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Microbiology- pharmacy – lecture 10 of these microorganisms (bergey’s manual is used for microorganisms, like pharmacopeia is used for drugs) In the classification of microorganisms we have key elements that we use to identify which type we’re dealing with; Examples: -spirochaete bacterium Treponema pallidum which causes syphilis disease First we ask about Its Microscopic morphology (shape , motility), but this doesn’t give us enough information so as to find out what type of microorganism it is, so we start with biochemical properties (gram reaction , aerobic or non-aerobic), and then the molecular properties (PCR, DNA hybridization)which give us the best results, we can use phage typing, and serological tests (antibody-antigen). • • • -Aerobic motile helical gram-negative bacteria Helicobacter (H.pylori) which causes peptic ulcer, Campylobacter (both bacteria related to GI disease) - Gram-negative aerobic rods and cocci pseudomonas : burn infection, UTI Pseudomonas doesn’t need a lot of nutrition, it is non fastidious, its enzymes are complex and it is able to synthesize nutrients; that’s why its capable of living in water even though water has little amount of nutrients. Most macroscopic organisms can preliminarily be classified according to observable structural characteristics but many of the bacteria have similar structures (when it is found in a burn infection, it forms a green color,, Separating the bacteria according to cell shape, size, and arrangement does not produce a very useful classification system Nor does the presence of specific structures such as flagella, endospores, or capsules It can also be found in eye drops and eye solutions if not handled carefully, which might eventually cause eye infection and might cause blindness). It is a very important gram negative problematic microorganism the Gram stain, were among the first properties other than morphology to be used to classify bacteria . Other properties now in use include features related to growth, nutritional requirements, physiology, biochemistry, genetics, and molecular analysis. These features include properties of DNA and proteins An example of Gram negative rods: Escherichia coli which is the main cause if UTI infections !! --> Escherichia coli is the main causitive agent for UTI (urinary tract infections) - some types of E.coli are found in the GI as part oof the normal flora. nevertheless it could cause unirary tract infection ##REMEMBER## UTI infection E. coli. Accordingly we have Bergey’s manual which lists characteristics of microorganisms and disease and products 1 - Neisseria: Neisseria gonorrhoeae causes STD gonorrhea Irregular non spore forming gram positive bacteria: dyfteria مرض الخانوق, propioni acne bacteria - salmonella, shigella, and other types of microorganisms, and anaerobic gram negative rods “bacteroides” that is found in the GI and can cause infection in different sites of the body - Mycobacteria is an acid fast bacteria -Nocardia: “Obligate intracellular microorganism” (has to be inside a cell in order for it to grow) viruses : they are called obligate intracellular parasites by (look at the table , memorize the ticked lines ) Rickettsiae and Chlamydiae, are “Obligate intracellular microorganism” and contain rather unusual organisms that have different Methods of reproduction other than the conjugation and binary fission. Chlamydia may be found in the form of an elementary body and a reticulate body; a reticulate body is highly involved in the process of replication and growth of these bacteria Mycoplasma; it is a type of bacteria that lack the cell wall. It contains steroids in its cytoplasmic membrane; an important cause of atypical pneumonia cocci: caused Actinomyces and Streptomyces: they are bacteria but they divide in more than one plane, filamentous growth, we use it to form over 500 antibiotics , they look like fungus but they are not. Aerobic gram negative bacteria may be present in the GI tract and can cause infections. Gram positive streptococcus nocardioform, staphylococcus, -Endospore- forming gram positive bacteria : Bacillus that causes anthrax - Anaerobes and endospores-forming: clostridium (clostridium tetani, clostridium perfringens) -Regular non spore forming gram positive bacteria: lysteria 2 *DNA: - single-stranded - double- stranded * RNA: - single-stranded: (positive sense ssRNA, or negative sense ssRNA ) -double-stranded RNA (classification according to their genetic material) **Viruses ** General viruses: - - - - - characteristics of Viruses are microorganisms (بين )الحياة والال حياة They can replicate, or multiply, only inside a living host cell (obligate intracellular parasites) They can’t be seen by light microscopes , we need electron microscopes to be able to see them Some viruses cause infections to humans only, some cause infections to animals only, and some cause both, and these viruses are transferred from animals to humans and the other way around as well,. When they invade susceptible host cells, viruses display some properties of living organisms and so appear to be on borderline between living and nonliving Viruses contain DNA or RNA but never both • Some viruses are composed of only the genetic material, surrounded with a capsid Other viruses have another layer that surrounds the capsid; called the envelope (additional surrounding lipid bilayer membrane) Components of Viruses: capsid: Surrounding protein coat core: that contains