Microbe Mission

In Microbe Mission, teams will answer questions, solve problems, and analyze data pertaining to microbes and microscopes. The event was run as a trial event before being made an official event in 2011 and 2012. It is returning for the 2017 season.

If you are interested in helping by improving the Microbe Mission page(s) for 2012, see this page.

The Stations
If there are stations, there will be 8-20 of them. They will be marked with roman numerals (I, II, III...) or they will be numbered (1, 2, 3...). There will be sections in the test corresponding to each of the stations with questions (the format of which is decided by the tester, and can vary widely from tester to tester). Students typically have a time limit at stations (i.e. 5 minutes per station, then rotate).

The Test
The test will pages/sections corresponding to the individual stations (if there aren't stations then it will be a normal test). It will have blank lines for you to record your answer. There will be no questions/diagrams in the packet, so all work must be done at the corresponding station. At some competitions, the questions will be at the station. All answers must be recorded in the packet. Spelling does count in the packet. Points may also be taken away if the packet is not neat or legible. As you record your answers, make sure that you are recording on the right page/section/question. This may save you time and effort.

Please note that there may be lines for your team name, team number, or the participants' names on each page. No matter what, ALWAYS make sure you fill out that information on each page. If you don't, points can be taken off.

Materials
Each participant must bring Z87 chemical splash goggles and a writing implement. They may bring a non-programmable, non-graphing calculator and a 2-sided 8.5" x 11" page of notes which can contain any information in any form, including diagrams, from any source.

No other resources will be allowed. Students should remember all diagrams and study material. Make sure you print the guides to this event in the event info on soinc.org.

Preparing for This Event
Make a binder! This will help you tremendously in preparing for this event. Even though you can't bring it in, it's a great way to keep all your information in the same place and to remember it.

With your notes page, include pictures and charts of things you need to remember. Also remember how your page is laid out and where you put everything. In a timed test, trying to find things on your notes page is a waste of time.

If you can acquire an AP Biology textbook, it will help tremendously with learning terms and concepts.

It is also very helpful to practice, because the type of questions can vary widely from test to test. Practice tests are extremely helpful in preparing for this event.

Tips for Making the Note Sheet


 * Use as small of a font as you can. Go as small as you can, but make sure to keep it readable. There's no point in having volumes of information if you can't even interpret it.


 * Make your own diagrams, either by hand or with an image manipulation program (paint).


 * Color code. Use a different (readable) color for notes on each system. This will make things easy to find at competition day. Also color-code your diagrams if you can for maximum efficiency (as seen in the picture above). It's much easier to find a bright orange muscle than one outlined lightly in black. Keep the coding consistent so that by the end of the season you automatically associate a color to a type of information (ex: pink = muscles; blue = respiratory; green = endocrine and etc.) Hi-lighting will save you alot of time at competition.


 * Type your sheet up, then hand-write extra notes in the margins. You can write in places where the printer might not be able to print. This is time consuming but well worth the time spent.


 * Source-check before doing anything. The last thing you need is to realize you put incorrect info on your note sheet, then have to do it all over again.


 * Use space efficiently by prioritizing. Include the things you have the most trouble remembering first. Extra information can be added later if you have room.


 * Use charts, as they are life-savers.You can make your own chart with specific information you need - the simple act of making a chart can help tremendously to maximize space. Making your own charts can also help you get a better understanding of it too.


 * Laser printers are recommended if your font is that small. Font sizes can be reduced manually if you treat text like a picture (by typing it onto an image manipulation program and then shrinking the image), though this may reduce the readability of your notes.


 * Please communicate with your partner (if you have one). This is vital in every event. You do not want to be the only person on your team who knows how the sheet is laid out - if this happens, during the test your partner will be asking you continuously where things are, which will be distracting. If you don't trust your partner enough to make the note sheet, at least show it to them/take a practice test with it so they can familiarize themselves with it.


 * A good font for your Microbe Mission notes (actually for any event that lets you bring notes) is BenchNine, in either 6 or 7 font size, depending on which one you and your partner can read better.

Covered Information
You will be tested on topics relating to microbiology, ranging from different types of microscopes and microbes to learning about cell structure and uses for microbes. You will also be tested on being able to read a dichotomous key and understanding the principles of microscopy.

