICROBIOLOGY 1.4 MICROBIAL ECOLOGY AND ENVIRONMENT 1.5 THE MICROBIAL FAMILY TREE 1.6 CELL BIOLOGY AND THE AMAZING DNA REVOLUTION Origins of Medical Microbiology ▪ Miasma vs Germ theory - Miasma theory of disease is an early belief that diseases are caused by miasma or bad air. An 1831 color lithograph by Robert Seymour depicting cholera as a skeleton emanating a deadly black cloud.  Origins of Medical Microbiology ▪ Robert Koch (1843–1910) - German physician and bacteriologist - Founder of the scientific method of microbiology - Provided proof of germ theory of disease - Applied his methods to numerous lethal diseases around the world ▪ Germ theory postulates that many of the diseases are caused by microbes ▪ Working with anthrax, Koch demonstrated an important principle of epidemiology: the chain of infection, or transmission of a disease Koch’s Postulates ▪ Criteria for establishing a causative link between an infectious agent and a disease 1. Microbe is always present in diseased host and absent in healthy 2. Microbe is grown in pure culture without other microbes present 3. Introduce pure microbe into healthy host and the individual becomes sick 4. Same microbe re-isolated from now- sick individual Microbial Growth in Pure Culture ▪ To prove a particular bacterium caused a specific disease, pure culture of microorganisms were needed Angelina and Walther Hesse developed solid medium using agar Julius Petri invented a double-dish container (Petri dish) Immunization Prevents Disease ▪ In the eighteenth century, smallpox infected a large fraction of the European population (10-20%) ▪ Lady Mary Montagu introduced the practice of smallpox inoculation (variolation) to Europe in 1717 ▪ Edward Jenner (1749–1823) discovered that cowpox infection protects patients from smallpox - The practice of cowpox inoculation was called vaccination (Latin vacca for “cow”) Immunization Prevents Disease French newspaper ▪ Louis Pasteur (1822–1895) depicts Louis developed the first vaccines based Pasteur protecting children from rabid on attenuated (weakened) strains dogs - Fowl cholera - Rabies ▪ Immunization is the stimulation of an immune response by deliberate inoculation with an attenuated pathogen  We Have Come a Long Way The mRNA vaccine causes host cells to make viral spike proteins and process antigens to stimulate an immune response. Antiseptics ▪ In 1847, Ignaz Semmelweis ordered doctors in Vienna General Hospital First Obstetrical Clinic to wash their hands with chlorinated lime solution, an antiseptic agent - Mortality rates due to postpartum infections fell from 18% to 2% - Nicknamed “saviour of mothers” ▪ In 1865, Joseph Lister developed carbolic acid to treat wounds and clean surgical instruments ▪ In the twentieth century, aseptic surgery was developed - Environments completely microbe-free Discovery of Antibiotics ▪ In 1929, Alexander Fleming discovered that Penicillium mold generated a substance that kills bacteria ▪ In 1941, Howard Florey and Ernst Chain purified penicillin - The first commercial antibiotic to save human lives Discovery of Viruses ▪ In 1892, Dmitri Ivanovsky studied tobacco mosaic disease - Agent of transmission could pass through a porcelain Pasteur- Chamberland filter that blocked all known microbes ▪ In 1898, Martinus Beijerinck established that the agent of tobacco mosaic disease is not a bacterium, because it passes through a filter that retains bacteria, called it contagious living fluid ▪ In 1935, the “filterable agent” was purified and crystallized by Wendell Stanley earning him the 1946 Nobel Prize in Chemistry - Tobacco mosaic virus (TMV) Tobacco mosaic virus (TMV) A. Particles of tobacco mosaic virus (colorized transmission electron micrograph). B. A capsid of proteins surrounds an RNA chromosome  Viruses ▪ Viruses are considered by most scientists to be non-living particles - Acellular - Obligate parasites - No metabolism - Do not respond to stimuli - Assemble rather than grow (Wasser et al 2009)  OVERVIEW 1.1 WHAT IS A MICROBE? 