the genetic material which is either the DNA or the RNA Major groups of viruses are distinguished first by their nucleic acid content as either DNA or RNA Because most eukaryotic cells do not have the enzymes to copy viral RNA molecules, the RNA viruses must either carry the enzymes or have the genes for those enzymes as part of their genome. (VERY IMPORTANT) - 3 Naked viruses: are viruses with a nucleocapsid and no envelope Enveloped viruses: viruses with additional envelope (they have genes for forming an envelope) (classification according to their structure) On the other hand, a naked virus activates the immune system because the body recognizes a foreign object (from its outer membrane), nevertheless; the protein that surrounds naked viruses is very tough and is very resistant to chemicals, that’s why they are found in the environment in large numbers. -Virion: A complete virus particle (in a naked virus; the virion is the genetic material with the capsid. In an enveloped virus; a virion is the genetic material with the capsid and envelope) A capsid is composed of polymers of capsomeres (polymer of protein) Protrusions called spikes are found on an envelope (attachment site) • • • The enveloped viruses are very sensitive to antimicrobial treatments or to virusoid treatment . Viruses use their nucleic acids (genome) to replicate themselves in host cells Capsids also play a key role in the attachment of some-naked- viruses. Each capsid is composed of protein subunits called capsomeres. (capsomeres have different shapes, which means that viruses can be classified according to the shape of the capsid or the capsomere) Enveloped viruses have a typical bilayer membrane outside their capsids and acquire their envelope after they are assembled in a host cell and “bud” through host’s membrane (we mentioned in a previous lecture that yeasts also undergo “budding”) *budding: the virus forms its envelope though the process of budding out of the host cell . Which means that the outer membrane is very similar to a human cell membrane, that’s why it is very difficult for the immune system to recognize such a virus. - It is very resistant to the immune system because of the budding process Lets take “hepatitis A” for an example; hepatitis A is transferred by food, it is a naked virus, and considered one of the most resistant viruses to disinfectants and antimicrobial agents because it has a capsid. HIV & hepatitis B are more dangerous than hepatitis B because they are enveloped; Hepatitis B is more dangerous because it causes chronic infection and might cause cancer, while hepatitis A causes acute infection. Hepatitis B has little resistance to antimicrobial agents, that’s why it is considered fragile, For an instance if we have blood spillage containing hepatitis B and we put an antimicrobial agent, it will kill the virus, while if we had hepatitis A in the blood, it would be very hard to kill it using the antimicrobial agent. (because hepatitis A has a capsid, and hepatitis B has an envelope) 4 NOTE: hepatitis A activates the immune system more than hepatitis B -As seen in the graph, viruses fit inside the bacteria which means they are very small, some are even as tiny as a ribosome ------------------------------------------• Nucleocapsid comprises the viral genome together with the capsid • Naked viruses: viruses with a nucleocapsid and no envelope • Spikes: projections that extend from the viral envelope that may aid in attachment to the host cell (made out of glycoproteins) • Glycoprotein: these surface projections serve to attach virions to specific receptor sites on susceptible host cell surfaces • Envelopes help the virus in evading detection by the host’s immune system -The triangled structure is capsomere (it is polyhedral) a -The structure that looks like a spaceship is a bacteriophage which is a virus that causes an infection to bacteria, it has a core and tails (resembles a spider), it ejects its genetic material into the bacteria. Virus shape: • Some viruses are variable in shape, but most have a specific shape that is determined by the capsomeres or envelope (most envelopes are spherical) • Helical capsid: consists of a ribbonlike protein that forms a spiral around the nucleic acid • Polyhedral capsid: many-sided, and one of the most common polyhedral capsid shapes is the icosahedron (20 triangle faces) • Complex capsid: a combination between helical and icosahedral • Some viruses have a bullet-shaped capsid and some are spherical Viral sizes and shapes - They are too tiny and can’t be seen by light microscope - Variations in shapes and sizes of viruses compared with a bacterial cell, an animal cell, and a eukaryotic ribosome Classification of viruses: Studying viruses is harder, because the growth of viruses has to happen in a tissue culture unlike bacteria which could grow if we put it under optimum temp optimum PH and optimum nutrition. 