Micro (BIO 246) Week 1 Notes and Reading Outline
Micro (BIO 246) Week 1 Notes and Reading Outline Bio 246
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This 10 page Class Notes was uploaded by Julianna Umbehr- Notetaker on Friday August 28, 2015. The Class Notes belongs to Bio 246 at University of North Carolina - Wilmington taught by Dr. Kiser in Summer 2015. Since its upload, it has received 234 views. For similar materials see Microbiology in Biology at University of North Carolina - Wilmington.
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Week 1 Notes and Supplemental Reading Outlines Microbiology BIO 246 Kiser August 20 2015 11 Microbiology The study of small living things or microorganisms 2 mm is the visual capability of the eye Microbes are smaller than 2 mm Micro millionth A micrometer um 10 quot 6 Nano billionth A nanometer nm 10 quot 9 12 Discovery of Microbes 16605 Robert Hooke used a microscope to describe cells 16705 Antonie van Leeuwenhoek Used microscope to see microbes single cell organisms from puddle water He noticed they were living because of their movement and called them quotanimalculesquot 18605 Louis Pasteur Discovered the importance of microbes Performed the swan neck flask experiment using an exposed flask and an intact flask In the exposed flask he noticed microbial growth 0 Created the term quotpasteurizationquot in his beer fermentation experiments Wanted to keep beer from spoiling He figured out that yeast was converted to alcohol Proposed the idea of boiling the beer before storage so microbes would be killed off and therefore could not spoil the beer 0 Biogenesis The idea that life can only come from other life Late 18005 Robert Koch Discovered anthrax cattle disease was caused by a soil bacterium called quotbacillus anthracis o Etiology The cause of a disease quotEtiologic agent 0 Epidemiology Studying disease trends in populations August 25 2015 12 Continued Septicemia the 10 top killer in the US Bloodstream infection Causes could be due to drugs antibiotics more invasive procedures in hospitals Our access and improvements in health care actually create more problems There are unintended consequences in technology Microbes are ubiquitous they are in food water soil In our bodies there are more bacterial cells a 101 ratio then our own cells However only a small percentage are disease causing Normal Flora normal inhabitants in the body take up space and outnumber invaders so there is no room for bad bacteria to colonize These are the good bacteria that we cannot live without 0 Ex there is good bacteria in our digestive track to aid digestion People without these good bacteria due to long term antibiotic use etc in their digestive track can get a CDiff Infection The treatment is having other healthy people donate their feces which is full of good bacteria which must be entered into the infected person s body by means of oral or nasogastric tube or rectal insertion 0 Good microbes can be found in alcoholic beverages tasty foods vaccines fuelbiofuel and as a helpful oil spill chemical waste cleanup tool 13 Prevention Treatment of Microbial Disease 0 1840s Ignaz Semmelweis Hungary Found that mothers who gave birth in the hospital with help of a doctor had more infection in their babies known as quotchildbed fever Mothers who gave birth with the help of nurses and midwives had much lower rate of infection 0 Realized the doctors were actually medical students who would handle cadavers and immediately aid a childbirth within the same hour without cleaning their hands whereas nurses and midwives did not do any dirty work beforehand 0 At the same time as Semmelweis Oliver Wendell US found that home deliveries had less infection rate versus hospital deliveries o The relationship between and importance of hand hygiene and infection 0 1860s Joseph Lister Medical Aseptic Technique used carbolic acid spray on and around a patient during surgeries to prevent microbial entrance to the patient s body 0 Modern day Surgeons use sterilization gloves masks goggles gowns and one timeuse tools for patients to prevent spread of infection 0 1790 Edward Jenner created the first vaccine Used a weak disease cowpox on a small boy then introduced a deadly disease smallpox to the child afterwards to see if the body built immunity against the disease and it did The boy lived o 1920 Alexander Fleming discovered the first antibiotic penicillin Observed a mold killing staph bacteria and saved many lives at war 0 MRSA Methicillin Resistant Staphylococcus Aureus The overuse and misuse of antibiotics has led to the emergence of antibiotic resistant quotsuperbugsquot These antibiotic resistant infections keep adapting and changing to the new antibiotics being used and keep becoming more and more resistant to our efforts to stop them 14 Cells and Microbes o A cell is the smallest unit of life 0 Cell membrane made of lipids which have a hydrophobic tail and polar head repel water and separate the inside of the cell from the extracellular matrix Contain proteins for transport regulation communicating and signaling I The extracellular matrix contains substrates that are used with enzymes 0 Cytoplasm Contains water salts amino acids nucleotides carbs and vitamins I Energy ATP is used in the cell and created by the mitochondria I DNA 9 RNA 9 Protein 0 Genes RNA is made first by copying the strands of DNA The RNA has a list of amino acids Ribosomes read these amino acids sequences and combine for protein synthesis These proteins function for metabolism transport communication