PRINCIPLES OF VIRUS STRUCTURE Genetic economy requires that a viral structure be made

Transcription

1 1. History of microbiology 2. Cell structure 3. Taxonomy 4. Growth and death of microorganisms 5. Cultivation of microorganisms 6. Microbial metabolism 7. Microbial genetics 9. Normal human microbiota 10. Pathogenesis of bacterial infection (general) 11. General properties of viruses 12. Pathogenesis and control of viral diseases (general) 13. General properties of fungi 14. Pathogenesis of fungal disease 15. General properties of parasite 16. Pathogenesis of parasitic disease PRINCIPLES OF VIRUS STRUCTURE Genetic economy requires that a viral structure be made First Course 8. Second Course from many identical molecules of one or a few proteins. Viral architecture can be groupe d into three types based on the arrangement of morphologic subunits: (1) cubic symm etry (eg, adenoviruses), (2) helical s ymmetry(eg, orthomyxoviruses),and(3)complexstructures(eg, poxviruses ) A. Cubic Symmetry All cubic symmetry observed with animal viruses is of the icosahedral pattern, the most efficient arrangement for subunits in a closed shell. The icosahedron has 20 faces (each an equilateral triangle),12 vertice s, and fivefold, threefold, and twofold axes of rotational symme try. The vertex units have five neighbors (pentavalent), and all others have six (hexavalent). The viral nucleic acid is condensed within the isometric particles; virus-encoded core proteins or, in the case of polyomaviruses and papillom aviruses, cellular histones are involved in condensation of the nu cleic acid into a form suitable for packaging. Packag ing sequences on viral nucleic acid are involved in assembly into virus particles. There are size constraints on the nuc leic acid molecules. Both DNA and RNA viral groups can be exhibit examples of cubic symmetry. B. Helical Symmetry In cases of helical symmetry, protein subunits are bound in a periodic way to the viral nucleic acid, winding it into a helix. The filamentous viral nucleic acid protein complex (nucleocapsid) is then coiled insi de a lipid-containing envelope. Thus, as is not the case with icosahedral structures,

2 there is a regular, periodic interac tion between capsid protein and nucleic acid in viruses with helic al symmetry. It is not possible for empty helical parti cles to form. All known examples of animal viruses with helical symmetry contain RNA genomes and, with the exception of rhabdoviruses, have flexible nucl eocapsids that are wound into a ball inside envelopes. C. Complex Structures Some virus particles do not exhibit simple cubic or helical symmetry but are more complic ated in structure. For example, poxviruses are b rick shaped, with ridges on the external surface and a core and lateral bodies inside. CHEMICAL COMPOSITION OF VIRUSES 1-Viral Protein The structural proteins of viruses have several important functions. 1- Their major purpose is to facilitate transfer of the viral nucleic acid from one host cell to another. 2- They serve to protect the viral genome against inactivation by nucleases, 3- participate in the attachment of the virus particle to a susceptible cell, 4- and provide the structural symmetry of the virus particle. 5- The proteins determine the antigenic characteristics of the virus. The host s protect ive immune response is directed against antige nic determinants of proteins or glycoproteins exposed on the surface of the virus particl e. 6- Some surface proteins may also exhibit spe cific activities (eg, influenza virus hemagglutinin agglutinates red blood cells).

