Microbiology test 2

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kmbaker2
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Microbiology test 2
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2013-10-09 16:40:42
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Microbiology
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Microbiology
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  1. Viruses Associated with Tumor
      • Adult T cell Leukemia
      • Burkitts Lymphoma
      • Skin and Cervical cancer
      • Liver Cancer
  2. Adult T Cell Leukemia
      • Human T cell Leukemia virus- Retrovirus
      • RNA<-> DNA
      • Rare
  3. Burkitt's Lymphoma
      • 95% US population has it
      • Herpes
      • Epstein- Barr Virus
      • DNA
  4. Skin and Cervical Caner
      • Papilloma Virus
      • vaccine available
      • papova
      • DNA
  5. Liver Cancer
    • -Hepatitis B Virus (vaccine, DNA)
    • -Hepadnavirus
    • -Hepatitis C Virus (no vaccine, RNA)
  6. Positive stranded RNA virus
      • Picornavirus (small RNA virus)
      • poliovirus
      • rhinovirus
      • hepatitis A virus
  7. Lifecycle of Pos. Strand RNA Viruses
    • -1 piece of RNA infective.
    • -Cell is machine to read RNA
    • -5' end is vpg
    • -viral protein synthesis is enhanced, cell protein is restricted
    • -1 large protein cleaved into many i.e. ( proteases, RNA polymerase, structural coat proteins
  8. Replication of Poliovirus positive strand
    • -enteric virus
    • may infect nervous system causing poliomyelitis
    • -vpg at 5', only 22 aa, primer for transcription
    • -vpg inhibits host protein synthesis, disrupt cap-binding protein
    • -early genes can be oncogenes
    • -viral protease- cannot replicate
    • -vaccine available
    • -U.P. septic tanks = 15 years returning
  9. Rhinovirus pos. strand
    • -70%= major cause of common cold
    • -different types of the same virus make immune system ineffective
    • -115 types
    • -disease is transmitted through respiratory tract
  10. Hepatitis C Virus Pos strand
    • -enveloped positive stranded RNA virus
    • -chronic infection causes liver cirrhosis and cancer
    • -transmission by blood, heterosexual transmission rate is low
    • -treatment with interferon and anti-viral agents
    • -social problem , homosexual transmission
  11. Negative stranded RNA viruses
    • -Enveloped
    • -Rhabdovirus
    • -paramyxovirus
    • -orthomyxovirus
  12. Rhabdovirus
    • -rabies
    • -vesicular stomatitis virus
  13. Paramyxovirus
    • -non segmented (Opposite side-mucous)
    • -one piece of neg strand
    • -mumps, measles, respiratory syncytial virus
    • -MMR- vaccination
  14. Orthomyxovirus
    • -segmented
    • -(severe, mucous)
    • -influenza
  15. Rabies
    • -transmitted by animal bite (zoonoses)
    • -wild animal has virus reservoir
    • -after transmission, incubation can be 9 mo
    • -vaccination after bite is still effective
    • -once symptoms are apparent, 100% death
  16. Replication of Rabies Virus
    • -enveloped, non segmented virus
    • -once the nucleocapsid gets into the cytoplasm. mRNA, +RNA are synthesized (early genes)
    • -1 area controls cell, 1 area replicates genome
    • -late genes develop then can synthesize structural genes
    • -Assembly of viral particles are on the cell membrane. Need membrane to get out.
  17. Orthomyxovirus
    • -(Influenza)
    • -enveloped and 8 segments
    • -hemagglutinin on viral surface- binds sialic acid on the respiratory epithelial cells
    • -neuraminidase- cleaving the virus from attachment on sugars and spreads virus
  18. antigenic drift
    • -virus mutation due to no proof reading.
