Bacteria & Viruses

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Bacteria & Viruses

  1. 1. Bacteria & Viruses Prokaryotes and Beyond
  2. 2. The Prokaryotes <ul><li>Prokaryotes = Monerans </li></ul><ul><li>The earliest organisms </li></ul><ul><ul><li>lived & evolved alone on earth for 2 x 10 9 years </li></ul></ul><ul><li>The smallest independently living things </li></ul><ul><ul><li>Much smaller than single celled eukaryotes </li></ul></ul><ul><ul><li>Typical bacteria = 2 µ </li></ul></ul><ul><ul><li>Average eukaryotic cell = 50-200 µ </li></ul></ul><ul><li>Outnumber all eukaryotes combined </li></ul><ul><ul><li>more inhabit your mouth than the total # of people who ever lived! </li></ul></ul>
  3. 3. Diversity & Classification <ul><li>2 branches </li></ul><ul><li>Archebacteria </li></ul><ul><ul><li>Confined to extreme environments </li></ul></ul><ul><ul><li>Similar to early earth </li></ul></ul><ul><ul><li>More closely related to eukaryotes than to modern bacteria </li></ul></ul><ul><li>Only a few genera: </li></ul><ul><ul><li>Methanogens - reduce CO 2 to CH 4 </li></ul></ul><ul><ul><li>Extreme halophiles - salt loving </li></ul></ul><ul><ul><li>Thermoacidophiles </li></ul></ul><ul><li>Eubacteria </li></ul><ul><ul><li>most modern bacteria </li></ul></ul><ul><ul><li>very diverse </li></ul></ul>
  4. 4. Bacterial Classification
  5. 5. Prokaryotes vs. Eukaryotes <ul><li>No mitochondria, chloroplasts, or other membrane bound organelles </li></ul><ul><li>Most are unicellular and much smaller </li></ul><ul><li>Smaller, simpler genomes </li></ul><ul><ul><li>DNA not arranged in chromosomes </li></ul></ul><ul><li>Cell wall is different from plants, fungi, protists </li></ul><ul><ul><li>contains murein / peptidoglcan (a nitrogen containing polysaccharide) </li></ul></ul><ul><li>Differ in mechanisms of genetic replication, expression, and recombination </li></ul>
  6. 6. Prokaryotic & Eukaryotic Cells
  7. 7. Function & Interactions <ul><li>Only a minority cause disease </li></ul><ul><li>Many are essential to life on earth </li></ul><ul><li>Decomposers </li></ul><ul><ul><li>essential to chemical cycles </li></ul></ul><ul><li>Often live in symbiotic relationships with other organisms </li></ul>
  8. 8. Form & Function <ul><li>Single celled </li></ul><ul><ul><li>some aggregate in 2-celled or several celled groups </li></ul></ul><ul><ul><li>some form colonies </li></ul></ul><ul><li>Diversity of shapes </li></ul><ul><li>3 most common: </li></ul><ul><ul><li>spheres = cocci </li></ul></ul><ul><ul><li>rods = bacilli </li></ul></ul><ul><ul><li>spirals = spirilla </li></ul></ul>
  9. 9. Bacterial Shapes
  10. 10. The Bacterial Cell Wall <ul><li>Instead of cellulose, contain peptidoglycan </li></ul><ul><ul><li>A polymer of modified sugars cross-linked with amino acids </li></ul></ul><ul><li>The gram stain distinguishes many disease causing bacteria based on the type of cell wall </li></ul><ul><li>Many antibiotics work by attacking the bacterial cell wall </li></ul>
  11. 11. The Gram Stain <ul><li>A valuable tool for distinguishing types of bacteria based on the cell wall </li></ul><ul><li>Gram (+) </li></ul><ul><ul><li>accept gram stain </li></ul></ul><ul><ul><li>have simpler cell walls with large amounts of peptidoglycan </li></ul></ul><ul><li>Gram (-) </li></ul><ul><ul><li>do not stain </li></ul></ul><ul><ul><li>have more complex cell walls with less peptidoglycan </li></ul></ul><ul><ul><li>cell walls contain lipopolysaccharides </li></ul></ul><ul><ul><li>are more likely to be pathogenic (cause disease) </li></ul></ul><ul><ul><li>more resistant to antibiotics </li></ul></ul>
  12. 12. The Cell Wall & Gram Stain
  13. 13. Gram (+) and (-) Bacteria