3 7 - Some viruses carry enzymes (which are proteins) inside the virions. The enzymes ar e present in very small amounts and are probably not importan t in the structure of the virus particles; however, they are essential for the initiation of the viral replicative cycle when the virion enters a host cell. Examples include an RN A polymerase carried by viruses with negative-sense RNA genomes (eg, orthomyxoviruses, rhabdoviruses) that is need ed to copy the first mrnas, and reverse transcriptase, an en zyme in retroviruses that makes a DNA copy of the viral RNA, a n essential step in replication and transformation. At the extreme in this respect are the poxviruses, the cores of which contain a transcriptional system; many different e nzymes are packaged in poxvirus particles. 2- Viral Nucleic Acid Viruses contain a single kind of nucleic acid either DNA or RNA that encodes the genetic information necessary for replication of the virus. The genome may be single or double stranded, circular or linear, and segmented or nonsegmented. The type of nucleic acid, its strands, and its size are major characteristics used for Classifying viruses into families 1- All major DNA viral groups have genomes that are single molecules of DN A and have a linear or circular configuration. 2- Viral RNAs exist in several forms. A-The RNA may be a single linear molecule (eg, pic ornaviruses). B- For other viruses (eg, orthomyxoviruses), the geno me consists of several segments of RNA that may b e loosely associated within the virion. The isolated RNA of viruses : classified depend on strandes in to 1- The isolated RNA of vi ruses with positive-sense genomes (ie, picornaviruses, togaviruses) is infectious, and the molecule functions as an mrna within the infected cell. 2- The isolated RNA of the nega tive-sense RNA viruses, such as rhabdoviruses and orthomyxoviruses, is not infect ious. For these viral families, the virions carry an RNA polymerase that in the cell transcribes the genomic RNA molecules into several complementary R NA molecules, each of which may serve as an mrna. 3- Viral Lipid Envelopes A number of different viruses contain lipid envelopes as part of their structure. The lipid is acquired when the viral nucleocap sid buds through a cel lular membrane in the course of maturation. Budding occurs onl y at sites where virus-specific proteins have been inserted i nto the host cell membrane. The budding process varies marked ly depending on the replication strategy of the v irus and the structure of the nucleocapsid.budding by influenza virus is illustrated in next Figure : The specific phospholipid composition of a virion envelope is determined by the specific type of cell membrane involved in the budding process. For examp le, herpesviruses bud through the nuclear mem brane of the host cell, and the phospholipid composition of the purified virus reflects the lipids of the nuclear membrane. The a cquisition of a

4 lipidcontaining membrane is an integral step in virion morphogene sis in some viral groups. Lipid-containing viruses are sensitive to treatment with ether and other organic solvents indicating that disruption or loss of lipid results in loss of infectivity. Nonlipid-containing viruses are generally resistant to ether. 4- Viral glycoproteins Viral envelopes contain glycoprot eins. In contrast to the lipids in viral membranes, which are derived from the host cell, the envelope glycoproteins are virus encoded. However, the sugars added to viral glycoprote ins often reflect the host cell in which the virus is grown. 1- The surface glycoproteins of an enveloped virus attach the virus particle to a target cell by interacting with a cellular receptor. 2-They are also often involved in the membrane fusion step of infection. 3-The glycoproteins are also important viral antigens. As a result of their position at the outer surface of the virion, they are frequently involved in the interaction of the virus particle with neutralizing antibody. Extensive glycosylation of viral surface proteins may prevent effective neutralization of a virus particle by specific antibody. Pathogenesis and Control of Viral Diseases PRINCIPLES OF VIRAL DISEASES 1-Th e fundamental process of viral infection is the viral replicative cycle. 2-Th e cellular response to infection may range from no apparent effect to cytopathology with accompanying cell death to hyperplasia or cancer. 3- Clinical disease in a host consists of overt signs and symptoms. Therefore Viral disease is some harmful abnormality that results from viral infection of the host organism. 4- A syndrome is a specifi c group of signs and symptoms. 5- inapparent (subclinical) Viral infections is that fail to p roduce any symptoms in the host, In fact, most viral infections do not result in the production of disease 6- Important principles that pertain to viral disease include the following: (A) many viral infections are subclinical; (B) the same disease may be produced by a variety of viruses; (C) the same virus may produce a variety of diseases; (D) the disease produced bears no relationship to viral morphology; and (E) the outcome in any particular case is determined by both viral and host factors and is infl uenced by the genetics of each. 7 - Disease pathogenesis is a subset of events during an infection that results in disease manifestation in the host. Therfore Viral pathogenesis is the process that occurs when a virus infects a host. Depend on this principle A virus is become pathogenic for a particular host if it can infect and cause signs of disease in that host. 8- A strain of a certain virus is more virulent than another strain if it commonly produces more severe disease in a susceptible host. P REVENTION AND TREATMENT OF VIRAL INFECTIONS 1- Antiviral Chemotherapy