    • -point mutation in hemagglutinin or neuraminidase leads to drift. (antigens change slowly)
    • -causes influenza endemic
  19. Antigenic Shift
    • -exchange a segment with another strain of virus causes antigentic shift, which will cause influenza epidemic and pandemic (reassortment)
    • -H1N1
  20. Pandemic of Influenza Virus
    • 1918-1919 Spanish Flu
    • 1957-1958 Asian Flu
    • 1968-1969 Hong Kong Flu
    • 2008-2009 Swine Flu

    Happened every 40 years
  21. Asian Flu
    Antibiotics significantly lowered death rate
  22. double stranded RNA Virus
    • -reovirus----rotavirus
    • -causes diarrhea in infants
    • -non-enveloped
    • -double stranded RNA cannot serve as mRNA- needs transcription (mRNA synthesis)
    • -one mRNA = two proteins
    • -ribosome skips first AUG
    • -frame shift
  23. Polyomavirus
    • -non-enveloped, icosahedral, circular double stranded DNA virus
    • -Uses DNA polymerase in host cell to replicate in nucleus vs cytoplasm
    • -RNA has introns (noncoding regions)
    • -Simian virus 40 encodes two proteins that transform the host cell
  24. Permissive Cell
    simian virus 40 replicate here to produce progeny
  25. Non-permissive cells
    SV 40 integrates into the host cell and transforms cell
  26. Herpes Virus
    • A large group of double stranded DNA virus
    • - Herpes simplex virus 1 and 2, fever blisters
    • - Varicella-zoster virus, chicken pox and shingles
    • - Epstein- Barr virus, infectious mononucleosis
  27. Chicken Pox
    • -transmitted by infectious droplets
    • -replicate in respiratory tract, spreads to body in blood
    • - virus can go latent in neurons and remain dormant for years
    • - when host is weak, migrates to skin cause shingles
    • - infection in kids- nonlife threatening, adults it can be deadly
    • - vaccine is effective
  28. Herpes Simplex Virus
    • - HSI normally associated with fever blisters and cold sores around mouth
    • - HSII associated with genital blisters
    • - sexually transmitted
    • - HSV can establish latent infection in neuron and recurrent infection occurs when host immune system becomes weak
  29. Replication of Herpes Viruses
    • - Viral DNA circulates upon getting in nucleus
    • - synthesis of alpha beta and gamma
    • -viral nucleocaspid is assembled in the nucleus
    • - assembly of viral particles is in the inner nuclear membrane
    • - virus buds into the endoplasmic reticulum
  30. Adenovirus
    • -causes mild respiratory infection
    • - double stranded/ DNA virus/ non-enveloped/ icosahedral
    • - infects many cell types
    • -widely used for gene therapy to deliver genes
    • - recently, Adeno-Associated virus (AA1) seems to be more popular for gene therapy
  31. Pox Virus
    • -largest animal virus
    • - DNA synthesis in cytoplasm
    • - small pox virus eradicated by vaccination
    • - very large virus, immune response against Cow pox virus (vaccinia) is protective for small pox virus
  32. Replication of Pox virus
    • -Virus gets into cytoplasm, inclusion body is formed
    • - where the virus replication starts and progeny is generated
    • - The number of inclusion body directly reflect the multiplicity of infection
    • -as host cell disintegrates, viruses are released
  33. Piron
    • -completely made of proteins
    • -Slow incubation and cause neurological disease in a long period
    • -Bovine spongiform encephalopathy (Mad Cow Disease)
    • - Creutzfeldt- Jakob disease in human
    • -Autoclaving cannot inactivate
  34. Viroid
    • -Circular single stranded RNA as short as 250nt
    • - does not code for a protien
    • - Causes coconut cadangcadang disease
    • - RNA minics DNA so that the host RNA polymerase can replicate the genome.
  35. Phenotype verse Genotype
    • phenotype- a property that is easily observable
    • genotype- gene structure of the organism
  36. Auxotroph
    • -mutants lost ability to synthesize certain growth factor
    • -must provide nutrients for growth
  37. Temperature Sensitive
    • -optimal growth temperature of the mutants has changes
    • -denatured at normal (optimal temp) lower a few degrees
    • used to make mutants for vaccine
    • - keeps us safe, denatures virus a few degrees under ours
  38. Sugar Fermentation
    • -loss ability of the bacteria to ferment certain sugars
    • - lost enzymes
  39. Kinds of Mutants
    auxotroph, drug resistant, virus resistant (resist HIV), non-motile, temp sensitive, non-capsulated (lost ability to synthesize capsule- non infective), sugar fermentation, pigmentless
  40. Insert Mutation
    altered reading frame
  41. missense
    different codon - different aa
  42. nonsense
    stop codon made
  43. silent
    aa does not change while nucleotide does
  44. deletion mutation
    altered reading frame
  45. Mutation Rate
    • -spontaneous mutation occurs at 10^-6
    • -RNA 1000x higher mutation rate than DNA, lack of proof reading in RNA dependent RNA polymerase or reverse transcriptase or lack of repair system
    • - RNA viruses will have a mutant genome after 1 month, no gene untouched = diversity
  46. Ames Test
    • - Use Microorganisms to detect mutation
    • - A back mutation (revertant) of autotroph can be used to test chemicals that can mutate (mutagen)
    • - Hitamine of salmonella typhimurium and Trp- or EColi commonly used.