homeostasis growth and reproduction I Prokaryotes No nucleus no organelles no intracellular organization Ex Bacteria archaea I Eukaryotes true nucleus has organelles compartmentalized organization Ex animals plants fungi protists 0 Evolution Biodiversity There are many different forms of life 0 22 billion years ago living organisms learned how to use the most abundant source of energy SOLAR Photosynthesis began o Shortly after about 18 billion years ago eukaryotes appeared o Are viruses living 0 Why yes I Have genes DNARNA carbs lipids they reproduce are infectious 0 Why not I They are dependent on a host for reproduction have no metabolism no synthetic machinery o Taxonomy 3 domains 0 Bacteria Archaea Eukarya AUGUST 27 2015 Taxonomy Carl WoeseFox System Used genetic techniques to identify archaea as a unique domain of life in 1977 Made a tree of life based upon genetic phylogeny How is life classified 3 domains 0 Domain Bacteria ex Cyanobacteria 0 Domain Archaea Methane producers contain prokaryotes than live in extreme salt and in extreme heat Actually more like eukaryotes then prokaryotes 0 Domain Eukarya ex plants animals fungi They are different from one another 0 Domain Kingdom Phylum Class Order Family Genus Species o Genus and Species I Ex Escherichia genus capitalized coli species lowercase I Strains small differences can be very influential 0 Laboratory Strain E coli K12 harmless o Pathogen E coli 0157H7 fatal causes blood in diarrhea o S aureus MRSA resistant strain or MSSA sensitive strain 31 Bacteria o Prokaryotes are simple cells without a nucleus 0 Heterotrophs feed on organic substrates Decomposers and pathogens Some are intracellular parasites that invade cells They produce enzymes that digest material absorb nutrients and use them as energy 0 Autotrophs selffeeders utilize inorganic substrates Ex photosynthetic cyanobacteria Do not typically cause disease in humans Often use photosynthesis o All bacteria cells have cell membrane cytoplasm ribosomes DNA in a nucleoid region NO nucleus 0 Some bacteria have cell wall flagellum fimbria plasmid pilus actin cytoskeleton 32 Surface Structures 0 Flagellum singular flagella plural means whip 0 Made up of subunits of protein called flagellin 0 Attached to the body of cell by quotbasal body which has rotation and SPINS like a propeller to mobilize the cell I Chemotaxis Movement of a cell in a direction of a favorable chemical stimulus Cells can sense and are dictated by chemical gradients of food or other necessities and move toward them The bacteria are influenced to move by the need for food and by the need to get away from toxins predators or pHtemperature changes negative chemotaxis o Flagella classification I quotAtrichousquot without flagella These bacteria move by relying on quotcurrentsquot outside forces that cause the movements They are immobile They can also attach themselves to something that does move 0 Monotrichous 1 flagella o Lophotrichous all flagella at one pole of the bacteria 0 Amphitrichous flagella are at opposite poles of the bacteria 0 Peritrichous Flagella surround or cover the surface 0 Uropathogenic E coli UPEC Causes UTI s when transferred via fecal contamination into urethra The strain has no flagella in the bladder but does so in the ureters I Produces flagella because it must fight gravity and peristalsis in the ureters I Advantages of not having flagella conserves energy why use energy whipping around a tail when it is unnecessary o Periplasmic Flagella or Axial Filaments When the flagella are wrapped around a cell These spirochetes move with a corkscrew like motion I Ex Treponema Pallidum Syphilis an STD where the bacteria corkscrews into the epithelium and causes infection 0 Fimbria singular fimbriae plural Means fringe 0 Made up of subunits of a protein called pilin 0 Used for attachment and colonization Attachment is specific to epithelial tissues I Colonization Gonorrhea STD urethral vaginal anal pharyngeal throat due to oral sex Inside of the urethra vaginal tract is susceptible where things like bacteria stick to the surface of any epithelial tissue 0 Pilus singular Pili plural Means hair 0 Made up of pilin subunits 0 Mostly used in attachment and colonization 0 Type IV Pilus Crawls for motility Has a twitching motion Looks like it quotthrows a rope out in front of itself then jumps forward Then it grows a new pilus 0 Sex Pilus Tube that connects similarly related bacterial cells and transfers material This process is called conjugation A copy of a piece of DNA is sent and is called a plasmid separate from main chromosome I Plasmid DNA can carry resistance gene R factor Resistance develops and then spreads easily between bacterial cells 0 Glycocalyx Means quotsugar coat Are polysaccharides o Slime Layer excreted by the cell covers the cell and neighboring area 0 Capsule Distinct layer around the cell related to cell organization I Slime Layer and Biofilms streptococcus mutans coverts sugars to polysaccharides and attach to tooth surface then salivawater cannot wash it off Bacteria stick to sticky surfaces and it becomes the plaque you find on your teeth It must be removed because they release organic acid that corrodes the enamel on your teeth and causes cavities or calculus I Staphylococcus Epidermidis A skin bacterium that can form biofilms on IV catheters Slime layer is attached to IV Catheter then enter your bloodstream and begin circulation Biofilm on catheters will remain until removed Antibiotics cannot penetrate the layer of polysaccharides quotCapsular polysaccharide anti phagocytic