Prions
Prions (proteinaceous infectious particles) are infectious proteins that are responsible for a class of diseases known as the Transmissible Spongiform Encephalopathies, which are neurodegenerative diseases including Mad Cow Disease and kuru. Prions destroy the tissue of the nervous system, forming holes in the brain and nervous systems. Prion diseases all involve modification of the prion protein, a normal part of mammalian cells. They are also all fatal and rapidly progressive. Like viruses, prions cannot replicate on their own and rely on other organisms. Unlike other microbes, prions do not contain nucleic acids. Prions are thought to have originated from ZIP proteins.

Viruses
Viruses are microorganisms much smaller than bacteria that invade other cells in order to replicate. Viruses are responsible for a variety of diseases, such as chicken pox. The origin of viruses is unclear; some may have come from plasmids (pieces of DNA that can travel between cells) or transposons (pieces of DNA that can move themselves to different places in a cell's genome) while others may have evolved from bacteria.

Some viruses, known as bacteriophages, infect bacteria. Their appearance is often compared to that of an alien landing pod. Typically, their genome is composed of DNA rather than the RNA of retroviruses. Other viruses, most famously Sputnik, infect other viruses. These are known as virophages.

Viruses can be cause either lytic or lysogenic infections. In a lytic infection, the virus injects its genome into the host cell, which cannot differentiate between viral DNA and its own DNA. The cell begins to make mRNA from the viral DNA, which is then made into viral proteins that destroy the cell's DNA. When the cell eventually shuts down, the virus continues to use the cell to replicate. Enough viruses are made to cause the cell to burst, or lyse. Hundreds or thousands of released viruses then go on to infect other cells.

In a lysogenic infection, a virus integrates its DNA into the host cell's DNA. This viral DNA is known as a prophage. The propahge remains dormant in the cell's DNA for several generations before becoming active, leaving the cell's DNA, and directing the synthesis of new viral proteins. HIV, which causes AIDS, is a lysogenic virus.

Cellular Microbes
Cellular microbes are microbes that are made up of cells. Their are two main types of cellular microbes; prokaryotes and eukaryotes. Prokaryotes differ from eukaryotes with their lack of nuclei and membrane bound organelles.

Bacteria
Bacteria are single-celled, prokaryotic microorganisms. Some bacteria are beneficial to humans while others are pathogenic, but a majority of bacteria are harmless to humans. Pathogenic bacteria are responsible for a variety of diseases including strep throat and tetanus. Bacteria come in 3 shapes: coccus(circular), bacillus (rod-shaped), and spirillum (spirally). Bacteria originate from the single-celled organisms that were the first to inhabit the Earth.
 * Note: The bacterial shapes are only necessary to remember for division C, although it is always helpful to know them.

Organisms are often classified by their source of energy and source of carbon. Bacteria may be photoautotrophic, utilizing photosynthesis to produce food and oxygen and using carbon dioxide as their source of carbon. This category includes purple and green sulfur bacteria. They may also be chemoautotrophic, making food using the energy from chemical reactions and using carbon dioxide as their source of carbon - these bacteria serve an important role in the nitrogen and sulfur cycles. The two other types are photoheterotrophs (including purple and green non-sulfur bacteria) and chemoheterotrophs (including most bacteria, animals, fungi, and protozoa). Motile bacteria may utilize rotating flagella to move, or they may secrete slime to slide around like a slug. Bacteria may also be nonmotile.

Archaea
Archaea are a group of single-celled microorganisms that were previously thought to be bacteria. Archaea are prokaryotes. Their origin and potential for causing disease are currently unclear; however, archaea are thought to be ancestors of eukaryotes or very close descendants because of their many similarities, including genes and inclusion of enzymes in translation and transcription processes. Unlike bacteria, no known species of archaea form spores.

Archaea are capable of living in extreme habitats and anaerobic environments. They are extremely tolerant to heat, acid, and toxic gases. Archaea are variously involved in the carbon and nitrogen cycles, assist in digestion, and can be used in sewage treatment.

Fungi
Fungi are eukaryotic organisms that can be single-celled or multi-celled. Fungi have cell walls composed of chitin, unlike the cellulose walls of plants. Fungi are heterotrophic and do not have chloroplasts like photoautotrophs. They grow best in slightly acidic environments and can grow in areas of low moisture. Technically, fungi are more closely related to animals than they are to plants and likely shared a common ancestor with animals. Fungi are responsible for diseases such as athlete's foot. Baker’s yeast (a fungi) is used for bread and brewing. Some fungi are used for antibiotics and others are important decomposers in the ecosystem.