5 Unlike viruses, bacteria and protozoans do not rely on host cellular machinery for replication, so processes specific to these organisms provide ready targets for the development of antibacterial and antiprotozoal drugs. Where t he discovery of Antiviral Chemotherapy is difficult because. 1-Because viruses are obligate intracellular parasites, a ntiviral agents must be capable of selectively inhibiting vir al functions without damaging the host, making the development of such drugs very difficult. 2- Another limitation is that m any rounds of virus replication occur during the incubation period and the virus has spread before symptoms appear, making a drug relatively ineffective. 3- There is a need for antiviral drugs active against viruses for which vaccines are not available or not highly effective the latter perhaps because of a multiplicity of serotypes (eg, rhinoviruses) or because of a constantly changing virus (eg, influenza, HIV). Antivirals can be used to treat established infections when vaccines would not be effective. Antivirals are needed to reduce morbidity and economic loss caused by viral infections and to treat increasing numbers of immunosuppressed patients who are at increased risk of infection. it has been very difficult to develop antivirals that can distinguish viral from host replicative processes. S ome Types of Antiviral Agents A number of types of compounds have been shown to possess some antiviral activity under certain conditions. 1- Fuzeon is a large peptide that blocks the virus and cellular membrane fusion step involved in entry of HIV-1 into cells. 2 - Foscarnet (phosphonoformic acid) is an organic analog of inorganic pyrophosphate. It selectively inhibits viral DNA polymerases and reverse transcriptases. 3- Methisazone is of historical interest as an inhibitor of poxviruses. It was the first antiviral agent to be described and contributed to the campaign to eradicate smallpox. It blocked a late stage in viral replication, resulting in the formation of immature, noninfectious virus particles. 2- interferons A-They are host-coded proteins that are members of the large cytokine family that B- They are inhibit viral replication. c- They are produced very quickly (within hours) in response to viral infection or other inducers and as one of the body s first responders in the defense against viral infection. D- interferons are central to the innate antiviral immune response. They also modulate humoral and cellular immunity and have broad cell growth regulatory activities, but the focus here is on their antiviral effects. 3- Viral Vaccines A- The purpose of viral vaccines is to use the immune response of the host to prevent viral disease. B- Several vaccines have proved to be remarkably effective at reducing the annual incidence of viral disease. C- Vaccination is the most cost effective method of prevention of serious viral infections. some example Attenuated Live-Virus Vaccines and Killed-Virus Vaccines

6 Normal Human Microbiota The term normal microbial fl ora denotes the population of microorganisms that inhabit the skin and mucous membranes o f healthy normal persons. Th e genomes of these microbial symbionts are collectively defi ned as the microbiome. Research has shown that the normal microbiota provides a fi rst line of defense against microbial pathogens, assist in digestion, play a role in toxin degradation, and contribute to maturation of the immune system. Shift s in the normal mi crobiota or stimulation of infl ammation by these commensals may cause diseases such as infl ammatory bowel disease. HUMAN MICROBIOME PROJECT in 2007, the National Institutes of Health launched the Human Microbiome Project. One of the main goals of this project is to understand the range of human genetic and physiologic diversity, the microb iome, and the factors that infl uence the distribution and evolution of the constituent microorganisms. One aspect of this project involves having several research groups simultaneously embark upon surveying the microbial communities on human skin and in mucosal areas such as the mouth, esophagus, stomach, colon using small-subunit (16S) ribosomal RNA gene sequencing. Numerous observations have already been made. For example, it has been determined that there are large diff erences among individuals in terms of the numbers and types of species of microorganisms inhabiting the colon and that obesity may be correlated with the types of microbes involved in specifi c metabolic pathways in the gastrointestinal tract. Readers should be aware that this fi eld is rapidly evolving, and our understanding of the human microbiota will necessarily change as more information about resident microbial communities becomes available through the Human Microbiome Project. ROLE OF THE RESIDENT MICROBIOTA Th e skin and mucous membranes always harbor a variety of microorganisms that can be arranged into two groups: (1) the resident microb iota consists of relatively fi xed types of microorganisms regularly found in a given area at a given age; if disturbed, it promptly reest ablishes itself; (2) the transient microbiota consists of nonpathogenic or potentially pathogenic microorganisms that inhabit the skin or mucous membrane s for hours, days, or weeks. Th e transient microbiota is derived from the environment, does not produce disease, and does not establish itself permanently on the surface. Members of the transient microbiota are generally of little significance so long as the N ormal resident flora remains intact. However, if the resident microbiota is disturbed, transient microorganisms may colonize, proliferate, and produce disease. The microorganisms that are constantly present on body surfaces are commensals. Their flourishing in a given area depends on : physiologic factors of temperature, moisture, and the presence of certain nutrients and inhibitory substances. Their presence is not essential to life because : germ-free animals can be reared in the complete absence of a normal microbiota. Yet the resident flora of certain areas plays a definite role in maintaining health and normal function because :1- Members of the resident microbiota in the intestinal tract synthesize vitamin K

