Microbiology Exam Four

Fungal Pneumonia Agents

True or primary fungal pathogens that can invade and grow in a healthy, immunocompetent host. Thermal dimorphism; grow as molds at 30 celsius and as yeasts at 37 celsius or when in human body.

After Glycolysis and TCA Cycles

we started with one glucose entering glycoclysis and coming out as 2 pyruvates. Glycolysis also gave us a yield of 2 ATP and 2 NADH. The 2 pyruvate then enter into the TCA cycle where they are broken down into 6 CO2 and we get 2 more ATP, 8 NADH and 2 FADH2 as well. So far per glucose we have made 4 ATP that can be used to power anabolic processes in the cell. The 6 CO2 have very little energy so they are released as waste products from the cell. We also have 10 NADH (2 from glycolysis and 8 from TCA) and 2 FADH2. It turns out that these molecules have been storing some energy and they are headed to the final step of aerobic respiration to release that energy.

Symptoms of URI

Runny/stuffy nose. Sore throat. Fever

URI Treatment for Bacteria

Use antibiotics.

Tracheitis

Inflammation of the trachea.

Common URI Bacteria

Streptococcus (Strep A)

Reasons why Bacteria Make Proteins Faster than Eukaryotes

1) Lack of a nucleus: Since bacteria do not sequester their DNA into a membrane bound nucleus, the process of translation can actually start before transcription has finished. 2) Lack of introns: Bacteria do not have introns in their DNA, it is all coding exons. Therefore, bacteria do not need to splice out introns before their mRNA is translated. This is a clear example of bacteria evolving for speedy responses while eukaryotes have evolved for complexity, two different evolutionary strategies. 3) Bacteria have operons that allow them to respond quickly to their changing environment and make only those enzymes that will be useful for their current circumstances.

Events in Coccidioides Infection

1. Digging in soil produces aerosol of arthrospores. 2. Inhaled athrospores establish a lung infection. 3. An arthrospore develops into a spherule that produces endospore; endospores are released in the lungs. 4. Immunocompromised persons effectively fight infection and return to health. Inhaling arthrospores causes Valley Fever; type of fungal pneumonia causing cough, fever, chest, pain, flu-like symptoms. Common in children and newcomers to endemic areas. 5. Compromised people can develop meningitis, osteomyelitis, and skin granulomas.

Helminth Classification

1. Roundworms (Nematodes) - round non-segmented bodies with a complete digestive tract. 2. Flatworms - flat multi-cellular worms including Trematodes (flukes) which are flat, non-segmented with "sucking" mouthparts and custodies (tapeworms) which are long and segmented.

Events in Histoplasma Infection

1. Soil containing bird droppings is whipped up by wind. 2. Microconidia are inhaled and develop into yeast. 3. Patient develops mild pneumonitis, which might recur. 4. In the tissue phase of infection, the yeast phase develops, is phagocytize and reproduces by budding intracellularly. Causes Ohio Valley Fever; asymptomatic to self-resolving fungal pneumonia in 95% of cases, causes cough, fever, malaise, chest pain, headache, weight loss. Most recover without complications. 5. In some cases, phagocytes enter the mood and cause disseminated (spreading of yeast) disease in a number of organs; typically in immunocompromised. Diagnosed by speutem sample exposing intracellular yeasts.

Catabolic Strategies for Getting ATP

3 main strategies to make ATP used by organisms on planet Earth. 1. Aerobic Respiration Aerobic respiration is the most common form of catabolism and it is used by most organisms on the planet including ALL eukaryotes and many of the prokaryotes. 2. Anaerobic Respiration Anaerobic respiration is a relatively unusual strategy and is only done by SOME prokaryotes. 3. Fermentation Fermentation is done by a FEW eukaryotes and SOME prokaryotes but is only used as a last resort by the organisms that can ferment.

DNA-Protein Relationship

3 nucleotides (codon) are the information for one amino acid. tRNAs interpret the DNA code and translate it into amino acids. All proteins are made methionine first.

