Microbiology Quiz One (PDF)

Lecture Summary Lecture 1 will cover the following: Lecture 1 Definition of microbiology. The Scope of Microbiology...

Lecture Summary Lecture 1 will cover the following: Lecture 1 Definition of microbiology. The Scope of Microbiology Types of microorganisms. Types of biological entities. 1 2 Scope of Microbiology Organisms are composed of cells (cellular) and include: ⚫ Bacteria Definition of Microbiology ⚫ Archaea It is the study of organisms and biological entities that most of them are very ⚫ Fungi small in size to the extent we can not see them by our eyes. ⚫ Protists Comments on the definition: ⚫ A cell is defined as the smallest, basic unit of life that is responsible for all Microbiology study everything related to the organisms and the biological processes of life such as growth. entities such as: ⚫ Types ⚫ Structure and function ⚫ Distribution on earth ⚫ Interaction with each other ⚫ Interaction with other living organisms e.g. plants and humans ⚫ Interaction with the nonliving matter e.g. rocks and metals ⚫ Benefits and harms e.g. production of food and causing diseases. ⚫ Thus, in order to study these organisms, we must be able to grow them in the lab which led to the development of microbiology. 3 Biological entities are not composed of cells (acelluar) include the following: The majority of organisms and the biological entities are very small in size, thus: ⚫Viruses ⚫ Can not be seen by the human eyes. ⚫ Viroids ⚫ Are 1mm or less in diameter. ⚫ Satellites ⚫ Usually measured in micrometres (µm). ⚫ Prions ⚫ Because they are very small, they are called microorganisms (micro: means small). They are described as biological entities but not organisms because: ⚫ Only can be seen by microscopes and that is why microbiology developed They are not composed of cells like organisms. A cell is defined as the after the invention of the microscope. smallest, basic unit of life that is responsible for all processes of life such as ⚫ However, some organisms are big and can be seen by the human eyes, so growth. these are called macroscopic (macro means big) e. g. mushrooms. They are biological because they are composed of biological materials such as protein and/or DNA and/or RNA. They are entities because they can survive but cannot reproduce independently of living host. 5 6 Therefore, based on previous slides, microbiology study the following: Lecture 2 Classification of living organisms and The Development of Microbiology-1 7 1  Classification of living organisms Lecture Summary The discovery and observation of living organisms resulted in lots of information Made biologists to classify living organisms in order to study them more Lecture 2 will cover the following: Classification of living organisms. How to classify living organism: Using these a) by using apparent properties e.g. similarity in shape (morphology Comments on the Most recent accepted (domain system) classification characteristics or outer appearance) scheme for living organisms. resulted in the b) by using structures e.g. presence of nucleus five-kingdom Development of microbiology and the factors that led to the development system c) by Mode of nutrition e.g. photosynthesis of microbiology. Biologists decided to use specific fingerprint that is unique to each living organism i.e. sequence of ribosomal rRNA (rRNA) For this purpose, Carl Woese compared the sequences of rRNA of all living organisms in order to classify them This method resulted in the following domains 2 3 Domains of living organisms Comments on the domain system for the classification of living organisms ⚫ It was proposed by Carl Woese in 1971. ⚫ Used sequences of rRNA of all living organisms because: Other schemes of classification are not applicable to all organisms. rRNA sequences are unique to each living organisms so they are fingerprints that distinguish each living organisms. ⚫ Resulted in grouping organisms into three domains: 1. Bacteria (prokaryotes) 2. Archaea (prokaryotes) 3. Eukarya (eukaryotes- protists and fungi) 4 5  Development of microbiology Development of microbiology - Continued Microbiology has developed due to