7 and aid in the absorption of nutrients. 2- On mucous membranes and skin, the resident microbiota may prevent colonization by pathogens and possible disease because : bacterial interference. The mechanism of bacterial interference may involve competition for 1- receptors or binding sites on host cells, 2- competition for nutrients, 3- mutual inhibition by metabolic or toxic products, 4- mutual inhibition by antibiotic materials or bacteriocins, or other mechanisms. Suppression of the normal microbiota clearly creates a partial local void that tends to be filled by organisms from the environment or from other parts of the body. Such organisms (may be normal microbiota from other parts ) behave as opportunists and may become pathogens. the important point is that the normal resident microbiota is harmless and may be beneficial in their normal location in the host and in the absence of coincident abnormalities. They may produce disease if introduced into foreign locations in large numbers and if predisposing factors are present. There are many examples 1- streptococci of the viridans group are the most common resident organisms of the upper respiratory tract. If large numbers of them are introduced into the bloodstream (eg, after tooth extraction or oral surgery), they may settle on deformed or prosthetic heart valves and produce infective endocarditis. Small numbers occur transiently in the bloodstream with minor trauma(eg, dental scaling or vigorous brushing). 2- Bacteroides species are the most common resident bacteria of the large intestine and are quite harmless in that location. However, if introduced into the peritoneal cavity or into pelvic tissues along with other bacteria as a result of trauma, they cause suppuration and bacteremia. Medical Mycology General principle 1- Mycology is the study of fungi, 2- Fungi are eukaryotic organisms 3- unlike animals, most fungi are nonmotile and possess a rigid cell wall. 4- Unlike plants, fungi are nonphotosynthetic. 5- Approximately 80,000 species of fungi have been described, but fewer than 400 are medically important, and less than 50 species cause more than 90% of the fungal infections of humans and other animals. 6- most species of fungi are beneficial to humankind. a- Th ey reside in nature and are essential in breaking down and recycling organic matter. b- Some fungi greatly enhance quality of life by contributing to the production of food and spirits, including cheese, bread, and beer. c- Other fungi have served medicine by providing useful bioactive secondary metabolites such as antibiotics (eg, penicillin) and immunosuppressive drugs (eg, cyclosporine). 7- Overall, fungi exert their greatest economic impact as phytopathogens; the agricultural industry sustains huge crop losses every year as a result of fungal diseases of rice, corn, grains, and other plants. 8- Like all eukaryotes, each fungal cell has at least one nucleus with a nuclear membrane, endoplasmic reticulum, mitochondria, and secretory apparatus. Nutrition of fungi

8 1- Most fungi are obligate or facultative aerobes. 2- They are chemotrophic, secreting enzymes that degrade a wide variety of organic substrates into soluble nutrients which are then passively absorbed or taken into the cell by active transport. Fungal infections. 1- Fungal infections are mycoses 2- Most pathogenic fungi are exogenous, their natural habitats being water, soil, and organic debris. 3 Th e mycoses with the highest incidence candidiasis and dermatophytosis are caused by fungi that are part of the normal human microbiota and highly adapted to survival on the human host. 4- mycoses may be classified as superfi cial, cutaneous, subcutaneous, or systemic, 5- Th e systemic mycoses may be caused by endemic fungi, which are usually primary p athogens, or by ubiquitous, oft en secondary opportunistic pathogens. Grouping mycoses in these categories refl ects their most common portal of entry and initialsite of involvement. However, there is considerable overlap, since systemic mycoses oft en exhibit subcutaneous manifestations and vice versa. 6- Most patients who develop opportunistic infections have serious underlying diseases and compromised host defenses. But primary systemic mycoses also occur in such pat ients, and the opportunists oft en infect immunocompetent individuals. 7- During infection, most patients develop significant cellular and humoral immune responses to the fungal antigens. 8 - Pathogenic fungi do not produce potent toxins, and the mechanisms of fungal pathogenicity are complex and polygenic. 9- Most mycoses are difficult to treat. Because fungi are eukaryotes, they share numerous homologous genes, gene products, and pathways with their human hosts. Consequently, there are few unique targets for chemotherapy and effective antibiotics. Fortunately, there is growing interest in medically significant fungi and in the search for virulence factors and potential therapeutic targets. GENERAL PROPERTIES of structure and classification 1- Like all eukaryotes, each fungal cell has at least one nucleus with a nuclear membrane, endoplasmic reticulum, mitochondria, and secretory apparatus. 2 - Fungi grow in two basic forms, as yeasts and molds (or moulds). First molds (or moulds). 1 - Growth in the mold form occurs by the production Of multicellular filamentous colonies. 2 - These colonies consist of branching cylindric tubules called hyphae, varying in diameter from 2 to 10 μm.