Tuberculosis

A complicated illness caused by Mycobacterium tuberculosis, an acid-fast bacillus that has a tendency to grow in cords. They do not produce exotoxins or enzymes characteristic of other bacterial pathogens. Instead, the ability to produce the cord-like colonies is used as an indicator of virulence. Cord formation is thought to impede the ability of macrophages to ingest and destroy M. tuberculosis; instead they take them to lymph nodes in lungs where they are latent. 1/3rd of the population has TB, only a small amount become sick. Latent tuberculosis they are infected but not sick, but can become active years later, especially in people who have HIV, organ transplant, or chemo. Drop of blood or urine can tell TB in 2 hours with new test looking for TB or antibodies. Treatment is same in the last 50 years, 4 antibiotics every day for 6-9 months. For drug resistant forms, 2 years of treatment with pills and injections, cures 1/2. Vaccine prevents the most serious forms for children but not transmission.

Operon

A coordinated group of genes under the control of a single promoter. In an operon, all of the genes needed for one function (like digesting lactose) are all together under one single promoter. Since there is one promoter, those genes will get transcribed together. So RNA polymerase will bind to the promoter and transcribe all of the enzymes needed to digest lactose at once. This is convenient for the bacteria because one single transcription event can start the production of all of the needed enzymes. There is nothing like operons in Eukaryotes.

Epiglottitis

A disease in which the epiglottis becomes inflamed and enlarged and may cause an upper airway obstruction.

Norovirus

A highly contagious naked, RNA virus that is thought to be the cause of almost 90% of all viral gastroenteritis infections. It is the most common cause of food-borne illness in the United States, sickening nearly 21 million people each year. Norovirus is transmitted by coming in contact with an infected person, consuming contaminated food or water, or by coming in contact with contaminated surfaces. The virus causes inflammation in your stomach and/or small intestine, leading to stomach pain, nausea, diarrhea, and vomiting. Symptoms usually appear within 12 to 48 hours of exposure and patients recover within 1 to 3 days. Norovirus is easily transmitted in crowded situations, such as schools, cruise ships, nursing homes, or restaurants, and is not restricted to particular age groups. i.e. stomach bug. Can spread even after your symptoms go away. Can avoid it by bleaching items, cleaning shellfish. #1 cause of diarrhea in kids. Because the Norovirus is so contagious, it commonly crops up as an epidemic in people that are in close contact with one another like school children.

Rotavirus

A naked, RNA virus that is most common in infants and young children, and is the leading cause of severe diarrhea in these age groups. Older children and adults can be infected with rotavirus, but they will typically exhibit milder symptoms. Symptoms appear approximately 2 days after exposure to infected individuals or contaminated surfaces and include severe watery diarrhea, vomiting, fever, and abdominal pain. Rotavirus is a very serious illness and is responsible for the deaths of over 500,000 infants and children each year, worldwide. The CDC recommends an oral vaccine be given to infants in the US. Almost every child has by age 5, but breastfeeding helps. No way to treat, just need to hydrate. Avoid infection by vaccination.

Giardia Intestinalis

A protist in the supergroup Excavata, more specifically the Diplomonads. Many Diplomonads are parasites, thrive in oxygen poor environments, and are symmetrical - with two equal-sized nuclei and four flagella on each side. This symmetry can be seen in the image above of Giardia, the two dark circles are the nuclei of the cell. Giardiasis is the most common intestinal parasite found in the United States, although the majority of infections are asymptomatic. Human infection is often seen in campers and hikers who drink water from rivers and streams without proper filtering or boiling the contaminated water. Symptoms such as loss of appetite, diarrhea, stomach cramps and upset, projectile vomiting, excessive gas, and lactose intolerance, can arise within one to three weeks of exposure to contaminated water. The symptom of lactose intolerance is typically temporary, but can become permanent. Cysts are shed in the fecal matter of infected vertebrates, which can survive in cold water for up to three months. Diagnosis is achieved through examination of the patient's stool for trophozoites (pictured above) and cysts.

Why is it vital for no oxygen to be present for fermentation to occur?

