Bio320 Midterm 1

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Bio320 Midterm 1
2014-01-28 23:47:56

Flash cards for Biomidterm 1 Vocab
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  1. Eubacteria
    Means true bacteria. Form the domain bacteria. Basically all bacteria fall here, except archaebacteria. Prokaryotic, mostly unicellular, DNA is in a single circular chromosome, peptidoglycan on cell wall.
  2. Archaea
    Domain of life containing anucleate cells that have unique lipids in their membranes, distinctive rRNA sequences, and cell walls that lack peptidoglycan.
  3. Peptidoglycan
    Component of bacterial cell walls. It is composed of long chains of alternating N-acetylglucosamine and N-acetylmuramic acid residues, with the chains linked to each other by short chains of amino acids
  4. Peptide cross-bridge
    A short peptide chain that connects the tetrapeptide chains in the peptidoglycan of some bacteria. Can vary from species to species. In Gram negative, uses D-amino acids. In Gram positive, pentaglycine. Attached to NAM.
  5. NAM
    N-acetylmuramic acid. Part of peptidoglycan subunit. Alternates NAM/NAG along the peptide chain.
  6. NAG
    N-acetyl-glucosamine. Part of peptidoglycan, attached to NAM
  7. Two component regulator
    Stimulus response coupling mechanism. Allows organisms to sense and respond to different environmental conditions. Membrane bound histidine kinase that senses stimulus, and a corresponding response regulator that mediates cellular response. Does this through differential expression of target genes. Transfer of phosphoryl groups from ATP to Histidine kinases.
  8. Caulobacter crescentus
    Bacteria that has two different types of cells for differentiation. Stalked cells that reproduce. Asymetric division. Produces a swarmer cell that is flagellated, finds a new surface attachment site, and then turns into a stalked cell. Gram negative, oligotrophic
  9. S. aureus
    Staphylococcus aureus - member of the Firmicutes, Found in human respiratory tract and on skin. Facultative anaerobic Gram-positive coccal bacterium. Used to discover penicillin.
  10. E. coli
    Gram-negative, facultative anaerobic, rod shaped bacterium, found in lower intenstine of warm blooded beings. Also found with contaminated water.
  11. Mesophile
    A microorganism with a growth optimum around 20 to 45°C, a minimum of 15 to 20°C, and a maximum of less than 45°C
  12. Chemiosmosis
    Chemiosmosis is the movement of ions across a selectively permeable membrane, down their electrochemical gradient. More specifically, it relates to the generation of ATP by the movement of hydrogen ions across a membrane during cellular respiration.
  13. Turgor pressure
    Pressure placed on the outer membrane from the inside due to influx of water from higher solute concentration within the cell.
  14. Matric Pressure
    Pressure made by water adhering to solids. Can lead to desiccation.
  15. Osmotic pressure
    Pressure needed inside an area to stop the flow of solvent into the cell, which is created by higher solute concentration within the cell.
  16. LPS
    Lipopolysaccharides. Found on the outer membrane of gram negative bacteria. Has 2 major components, O antigen repeating polysaccharide and Lipid A which attaches it to the outer membrane. LPS is an endotoxin, and Lipid A is the causative agent of gram negative septic shock.
  17. Lipoteichoic acid
    Found on gram positive cell wall. Polymers of glycerol or ripitol joined by phosphate groups. Covalently connected to plamsa membrane lipids.
  18. Spirillum
    A spiral shaped bacteria with 1 or 2 turns around helical axis. Has external flagella. Rigid structure usually.
  19. O-antigen
    Part of LPS that extends outward from the core. Polysaccharide chain.
  20. Methanogen
    Strictly anaerobic archae that dervie energy by converting CO2, H2, formate, acetate, and other compounds to either methane or methane and CO2.
  21. Oscillatoria
    A Cyanobacteria. Fillamentous bacteria which moves in a oscillatory fashion.
  22. Pseudomurein
    aka psuedopeptidoglycan, a complex polysaccharide observed in the cell walls of some archaea ,it resmbles peptidoglycan in structure and chemical make-up.
  23. Methanococcus
    A methanogen, an archael cell that has a cell wall which is an S-layer. Composed of glycoprotein or protein. 20-40 nm thick.