Supplemental Reading Outlines 1 Lemon Bacteria a Anne Loving did an experiment on lemons served in drinks in restaurants She took swabs of the rind and swabs of the pulp on 76 lemons at different restaurants and analyzed for microbes i 25 different germs were found on 5376 lemons sampled Some of the germs included fecal matter and saliva ii 29 had germs on both the rind and pulp In 15 instances the germs on the pulp differed from the germs on the rind indicating the lemons touched contaminated surfaces after they were cut 2 Bacteria in Ice a Jasmine Roberts 7th grader conducted an experiment that showed that ice in some fast food restaurants contains more bacteria than toilet water from the same restaurants i Toilet water contained less bacteria 70 of the time ii 35 samples tested positive for fecal matter or E coli 3 5 Second Rule a Jillian Clark conducted an experiment about people using the 5 second rule about dropping food on the floor and eating it She dropped food on tiled and carpeted floors contaminated with salmonella and E coli and discovered that before the 5 seconds were up the food had been contaminated i To test how long the bacteria live on these surfaces she did an experiment and found that after 24 hours of exposure to air thousands of bacteria per cmquot2 had survived on the tile and wood and tens of thousands on the carpet Hundreds of salmonella were still alive after 28 days ii On surfaces that had been contaminated 8 hours earlier slices of bologna and bread left for 5 seconds gained from 150 to 8000 bacteria iii For 1 minute slices collected about 10x more than that from the tile and carpet iv Quickly grabbing the food does therefore mean LESS bacteria but you should still consider where you dropped the food and how long it was sitting there 4 Gas Pumps a KimberlyClark swabbed many surfaces found that gas pumps are the filthiest surfaces Americans touch followed by public mailboxes escalator rails and ATM buttons i Germs from people s hands can transfer 7 times before leaving the skin so handwashing often is very important 5 Shopping Carts a Of the 85 carts examined in this study 72 contained fecal material b When examining 36 of the carts there was E coli on 50 of them c Shopping carts are not routinely wiped and people should wipe them down before placing their children into them CHAPTER 2 OUTLINE Tools of the Laboratory 21 How to Culture Microorganisms o The 5 I s basic techniques to examine microbes o Inoculation Growing or quotculturingquot microorganisms is introducing a sample into a container of nutrient medium which gives them an environment where they can multiply Equipment must be sterile People can analyze specimens from body fluids or from natureinanimate objects 0 Incubation This is placing the container of medium in a temperature controlled chamber to encourage multiplication normally 2045 C Controls gases in the chamber Can range from one day to several weeks Makes it able to observe macroscopically I Media are helpful for culture growth Classified by 3 properties physical state chemical composition and functional type purpose 0 Physical Liquid semisolid solid can be liquidated solid cannot be liquidated Ex Agar is an important and useful complex polysaccharide 0 Chemical Chemically defined media are called defined or quotsyntheticquot Have organic and inorganic compounds Are standardized and reproducible Not chemically defined media are quotcomplexquot Ex blood serum meat extracts 0 Functional o Generalpurpose media grow a broad spectrum of microbes they are complex media Ex brainheart infusion Enriched Medium has complex organic substance like blood serum growth factors and are useful in growth of pathogens that are present in small numbers Bacteria that need growth factors are fastidious o Selective and differential media are used for specific microbial groups useful in isolation and identification A selective medium has one or more agents that inhibit the growth of certain microbes but not others Differential Media allow multiple types of organisms to grow but show differences in how they grow size color bubbles A single medium can be both selective and differential allow isolation and identification at same time Dyes are used as differential because they are pH indicators 0 Miscellaneous Media A reducing medium contains substance that absorbs 02 reducing its availability important for growing anaerobic bacteria O I Carbohydrate fermentation Media contains sugars that can be converted to acids and pH indicators I Transport Media maintain and preserve specimens that have to be held for time before clinical analysis I Assay Media test effectiveness of antimicrobial drugs check effect of disinfectants antiseptics cosmetics etc I Enumeration Media count the number of organisms in milk water food soil etc Isolation If an individual bacterial cell is separated from other cells given nutrients amp large volumemedium it will grow into a colony f formed from a single cell colony has just that species alone Includes spread plate and streak plate methods lnspection Identification Microscopic appearance differentiates bacterial cells from eukaryotes and can pick out genusspecies of eukaryotes Biochemical tests are used to determine fundamental chemical characteristics such as nutrient requirements products emitted during growth enzyme presence and ways they derive energy 22 The Microscope o Microbial Size microorganisms fall within a range of micrometers 10 quot 6 pm and nanometers 10quot 9 nm 0 Magnification and Microscope Design Microscopes have