ALL fermenters can also do aerobic respiration.... in other words they can choose to do aerobic respiration and get 38 ATP per glucose or do fermentation and get 2 ATP per glucose. For that reason, organisms that can do fermentation will only do it when there is no oxygen present to do aerobic respiration. Some bacteria, like E. coli can actually do all 3 catabolic strategies. When oxygen is present, E coli will use aerobic respiration to maximize the ATP yield but without oxygen, E coli will do anaerobic respiration if a suitable salt is found for it's final electron acceptor. If there is no oxygen and no salt, E coli will use fermentation since 2 ATP is better than nothing!

Liver

Acts an accessory organ of the digestive system by producing a number of different hormones, enzymes and other substances essential to digestion. Other important contributions from the liver are the production of lectin (helpful in complement activity) and filtering of blood to remove old blood cells and various toxins. Because the liver doesn't have contact with the outside environment, it does not have any normal microflora and is sterile in a healthy human.

Acute Respiratory Distresses

Acute Respiratory Distress Syndrome (ARDS) is a severe, life-threatening medical condition characterized by widespread inflammation of the lungs, fluid accumulation, and breakdown of the cells lining the lung's blood vessels. Diseases that cause this are: Sin Nombre Hantavirus SARS-Coronavirus MERS-Coronavirus

Complete Tally for Aerobic Respiration

Aerobic respiration has 3 steps, Glycolysis, the TCA cycle and the Electron Transport System. Through these 3 steps a single glucose molecule is broken down to yield 6 CO2 and a total of 38 ATP (2 ATP from Glycolysis, 2 ATP from TCA and 34 from the ETS.) Aerobic respiration requires oxygen because it is the final electron acceptor for the ETS. Aerobic respiration is the most common catabolic strategy on the planet, all eukaryotes and many prokaryotes use it.

Enterohemorrhagic E Coli (EHEC)

Also called STEC (shiga toxin-producing E coli) and VTEC (verotoxic E coli). Non-invasive but causes attaching and effacing lesions, similar to EPEC but this one is only in the LARGE INTESTINE (i.e. colon). Produces a hemorrhagic toxin called shiva-like toxin or verotoxin, which nicks the colon cells' 60S ribosomes, shutting down eukaryotic protein synthesis. Includes O157:H7 and O104:H4 which are found in food or water contaminated by catal feces (mainly hamburger), sometimes through sewage contaminating water. Person to person transmission also occurs. Less than 100 cells needed for infection. Shiga-like toxin can also enter the bloodstream and travel to the kidney, whose cells are particularly vulnerable to the toxin. Disease may progress to hemolytic uremic syndrome (HUS) and acute renal failure, can cause many complications and should be treated quickly.

Entamoeba Histolytica

An Amoebozoan, a protistan supergroup we first learned about when discussing amoebic encephalitis. Amebiasis symptoms include loose stool, abdominal pain, weight loss, and fatigue, but only 10 to 20% of infected individuals will display these symptoms. Amebic dysentery is the term given to severe E. histolytica infections, with the added symptoms of bloody diarrhea and fever. Symptoms typically take one to two weeks to arise, although there has been cases of symptoms taking longer to develop. Diagnosis is achieved through microscopical analysis of stool samples. During diagnosis, it is important not to confuse E. histolytica with another amoeba, Entamoeba coli which is a non-pathogenic amoeba that may be found in the human GI tract. To distinguish the two, the E. histolyticatrophozoite often presents with ingested human red blood cells. Cysts released in the feces of infected vertebrates can persist in soil or water for weeks up to several months.

Cryptosporidium Spp.

An Apicomplexan, a protistan group of animal parasites we first encountered when learning about malaria. The most common way to be infected with cryptosporidiosis is through the consumption of water contaminated with Cryptosporidium spp. cysts. The cysts enter the water when fecal matter from infected vertebrates is introduced, and they can last for several days to weeks in the water. Common sources of human outbreaks are in water parks or municipal water systems. Cryptosporidium is resistant to chlorine and oftentimes swimming pools have to be shut down and drained when fecally-contaminated. Symptoms arise within 2 to 10 days of consuming the contaminated water, and can last for a week or more. The illness is most severe for immuno-compromised patients, and healthy patients may not experience any symptoms. The primary symptom is watery diarrhea, but other symptoms include stomach pain, nausea, vomiting, fever, weight loss, and dehydration. Proper diagnosis is made by examining the patient's stool. The stool can be examined for cysts via microscopy using an acid fast stain, or it can be checked for Cryptosporidium anitgens via ELISA.