Protists
Protists are eukaryotic but do not have specialized tissues. Algal protists are similar to plants and can go through photosynthesis, but do not have cuticles that prevent water loss. As a result algal protists must live in water. Animal like protists are called protozoa and are eukaryotic and heterotrophic. These protists consume other protists and bacteria for food. Some have two nuclei: the macronucleus and the micronucleus. Many move with cilia, flagella, or pseudopodia (in the case of amoebae). They also have complex life cycles. For example, they may exist in a trophozoite, or feeding, form. They can also change into a dormant form known as a cyst, which can help in reproduction.

Endosymbiotic Theory
Championed by Lynn Margulis in the 1960s, the endosymbiotic theory holds that mitochondria and chloroplasts in eukaryotic cells originated from proteobacteria and cyanobacteria, respectively. Evidence for this theory includes that mitochondria and chloroplasts divide through binary fission, not mitosis like the rest of the cell. These organelles, which are the same size as bacteria, also have their own different, circular DNA, their own ribosomes and two membranes. The two membranes have different chemical compositions, with the outer being similar to the eukaryotic plasma membrane and the inner being similar to bacterial membranes. Chloroplasts in some algae have cell walls of peptidoglycan.

Microbial Growth Curve


When microbes (bacteria) are put in a favorable environment, they usually follow a characteristic pattern of growth. This is represented using the microbial growth curve.


 * Lag Phase

*During the lag phase of the microbial growth cycle, cells are maturing for doubling; synthesis of RNA, enzymes, etc. Therefore, lag phase in the microbial growth curve is represented by the initial horizontal line.


 * Exponential Growth Phase

During the exponential growth, the microbial population undergoes constant doubling. The more "favorable" conditions are, the longer the slope will be, and the faster the growth, the steeper the slope. This is the phase which generation time can be calculated as well.


 * Stationary Phase

The stationary phase is another flat potion of the microbial growth curve where it appears that there is no significant increase in the number of cells; showing a stabilization of the population. This is due to the fact that the amount of dying cells is equal to the amount of new cells.


 * Decline or Death Phase

Unless the microbes have an infinite source of nutrients, the microbes begin to use up all of the surrounding resources and the waste products begin to pile up. This leads to an unfavorable environment which causes the amount of dying cells outnumber the amount of new ones.

Gram Staining

 * This topic is only tested in Division C.

Gram staining is a type of differential staining, meaning it separates bacteria into two different groups (Gram-positive and Gram-negative) based on their reactions to the procedure. Because of widely varying responses, Gram staining cannot be performed on archaea.

The first step in the procedure is to heat fix the bacteria; then, those bacteria are stained with crystal violet, the primary stain, for one minute. In an aqueous solution, crystal violet disassociates into CV and Cl ions, which penetrate through the cell wall. CV ions react with negatively charged particles in bacterial cells and stain them purple.

The third step is to apply iodine as a mordant, or trapping agent, for one minute. It reacts with the crystal violet and prevents removal of the purple stain. After the remaining iodine is rinsed away, alcohol decolorizer (sometimes acetone) is added until the primary stain is removed in Gram-negative bacteria because alcohol dissolves the outer membrane. In contrast, Gram-positive bacteria retain the primary stain because it becomes trapped in their thick, multi-layered walls of peptidoglycan.

The final step is to apply safranin (sometimes basic fuchsin) as a counterstain. This gives the Gram-negative bacteria their final red-pink color.

Characteristics of Gram-Positive Bacteria
Typically, Gram-positive bacteria produce exotoxins and are susceptible to phenol disinfectants. They retain the blue-purple color of crystal violet in Gram staining because of their thicker walls of peptidoglycan. Unlike Gram-negative bacteria, they lack the periplasmic space between the cytoplasmic and outer membranes because Gram-positive bacteria lack an outer membrane. Certain types of Gram-positive bacilli, most importantly Lactobacilli (used in milk and dairy products), cannot form spores.