  24. Enterobacteriaceae
    Large family of gram negative bacteria that are rod shaped and 1-5 micrometers in length. Facultative anaerobes
  25. Chlamydiae
    An obligate intracelluar bacteria, can only be grown as a parasite in mammalian cell tissue culture.
  26. PTS System
    Group translocation system. Sugars are brought into the cell and then transformed by phosphorolation, using PEP as a phosphate donor.
  27. Symport
    Linked transport of two substances in the same direction. Usually using one substance to move another substance across its concentration gradient.
  28. DNA gyrase
    A topoisomerase enzyme that relieves tension generated by the rapid unwinding of DNA during DNA replication.
  29. Plasmodium
    A stage in the life cycle of myxogastria protists; a multinucleate mass of protoplasm surrounded by a membrane. Also the parasite responsible for malaria. 
  30. BSE/Mad Cow
    Caused by infectious protein particles (prions). Spread through cattle population by rendering dead cow and sheep into feed. Contaminated british beef in the 90's. May be widespread in animal populations.
  31. H1N1/H5N1/H3N2
    • H1N1 (Swine flu) Type of respiratory influenza
    • H5N1 (Bird flu) Humans and birds - Pandemic
    • H3N2 another influenza that is in pigs/birds/humans.
  32. Diarrheal disease
    Disease that causes diarrhea, usually leading to dehydration and shock.
  33. Influenza
    Influenza, commonly known as "the flu", is an infectious disease of birds and mammals caused by RNA viruses of the family Orthomyxoviridae, the influenza viruses. The most common symptoms are chills, fever, runny nose, sore throat,muscle pains, headache (often severe), coughing, weakness/fatigue and general discomfort.
  34. Gram positive
    Retains cyrstal violet when stained with Gram's stain and then decolorized. Outer cell wall has a thick peptidoglycan layer and uses lipotechoic acid. Cell wall uses glycine, serine, and Threonine
  35. Gram Negative
    Looks pink after gram's stain and decolorizer is applied. Outer membrane is another lipid bilayer with LPS embedded. Has a very thin peptidoglycan layer. Helps to keep antibiotics out with porin channels. that only allow certain sized antibiotics through.
  36. Myxobacteria
    Predatory bacteria, hunt down other bacteria and eat them.Have swarming motility and move through the soil. Very loose communities, not highly differentiated. When starved, they create fruiting bodies.
  37. Fruiting body
    Made of lots of bacterial cells. Formed through cell to cell contact. Form myxospores. Will disperse and fly through the air, looking for more nutrients. Created when no more nutrients about.
  38. Autolysin
    Enzymes that partially digest peptidoglycan in growing bacteria so that the cell wall can be enlarged.
  39. Spirochete
    A spiral shaped bacteria where the flagella run along the length of the cell, giving corkscrew like motility.
  40. Flagellum
    • Have 3 parts, Filament - end, made up of protein flagellin
    • Hook, different protein 
    • Basal body
    • Peritrichous - all over cell body
    • Can be at the poles - rods and spirilla
    • Monotrichous - single at one end
    • Lophotrichous - clump of flagella at one end
    • Amphitrichous - flagella at both ends
  41. Hook
    A flexible joint in the flagella that allows movement.
  42. Glycolysis
    The conversion of glucose to pyruvic acid by certain metabolic pathways. Allows creation of ATP.
  43. Catabolism
    That part of metabolism in which larger, more complex molecules are broken down into smaller, simpler molecules with the release of energy
  44. Anabolism
    Build up of larger molecules from smaller subunits.
  45. Chemotaxis
    The pattern of microbial behavior in which the microorganism moves toward chemical attractants and away from repellents.
  46. Psychrophile
    Cold loving. A microorganism that grows well at 0° C and has an optimum growth temperature of 15°C or lower and a temperature maximum of 20°C.
  47. Thermophile
    A microorganism that can grow at 55°C or higher, the minimum is usually around 45°C
  48. Alkaliphile
    A microorganism that grows best at pHs from about 8.5 to 11.5
  49. Acidophile
    A microorganism that has its growth optimum between about pH 0 and 5.5
  50. Dissimilatory
    The use of a substance as an electron acceptor for an electron transport chain. The acceptor sulfate or nitrate is reduced but not incorporated into organic matter.
  51. Assimilatory
    The reduction of an inorganic molecule to incorporate it into organic material. No energy is conserved during this process.