Fungal Pneumonia

An infection of the lungs caused by endemic fungi. It accounts for only a small portion of pneumonia cases in this country; however, fungal pneumonia generates concern in the ever-growing population of immunosuppressed people. Portal of entry: cutaneous and superficial (contamination of skin), subcutaneous (inoculated skin, trauma), and systemic mycoses (respiratory poral, inhaled spores). Histoplasma capsulatum Blastomyces dermatitidis Coccidioides immitis

Sinusitis

An inflammatory condition of any of the four pairs of sinuses in the skull (see picture below). Sinusitis is commonly called a sinus infection and can be caused by allergy or by infectious agents which include a variety of viruses or bacteria. In fact, the same bacterial organisms that cause otitis media can also cause sinusitis (in the same order of most common to least common). Bacterial sinusitis is not a communicable disease and infections most often arise from the normal microflora of the host following a viral URI (e.g. common cold).

Rheumatic Fever

Antibodies made against S. pyogenes M-protein cross react and bind to the heart. This immune reaction on the heart can cause permanent heart valve damage and is very serious. Strep throat must always be treated immediately and aggressively with antibiotics to prevent these deadly complications.

Glomerulonephritis

Antibodies made during a strep throat infection form large immune complexes of antibodies and antigens that deposit in the kidneys as they filter the blood. The result is nephritis as the kidney function is blocked. Symptoms of nephritis are extreme swelling, low urine output, blood in the urine, increased blood pressure, possible heart failure and permanent kidney damage. Yet another example of why it is so important to treat strep throat infections immediately and aggressively with antibiotics.

Cestodes (Tapeworms)

Are long, very thin, segmented flatworms divided into 3 sections. 1. Scolex = head, which attaches to intestinal wall via hooks and/or suckers. 2. Neck and 3. Body which is ribbon-like and resembles tape; made up of individual segments called proglottides. Proglottids absorb nutrients directly and filled with eggs. Definitive hosts (humans) ingest larvae from infected tides (cysticercus), i.e. undercooked beef, pork, or fish. Larvae develop into adult tapeworms in the intestines. Adult tapeworms develop in the intestine and can grow up to 5 meters long and live up to 30 years. Tapeworm infections are often asymptomatic unless there is a heavy worm burden. Taenia saginata (beef tapeworm) Humans acquire by ingesting inadequately cooked beef containing the cysticerci (encysted larval stage). Larvae hatch in intestine and mature to an intestinal tapeworm. Adult beef tapeworms remain in intestines. Infection called taeniasis (any tapeworm infection); intestinal infection is asymptomatic to mild, diarrhea and weight loss. Adult tapeworms grow up to 5m and live in intestines for several decades. Diagnosis by microscopy fecal sample: thick-walled spherical, dark brown eggs, and/or proglottids in stool. Taenia solium (pork tapeworm) Life cycle mirrors T saginata but with pigs as intermediate host. Infection by ingestion of cysticerci in undercooked pork causing tapeworm (Taeniasis): asymptomatic to mild; diarrhea and weight loss. Infection can also occur via ingestion of eggs in contaminated food and develop a serious condition known as cystericercosis (when you eat the eggs, not the pig or cow that eats the egg). Leads to larvae hatching from eggs and migrating throughout the body and becoming encysted in muscles, bladder, eyes, and brain. Cystericercosis is one of the highest causes of seizures in adults.