the following three events: Second: The ability to grow microorganisms in the lab because without growing microorganisms microbiologists can not study and characterize them. First: ⚫ The discovery of the microorganisms has started by observing ⚫Therefore, we can conclude that the Second Stage of the history of microbiology microorganisms. has started when microbiologists managed to isolate and hence grow microorganisms ⚫ There are two types observations: in the lab. Observation of the effects of microorganisms, for example, observing the symptoms of infectious diseases, such as: Third: The ability to isolate and analyze nucleic acids of microorganisms [a] the plague specially DNA. [b] leprosy [c] smallpox. ⚫ This Third Stage of microbiology development has started in the seventies and still in progress. Observation of microorganisms that started with/after the discovery of the microscope that enabled microbiologists to see microorganisms. ⚫Therefore, we can conclude that the history of microbiology has started by observing microorganisms (First stage of the history of microbiology). 6 7 Lecture Summary Lecture 3 Lecture 3 will discuss the following: The Development of Microbiology-2 The Three stages of Microbiology History (History of Microbiology) Stage 1: The Observation Stage of Microbiology History. The contribution of Lisan ad-Din Ibn al-Khatib (1313-1374). The contribution of Abū Jafar Aḥmad ibn Khātima Al-Anṣārī (1324 – 1369). The history of leprosy. 1 2  The Three stages of Microbiology History Stage 1: The Observation Stage of Microbiology History First: Observing the effects of microorganisms (the plague, leprosy and smallpox) As mentioned in the previous lecture, the history of microbiology can be ⚫ In this stage, microbiologists started to observe the effects of microorganisms, for divided into three stages: example, the ability to cause diseases with apparent symptoms. ⚫ The first documented event of the plague (also called black death) was dated 1346. Stage 1: The observation (observing the effects and direct observation) of microorganisms. The observation stage (early human history – 17th century). ⚫ The causative agent of the plague is a bacterium named Yersinia pestis (identified in1894) that first caused the plague in Mongolia in East Asia. ⚫ Then, the Mongols carried the plague to the Black Sea area. Stage 2: The ability to prepare pure culture of microorganisms (pure culture ⚫ In May 1347, a ship carrying infected people arrived in Constantinople (Istanbul, Turkey), means presence of grown one type of microorganism). The pure culture stage which resulted in loses as much as 90 percent of its population. (18th century – mid 19th century). Stage 3: The ability to isolate and analyze nucleic acids of microorganisms. The microbial molecular biology stage (mid 19th century – now). In this lecture, we will start studying these three stages ⚫ In October 1347, another ship carrying infected people docks in Sicily, with the crew barely alive. Then, the plague spread to Italy from which the disease was transmitted to the rest of 3 Europe. 4 Lisan ad-Din Ibn al-Khatib (1313-1374) ⚫ Ibn al-Khatib explored the idea of transmission of the plague through infectious particles that he called contagion, centuries before Louis Pasteur conducted his experiments in Europe. ⚫ On the Plague, Ibn al-Khatib wrote: The existence of contagion is established by experience and by trustworthy reports on transmission. Transmission occurs by: [a] garments [b] vessels [c] ear-rings [d] by persons from an infected house [e] by infection of a healthy sea-port by an arrival of ships from an infected land [f] by the containment (quarantine) of isolated individuals. 5 6 Abū Jafar Aḥmad ibn Khātima Al-Anṣārī (1324 – 1369) ⚫ Is one of the most important intellectuals of the Medieval Moorish Spain ⚫ The first documented event of leprosy ( ‫ )مرض الجذام‬was dated to 4000 years ago. ⚫ ‫ابن خاتمة األنصاري‬ ⚫ Leprosy was found in a 4,000-year-old human skeleton uncovered in India in 2009. ⚫ Tahsil garaḍ al-qāṣid fī-tafṣīl al-maraḍ al wāfid “ ‫تحصيل غرض القاصد في تفصيل‬ ‫”المرض الوافد‬ ⚫ In 1874, Gerhard-Henrik Armauer Hansen, a Norwegian scientist, discovered the bacterium ⚫ Investigated: Mycobacterium leprae as the causative organism for leprosy. ⚫ The causes of plague (black death). ⚫ The contagion theory in the disease: [a] The plague happened because of the change in the air that can cause damage to the body. [b] Breathing corrupted air causes the damage to the heart. 