  52. Lipid A
    Part of LPS, helps to anchor LPS to outer membrane of Gram Negative bacteria. Also the endotoxin part of LPS.
  53. Clostridia
    Endospore. Class of Firmicutes. Lack Aerobic respiration. Obligate anaerobes. All gram positive.
  54. Mycoplasma
    Bacteria that are members of phylum Firmicutes, cklass mollicutes, and order mycoplasmatales. Lack cell walls and cannot synthesize peptidoglycan precursers, most require sterols for growth.
  55. Calvin-Benson Cycle
    The main pathway for the fixation (reduction and incorporation) of C02 into organic material by photoautotrophs and chemolithoautotrophs. AKA dark cycle. Uses Rubisco as a major enzyme.
  56. Halobacterium
    A group of archaea that depend on high NaCl concentrations for growth and do not survive at a concentration below about 1.5 M NaCl
  57. filamentous
    Long strands of bacterial cells that do not seperate, knock out genes for cleavage.
  58. Autotroph
    An organism that uses CO2 as its sole or principal source of Carbon. Either phototrophs (carbon from light) or lithotrophs, which is done by inorganic chemistry. Does not rely on organic material for carbon.
  59. Rickettsiae
    Obligate intracellular bacteria, gram negative
  60. Antiport
    Coupled transport where one molecule enters the cell as the other leaves the cell.
  61. Neisseria
    Genus of commensal bacteria, including Neisseria gnorrheoeae and Neisseria menigitidis. Gram negative, cause symptomatic infections. Fimbriae are well studied in N. gonorrheoea, the small hair like structures that are often used for surface attachment.
  62. B. anthracis
    Gram positive, endospore forming rod like bacteria that is responsible for Anthrax.
  63. Bent-neck flask
    Flask used by pasteur to show that growth of microbes was prevented in a heated broth.
  64. Quinine
    Drug used against malaria.
  65. HIV/Aids
    • Human Immunodeficiency Virus/ Acquired Immune deficiency syndrome. 
    • Leading global infectious disease killer worldwide. More than 3 million die each year. Many die from TB. Virus infects immune system cells and destroys t-cells.
  66. Epidemic/Pandemic
    Epidemic A wide spread occurrence of a disease in a community at a certain time.

    Pandemic - An epidemic that has spread through many large communities/populations.
  67. Transpeptidase
    Enzyme that cross links peptidoglycan chains to form rigid cell walls.
  68. Transglycosylase
    An enzyme that catalyzes the transfer of glycosyl groups from one compound to another.
  69. TCA Cycle
    Citric acid cycle or kreb's cycle, Oxidation of acetate to form ATP.
  70. Photosynthesis
    Conversion of light energy into chemical energy. Mostly in plants, some other bacteria.
  71. Lithotropy
    Organisms that use reduced inorganic compounds as its electron source.
  72. Green sulfur
    Family of obligate anaerobic photoautotrophic bacteria
  73. Redox
    Transfer of electrons between species. Reduction/oxidation
  74. Flagellin
    Protein that makes up the filament part of the protein.
  75. fermentation
    metabolic process that converts sugars to acids, gases and or alcohol.
  76. Streptococcus
    Spherical gram positive bacteria. Divide down one axis, so grow in chains or pairs.
  77. Staphylococcus
    Normally found on skin and mucous membranes, grape like clusters, round, gram positive.
  78. Bacillus
    Genus, gram positive rod shaped. obligate aerobes or facultative anaerobes.
  79. Magnetosome
    A functional inclusion, magnetic particles in manetotactic bacteria that are tiny manets and allow bacteria to orient themselves in magnetic fields.
  80. Gas vacoule.
    Functional inclusion, gas filled, found in cyanobacteria, and other bacteria/archae that provide flotation.
  81. Quorum sensing
    The process in which bacteria monitor their own population density by sensing the levels of signal molecules that are released by the microorganisms. when these signal molecules reach a threshold concentration, quorum dependent genes are expressed.
  82. Nitrogenase
    Enzyme that fixes atmospheric nitrogen gas.
  83. N fixation
    Process by which nitrogen gas is converted into ammonium.
  84. Sulfur cycle
    Use of sulfur as an electron acceptor/donor. Assimilatory and dissimaltory processes using Sulfur.