  14. 14. Antibiotics <ul><li>Many antibiotics work on the cell wall </li></ul><ul><li>Common antibiotics (e.g. penicillin) work by preventing cross-linking of peptidoglycan </li></ul><ul><li>Therefore bacteria can’t form new cell walls </li></ul><ul><li>Therefore no new bacteria are formed </li></ul><ul><li>Doesn’t effect the host, because only monerans have peptidoglycan </li></ul><ul><li>Explains added resistance of gram (-) bacteria to these antibiotics </li></ul>
  15. 15. Secretion of Antibiotics <ul><li>Most micro-organisms (including protists, monerans & fungi) release antibiotics </li></ul><ul><li>An evolutionary advantage </li></ul><ul><li>Helps the organism compete for food and space </li></ul>
  16. 16. The Capsule <ul><li>Many bacteria secrete a sticky substance that forms another protective layer, the capsule </li></ul><ul><li>Outside the cell wall </li></ul><ul><li>Helps them stick to things </li></ul><ul><li>Provides protection </li></ul>
  17. 17. Motility <ul><li>About half of all monerans are capable of directional movement. </li></ul><ul><li>3 mechanisms: </li></ul><ul><ul><li>flagella - different from eukaryotes </li></ul></ul><ul><ul><li>spiral shaped bacteria ( spirochetes ) have a filament that spirals around the cell under the outer sheath </li></ul></ul><ul><ul><ul><li>causes the cell to move like a corkscrew </li></ul></ul></ul><ul><ul><li>some bacteria secrete slimy chemicals & glide </li></ul></ul><ul><li>Taxis </li></ul><ul><ul><li>movement toward or away from a stimulus </li></ul></ul><ul><ul><li>many bacteria exhibit this form of movement </li></ul></ul>
  18. 18. Structure of Prokaryotic Flagella
  19. 19. Structures of Movement
  20. 20. Prokaryotic Ribosomes <ul><li>Slightly different from eukaryotic ribosomes </li></ul><ul><li>The basis of some antibiotics </li></ul><ul><ul><li>tetracycline & chloramphenicol </li></ul></ul><ul><ul><li>block protein synthesis in prokaryotes only </li></ul></ul>
  21. 21. Metabolic Diversity <ul><li>A varied group, similar to eukaryotes </li></ul><ul><li>Three major groups: </li></ul><ul><li>Phototrophs </li></ul><ul><ul><li>use light energy to synthesize organic compounds from CO 2 </li></ul></ul><ul><ul><li>includes cyanobacteria (blue-green algae) </li></ul></ul><ul><ul><li>have chlorophyll but not chloroplasts </li></ul></ul><ul><li>Photoheterotrophs </li></ul><ul><ul><li>can use light to generate ATP </li></ul></ul><ul><ul><li>must obtain carbon in organic form </li></ul></ul><ul><li>Chemoheterotrophs </li></ul><ul><ul><li>Must consume organic molecules for both energy & carbon </li></ul></ul><ul><ul><li>Most bacteria are chemoheterotrophs </li></ul></ul>
  22. 22. Chemoheterotrophs <ul><li>Most bacteria are chemoheterotrophs </li></ul><ul><li>Consume organic molecules for both energy and carbon </li></ul><ul><li>Secrete an enzyme that breaks down large molecules of food to smaller molecules that can be absorbed through the cell membrane </li></ul><ul><li>Many bacteria are saprobes </li></ul><ul><ul><li>feed on dead plants or animals </li></ul></ul><ul><ul><li>also called decomposers because they break down decaying material </li></ul></ul><ul><li>Other bacteria live in or on the bodies of other living organisms </li></ul><ul><ul><li>some are beneficial ( symbiosis ) </li></ul></ul><ul><ul><li>some are harmful = parasites </li></ul></ul>
  23. 23. Oxygen <ul><li>The effects of oxygen on growth are varied </li></ul><ul><li>Obligate aerobes </li></ul><ul><ul><li>cannot grow without O 2 for cellular respiration </li></ul></ul><ul><li>Facultative aerobes </li></ul><ul><ul><li>use O 2 if available but can also use fermentation </li></ul></ul><ul><li>Obligate anaerobes </li></ul><ul><ul><li>cannot use O 2 and are poisoned by it.  </li></ul></ul><ul><li>Facultative anaerobes </li></ul><ul><ul><li>don't use O 2 , but aren't harmed </li></ul></ul><ul><li>Many heterotrophic bacteria are anaerobes </li></ul><ul><ul><li>classified by their metabolic wastes (acetic acid, lactic acid, etc.) </li></ul></ul>