5 Viruses need live cells in order to grow and replicate, that’s why – compared to bacteria- we have very little information about viruses; The classification of viruses is simpler than that of bacteria ( )التقسيماتbecause we don’t have enough knowledge to use complicated classifications • • Historically, virologists classified viruses by the type of host/host structures they infected (human virus, animal virus, and plant virus)/(skin virus) Bacteriophages: cells In 1977 of the International Committee on Taxonomy of Viruses (ICTV) formed to establish a single, universal taxonomic scheme for viruses • They concluded that it is very difficult to classify viruses according to typical taxonomical categories, it is not as easy as classifying bacteria • Therefore: - - infect bacterial - • Plant viruses infect plant cells • Animal viruses are subgrouped by the tissues they attack: 1. Dermotrophic: skin • - if they infect the 2. Neurotrophic: if they infect nerve tissue Discoveries into biochemical and molecular allowed for viruses to be classified based on: 1. Type and structure of their nucleic acids family is the highest taxonomical category by the ICTV Viral genera have been established Species is the common name of the virus (English name) Example: family: rhabdoviridae Genus: Lyssavirus , species: rabies (English name) Family: Coronaviridae: Coronavirus got their name (corona, Latin for “crown”) ---------------------------------------------*single- stranded RNA are major *double- stranded RNA are less * double- stranded DNA are major * single-stranded DNA are less RNA viruses: 2. Method of replication • Many ssRNA viruses contain positive (+) sense RNA, and during an infection acts like mRNA and can be translated by host’s ribosomes • Other ssRNA viruses have negative (-) sense RNA and the RNA acts as a 3. Host range 4. Other physical characteristics and chemical 6 template during transcription to make a complementary (+) sense mRNA • enters through the mouth (that’s why the vaccine is given orally, since the form of administration of this virus is orally- )المطعوم الثالثي epidemic polio is transferred by water and food Rhino virus (common cold virus) and hepatitis A belong to the same group : positive sense RNA Togaviridae family: rubella: German measles : الحصبة األلمانية: naked virus: very contagious because it is less fragile since it can withstand environmental conditions Negative (-) sense RNA must carry an RNA polymerase within the virion positive sense ssRNA: act as messenger RNA: undergoes translation by ribosomes forming proteins of the capsid Negative sense ssRNA : does not undergo translation: instead it forms complementary RNA (positive sense) using reverse transcriptase, the positive sense RNA(messenger RNA) then undergoes translation to proteins Example: -positive sense: picornaviridae family:very small, naked, polyhedral, (+) sense RNA viruses, include: enteroviruses (related to the GI tract,) rhinoviruses and hepatoviruses (related to the liver) As we said earlier: hepatitis A is a naked virus, and hepatitis B is enveloped; and it causes cancer (anything that causes cancer has DNA as its genetic material), therefore we cannot say that hepatitis A,B,&C belong to the same family, since they are completely different and they differ in their genetic material, and differ in being enveloped or naked Poliovirus : enterovirus: مسبب شلل األطفال: Retroviruses(retroviridi): “retro= bacteria that have reverse transcriptase” They are enveloped viruses that have two complete copies of (+) sense RNA. They also contain the enzyme reverse transcriptase, which uses the viral RNA to form a complementary strand of DNA, which is then replicated to form a dsDNA (such as HIV virus and human leukemia virus(which is a type of cancer: cancer means abnormal growth of cells; it can be caused by viruses when a virus injects its genetic material into a human cell which leads to abnormal growth, 7 in order for that to happen, the genetic material of both the virus and the human should be the same : double stranded DNA )) vaccine contains antigens from influenza A & B viruses) **examples on double stranded RNA viruses: Any virus that causes cancer has to have double stranded DNA Retroviruses don’t originally have dsDNA but the presense of reverse transcriptase leads to forming dsDNA dsRNA ; least number (less than ssRNA) Reoviruses : cause upper respiratory infections DNA viruses: ( dsDNA more than ssDNA) **Examples: - negative sense RNA: Paramyxoviruses: myxo = mucous membrane; like measles ()الحصبة Rhabdoviruse : (-) sense RNA virus group consists of medium-sized, enveloped viruses. The capsid is helical and makes the virus nearly rod or bullet-shaped. Contain an RNA-dependent RNA polymerase that uses the (-) sense strand to form a (+) sense strand that serves as a mRNA and template for synthesis of new viral RNA مسبب مرض الكألrhabidis Orthomyxoviruses: “myxo” = mucous membrane, medium-sized, enveloped, (-) sense that vary in shape from spherical to helical. Their genome is segmented into eight pieces (mutation to influenza A and B happens in these segments, the *double stranded: adenoviridae : adenovirus, which causes human respiratory infection Herpesviruses: herpes disease(oral & genital), chickenpox(varicella) and shingles(zoster)-( الحزام )الناري ,smallpox and cowpox Papovaviruses: Named for three related viruses, the papilloma, polyoma, and vacuolating viruses, papillomaviruses cause both benign and malignant warts in humans, 90% of cervical cancer in females is caused by papilloma virus 8, which has double stranded DNA. A new vaccine is being used in the USA so as to prevent females from being infected with papillomavirus which causes cancer and opposing death. Papillomavirus is considered a sexually transmitted disease (STD) 8 hepadnaviruses :Their name comes from the infection of the liver— hepatitis—by a DNA virus. In humans, the hepatitisB virus causes hepatitis B, which can progress to liver cancer next lecture we will talk about virus replication.. good luck all :) done by: Lana Hammad 9