  85. Phosphatase
    Enzyme that removes phosphate group from a substrate. Helps bacteria to get a limiting nutrient.
  86. Treponema
    Spirochete bacteria that can cause diseases like syphilis.
  87. biofilm
    Group of microorganisms that stick together on a surface. Usually imbedded in an EPS (extracellular polymeric substance).
  88. FtsZ
    Filamenting temperature sensitive mutant Z. Protein used in septum formation in bacteria, almost like tubulin in eukaryotic cells.
  89. Borrellia
    form of spirochete.
  90. Heterotroph
    Uses organic carbon for energy/carbon source.
  91. 70S/50S/30S
    Bacterial ribosomal subunits  Initial subunits is 50S and 30S, and the final subunit is 70S
  92. Rhizobium
    Gram negative bacteria that fix nitrogen in the soil. Can be different shapes.
  93. Variola
    Small pox virus
  94. Vaccinia
    Vaccine virus that helped to eradicate small pox.
  95. CCR5
    C-C chemokine receptor type 5, also known as CCR5 or CD195, is aprotein on the surface of white blood cells that is involved in the immune system as it acts as a receptor for chemokines. This is the process by which T cells are attracted to specific tissue and organ targets. Many forms of HIV, the virus that causes AIDS, initially use CCR5 to enter and infect host cells. A few individuals carry a mutation known as CCR5-Δ32in the CCR5 gene, protecting them against these strains of HIV
  96. What were the contributions to microbiology of Van Leeuwenhoek and Hooke?  Koch and Pasteur?  Beijerinck and Winogradsky?
    • Van Leeuwenhoek and Hooke - Early microscopy, hooke showed cells in a piece of cork with a single lens, Leeuwenhoek used stains and very well crafted lenses to look at bacteria.
    • Koch and Pasteur - Pasteur - bent neck flask that showed that microbes will not grow in a heated both. Koch, discovered Bascillus anthrax. Came up with 3 postulates - Isolate organisms from the diseased patient - Show that inoculation of the organism in an animal model causes the disease - reisolate the organism from the diseased animal, show it is the same organism. 
    • Beijernick and Winogradsky - showed that bacteria are important factors in cycling of nutrients in the environment.  Life depends on microbial nitrogen fixation from the atmosphere. Microbial consortia in environment were important to understand.  Developed methods for studying bacterial and fungal growth, metabolic processes in complex systems.
  97. What are the different types of organisms we will be studying in this
    class?  Which are eukaryotes, which
    prokaryotes?  Give an example of
    each type of microorganism.
    We are going to be studying Archaea, Bacteria, Eukarya, fungi, protists, prions and Viruses. Archae and Bacteria are considered prokaryotes, or non compartmented interior of cells. Fungi and protists are considered eukaryotes.  Viruses are acellular, and prions are made up of proteins only. An Example of archaea are methanobacteria, or archae that creates methane. An example of a Bacteria is E. coli, and common enteric bacteria. An example of fungi would be a yeast cell. A protist example is algae. An example of a Virus is small pox, and an Example of a prion is BSE, or mad cow disease.
  98. What are some examples of emerging infectious diseases?  What are some diseases that are major
    problems in the developing world v. the developed world? What are some
    examples that transcend that divide?
    VRE, MRSA, MDR TB. HIV, West Nile, Ebola. Diseases in the developing world are TB, Malaria, diseases caused by fowled water, and HIV. Diseases in the developed world that cause problems are Drug resistant bacteria like MRSA and VRE. Some examples that transcend the divide are HIV, which can infect anyone and travel long distances, and is unable to be cured. Hepatitis C is another example of this.
  99. What is the global burden of tuberculosis? 
    Why is this much less of an issue in the US?  What is the global burden of HIV?  Why do the interactions of these
    diseases seem to matter?
    The global burden of tuberculosis is about 2 million deaths per year, leading killer among HIV infected people. 1/3 of the world's population is infected. Advanced healthcare  makes TB not a large issue in the United States, including antibiotics. The global burden of HIV is approximately 6 million a year. These are connected because HIV makes people susceptible to other diseases, and allows TB to grow in the body.