Bacillus Cereus Exotoxins

Bacillus cereus is an endospore-forming gram-positive bacilli that is a common soil microbe that can be an airborne and dust-borne contaminant. As a result, it is a common resident on vegetables and food products in close contact with soil. B. cereus multiplies very readily in cooked foods, most notably fried rice. In fact, oubreaks of food poisoning from this bacterium are often associated with Chinese restaurants. Other foods implicated with B. cereus are cooked potatoes and meat and vegetable dishes. Bacillus cereus spores and toxins survive short periods of cooking and reheating; when the food is stored at room temperature, the spores germinate and release exotoxins. B. cereus produces two exotoxins, one of which causes an emetic (or vomiting) disease, the other causes a diarrheal-type disease. The emetic form of the disease is the most frequently linked to fried rice and food intoxication results from ingestion of a heat-stable exotoxin that causes acute vomiting, usually within 1-4 hours post-ingestion. The diarrheal form of the disease is associated with cooked meats or vegetables that are held at warm temperatures for long periods of times. These conditions cause B. cereus to produce a heat-labile (or heat-sensitive) exotoxin that causes watery, profuse diarrhea, nausea, and abdominal cramps. The symptoms generally disappear in 24 hours with no lasting effects or required treatments.

Streptococcus Pneumoniae

Bacteria is found as normal microflora in the nasopharynx of a good portion of healthy humans. A gram positive cocci in pairs (diplococcus) and short chains. It can cause ear infections (otitis media) when it passes through the eustachian tube into the middle ear, can also cause meningitis when it gets into CSF. If S. pneumoniae moves from the normal flora location of the nasopharynx into the lungs, it can cause pneumonia. Many Streptococci (including S. pneumoniae) are fastidious and must be grown on Blood Agar. The pneumococcus displays alpha hemolysis on blood agar plates. The major virulence factor for S. pneumoniae is it's capsule which is particularly thick and protects the bacteria from phagocytosis by phagocytic leukocytes. The large capsule causes the colonies to be mucoid (see figure below) which means that they are thick, moist, smooth and kind of mucous-like in consistency. This capsule is so important to the bacteria that if you remove the capsule, it can no longer infect! This capsule is often identified in a patient's sputum sample by using a serological test called the Quellung reaction.

Tooth and Gum Infections

Bacteria live on the teeth and throughout the soft structures of the mouth. Normal biota (resident microbes) live on the teeth by forming dental plaque, a kind of biofilm. Over time, the plaque can accumulate more and more bacteria, especially anaerobic bacteria which can damage the soft tissues and bones surrounding the teeth. Additionally, introducing sugary substances into the mouth can result in the breakdown of teeth due to the production of acid by certain oral streptococci in the biofilm.

Adenosine Triphosphate (ATP)

Because of it's role as an energy storage molecule between catabolism and anabolism, adenosine triphosphate (ATP) is absolutely vital to the cell. It absorbs and stores energy released by catabolism and then releases that energy when it's need to run anabolism. This incredible ability is because of the ATP structure. ATP is made of adenosine (ribose and the nitrogenous base adenine) with 3 phosphate groups attached in a row. phosphate groups have a negative charge... so, do those 3 phosphate groups like being attached to one another...... heck no! Just like 3 small children strapped into the back seat together for a long car ride, they are dying to get away from one another! The bonds between phosphate groups are often called "high energy phosphate bonds" because they hold so much potential energy between the 2 negatively charged phosphate groups! When there are only 2 phosphate groups attached to the adenosine it's called adenosine diphosphate (ADP). This is how ATP can store and release energy so readily. The cell has a constant pool of ADP and it can constantly alternate between ADP and ATP. During catabolism, the released energy is used to load a phosphate group onto ADP forming ATP. When the cell needs to get energy to run anabolism, it will cut off that last phosphate group from ATP releasing energy and forming ADP. So the same adenosine molecule alternates between ADP and ATP hundreds of times a second as it stores energy with that phosphate group and then releases the energy when it's needed.

Gene Regulation in Bacteria

Being tiny unicellular cells, bacteria have evolved to be able to respond to their environment quickly. Humans are large organisms that have evolved the ability to control our inner environments but bacteria have a very different evolutionary strategy, they need to be able to adapt to rapidly changing conditions. Therefore, it is no surprise that bacteria are able to respond to their environment by quickly changing the enzymes that they are producing. This ability to sense changes in their environment and change enzyme expression accordingly is a tremendous benefit to bacteria.