  24. 24. Nitrogen Metabolism <ul><li>Also diverse </li></ul><ul><li>Monerans are able to metabolize most nitrogen compounds </li></ul><ul><li>Key to cycling nitrogen through the ecosystem </li></ul><ul><li>Nitrogen fixation </li></ul><ul><ul><li>Some monerans can capture N 2 in the atmosphere </li></ul></ul><ul><ul><li>They have an enzyme that converts N 2 gas to nitrates (NO 3 ) - a form other organisms can use </li></ul></ul><ul><ul><li>This is the only mechanism that makes atmospheric nitrogen available to other organisms </li></ul></ul><ul><ul><li>Some plants (clover, beans, etc.) have nitrogen fixing bacteria growing in their roots </li></ul></ul>
  25. 25. The Bacterial Genome <ul><li>Bacteria have ~ 1/1000 as much DNA as eukaryotes </li></ul><ul><li>DNA is one double stranded molecule in the form of a ring </li></ul><ul><li>No nucleus, so DNA is in the cytoplasm </li></ul>
  26. 26. Plasmids <ul><li>Bacteria may also have smaller rings of DNA called plasmids </li></ul><ul><li>Each plasmid is only a few genes </li></ul><ul><li>Plasmids carry non-essential genes such as antibiotic resistance, metabolism of special nutrients, etc. </li></ul><ul><li>Plasmids can carry a sex factor </li></ul><ul><ul><li>bacteria with the sex factor can conjugate with cells that do not carry the factor. </li></ul></ul><ul><li>Plasmids replicate independently </li></ul><ul><li>Can be transferred when bacteria conjugate </li></ul>
  27. 27. Growth & Reproduction <ul><li>Neither mitosis nor meiosis occurs in prokaryotes </li></ul><ul><li>Prokaryotes reproduce asexually by binary fission </li></ul><ul><li>Genetic recombination does occur in bacteria </li></ul>
  28. 28. Genetic Exchange <ul><li>3 mechanisms of exchange of genetic material: </li></ul><ul><li>transformation - </li></ul><ul><ul><li>genes taken up by bacteria from the surrounding environment </li></ul></ul><ul><li>conjugation - </li></ul><ul><ul><li>genes are transferred directly from one bacteria to another </li></ul></ul><ul><li>transduction - </li></ul><ul><ul><li>genes are transferred between bacteria by means of viruses </li></ul></ul><ul><li>All are unilateral passage of variable amounts of DNA </li></ul><ul><li>Mutation is the major source of genetic variation in prokaryotes </li></ul>
  29. 29. Bacterial Conjugation
  30. 30. Endospores <ul><li>Some bacteria form resistant cells called endospores </li></ul><ul><li>Can live in stasis indefinitely </li></ul><ul><ul><li>found 11,000 y.o. bacteria </li></ul></ul><ul><li>Resist extremes of temperature, pH, etc. </li></ul>
  31. 31. Classes of Bacteria <ul><li>The Eubacteria include: </li></ul><ul><ul><li>Proteobacteria </li></ul></ul><ul><ul><li>Chlamydia </li></ul></ul><ul><ul><li>Spirochetes </li></ul></ul><ul><ul><li>Gram-positive bacteria </li></ul></ul><ul><ul><li>Cyanobacteria </li></ul></ul><ul><li>The Archebacteria include: </li></ul><ul><ul><li>Euryarchaeota </li></ul></ul><ul><ul><li>Crenarchaeota </li></ul></ul>
  32. 32. Prokaryotic Phylogeny
  33. 33. <ul><li>There are 5 major clades (divisions) of eubacteria </li></ul>
  34. 34. The Proteobacteria <ul><li>A diverse group of gram-negative bacteria </li></ul><ul><li>Includes photoautotrophs, chemoautotrophs & heterotrophs </li></ul><ul><li>Includes both anaerobic & aerobic species </li></ul><ul><li>5 subgroups: </li></ul><ul><ul><li>Alpha proteobacteria </li></ul></ul><ul><ul><li>Beta proteobacteria </li></ul></ul><ul><ul><li>Gamma proteobacteria </li></ul></ul><ul><ul><li>Delta proteobacteria – myxobacteria </li></ul></ul><ul><ul><li>Epsilon proteobacteria - helicobacter </li></ul></ul>