1.2 IMPACT OF MICROBES ON HUMAN HISTORY 1.3 ORIGINS OF MEDICAL MICROBIOLOGY 1.4 MICROBIAL ECOLOGY AND ENVIRONMENT 1.5 THE MICROBIAL FAMILY TREE 1.6 CELL BIOLOGY AND THE AMAZING DNA REVOLUTION Microbes Support Natural Ecosystems ▪ Microbes cycle the many minerals essential for all life, including all global N2 and much of the O2 - Yet less than 0.1% of all microbial species can be cultured in the laboratory - The remainder make up the majority of Earth’s entire biosphere ▪ Only the outer skin of Earth supports complex multicellular life Microbes Support Natural Ecosystems ▪ Sergei Winogradsky (1856–1953) - A Ukrainian scientist who was among the first to study microbes in natural habitats - Discovered lithotrophs - Organisms using inorganic materials for biosynthesis - Developed enrichment cultures - Built the Winogradsky column - A wetland model ecosystem containing regions of enrichment for microbes of diverse metabolism Wikimedia commons Winogradsky Column  Winogradsky Pioneered the Concept of Geochemical Cycling ▪ The global nitrogen cycle - All life depends on oxidative and reductive conversions of nitrogen - most of which are performed only by microbes Wikimedia commons Bacterial Endosymbiosis ▪ Endosymbionts are microbes living symbiotically inside a larger organism, usually in a mutualistic relationship ▪ Endosymbiotic bacteria known as rhizobia induce the roots of legumes to form special nodules to facilitate nitrogen fixation ▪ Endosymbiotic microbes make essential nutritional contributions to host animals (e.g. vitamins) - Colonic bacteria such as Escherichia coli and Bacteroides species grow as biofilms Microbes Support Natural Ecosystems An extreme thermophile reduces iron oxide to magnetite. A. Hydrothermal vent at ocean floor. B. Geogemma barossii is a round archaeon with a tuft of flagella (transmission electron micrograph). C. Kazem Kashefi, now at Michigan State University, pulls a live culture of “strain 121” (Geogemma) out of an autoclave generally used to kill all living organisms at 121°C (250°F). Microbial Life on Other Planets? Mars Curiosity rover. The rover explores Mars for evidence of microbial life.  OVERVIEW 1.1 WHAT IS A MICROBE? 1.2 IMPACT OF MICROBES ON HUMAN HISTORY 1.3 ORIGINS OF MEDICAL MICROBIOLOGY 1.4 MICROBIAL ECOLOGY AND ENVIRONMENT 1.5 THE MICROBIAL FAMILY TREE 1.6 CELL BIOLOGY AND THE AMAZING DNA REVOLUTION Microbial Family Tree ▪ The bewildering diversity of microbial life-forms presented nineteenth-century microbiologists with a seemingly impossible task of classification ▪ So little was known about life under the lens that natural scientists despaired of ever learning how to distinguish microbial species ▪ The famous classifier of species, Swedish botanist Carolus Linnaeus (1707–1778) called the microbial world “chaos” Challenge of Classifying Microbes ▪ While animals and plants can be classified based on physical features, early taxonomists faced two challenges as they attempted to classify microbes 1. Resolution of the light microscope was too low - Challenge was overcome via advances in biochemistry and microscopy 2. Microbial species are hard to define because they share common features - With the ability to sequence microbial genomes, microbiologists have devised working definitions of microbial species - 95% similarity of DNA sequence Microbes include Eukaryotes and Prokaryotes ▪ Ernst Haeckel (1834–1919) referred to microbes as neither plant nor animal - a third kind (kingdom) of life classified as Monera ▪ Herbert Copeland (1902–1968) divided Monera into two groups - protists (eukaryotic protozoa and algae) - prokaryotes (bacteria) ▪ Robert Whittaker (1920–1980) added Fungi as a fifth kingdom of eukaryotic microbes ▪ Five kingdoms classification: Animals, Plants, Fungi, Protists, Prokaryotes Eukaryotes Evolved through Endosymbiosis ▪ The five-kingdom system was modified dramatically by Lynn Margulis (1938–2011) - She proposed that eukaryotic organelles, such as mitochondria and chloroplasts, evolved by endosymbiosis from prokaryotic cells engulfed by pre-eukaryotes ▪ The endosymbiosis theory was highly controversial - It implied a polyphyletic ancestry (species emerging from several common ancestors) of living species, instead of the long-held assumption that species evolve only by divergence from a common ancestor (monophyletic ancestry) Endosymbiosis and the Five Kingdoms of Life Lynn Margulis and the serial endosymbiosis theory. A. Five-kingdom scheme, modified by the endosymbiosis theory. B. Lynn Margulis (University of Massachusetts, Amherst) proposed that organelles evolve through endosymbiosis. Development of Phylogenetics ▪ In 1977, Carl Woese was studying recently discovered prokaryotes that: - Live in hot springs - Produce methane ▪ Analysis of the 16S rRNA revealed that these prokaryotes were a distinct form of life - He called them archaea - Modern day phylogenetics based on 16S rRNA sequence Illinois Distributed Museum Archea Archaea, newly discovered life-forms. A. Finding archaea in the hot-spring Obsidian Pool at Yellowstone. B. Pyrococcus furiosus, an organism that lives at temperatures above 100°C (transmission electron micrograph). Three Domains of Life Three domains of life phylogenetic tree. Three domains form a monophyletic tree that is based on the 16S small- subunit ribosomal RNA (rRNA) sequences. The length of each branch approximates the time of divergence from the last common ancestor. Woese et al.; Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. PNAS 1990  OVERVIEW 1.1 WHAT IS A MICROBE? 