  100. What feature makes a person not susceptible to HIV?  How common is this?  How does this impact possible
    A mutation that makes the CCR5 protein smaller, denying HIV access to a cell. This is not very common, approximately 1% of all caucasions. This directs treatment towards gene therapy and figuring out how to manipulate cells to not let the HIV virus into the cell.
  101. What is the fundamental difference between a
    eukaryotic cell and a prokaryotic cell? 
    What are some characteristics that bacteria have that eukaryotes lack
    The fundamental difference between eukaryotic cells and prokaryotic cells is the fact that eukaryotic cells have a nucleus and membrane bound organelles, and prokyarotes do not. Bacteria cells have plasmids, flagellum, and capsules, and eukaryotic cells lack these.
  102. Describe the physical structure of a biofilm, and some characteristics organisms in
    a biofilm possess.
    A biofilm is a community of microorganisms. An EPS is formed which allows microbes to stick easly to a surface. Microbes then reproduce and continue to secrete polymers. Different types of cells will differentiate throughout the matrix. Fast growers are usually on the outside, and slow growers are on the inside, having to do with nutrient availability. Organisms in a biofilm are protected from harmful agents, like UV light, antibiotics and antimicrobial agents.  Cells are also to communicate with each other as well as share nutrients.
  103. What are the three domains of life? 
    Which contain prokaryotic organisms?
    Three domains are Bacteria, Eukaryota, and Archaea. Bacteria and Archaea contain prokaryotes.
  104. Describe the genetic methods used to distinguish and identify unknown microorganisms. Describe the biochemical approaches.
    Genetic methods used are sequencing genome of the organism and comparing it to a known register. Biochemical methods include using different type of media to differentiate microorganisms, such as EMB plates to differentiate gram positive and negative cells.
  105. What is the difference between the gram negative cell wall and the gram
    positive cell wall?
    The gram positive cell wall has a plasma membrane and an external petidoglycan layer. Gram negative cell walls have a plamsa membrane, a periplasmic space that contains a small peptidoglycan layer, then an outer lipid bilayer membrane on the outside that contains LPS.
  106. What purpose does the cell wall serve for bacterial cells? Explain turgor pressure and why it is an issue for living cells.
    Turgor pressure is the pressure placed on the inside of the cell wall from osmosis. If bacteria did not have a cell wall to maintain form, they would explode, lysing.
  107. What are the chemical constituents of peptidoglycan? What part of the macromolecule is responsible for cross-linking? What is pseudomurein?
    Peptidoglycan is composed of N-acetyl glucosamine and N-acetyl muramic acid building blocks. The cross linkers are conected to NAM and are D-amino acids in G negative and penta glycine in G positive. Pseudomurein is the cell wall component in Archaea, and has a different sugar building block than NAM
  108. What is the significance of the outer membrane of gram negatives? What purpose does it have for the cell? What is the space between the membranes called?
    The outer membrane of the gram negative bacteria is another lipid bilayer which is semipermeable to most molecules. It has porin channels which allow select molecules in. This helps to protect the cell from outside toxins such as antibiotics. The space between the membranes is called the periplasmic space, which is where nutrients are stored/used.
  109. What part of the gram negative cell is endotoxin?
    LPS - Lipopolysaccharide, and more specifically, Lipid A portion of it.
  110. How do bacterial flagella work? How do they relate to chemotaxis?
    Flagella rotate like a propeller on a boat. Depending on how they rotate is how the cell moves. If it rotates counterclockwise, the cell will move forward in a run. If it moves clockwise, the cell will tumble in place. The rotation is generated by the flagellar motor. This is related to chemotaxis because the bacteria will run for longer periods either towards or away from a chemical, depending on if it is helpful or harmful.
  111. What are some of the functions of glycocalyx or exopolysaccharide? How can we detect the presence of a polysaccharide capsule around a bacterial cell?
    Helps to trap nutrients and adhere to surfaces. Creates a biofilm which bacteria can live in, also gives antibiotic resistance, and protection against environmental stresses. We can detect the presence of a capsule through antibody staining and microscopy. You can also use a regular stain, and the capsule will appear to be a clear halo around the cell.
  112. Why do some bacteria form endospores?
    Endospores are formed when there are environmental stressors. This is done in Gram positive bacteria.
  113. What is the mechanism of bacterial replication? What are some aspects of the DNA replication process that are similar and what are some that are different between bacteria and eukaryotes?
