Microorganisms and Disease Class 02 Slides PDF - Microbiology Course

1/23/25 Microorganisms and Disease Class 02, Jan 23, 2025 Micro Universe and Impacts Reading: Ch...

1/23/25 Microorganisms and Disease Class 02, Jan 23, 2025 Micro Universe and Impacts Reading: Chapter 1-intro, 1.1, 1.2, & 1.3 Note that unannotated Figures in these powerpoint presentations are derived from Nester’s Microbiology, © McGraw Hill (course Textbook), with permission 1 Announcements Pre-class quiz for Class 01 is still open (until next Thursday). Pre-class quiz for today is closed – 30 people missed! In-Class Assessment 01 – graded. If questions, see me. HW for Class 01 is a special case – due Week from today! è must be in person to me in my office! HW for Class 02 available after today’s class, due Sunday Pre-quiz for Class 03 open after today’s class 2 1  1/23/25 Review Syllabus states class policies and rules Some key elements Regular assignments for each class: quiz, in-class, HW Five exams on fixed schedule No late work No “make up” work No “extra credit” work Encouraged to talk to professor – email or in person, any topic 3 Today’s Agenda: Stories and “what to memorize” Philosophy of Evidence and Rules Historical Example(s) Microorganism learning Microorganism examples – first pass 4 2  1/23/25 Some “ A Yes” or B “No” Questions Can Micro-Organisms [MOs] Learn and Remember? Can MOs make decisions based on data? Do MOs have a brain? IF we accept Mos do not have a brain, but do Learn and remember, where do they store the information and how do they retrieve it? 5 Más sabe el diablo por viejo que por diablo Paraphrased: The devil knows more by being old than by being a devil. And Bacteria and Archaea are very old… 6 3  1/23/25 Information Stored in Nucleic Acids (DNA or RNA) MO Instruction and Grading are tougher than any course you’ve taken. Given a situation – you have to guess. If you guess wrong, you die. If you guess right, live, and reproduce -- Not only do you remember, but so do your offspring. Very slow process, and a lot of dead ends (literally!) But the time scale we are looking at is hard to imagine. 7 Each Micro-Organism has Memorized (written in DNA) 3.8 Billion Years of experience In this class we have 13 weeks… What do you expect to learn? And how will you learn it? 8 4  1/23/25 What is Learning? DNA of every cell alive today contains almost 4 billion years of memory of trial and error. Hard wired learning on day-to-day survival, growth, and reproduction. Response to stimuli. Other innate learning includes response to stimuli or learned behaviors. Some animals can learn new behaviors that have short term positive feedback. Some can even be seen teaching others by example 9 We do all those things Trial and Error Immediate rewards Memorize examples. But we are capable of so much more. 10 5  1/23/25 ”What?” is not enough We have a need for “Why?” 11 We need a story…. Humankind has long recognized infectious diseases as responsible for Illness and even death not related to physical injury and distinct from effect of poisons – but not knowing why, they invented reasons. In the book of Deuteronomy 23:12-14 we find explicit instructions for camp sanitation, requiring burial of human excrement outside of the camp. With no concept of infectious agents, the justification provided was that God walks through the camp at night, and we wouldn’t want his shoes to get dirty! In many cases, the diagnosis of the disease was remarkably accurate, but without knowledge of MOs, etiology explanations were haphazard. Roman medicine included accurate descriptions of periodic fevers, but the only cause they could imagine was the poison of the “bad air” [“mal” “aria”] associated with swamps à calling the disease malaria! 12 6  1/23/25 Trying to memorize everything in this course is poor strategy… You only “learn” what told. If you forget any item, it is gone… 13 But if you understand the story… You still know what you remember You can interpolate to fill holes in your memory. And you also can predict and extrapolate to new circumstances 14 7  1/23/25 In the Stories of Science, the focus is on …. Understanding Why? About extrapolating and predicting About rules and principles à but only if the story is correct! è and self correcting! 