Characteristics of Gram-Negative Bacteria
Gram-negative bacteria have thinner walls of peptidoglycan and two membranes and periplasmic space between them. Because of the safranin counterstain, they become red-pink after Gram staining. There are many Gram-negative aerobic (oxygen-using) bacteria.

Types of Microscopes

 * Optical Microscopes: Optical microscope uses visible light (or UV light in the case of fluorescence microscopy) to sharply magnify the samples. The light rays refract with optical lenses. Dating back to the first microscopes that were invented, it is found that they belonged to this category. Optical microscopes can be further subdivided into several categories:


 * Compound Microscope: The compound microscope is built of two systems of lenses for greater magnification (an objective and an ocular: eyepiece). The utmost useful magnification of a compound microscope is about 1000x.


 * Stereo Microscope (dissecting microscope): The stereo microscope is an optical microscope which magnifies up to about maximum 100x and provides a 3-dimensional view of the specimen. Stereo microscopes are highly useful for observing opaque objects.


 * Confocal Laser scanning microscope: Unlike compound and stereo microscopes, Confocal Laser scanning microscopes are reserved for research organizations. Such microscopes are able to scan a sample also in depth. A computer can then assemble the data to create a 3D image.


 * Electron Microscopes:Electron microscopes are the most advanced microscopes used in modern science. The electron microscopes essentially function on the principle of a beam of electrons that strikes any objects that comes to its path to magnify it. Electron microscopes are designed specifically for studying cells and small particles of matter, as wells as large objects.


 * Scanning Electron Microscope: Scanning Electron Microscope is characterized as a microscope that has lower magnifying power but can provide 3 dimensional viewing of objects. The Scanning Electron Microscope captures the image of the object in black and white after being stained with gold and palladium.


 * Reflection Electron Microscope: Reflection electron microscopes are also designed on the principle of electron beams but they are characteristically different from transmission and scanning electron microscopes being that it is built to detect electrons that have been scattered elastically.


 * X-ray Microscope: An X-ray microscope uses a beam of x-rays to create an unparalleled high resolution 3D image. Due to the small wavelength, the image resolution is higher as compared to optical microscopes. The greatest useful magnification is therefore also higher and it lies between the optical microscopes and electron microscopes. X-ray microscopes hold significant importance in science and research and have got one special advantage over electron microscopes- it allows observing the structure of the living cells. It is adept at slicing together thousands of images to generate a single 3D X-ray image.


 * Scanning Helium Ion Microscope (SHIM or HeIM): Scanning Helium Ion Microscope is a new imaging technology which uses a beam of Helium ions beams to generate an image. This technology has several advantages over the traditional electron microscopes; one advantage lies in the fact that the sample is left mostly intact (due to the low energy requirements) and that it provides a high resolution. The first commercial systems were released in 2007.


 * Scanning acoustic microscope (SAM): Scanning acoustic microscope uses focused sound waves to generate an image. An acoustic microscope has a wide range of applications in materials science to detect small cracks or tensions in materials. The scanning acoustic microscope is a powerful tool which can also be used in biology to study the physical properties of the biological structure and help uncover tensions, stress and elasticity inside the biological structure.


 * Electron Microscopes: Modern electron microscope uses accelerated electrons and can magnify up to 2 million times due to the very small wavelength of high energy electrons. The high energy electrons as a source of illumination are quite tough on the sample being observed. Because of the much shorter wavelength, the electron microscope has a higher resolving power than a light microscope. To reveal the structure of objects, it may initially acquire a long time to completely dehydrate and prepare the specimen. A sleek layer of a metal could be on the other hand used to coat some of the biological specimens for easy observation.


 * Neutron Microscope: Still under an experimental stage, Neutron microscope generates a high resolution image and may offer better contrast than other forms of microscopy. The new technology would use neutrons instead of beams of light or electrons to generate high resolution images.


 * Scanning Probe Microscopes: Scanning Probe Microscope helps visualize individual atoms. The image of the atom is computer-generated, however. It provides the researchers an imaging tool for the future where a small tip measures the surface structure of the sample. These specialized microscopes provide high image magnification to observe three dimensional specimens. If an atom projects out of the surface, then a higher electrical current flows through the tip. The amount of current that flows is proportional to the height of the structure. A computer then assembles the position data of the tip. An enhanced 3D image is generated.

Viral Diseases
Viral diseases are immune to antibiotics; therefore, vaccines are typically the best form of prevention.