  35. 35. Subgroups of Proteobacteria <ul><li>Alpha proteobacteria </li></ul><ul><ul><li>Most are symbionts or parasites </li></ul></ul><ul><ul><li>Includes rhizobium, nitrogen fixing bacteria found in the roots of legumes </li></ul></ul><ul><li>Beta proteobacteria </li></ul><ul><ul><li>Includes nitosomonas – oxidize NH 4 producing nitrite </li></ul></ul><ul><li>Gamma proteobacteria </li></ul><ul><ul><li>Includes photosynthetic bacteria and many enterics such as E. coli , Legionella , Vibrio cholera , salmonella </li></ul></ul><ul><li>Delta proteobacteria </li></ul><ul><ul><li>Includes Myxobacteria which form elaborate colonies </li></ul></ul><ul><ul><li>Bdellovibrios – predators that attack other bacteria </li></ul></ul><ul><li>Epsilon proteobacteria </li></ul><ul><ul><li>Closely related to deltas </li></ul></ul><ul><ul><li>Includes helicobacter which causes stomach ulcers </li></ul></ul>
  36. 36. Chlamydia <ul><li>Parasites that can survive only within the cells of animals </li></ul><ul><li>Gram negative walls are unusual because they lack peptidoglycan </li></ul><ul><li>One species is the most common cause of blindness in the world </li></ul><ul><li>Another species causes the most common STD in the U.S. </li></ul>
  37. 37. Spirochaetes <ul><li>Helical heterotrophs </li></ul><ul><li>Have axial filaments = fibers between cell wall and cell membrane </li></ul><ul><ul><li>Filaments allow a corkscrew motion </li></ul></ul><ul><li>Many are free living </li></ul><ul><li>Includes anaerobes that live in mud or H 2 O </li></ul><ul><li>A few are parasites </li></ul><ul><li>Includes the organisms that cause syphilis and Lyme disease </li></ul>
  38. 38. Gram Positive Bacteria <ul><li>Includes all gram positive bacteria and also a few related gram negative bacteria </li></ul><ul><li>Colonial actinomycetes were once mistaken for fungus </li></ul><ul><ul><li>includes Streptomyces , the source of many antibiotics </li></ul></ul><ul><ul><li>Also includes species that cause tuberculosis & leprosy </li></ul></ul><ul><li>Includes spore formers such as such as Bacillus & Clostridium </li></ul><ul><ul><li>Bacillus anthracis </li></ul></ul><ul><ul><li>Clostridium botulinum </li></ul></ul><ul><ul><li>Also all Staphylococcus & Streptococcus </li></ul></ul><ul><li>Mycoplasmas </li></ul><ul><ul><li>The only bacteria lacking a cell wall </li></ul></ul><ul><ul><li>Smallest known cells </li></ul></ul><ul><ul><li>Most live in soil </li></ul></ul>
  39. 39. Cyanobacteria <ul><li>Only about 1,500 species </li></ul><ul><li>Sometimes called blue-green algae </li></ul><ul><li>Are photosynthetic </li></ul><ul><ul><li>Don't contain chlorophyll </li></ul></ul><ul><ul><li>Have 2 photosynthetic pigments not found in plants: </li></ul></ul><ul><ul><li>phycocyanin - a blue-green pigment </li></ul></ul><ul><ul><li>phycoerythrin - a red pigment </li></ul></ul><ul><li>Many are multicellular - form long filaments </li></ul><ul><ul><li>To reproduce, chains of cells break, and cells at ends of chains divide, increasing length of the filament </li></ul></ul><ul><li>Some contain heterocysts - thick walled cells that contain enzymes for nitrogen fixation </li></ul><ul><ul><li>supply other cells with nitrogen </li></ul></ul><ul><ul><li>other cells supply them with food from photosynthesis </li></ul></ul>
  40. 40. Viruses <ul><li>Much smaller than bacteria: .03 - .30 </li></ul><ul><li>Can't be seen with a light microscope </li></ul><ul><li>Consist of a single molecule of nucleic acid surrounded by a protein coat </li></ul><ul><li>The nucleic acid molecule can be single or double stranded DNA, or RNA </li></ul><ul><li>The amount of nucleic acid is much less than bacteria </li></ul><ul><ul><li>bacteria have enough DNA for 2000 genes </li></ul></ul><ul><ul><li>many viruses have only 10 genes; the largest is about 100 genes </li></ul></ul>