15 Scientific Stories Are Continually being Refined! I will frequently cite general rules and principles that reflect the level of understanding I think appropriate for an introductory course in Microbiology. For example: Information only flows from DNA à RNA à Protein Or, There are only four RNA BASES à A,G,C, & U Know that every rule has exceptions For scientists, understanding the exceptions actually strengthens the utility of the rule. For this course, focus will be on the general, sometimes simplistic rule – with important exceptions noted! If you want to better explore exceptions or refining of rules, that would be a good topic for office hours. FOCUS ON UNDERSTANDING THE STORY 16 8  1/23/25 Where do Stories Come From? People view the world through different lenses, including Art, Science, Philosophy, Religion, Politics, Law, or other personal bias. Each viewpoint has its own standard for evidence or measures of success, and they can give very different goals or valuations that are not always reconcilable. For Science, the stories have specific requirements, often summarized as the “Scientific Method” Based on observations and data. Makes predictions that are testable. Predicted outcomes are continually tested by the community If exceptions are found, the story is revised and communicated to the community. And the cycle continues. 17 The Story of Infectious Diseases Humankind has long recognized infectious diseases as responsible for Illness and even death not related to physical injury and distinct from effect of poisons Working theories of the day credited the unseen spirits or gods or magic or evil and the like. Then, in 1674, some of the unseen became seen… 18 9  1/23/25 The Birth of Microbiology Late 17th century, a Dutchman, Antonie van Leeuwenhoek, and an Englishman, Robert Hooke, independently created powerful magnifying devises and showed that there was a world of creatures so small that they could not be seen by the unaided eye. This did not immediately change the concept of disease, but it set the stage for change. 19 Death of Theory of Spontaneous Generation Late 19th century (200 years later), Louis Pasteur showed that spoilage of grape juice could be prevented by boiling the juice and the blocking access of microorganisms to the juice. à Proposed the hypothesis that life can only arise from life! Other experimenters disputed the generality of the claim, showing that some media (hay infusion broth) would grow organisms after boiling, even in isolation! (Exceptions!) Finally, John Tyndall showed that the exceptions were due to heat resistant bacteria (we will talk about endospores, later!) – which still supported that “all life comes from life.” Took years for this story to fully develop! 20 10  1/23/25 Birth of Story of Infectious Disease Still in the 19th century, Louis Pasteur and Robert Koch independently demonstrated that some diseases are due to infectious microorganisms Going back to dirty shoes and bad air – Public health and sanitation grew from an understanding of the role of fecal material in transmission of disease organisms. The “bad air” of the swamps was shown to be a matter of infected mosquitoes living in the swamps and flying through the air. Set off a bonanza of research into identifying the infectious agents of all diseases. Still ongoing. 21 “Round up all the usual suspects!” Cellular life forms Bacteria Archaea How many of you knew about Archaea before this week’s reading? And how many of you who knew could spell it correctly without first looking it up? Eukaryotes Single celled – like Protists, Fungi, Multi-cellular – like helminths Other infective agents Viruses Viroids Prions 22 11  1/23/25 Who are these ”Infectious Agents” Cellular Agents Visible (barely, in some cases) by light microscopy Originally classified into two broad groups Eukaryotes (true nucleus) And Prokaryotes (no nucleus) Special stains subdivided even further DNA analysis of shared genes (ribosomal genes) that caused us to rethink the world! 23 Universal Tree Assesses the accumulation of mutations in DNA Lengths of lines correlate with evolutionary time Simplest assembly – all cellular life evolved from one single-celled ancestor Geological timeline Earth is ca. 4.6 billion years old Life started 3.5 – 3.8 billion years ago By 2.5 million years ago, single celled organisms were terraforming the planet, adding oxygen to the atmosphere. Spread and evolved to fit essentially every habitable zone on the planet. 24 12  1/23/25 Universal Tree of Cellular Life Access the text alternative for slide im ages. © McGraw Hill LLC 25 25 Cellular Life Arose One Time And evolved to fit into every livable corner of the Earth. NSF estimates 1,000,000,000,000 different bacteria species on earth, 99.999% of which are not yet discovered! And only a handful cause disease in humans… We are just another environmental niche they may want to colonize… And we are back to learning by trial and error, and being very old: (Más sabe el diablo por viejo que por diablo.) – evolving to live and grow in different environments. 