7 8 Lecture Summary Lecture 4 will cover the following: The history of smallpox. Lecture 4 The development of vaccination. The Development of Microbiology-3 Continuation of stage 1 of microbiology history: the direct observation of (History of Microbiology) microorganisms. Stage 2 of microbiology history: The Pure Culture Stage. Hasan Ibn Al-Haytham contributions. Louis Pasteur contributions. Antonie van Leeuwenhoek contributions. Koch’s contributions and postulates. 1 2  The discovery of vaccination Still at the Observation stage: In old cultures, it was observed that people who recovered ⚫ The first documented event of smallpox was dated 1500 BC in Egyptian from smallpox would not be infected by the disease again mummies. The Chinese in the 10th century used to protect people from smallpox by ⚫ In the 18th century Europe, it is estimated that 400,000 people died annually deliberately inoculate healthy people with material from infected people from smallpox. ⚫ Up to 300 million people have died from smallpox in the 20th century. In 1756 in England, this method was applied to Edward Jenner at the age of 8 ⚫ Smallpox is caused by a virus called Variolae vaccinae (i.e. pustules of the cow) that was first seen under the electron microscope in 1948. After graduation from the medical school Edward Jenner heard about the ⚫ Smallpox was eliminated completely in 1980 by vaccination that was discovered possibility of inoculating cowpox material to protect people against smallpox by Edward Jenner in 1798. and people who had cowpox are resistant against smallpox, Edward Jenner investigated this method and showed its success in 1796 and called the material used for inoculating people for the purpose of protection as vaccine. Later in year 1800, the process of protecting people by introducing disease material from infected people into healthy people was called vaccination. 3 In 1885, Louis Pasteur and his colleagues invented the rabies vaccine 4 Second: The direct observation of microorganisms (refer to L3 slide 4 Observation Stage) ⚫ The first documented event of image magnification was attributed to the Islamic scholar Hasan Ibn Al-Haytham (Latinized as Alhazen; 965 – 1040) ⚫ Known as "the father of modern optics". ⚫ Kitāb al-Manāẓir or "Book of Optics" that he wrote during 1011–1021. ⚫ The name "Alhazen" was cited by Isaac Newton, and Galileo Galilei. ⚫ The first to investigate the following: ⚫ Principles of image formation and camera obscura. ⚫ Interaction of light with lenses. ⚫ Potential of lenses to magnify images. ⚫ Light refraction. ⚫ Principles of the scientific method. 5 6  ⚫ Antonie van Leeuwenhoek (1632-1723) ⚫ Dutch scientist, that made a primitive little microscope that could magnify about 50 – 300X. ⚫ His microscope Leeuwenhoek was the first to observe & describe microorganisms accurately, that’s why he is called the father of microbiology. ⚫ He called protozoa animalcules. Hevelius's Selenographia, showing Alhasen representing reason, and Galileo representing the senses (in Italy) 7 8 Stage 2: The Pure Culture Stage of Microbiology History Old beliefs regarding the origin of disease ⚫ Before the discovery of microorganisms and the development of microbiology as a field, many people believed that living organisms could arise out of dead/non-living matter. ⚫ That concept is known as the spontaneous generation theory: living organisms could arise from non-living or dead matter. Centuries ago, people used to believe ⚫ Great Aristotle the Greek Philosopher believed that simple invertebrates could arise that disease was caused by a number of spontaneously. (refer to slide 10). factors: 1. Supernatural forces ⚫ The scientist who formally disproved the spontaneous generation theory in 1861 was Louis Pasteur. 