9 3 - The mass of intertwined hyphae that accumulates during active growth is a mycelium. 4 - Some hyphae are divided into cells by cross-walls or septa, which typically form at regular intervals during hyphal growth. However, members of the Order Mucorales produce h yphae that are rarely septated. 5- Vegetative hyphae penetrate the supporting medium, anchor the colony, and absorb nutrients. In contrast, aerial hyphae project above the surface of the mycelium and usually bear the reproductive structures of the mold. 6- When a mold is isolated from a clinical specimen, its growth rate, macroscopic appearance, and microscopic morphology are usually sufficient to determine its genus and species. 7- The most helpful phenotypic features are the ontogeny and morphology of the asexual reproductive spores, or conidia. Second yeast 1-They are single cells, usually spherical to ellipsoid in shape and varying in diameter from 3 to 15 μm. 2- Most yeasts reproduce by budding. 3- Some species produce buds that characteristically fail to detach and become elongated; continuation of the budding process then produces a chain of elongated yeast cells called pseudohyphae. 4- Yeast colonies are usually soft, opaque,, and cream colored. 5- Because the colonies and microscopic morphology of many yeasts are quite similar, yeast species are identified on the basis of physiologic tests and a few key morphologic differences. 3- Some species of fungi are dimorphic and capable of growth as a yeast or mold depending on environmental conditions. 4- Cell wall of fungi 1- Fungi have an essential rigid cell wall that determines their shape and protects them from osmotic and environmental stress. 2 - Cell walls are composed largely of carbohydrate layers long chains of polysaccharides as well as glycoproteins and lipids. Some sugar polymers are found in the cell walls of many fungi, such as

10 chitin; glucans, which are glucose polymers); and mannans, polymers of mannose. In addition, other polysaccharides may be unique to specific fungal species. 3 - During infection, fungal cell walls exert important pathobiologic properties. 4 - The surface components of the cell wall mediate attachment of the fungus to host cells. Specific fungal cell wall moieties bind to pattern recognition receptors on host cell membranes to stimulate innate immune responses. Cell wall glucans and other polysaccharides may activate the complement cascade and provoke an inflammatory reaction. 5 - Most of these polysaccharides are poorly degraded by the host and can be detected with special histologic stains. 6 - Cell walls also release immunodominant antigens that may elicit cellular immune responses and diagnostic antibodies. 7 - In addition, some yeasts and molds have melanized cell walls, which impart a brown or black pigment to the fungal colony. Such fungi are dematiaceous. Several studies have shown that melanin protects these fungi from host defenses and is associated with virulence. Life cycles of fungi The life cycles of fungi are remarkably versatile. Depending on the fungal species, 1- the predominant nuclear chromosomal count may be haploid or diploid. 2- Some species exist entirely by clonal growth or asexual reproduction, and barring spontaneous mutations, every cell will be a genetic clone. 3- Other species are capable of sexual reproduction, which may or may not require genetically different partners for mating and meiosis. 4- Asexual as well as sexual reproduction can result in the production of spores, which enhance fungal survival. 5- Spores are usually dormant, readily dispersed, more resistant to adverse conditions, and germinate to form vegetative cells when conditions for growth are favorable. 6- Spores derived from asexual or sexual reproduction are termed anamorphic or teleomorphic states, respectively. 7- Like vegetative cells, asexual spores are mitotic progeny (ie, mitospores). 8- The medical fungi produce two major types of asexual spores, conidia, which are produced by most pathogenic fungi, and, in the Order Mucorales, sporangiospores. 9- Informative features of spores include their ontogeny (some molds produce complex conidiogenic structures) as well as their morphology (size, shape, texture, color, and unicellularity or multicellularity ).