26 13  1/23/25 With the discovery of a micro universe, people began to understand. Microorganisms can cause disease, but our disease and suffering is not their intent. Their billions of years of evolution have focused on surviving, growing, and reproducing. If they did want to kill us, we would be dead by now. Understand that these tiny things terraformed a planet! If we can understand their specific needs, we can manipulate their activities to our benefit, to control infections, preserve foods, and stimulate good health. We are finding more cases where MOs even have a commensal relationship with us – with us supporting their growth and reproduction and them protecting us for other MOs! 27 Generalizations about Human Infectious Diseases Microbes are not trying to kill us! We are just another potential environmental niche. Some Microbes that have interacted with Humans over generations and evolved to a kind of balance – whether symbiotic or parasitic, both organisms survive to reproduce and evolve! Other microbes had/have some characteristic, evolved for other environments, that happens to cause severe disease. 28 14  1/23/25 Remember how MOs “Learn”? If MO kills too quickly, no growth/transmission. (Ebola) àNo advantage à No learning. Continual short-term issue. If MO is quickly killed by host, no growth/transmission. (Tetnus) àNo advantage àNo learning. Continual short-term issue. But in some microbes (and some humans) can allow for evolution... MO and host can learn! Evolving into a kind of balance. Still can be a crappy deal for the patient... 29 Emerging Infectious Diseases Accidental crossover (e.g., zoonosis) E. coli O104:H4 Ebola HIV-1 COVID-19 Climate change exacerbated Lyme disease Chagas disease Malaria Societal exacerbation Drug resistance (e.g., Tuberculosis, Staph.) Rapid world-wide travel/connections. Unequal access to medical care and treatments. Misinformation preventing application of medical care and treatments. 30 15  1/23/25 Last Point (for now) on Universal Tree of Cellular Life Access the text alternative for slide im ages. © McGraw Hill LLC 31 31 Quick Check: Which emerging infectious diseases is least likely to evolve into a balance with humans? (A). COVID-19, respiratory infection that was epidemic and rapidly A evolving (B). Clostridium perfringens, a wound infection that causes gas B gangrene and rapidly kills the host unless all infected tissue is amputated. C (C). Ebola – an extremely contagious hemorrhagic virus that rapidly kills most infected humans. (D). Chickenpox virus – infecting children with a rash, but also D reemerging as “shingles” in older adults? 32 16  1/23/25 MOs don’t even have to infect us to impact us! The great famine in Ireland in the 1800s was largely due to a microbial disease of potatoes A bacterial disease that kills olive trees, first seen in southern Italy in 2013, has spread to Spain and France, contributing to a recent worldwide drop in olive oil production A fungal disease called “wheat blast” devastated wheat crops in South America, then spread to Bangladesh in 2016, resulting in the loss of over 35,000 acres of crops that year. Two years later it was found in Zambia Frog populations around the world have been decimated by a fungal disease called chytridiomycosis Not just impacting frog-leg diners – think insect control! 33 Back to Infectious Disease Focus Most microorganisms are not harmful – some are even beneficial Those that cause disease are called pathogens. They can cause disease by Directly damaging body cells and tissues. Creating toxins that damage cells and tissues. Releasing waste products (from MO growth) that damage cells and tissues. Stimulating the body’s defense mechanisms, resulting in collateral damage. 34 17  1/23/25 Their impact can far exceed anything we have done to ourselves (so far) Influenza in 1918 to 1919 killed more Americans than died in WWI, WWII, and the Korean, Vietnam, and Iraq wars combined The COVID-19 pandemic has resulted in the death of more than 15 million people worldwide, including over 1 million Americans 35 Some specific successes (but...) Smallpox eradicated! The disease once killed one-third of its victims; left others blind or scarred Devastated unexposed populations, such as native inhabitants of Americas World-Wide vaccination program – can tell you stories of real heroes! No reported cases since 1977, but laboratory stocks of virus remain And Monkey pox is emerging... Plague deaths less than 100 per year Killed one-third of population of Europe (approximately 25 million people) between 1347 and 1351 Control of rodent populations and human respiratory secretions to prevent spread Antibiotics for treatment But we still have plague throughout the southwest region, just not human spread! Polio nearly eliminated by vaccination Emphasis on “nearly”. Eliminating the last human reservoirs stymied by religion and politics. Measles also “nearly” in US. Don’t get me started... 