1.2 IMPACT OF MICROBES ON HUMAN HISTORY 1.3 ORIGINS OF MEDICAL MICROBIOLOGY 1.4 MICROBIAL ECOLOGY AND ENVIRONMENT 1.5 THE MICROBIAL FAMILY TREE 1.6 CELL BIOLOGY AND THE AMAZING DNA REVOLUTION Cell Biology and the Amazing DNA Revolution ▪ More than 99% of what we know about microbes today was discovered after 1900 - Advances in biochemistry and microscopy revealed the fundamental structure and function of cell membranes and proteins - The revelation of the DNA and RNA structures led to the discovery of the genetic programs of model organisms - Beyond microbiology, these advances produced “genetic engineering” and more Cell Membranes and Macromolecules ▪ Two instruments had exceptional impact on the study of cell structure: 1.The electron microscope - Developed by Ernst Ruska - Revealed internal structure of cells 2.The ultracentrifuge - Developed by Theodor Svedberg - Enabled separation of subcellular parts light-harvesting Chlorobium species, a photosynthetic bacterium Microbial Genetics ▪ In 1928, Frederick Griffith discovered transformation in bacteria ▪ In 1944, Oswald Avery and colleagues showed that the transforming substance is DNA ▪ In 1953, Rosalind Franklin used X-ray crystallography to determine that DNA is a double helix ▪ Later that year, James Watson and Francis Crick discovered the complementary bases and antiparallel nature of DNA DNA Double-Helix The DNA double helix. A. Rosalind Franklin discovered that DNA forms a double helix. B. X-ray diffraction pattern of DNA, obtained by Rosalind Franklin. C. James Watson and Francis Crick discovered the complementary pairing between bases of DNA and the antiparallel form of the double helix. Microbial Genetics ▪ The promise of DNA was first fulfilled in bacteria and bacteriophages - Bacteria readily recombine DNA from unrelated organisms - Recombinant DNA ultimately enabled us to transfer genes - A heat-stable bacterial DNA polymerase (Taq) was used for amplifying DNA via the polymerase chain reaction (PCR) - Gene regulation discovered in bacteria which provided models for animals and plants - CRISPR-Cas9 is a molecular mechanism of bacterial defense against bacteriophages, that has now been used for human genome editing and is revolutionizing eukaryotic genetics 2020 Nobel Prize for CRISPR-Cas9 Emmanuelle Charpentier and Jennifer Doudna won the 2020 Nobel Prize in Chemistry for CRISPR-Cas9 discovery and application for human genome editing. Microbial Discoveries Transform Medicine and Industry ▪ Research in microbiology finds applications in diverse fields Summary ▪ Microbes are microscopic organisms that include bacteria, archaea, fungi, algae, protists, and viruses ▪ Microbes have affected human civilization ▪ Many scientists have contributed to our understanding of microbiology. They include: - van Leeuwenhoek = observation of microbes - Pasteur = disproved spontaneous generation - Koch = developed the Four Postulates - Jenner = developed vaccination - Fleming = discovered antibiotics ▪ Microbes perform unique roles in geochemical cycling ▪ Eukaryotic organelles, such as mitochondria and chloroplasts, evolved by endosymbiosis from prokaryotic cells engulfed by pre-eukaryotes ▪ The three domains of life are Bacteria, Archaea, and Eukarya ▪ Advances in microscopy and biochemistry revealed the structure and function of the various cell components Suggested Reading ▪ Microbiology: An Evolving Science, 6th Edition – CHAPTER 1 ▪ Proposal paper for the three domains of life: Woese et al.; Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. PNAS 1990 ▪ Book about the early development of molecular biology and genetics: The Eighth Day of Creation: The Makers of the Revolution in Biology by Horace Freeland Judson ▪ Book about how plagues have shaped human civilization: Plagues and Peoples by William McNeill