  41. 41. Viral Strategy <ul><li>Viral genes carry instructions for the production of new virus particles </li></ul><ul><li>Viruses have no ribosomes or other cytoplasmic structures to carry out their genetic instructions </li></ul><ul><li>Viruses can't live independently; are all parasites of living cells </li></ul><ul><li>They use the energy and the protein producing machinery of the host cells to make new virus particles </li></ul>
  42. 42. Viral Protection <ul><li>The protein coat is made of several hundred protein molecules packed in a geometric pattern </li></ul><ul><li>Some have a complex capsule surrounding the protein coat </li></ul>
  43. 43. Viral Structure
  44. 44. Specificity <ul><li>Each type of virus infects a particular type of cell </li></ul><ul><li>Viruses that infect bacteria = bacteriophage </li></ul><ul><ul><li>have a ‘tail’ that attaches to bacteria </li></ul></ul>
  45. 45. A Bacteriophage
  46. 46. Elements of a Bacteriophage
  47. 47. Reproduction of Viruses <ul><li>Two primary life cycles </li></ul><ul><ul><li>Lytic cycle </li></ul></ul><ul><ul><li>Lysogenic cycle </li></ul></ul><ul><li>Some have one life cycle or the other </li></ul><ul><li>Some can shift life cycle type depending on environmental pressures </li></ul>
  48. 48. The Lytic Cycle <ul><li>Example E.coli phage: </li></ul><ul><li>The tail fibers match molecules in host cell membrane - so bind specifically </li></ul><ul><li>Once the phage is attached, it acts like a syringe - injects its DNA into the host </li></ul><ul><li>Inside the cell, the phage DNA takes over the cytoplasmic machinery of the host cell </li></ul><ul><li>The host cell makes copies of the phage DNA </li></ul>
  49. 49. The Lytic Cycle (Continued) <ul><li>Host cell ribosomes make proteins according to phage gene instructions. </li></ul><ul><li>New phage proteins and nucleic acids come together in the cell and form several hundred new phage particles </li></ul><ul><li>The phage DNA instructs the host cell to self-destruct </li></ul><ul><li>The host cell makes an enzyme that lyses or digests the bacterial cell wall </li></ul><ul><li>When the host cell lyses, it releases new phage particles </li></ul>
  50. 50. Lytic Cycle of the T4 Phage
  51. 51. Modified Lytic Cycle <ul><li>Some viruses have a modified lytic cycle </li></ul><ul><li>They don't lyse the host cell </li></ul><ul><li>The virus exits by pushing out through the cell membrane </li></ul><ul><li>These viruses have capsules that consist partly of host cell membrane & partly viral protein </li></ul><ul><li>Example: human influenza virus </li></ul>
  52. 52. Viral Latency <ul><li>Some viruses can take both active and latent forms. </li></ul><ul><li>During the active phase, the virus interferes with normal cell metabolism, causing disease symptoms </li></ul><ul><li>During the latent phase, it's as if the virus has gone to sleep. </li></ul><ul><ul><li>Although the host cells remain infected, the host is a symptom-free carrier of the disease. </li></ul></ul><ul><li>The difference between the active and latent manifestations of viral infection results from a switch in viral replication patterns. </li></ul><ul><ul><li>Some viruses can only replicate by the lytic pathway. </li></ul></ul><ul><ul><li>Other viruses can inject their DNA into the host cell, but the injected DNA can be inactive until the appropriate cellular event triggers its awakening. </li></ul></ul>
  53. 53. The Lysogenic Cycle <ul><li>The latter pathway is called the temperate or lysogenic pathway. </li></ul><ul><li>After entering the host cell, the viral DNA inserts into host DNA by recombination </li></ul><ul><ul><li>viral DNA becomes part of host DNA </li></ul></ul><ul><li>Viral DNA does not take over the host cell </li></ul><ul><li>When the host cell reproduces, viral genes are also duplicated </li></ul><ul><li>There may be no active viral particles produced for generations </li></ul><ul><li>Sporadically, viral DNA will become active and trigger reproduction </li></ul>