36 18  1/23/25 Cellular Infectious Agents – “Usual Suspects” All living cells can be classified into the three domains we saw earlier. Bacteria Archaea Eukarya All three domains include known or suspected pathogens (Archaea sidebar and optional reference) 37 ” A rose by any other name....” Quick sidebar on Binomial System of Nomenclature Generally two words Genus (capitalized) species name (not capitalized) Both genus and species are either italicized or underlined Genus may be abbreviated (E. coli) if clear from context But note Escherichia coli and Entamoeba coli are both E. coli! Also, can use ‘spp.’ for multiple species: Plasmodium spp. 38 19  1/23/25 More on Scientific Names Name often reflects characteristic of organism or honors a scientist who worked with the organism. Escherichia (honors Theodor Escherich) coli (indicates the colon, where these bacteria often live) Members of a species with important minor differences may be indicated with a strain designation (E. coli K12) Informal names that resemble genus names are not italicized Members of the genus Staphylococcus are often called staphylococci © McGraw Hill LLC 39 39 Members of the Microbial World—Table 1.1 Table 1.1 Characteristics of Members of the Three Domains Characteristic Bacteria Archaea Eukarya Cell type Prokaryotic Prokaryotic Eukaryotic Number of cells Unicellular Unicellular Unicellular or multicellular Membrane-bound No No Yes organelles Ribosomal RNA Yes Yes Yes sequences unique to the group Peptidoglycan in Yes No No cell wall Typical size range 0.3–2 μm 0.3–2 μm 5–50 μm © McGraw Hill LLC 40 40 20  1/23/25 Bacteria Single-celled prokaryotes Most have a Rigid cell wall containing ‘peptidoglycan’ (polymer that is unique to bacteria) Many move using one or more ‘flagella’ Multiply via binary fission Obtain energy from a wide variety of sources; some are photosynthetic Most species have a consistent, specific shape. 41 Names can derive from bacteria or cluster shapes... Recognize, don’t memorize… Coccus (plural: cocci) -- Spherical cells, Bacillus (plural: bacilli) -- A rod shaped, cylindrical cell) Vibrio (plural: vibrios) -- A short, curved rod Spirochete (plural: spirochetes) -- A long, spiral-shaped cell with a flexible cell wall Cocci that remain as pairs are called diplococci Bacteria that form long chains – Streptococcus (strepto means “twisted chain”) Cocci that form grape-like clusters -- staphylo means “bunch of grapes” 42 21  1/23/25 Archaea -- to date, minor player in human disease Single-celled prokaryotes similar in size, shape, and properties to bacteria Major differences from Bacteria in chemical composition Cell walls lack peptidoglycan Ribosomal RNA sequences different To date, most research is on “extremophiles” High salt concentration, temperature Many are common in moderate environments Also found in human microbiomes (intestine, oral cavity) See optional (i.e., not on exam) article from CDC, this year. 43 Eukarya Eukarya: single-celled or multicellular eukaryotes Eukaryotes studied by microbiologists include fungi, algae, protozoa, and helminths (worms) Algae and protozoa also referred to as protists Table 1.3 Eukaryotic Organisms Studied by Microbiologists Organism Characteristics Fungi Use organic material for energy. Size range from microscopic (yeasts) to macroscopic (molds; mushrooms) are the reproductive structures of some fungi. Algae Use sunlight for energy. Size range from microscopic (single- celled algae) to macroscopic (multicellular algae). Protozoa Use organic material for energy. Single-celled microscopic organisms. Helminths Use organic material for energy. Adult worms are typically macroscopic and often quite large, but their eggs and larval forms are microscopic. © McGraw Hill LLC 44 44 22  1/23/25 Fungi Fungi: diverse group ranging from single- celled yeasts to multicellular filamentous molds The microscopic filaments of molds, called hyphae, form a visible mat called a mycelium Filamentous molds spread by release of microscopic spores (conidia) Mushroom: macroscopic reproductive structure characteristic of some fungi Secrete enzymes onto organic materials, and then take in the released nutrients Opportunistic infections (e.g., yeast) Janice Haney Carr/CDC Also, systemic infections on skin and in lungs. Access the text alternative for slide im ages. © McGraw Hill LLC 45 45 Algae Diverse group of photosynthetic eukaryotes Single-celled or multicellular Photosynthesis in algae occurs in chloroplasts which contain chlorophyll or other pigments that give characteristic colors Usually live near surface of water or in moist habitat Rigid cell walls and flagella distinct from those of prokaryotes Only rarely a pathogen, but some species secrete toxins into water. (Note: Cyanobacter are bacteria, NOT algae) Lisa Burgess/McGraw Hill © McGraw Hill LLC 46 46 23  1/23/25 Protozoa Diverse group of single-celled eukaryotes Complex, larger than prokaryotes Most ingest organic compounds No rigid cell wall Most are motile Energy from ingested organic material Pathogenic protozoa are often included under the term Parasites. Melba Photo Agency/Alamy Stock Photo © McGraw Hill LLC 47 47 Helminths Parasitic helminths are worms that live at the expense of a host Adult worms of most species can be seen with the naked eye. However, these stages are often embedded within the body and not easily viewed. The diagnostic stages (larvae and ova (or eggs) usually require use of a microscope – hence their inclusion under Microbiology. Helminths include roundworms (Ascaris), tapeworms (Taenia), and flukes © McGraw Hill LLC 48 48 24  1/23/25 Acellular Infectious Agents As name implies – they are not cells à Not on the universal tree of life Unlike cells, they have originated many times They are the lawyers of the Microbiology Universe They take perfectly reasonable laws and rules Then twist them beyond recognition for their own benefit. Top category are Viruses! 