 * AIDS (caused by the HIV virus)
 * Chicken Pox and Shingles (caused by the varicella zoster virus)
 * Common cold (often caused by the rhinovirus but can also be caused by coronaviruses and adenoviruses)
 * Dengue fever (caused by the mosquito-borne dengue virus)
 * Ebola Haemorrhagic Fever (caused by the ebola virus)
 * Hepatitis
 * Influenza (caused by viruses of the family Orthomyxoviridae)
 * Measles (caused by the morbillivirus)
 * Mumps (caused by the mumps virus)
 * Mononucleosis, also known as mono or glandular fever (caused by the Epstein-Barr virus)
 * Polio (caused by the poliovirus)
 * Rabies (caused by the rabies virus)
 * Rubella
 * Small Pox
 * West Nile Virus
 * Yellow Fever

Bacterial Diseases
Bacterial diseases may often be treated by antibiotics.


 * Anthrax: Anthrax is an infection caused by the bacterium Bacillus anthracis; occur in four forms: skin, inhalation, intestinal, and injection; The skin form presents with a small blister with surrounding swelling that often turns into a painless ulcer with a black center. The inhalation form presents with fever, chest pain, and shortness of breath. The intestinal form presents with nausea, vomiting, diarrhea, or abdominal pain. The injection form presents with fever and an abscess at the site of drug injection. Most people who get sick from anthrax are exposed while working with infected animals or animal products such as wool, hides, or hair. Inhalation anthrax can occur when a person inhales spores that are in the air (aerosolized) during the industrial processing of contaminated materials, such as wool, hides, or hair. Cutaneous anthrax can occur when workers who handle contaminated animal products get spores in a cut or scrape on their skin. People who eat raw or undercooked meat from infected animals may get sick with gastrointestinal anthrax . This usually occurs in countries where livestock are not routinely vaccinated against anthrax and food animals are not inspected prior to slaughter. A newly discovered type of anthrax is injection anthrax . This type of anthrax has been seen in northern Europe in people injecting heroin.


 * Botulism: Botulism is a rare and potentially fatal illness caused by a toxin, produced by the bacterium Clostridium botulinum. Botulism can be spread several different ways. The bacterial spores which cause it are common in both soil and water. They produce the botulinum toxin when exposed to low oxygen levels and certain temperatures. Foodborne botulism happens when food containing the toxin is eaten. Symptoms: Difficulty swallowing or speaking, Dry mouth, Facial weakness on both sides of the face, Blurred or double vision, Drooping eyelids, Trouble breathing. Nausea, vomiting and abdominal cramps, Paralysis


 * Cholera: Cholera is an infection of the small intestine by some strains of the bacterium Vibrio cholerae. It is spread mostly by unsafe water and unsafe food that has been contaminated with human feces containing the bacteria. Undercooked seafood is a common source. The classic symptom is large amounts of watery diarrhea that lasts a few days. Vomiting and muscle cramps may also occur. Diarrhea can be so severe that it leads within hours to severe dehydration and electrolyte imbalance. This may result in sunken eyes, cold skin, decreased skin elasticity, and wrinkling of the hands and feet. The dehydration may result in the skin turning bluish. Symptoms start two hours to five days after exposure.


 * Chlamydiasis


 * Dental Caries (tooth decay): Breakdown of teeth due to bacteria; The cavities may be a number of different colors from yellow to black. Symptoms may include pain and difficulty with eating. Complications may include inflammation of the tissue around the tooth, tooth loss, and infection or abscess formation. The cause of caries is bacterial breakdown of the hard tissues of the teeth (enamel, dentin and cementum). This occurs due to acid made from food debris or sugar on the tooth surface. Simple sugars in food are these bacteria's primary energy source and thus a diet high in simple sugar is a risk factor. If mineral breakdown is greater than build up from sources such as saliva, caries results. Risk factors include conditions that result in less saliva such as: diabetes mellitus, Sjogren's syndrome and some medications. Medications that decrease saliva production include antihistamines and antidepressants. Caries is also associated with poverty, poor cleaning of the mouth, and receding gums resulting in exposure of the roots of the teeth.