  54. 54. The Lysogenic Cycle (Continued) <ul><li>When lysogenic viral DNA becomes active, it breaks out of the host DNA  lytic </li></ul><ul><li>As it breaks out, the viral DNA may take several bacterial genes with it </li></ul><ul><li>The virus can carry bacterial genes from the previous host to a new host during the infection cycle </li></ul><ul><ul><li>this process = transduction </li></ul></ul><ul><ul><li>used in recombinant DNA research </li></ul></ul><ul><li>It is possible to artificially induce all the cells in a lysogenic culture to enter the lytic pathway by exposing them to UV light, or X-rays. </li></ul><ul><li>Example: Herpes virus (causes cold sores; may cause cancers </li></ul>
  55. 55. Discovery of the Lysogenic Cycle <ul><li>The lysogenic pathway was first discovered in bacteriophages in the early 1920s </li></ul><ul><li>It was not really understood until the 1950s </li></ul><ul><li>First explored at the cellular level by Andre' Lwoff, a French scientist. </li></ul><ul><li>Lwoff knew that some bacterial cultures that grew normally and otherwise seemed perfectly healthy were infected by phage. </li></ul><ul><li>Although the phage didn't interfere with the host bacteria, such cultures had the ability to cause the lysis or rupture of other bacteria. </li></ul><ul><li>Thus, the culture was described as &quot;lysogenic.&quot; </li></ul>
  56. 56. Unraveling the Lysogenic Cycle <ul><li>It was known why such cultures were lethal to other bacteria. </li></ul><ul><li>The lysogenic effect didn't stem from phage particles floating in the culture </li></ul><ul><ul><li>The cultures remained lethal even after removal of any free floating phage. </li></ul></ul><ul><li>The effect was not due to a reserve of phage stored within the host cells </li></ul><ul><ul><li>No phage were released when the cells of a lysogenic culture were artificially burst open. </li></ul></ul>
  57. 57. Lwoff’s Discovery <ul><li>Lwoff observed the growth of single bacterial cells of Bacillus megaterium in tiny droplets of medium. </li></ul><ul><ul><li>Found that free phage particles were never found floating in droplets that contained only single cells </li></ul></ul><ul><ul><li>They were found in the colonies derived from single cells. </li></ul></ul><ul><ul><li>Occasionally, a single cell in a droplet being watched would spontaneously burst, releasing about 100 phage. </li></ul></ul><ul><li>Concluded that host cells weren’t entirely immune to the phage. </li></ul><ul><ul><li>When a phage became active, it forced the host to make more phage, eventually killing the host, and releasing new phage when the cell burst. </li></ul></ul><ul><ul><li>But, the switch from the lysogenic to the lytic pathway was the exception rather than the rule; most of the time the phage was in an inactive form. </li></ul></ul>
  58. 58. Phage Lytic & Lysogenic Cycles
  59. 59. Are Viruses Alive? <ul><li>Viruses contain nucleic acids & proteins </li></ul><ul><li>Viruses, by themselves, cannot make or use food, grow or reproduce </li></ul><ul><li>Some scientists believe viruses were never independently living organisms </li></ul><ul><li>Others believe viruses evolved from simple bacteria like mycoplasmas & rickettsiae </li></ul><ul><li>Another hypothesis: viruses are genes that have escaped from the genomes of living cells </li></ul><ul><li>Not much evidence to support any one of these </li></ul>
  60. 60. Beyond Viruses <ul><li>Viroids </li></ul><ul><ul><li>even smaller & simpler than viruses </li></ul></ul><ul><ul><li>cause some plant diseases </li></ul></ul><ul><ul><li>short pieces of RNA with no protein coat </li></ul></ul><ul><li>Prions </li></ul><ul><ul><li>Infectious agents that lack nucleic acids </li></ul></ul><ul><ul><li>“ protein only” </li></ul></ul><ul><ul><li>BSE </li></ul></ul>
  61. 61. Prion Action

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