49 Quick Check: Are Viruses living entities? A (A). They cannot reproduce on their own. Obviously, they are not alive. (B). Even though they need help to replicate, they can evolve B evolve independently of the host. Obviously, they are alive. 50 25  1/23/25 Quick Check: Are Viruses living entities? A (A). They cannot reproduce on their own. Obviously, they are not alive. (B). Even though they need help to replicate, they can evolve B evolve independently of the host. Obviously, they are alive (C). I don’t know if they are alive or dead, but most of the time I C want to kill them... 51 Another Group: Acellular Infectious Agents As name implies – they are not cells à Not on the universal tree of life Unlike cells, they have originated many times They are the lawyers of the Microbiology Universe They start perfectly reasonable laws and rules Then twist them beyond recognition for their own benefit. Not clear if they are alive (depends on definitions) but they all learn in the same evolutionary classroom as cells And two of them use the same nucleic acid memory. By definition, they are all pathogenic to something! 52 26  1/23/25 Acellular Infectious Agents—Table 1.4 Agent Characteristic Viruses Consist of either DNA or RNA, surrounded by a protein coat. Obligate intracellular agents that use the machinery and nutrients of host cells to replicate. Viroids Consist only of RNA; no protein coat. Obligate intracellular agents that use the machinery and nutrients of host cells to replicate. Prions Consist only of protein; no DNA or RNA. Misfolded versions of normal cellular proteins that cause the normal versions to misfold. © McGraw Hill LLC 53 53 Viruses Nucleic acid packaged in protein coat Infect living cells, referred to as hosts Obligate intracellular agents Multiply using host cell machinery and nutrients Inactive outside of host All forms of life can be infected by different types May kill host cell May remain within host cell and replicate viral genetic information as host cell multiplies Fun fact – your genome is carrying thousands of viral genomes (ca 8% of your DNA). Fortunately, most of them have been enjoying a free ride for so long they Cynthia S. Goldsmith and Thomas Rowe/CDC have forgotten how to get out, replicate, and kill us.... © McGraw Hill LLC 54 54 27  1/23/25 Viroids Consist only of a single short piece of RNA (They generally need a buddy to get them into the plant in the first place) Obligate intracellular agents Cause a number of plant diseases To date, only one known human disease – Hepatitis D © McGraw Hill LLC 55 55 Prions (aka “slow viruses”) Infectious proteins: misfolded versions of normal cellular proteins found in the brain Misfolded version in contact with normal version causes the normal protein to also misfold! Abnormal proteins form fibrils and aggregates Cells die leaving spaces in brain (spongiform encephalopathy) EM Unit, VLA/Science Source Resistant to usual sterilization procedures © McGraw Hill LLC 56 56 28  1/23/25 If time – Scientific Method and information transfer 1900s – was “obvious” that proteins were the only molecule sufficiently complex to transfer information. Carbohydrates were polymers of sugar, for energy. DNA was polymer of nucleic acids for nitrogen storage. 1930-1944, Avery, MacLeod, & McCarty claimed that DNA was actually the transmitting molecule. Long, drawn out fight. Final nail in coffin was Watson & Crick (& ) showing how DNA replicated information. 1970-1988, Pruisner claimed that protein, alone could carry the information to cause disease. Same long, drawn arguments as before, but with roles reversed. There are exceptions to every rule – whatever the rule is. And the Scientific Method will (eventually) sort it out! 57 Finish overview Stories vs memorization Scientific Method Rules and philosophy Disease Usual Suspects 58 29  1/23/25 Questions? 59 Class 02 Homework 1.Select and name an emerging infectious disease. 2.What is the scientific name of the infectious agent. 3.To what domain or group does the agent belong? 4.In a few sentences, describe which of the factors described in class contribute to this disease being emerging, and why? (remember -- if using chatGPT or other AI tool, be sure to follow guidelines in the syllabus) 60 30  1/23/25 In Class Assessment – Class 02 “MOD” 1. What was the most interesting thing you heard in today’s class that you had not known before? 61 31