the following parts ocular eyepieces body nosepiece objective lens mechanical stage diaphragm control base with light source arm coarse focus adjustment knob fine focus adjustment knob stage adjustment knobs 0 Principles of Light Microscopy 3 qualities Magnification resolution contrast 0 Magnification 2 phases The objective lens closest to specimen forms initial image called the real image The image is projected to the ocular lens or eyepiece and forms a second image called the virtual image which is what you see with your eye I The magnifying power normally ranges from 4x to 100x and the power of the ocular is usually 10x The total power product of power of 2 lenses 0 10x low power objective x 10x 100x 0 40x high dry objective x 10x 400x 0 100x oil immersion objective x 10x 1000x Resolution resolving power Capacity of an optical system to distinguishseparate 2 objects or points from each other Human eye can resolve points as long as objects are not closer than 2 mm apart A few bacteria and most viruses are too small for resolution and need an electron microscope rather than a light microscope Contrast The refractive index is the degree of bending that light undergoes as it passes from one medium such as water to another medium such as bacterium The higher the refractive index the sharper the contrast The iris diaphragm controls amount of light entering condenser to better the contrast Different Types of Light Microscopes Optical microscopes are characterized by nature of their field 4 types Bright field Darkfield Phasecontrast and Interference There is another called the Fluorescence microscope uses UV rays Another called the Confocal microscope uses a laser beam 0 BrightField Most common light is transmitted through specimen Used for both live unstained specimen and preserved stained material 0 DarkField Basically a brightfield but with an added stop to condenser that blocks the light except for the light reflected off sides of specimen Gives an image of an illuminated specimen with a dark field behind it Used for viewing living cells that cannot be stained o Phasecontrast Contains devices that transform the subtle changes in light waves passing through specimen into differences in light intensity Patterns coming from different regions of the cell denser than others will vary in contrast Useful for intracellular structures of cells 0 Differential Interference DIC shows detailed view of unstained living specimen by changing light Has 2 prisms that add colors to image and 2 beams of light instead of one Vividly colorful and appear 3D 0 Fluorescence UV ray illumination Use of dyes and minerals that show fluorescence Dyes emit light when hit with UV rays Useful in diagnosing infections caused by bacteria protozoan viruses 0 Confocal Laser beam of light to scan depths and gives a sharp image of one single plane Used on fluorescently stained specimen also used to visualize live unstained cellstissue 0 Transmission Electron Microscope TEM for viewing detailed structure of cells and viruses Transmits electrons through specimen that are extremely thin and stained 0 Scanning Electron Microscope Dramatic and realistic images Extremely detailed 3D view of a range of objects SEM covers specimen with electrons and scans it over and over They are vivid with color 0 Preparing specimens for Microscope depends on condition of specimen living or preserved goals of examiner observe overall structure identify microorganisms see movement and type of microscope available Living Preparations placed in wet mounts or in hanging drop mounts Suspended in a fluid that maintains viability and provides space for movement Provide true assessment of size shape arrangement color motility of cells Fixed Stained Smears Permanent mount for long term study Spreading thin film made from suspension of cells and air drying it then heating and killing the specimen and securing it to the slide Stains applies colored chemicals called dyes to specimens Can be classified as basic cationic dyes with a positive charge or acidic anionic dyes with a negative charge Negatively charged cell parts will attract basic dyes and positively charged parts will attract acidic dyes 0 Negative versus Positive Staining A positive stain is where the dye sticks to the specimen and gives it color and a negative stain is where the dye does not stick but settles a distance from its outer boundary and forms a silhouette Value of negative staining is simplicity and reduced distortion of cells 0 Simple versus Differential Staining Positive staining methods are simple differential or special Simple stains require a single dye and uncomplicated procedure but cause all cells in a sample to be the same color Differential stains use different colored dyes called the primary dye and counterstain to distinguish between cell parts these are more complex Types include Gram acidfast endospore stains o Gram Make infectious bacteria more visible Bacteria that stain purple are grampositive stain red are gramnegative Differences in Gram stain are due to structure of cell wall 0 Acidfast stain acidfast pink and nonacidfast blue detects Myobacterium tuberculosis in specimens 0 Endospore Distinguishes between endospores and the cells they come from called vegetative cells Ex Bacillus and Clostridium o Capsular Straining observing microbial capsule which surrounds cells of some bacteria and fungi Ex Cryptococcus o Flagellar Staining revealing flagella which are used by bacteria for movement Can identify presence number and arrangement on a cell to identify bacteria