  47. Modified Ames Test
    • - A lot of chemicals are not mutagens but there metabolic products are
    • - liver enzymes used
    • - bacteria behave differently in human body environment
  48. Griffith's Experiment
    • Streptococcus pneumoniae
    • - heat killed smooth and live nonvirulent-mouse  die
    • - live virulent smooth replicated
  49. Transformation
    • 1. naked DNA fragments form disinigrated cells, float in the area of potential recipeint cell
    • 2. entry of naked DNA into competent cell
    • 3. Recombination
    • - DNA has info for reproduction
  50. Homologous Recombination
    • - different copies of the same gene are called alleles
    • - different strains may have dif. alleles
    • - when 2 alleles come together, they have tendency to exchange with eachother, this is called recombination
    • - can be used to delete certain genes
  51. Transduction
    • -another way to pick up genes
    • -phage infects bacterial cell
    • -virus to use as a tool to induce genetic recombination with host DNA through transduction
    • - infects 1 cell, lytic cycle, released, infect 2nd bacteria cell
  52. Conjugation (bacteria to bacteria)
    • -F plasmid from donor from F+ to F-
    • - after passing through conjugation bridge F- becomes F+
    • - Species to other species = arbritary
  53. Conjugation Initiated by F Plasmid
    • F+  ->   F-
    • when F plasmid is integrated into the chromosome, the strain will be called HFr (high frequency of recombination)
    • - HFr strain can transfer chromosomal genes to another bacterium 
    • -transfer can be partial from HFr -> F- = recombination or go away
  54. DNA Transfer in Bacteria Horizontal Gene Transfer
    • Transformation= outside to bacteria
    • Transduction= virus to bacteria
    • Conjugation= bacteria to bacteria
  55. Plasmid
    • -circular- extra-chromosomal DNA, self replicative (SV40 virus)
    • - Conjugative plasmid can encode genes necessary for conjugation
    • -F plasmid can even initiate the transfer of chromosomal DNA
    • - Plasmid that can integrate into chromosome is called episome F Plasmid
  56. Phenotypes conferred by Plasmids
    • Antibiotic Production- streptomyces
    • Resistance- enteric bacteria, Neisseria (Goneria)
    • Physiological Function- DNA fragments responsible for so many phenotypes
    • conjugation- E. Coli, Peudomonas, Staphyococcus
    • Virulence- Yersinia, Salmonella, E. coli, plage. remove plasma-> non virulent
    • - picked up from outside.
    • -sm DNA 250 nucleotide- kill many people
  57. Polymerase chain Reaction
    • -primary primers
    • -start with a few copies of the DNA and amplifies it 
    • -~2 hrs
    • - each cycle doubles amt of gene copies
    • -use electrophoresis to ID a gene expressed
  58. Mutations can be easily Detected
    • - quantify RNA or DNA virus
    • - measure DNA after each cycle
    • - after certain spot the linear graph drops off
    • - max amt of DNA detectable
    • -less cycles= more DNA present
    • -2^6
    • - qPCR  = real time PCR
  59. Genomics
    • -sequence the whole genome (takes 1 week)
    • -ID the open reading frame (ORF) 
    • ---can find start/stop codon
    • - compare the gene among different species- same function
    • -identify the function of the genes
    • ----post genomic era
    • - ORF in microbiology is like a gene
  60. Overview of Genomics
    • -over 5000-10000 genes have been sequenced so far 
    • -prokariotic genomes published online NIH has site for humans
  61. Size of Prokaryotic Genome
    Bigger genome= more ORFs (genes present)
  62. Genomic Size
    • -min. amt of genes to make cell, 250-300 genes
    • -- mycoplasma
    • - parasitic or endosymbiotic bacteria tent to have smaller genome
    • --expected, they dont need genes, get all from host
    • - size can be from 160Kb to 12 Mbp between viruses and eukaryotic cells
  63. Bioinformatics
    • -ID the gene functions of the genome by computer analysis
    • --guess function of genes w/ computer analysis
    • - compare the unknown ORG with the genes of known function
    • - uncharacterized ORF - 30% in E. Coli still unknown
    • - Maybe redundant genes or genes used at special condition (less redundant means more efficient)
  64. Genome of Mitochondria
    • -Diverse
    • -Linear, circular, or both, and even with plasmid
    • - 4 genes to 400 genes, some mit have some 400/species
    • - Mit gene analysis can trace the maternal lineage
  65. Surprising facts About Genome
    • -8 of the 400 yeast mitochondrial genes are encoded in the mitochondrial genome
    • - among the 400 genes from saccharomyces cerevisiae mitochondria, only 50 genes are closely related to the proposed ancestor bacteria
    • - another 150 are related to bacterial genes
    • - 200 genes with no homologues in bacteria
    • - endosymbiosis hypothesis?
  66. Eukaryotic Genome
    • -unicellular organisms can have bigger genome that human (25000 genes)
    • - phenotype is misleading
    • - paramecium has 40,000 genes (more than humans)
    • - trichomonas has 60,000 genes and it is a human parasite
  67. Explain the genome versus size
    Unicellular organisms have such a large genome because one cell does everything.

    Additional cells give flexibility, variety of genes spread out and react cell to cell to carry out function.
  68. DNA Chip
    • -35,000 dots that correspond with 1 gene
    • - $1000
    • - purify gene from sample can hydridize to chip
    • -small amt = blue
    • -large amt = red
    • -compare two conditions pathogen/ non pathogen = ID gene
  69. Proteomics
    • -two dimensional SDS-Page
    • -Molecular size/ pH isoelectrical point
    • -charge by aa separate
    • -antibody can bind to protein
    • -1000 antibodies/ 1000 types of proteins
    • -tag proteins with fluorescence
    • - more difficult and more expensive
  70. Design of Protein Chip
    • 1. antibody against protiens
    • 2. proteins labeled w/ biotin
    • 3. fluorescence labeled streptavidin
    •  12,938 data points
  71. Chromosomal Islands
    • pathogenicity island- gene clustered together
    • pathogenic -> plasmids or pathogenic islands

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