    Divide cytoplasm in two, replicate DNA, Partition proteins, cofactors and substrates, and divide into two separate cell. Bacterial DNA is mostly circular. Unlike eukaryotes, DNA in bacteria only has one origin of replication. Replication is bidirectional. After the two forks meet, two copies of the original are released. DNA gyrase relieves tension as the DNA unwinds and prevents supercoiling. Has leading and lagging strands. Polymerase I Removes RNA primers and fills in gaps. Polymerase III Catalyzes most of the DNA synthesis.
  114. What are the three sources of energy for microorganisms in the environment?
    Light, organic compounds, and inorganic compounds.
  115. What are bacteria called that prefer High temperatures? Low Temperatures? Acidic environments? High levels of salt?
    Thermophiles or Hyperthermophile, Psychrophile, acidophile, Halophile.
  116. What is the difference between a photoautotroph and a photoheterotroph? What is a chemoheterotroph? Which of these types of microbe is mostly likely to be present in your gut?
    Photoautotrophs use light to synthesize energy and can use inorganic compounds. Photoheterotroph's have to use light and organic compounds outside themselves. Chemoheterotrophs use chemicals and organic compounds outside themselves, and would most likely find chemoheterotrophs in our gut, because light is not needed, and there is no light in our gut.
  117. What is the ecological significance of cyanobacteria?
    Cyanobacteria are one of the main oxygen producers on the planet, keeping oxygen in our atmosphere and fixing CO2. 
  118. If you isolated bacterium from slightly acidic soil outside your house, under what conditions of temperature and pH would you expect it to grow best? What if you isolated it from your throat?
    I would expect the bacterium to grow in an environment that is neutral acidity ( between 8.5 and 5.5 pH ,most likely around 7, and a temperature of approxmately 40-45°C. If i isolated i from my throat, I would expect it to grow optimally at 37° C and a pH of 7.35-7.45
  119. What atom makes up the largest percentage of the "dry weight" of a microorganism? What other nutrients might a microbe need?
    Carbon makes up the highest percentage of dry weight. Microbes also might  need nitrogen, sulfur, and phosphorus, along with other inorganic trace elements such as zinc, iron, copper, molybdenum. 
  120. If a bacterium cannot tolerate the presence of oxygen gas, what is it called? What about a bacterium that survives just fine in the presence or absence of oxygen?
    Obligate anaerobes. Facultative anaerobe.
  121. What are the enzymes that get rid of reactive oxygen species called? Which of the two organisms mentioned above would lack these enzymes?
    Catalases and Superoxide dismutases. Obligate anaerobes would lack both of these. 
  122. What are the two modes of bacterial culture in the laboratory?
    Batch and continuous culture. Batch is just on an augur plate/pour plate, continuous has a continual infusion of nutrients in order to keep bacteria alive. 
  123. What is the difference between defined and undefined media?
    Defined media has an actual breakdown of all the nutrients and how much there is. Undefined media will not give you a specific breakdown, such as "beef extract" instead of the chemical components. 
  124. Describe the four phases of growth in bacteria in culture. What equation is used to describe this growth, and what number is used to describe the growth rate?
    • Lag phase - where cells take time to adjust to their new environment, just after innoculation. 
    • Log/exponential growth phase - maximal growth rate. 
    • Stationary phase - number of cells is steady
    • Death phase - rate of death > cell division rate. 
    • N=Noe^kt
    • K = growth rate
  125. What types of industrial processes are microbes involved in? What is the microbial role in food processing? Sewage treatment?
    Food making and sewage treatment, as well as medicine. Yogurt, beer, wine and cheese are all made by microbes. Aerobic and anaerobic processes. Microbes digest the waste in sewers.
  126. Describe how you might do an enrichment and isolation experiment to identify an organism that can degrade atrazine (common herbicide use in agriculture that can be a carbon and nitrogen source). Where would you go to find this organism? How would you verify it? How would this change if you were enriching for an organism that tolerates high levels of uranium?
    We would find the the bacteria in an agricultural setting. Then you would use a defined media that had a carbon and nitrogen nutrient source, and enrich those cultures by diminishing other resources and maintaining carbon and nitrogen. I would change this for uranium by taking the bacteria by placing it in higher and higher levels of uranium in order to find the bacteria that live in Uranium.