 * Gonorrhea
 * Legionnaire's Disease
 * Lyme Disease
 * MRSA
 * Peptic Ulcer Disease


 * Pertussis (whooping cough): Pertussis is caused by the bacterium Bordetella pertussis. It is an airborne disease which spreads easily through the coughs and sneezes of an infected person. The classic symptoms of pertussis are a paroxysmal cough, inspiratory whoop, and fainting, or vomiting after coughing. The cough from pertussis has been documented to cause subconjunctival hemorrhages, rib fractures, urinary incontinence, hernias, and vertebral artery dissection. Violent coughing can cause the pleura to rupture, leading to a pneumothorax (collapsed lung). The pertussis vaccine became available in the 1940s. The antibiotics erythromycin, clarithromycin, or azithromycin are typically the recommended treatment.


 * Rocky Mountain Spotted Fever: Rocky Mountain spotted fever (RMSF), also known as blue disease, is the most lethal and most frequently reported rickettsial illness in the United States. The disease is caused by Rickettsia rickettsii, a species of bacterium that is spread to humans by Dermacentor ticks. Initial signs and symptoms of the disease include sudden onset of fever, headache, and muscle pain, followed by development of rash. The disease can be difficult to diagnose in the early stages, and without prompt and appropriate treatment it can be fatal. Appropriate antibiotic treatment (with Doxycycline and Chloramphenicol) should be started immediately when there is a suspicion of Rocky Mountain spotted fever on the basis of clinical and epidemiological findings.


 * Strep throat
 * Syphilis: Syphilis is a sexually transmitted infection caused by the bacterium Treponema pallidum. The signs and symptoms of syphilis vary depending in which of the four stages it presents (primary, secondary, latent, and tertiary). The primary stage classically presents with a single chancre (a firm, painless, non-itchy skin ulceration) but there may be multiple sores. In secondary syphilis a diffuse rash occurs, which frequently involves the palms of the hands and soles of the feet. There may also be sores in the mouth or vagina. In latent syphilis, which can last for years, there are few or no symptoms. In tertiary syphilis there are gummas (soft non-cancerous growths), neurological, or heart symptoms. The preferred antibiotic for most cases is benzathine penicillin G injected into a muscle. In those who have a severe penicillin allergy, doxycycline or tetracycline may be used. In those with neurosyphilis, intravenous penicillin G potassium or ceftriaxone is recommended.


 * Tetanus
 * Tuberculosis

Fungal Diseases
The technical term for a fungal disease is a mycosis.
 * Athlete's foot
 * Dutch Elm Disease
 * Ergotism
 * Histoplasmosis
 * Potato Blight
 * Ringworm
 * Thrush

Protozoan & Algal Diseases

 * Malaria
 * Paralytic Shellfish Poisoning
 * Estuary Associated Syndrome
 * Giardiasis
 * Cryptosporidiosis

Prionic Diseases

 * Scrapie
 * Kuru

Parasitic Worms

 * Hookworm
 * Pinworm
 * Schistosomiasis
 * Tapeworm
 * Trichinosis

Sample Exercises
1. Provide two differences between bacteria, viruses, and fungi.

2. Using the following key, determine (from pictures) which cell, A, B, or C is considered an alga.

3. Based on the following graph, determine which organism is best suited for growth in acid environments.

4. A cell is observed through a light microscope at 4x magnification. The cell takes up about half of the visual field. What is the approximate length of this organism?

5. Students observe a Petri plate with many different colonies on it. Based on the color of the colony, how many different kinds of organisms do you detect? Which type of organism appears to be the most prevalent?

6. From the following picture, identify the organelle, provide its function, and state which type of microbe it is unique to.

7. What type of microbe is involved in the production of most breads? What type of organism is responsible for polio?

8. Based on the following graph, what will be the microbial population/ml after 3.5 hours of growth?

9. Provide two distinctive properties of viruses, then provide the name of two diseases that are caused by viruses. As a variation on this type of question, match the disease with the type of microbe that causes it.

10. Match each microbe that causes the following disease: Rubella, Schistosomiasis, Ebola, Scrapie, Malaria.

Useful links

 * Has information specific to cells -- Has a lot of useful information -- Use the links on that page too!
 * Has vocabulary
 * Bacteriology text
 * Microbiology text
 * CellCraft -- a game which helps you to learn the basic organelles of a cell.
 * Microbiology Online -- a great place to find in-depth information on cell organelles