2. Poisonous air (miasma) 3. Imbalance between the “four humours” (liquids): blood, ⚫ Louis Pasteur is a French microbiologist and chemist famous for his discoveries related to phlegm, yellow bile, and black the process that was later named after him (pasteurisation) and (fermentation). bile With time, scientific inquiry laid waste ⚫ Pasteur formally supported the current theory called the germ theory that states the to these beliefs and provided more following: many diseases (especially infectious disease) are caused by microorganisms. substantial evidence that microbes can cause disease ⚫ The need to study microorganisms , that are known to exist (as shown in stage 1) In the next section, we will highlight made/encouraged/compelled microbiologists to search for suitable media to grow major scientific discoveries of microbe- microorganisms. associated diseases 9 10 ⚫ In 1861, Pasteur performed the famous “Swan neck flask experiment”, which showed that microorganisms arise from other microorganisms, not non-living matter: ⚫ Robert Koch is a German physician and microbiologist. ⚫ Considered the father of modern bacteriology. ⚫ Laid the foundation for relationship between disease and infectious agents ⚫ Famous for his postulates (Koch’s postulates). ⚫ First proposed during his studies on anthrax, which were published in 1876; later applied the same concepts to studies on tuberculosis. ⚫ Anthrax is caused by the bacterium Bacillus anthracis. ⚫ Tuberculosis is caused by the bacterium Mycobacterium tuberculosis. ⚫ Also, Pasteur showed how to keep solutions sterile by heating and subsequent cooling the liquids that later called pasteurisation. 11 12 Koch’s experiment on anthrax using mice Comments on Koch’s postulates Not all of Koch’s postulates are applicable Cultured agent could be entire bacterium or endospore (we will cover “endospores” later in Mycobacterium leprae, a bacterium which causes the disease “leprosy”, the course) CANNOT be isolated and grown in pure culture Ebola virus disease is so deadly that it would be unethical to use humans as experimental organisms Instead of attributing a disease to an entire microorganism, scientists started focusing on “genes” responsible for the microorganism’s pathogenicity and virulence ❑ Pathogenicity: ability to cause disease ❑ Virulence: extent/degree of damage done by a pathogen Molecular version of Koch’s postulates was proposed by Stanley Falkow in 1988. Koch was awarded the Nobel Prize in Physiology or Medicine in 1905 13 14  Lecture 5 The Development of Microbiology-4 (History of Microbiology) 15 1 Development of microbiology - Continued Lecture Summary Third: The ability to isolate and analyze nucleic acids of microorganisms specially DNA. ⚫ This third stage of microbiology development Lecture 5 will cover the following: has started in the seventies and still in progress. The third stage of microbiology development ⚫ Microbiology gradually shifted from relying heavily on traditional culture-based techniques to Discoveries/events of the third stage of microbiology development: non-culture-based, molecular techniques. Sequencing of nucleic acids ⚫ Culture-based methods rely on isolation of microorganisms from their environments and Polymerase Chain Reaction (PCR) growing them in pure cultures. ⚫ Molecular-based methods rely on isolation of Complete sequenced genome of Haemophilus influenza. DNA from microorganisms. Invention of the next-generation sequencing (NGS). ⚫ This required the ability to isolate DNA and RNA from microorganisms. Complete sequenced genome of SARS-CoV-2 virus. ⚫ In 1977, Frederick Sanger develops a DNA sequencing technique which he and his team” use to sequence the first full genome of a virus called phiX174. 2 3 ⚫ In 1985, the Polymerase Chain Reaction (PCR) technique, ⚫ In 1995, The first bacterium genome of Haemophilus influenza invented by Kary B. Mullis. was completely sequenced. 4 5 ⚫ In 2020, Following the pandemic outbreak of COVID-19, the ⚫ In 2019, Nick McCooke with his team at Solexa to invent the next- genome of the SARS-CoV-2 virus was sequenced. generation sequencing (NGS), a technology to read DNA at high speed that is nowadays used worldwide. 6 7