Human Rhinovirus (HRV)

Belong to picornavirus family which are non-enveloped RNA viruses. Main cause of common cold (30-50%) of cases. Over 110 serotypes cause rhinitis with many strains circulating in the population at one time. Infections peak around summer and early fall. Transmission from contaminated hands and fomites. Cannot catch a cold by going outside in the cold or getting wet in the cold. Only by transmission from a virus. More likely to catch a cold if you are tired, stressed, or have allergies. Sensitive to acidic environments (stomach) and their optimum temperature is 33 degrees Celsius (temperature of nose). Usual therapy is to relieve symptoms with various cold remedies and cough syrups containing nasal decongestants, antihistamines, and analgesics. Best prevention is hand-washing and care in handling nasal secretions. Common cold symptoms are headache, chills, fatigue, sore throat, cough, and rhinorrhea.

Parainfluenza Virus

Belongs to Paramyxovirus family (enveloped, RNA virus, with helical capsid). Widespread as influenza but more benign. Spread by respiratory droplets or fomites. Causes about 5% of common cold cases in older children and adults. No specific treatment available; supportive therapy. In infants and young children, can cause bronchitis, bronchopneumonia, and Croup (laryngotracheobronchitis). Croup manifests as labored noisy breathing with "seal bark cough".

Escherichia coli

Best known fecal coliform and most abundant intestinal facultative anaerobe. Most species are nonpathogenic and motile. Causes an opportunistic infection when it enters the urethra and is the most common cause of urinary tract infections (UTIs). Some strains are pathogens with differing virulence factors and effects. True pathogenic strains are all spread via fecal-oral route, from poor sanitation and fecal contamination; enterotoxigenic E coli, enteroinvasive E coli, enteropathogenic E coli, and enterohemorrhagic E coli.

URI Transmission

By touching nose or mouth after touching dirty surface. Getting coughed or sneezed around by someone with it.

Diptheria

C. diphtheriae causes the disease diptheria which starts as a local infection of the throat resulting in fever, sore throat and severe inflammation. A hallmark of diptheria is the formation of a "pseudomembrane" at the back of the tongue that looks thick and leathery. This pseudomembrane is made of dead tissue, bacteria and by products of the immune response and it can grow in size and even block the airway causing asphyxiation. Unfortunately, many strains of C. diphtheriae are lysogenic where a virus has integrated it's DNA into the bacterial genome. So the person is infected by the bacterium C. diphtheriae after it was already infected by a virus! The lysogenic bacterium makes a particularly virulent exotoxin that blocks translation by Eukaryotic ribosomes. Only 1 molecule of the diptheria exotoxin is enough to stop 90% of all protein synthesis in a cell! When the exotoxin is released, patients have symptoms all over the body from the lack of cellular function. The most dangerous complications are nerve damage and heart failure leading to paralysis and even death. Diptheria is pretty contagious through respiratory droplets, direct contact with infected people and even through fomites that can transmit the bacteria. While we can treat diptheria patients with antibiotics and antisera, they should also have heart and respiratory monitoring since those dangerous complications are possible. The good news, however, is that we have dramatically cut down on diptheria cases because of a very effective vaccine called the DTaP.

Gram + Bacilli causing Acute Diarrhea

Clostridium difficile Listeria monocytogenes

Clostridium Difficile

Can cause pseudomembranous colitis (also called antibiotic-associated colitis) after antibiotic therapy kills the competing microflora of the gut. Gram + spore-formign anaerobic bacillus. Normal resident fo colon, in low numbers. Treatment with antibiotics eliminates C. difficile's competition and it can cause pseudomembranous colitis (antibiotic-associated colitis) when it grows unchecked. Spread via fecal-oral route, organism is infested either as the vegetative form or as hardy spores, which can survive for long periods in the environment and can traverse the acidic stomach. In small intestine, spores germinate into vegetative form. In large intestine, C. difficile-associated disease can arise if the normal flora has been disrupted by antibiotic therapy. C. difficile reproduces in the intestinal crypts, releasing toxins A and B causing severe inflammation, mucous and cellular debris are expelled, leading to formation of pseudomembranes. Toxin A attracts neutrophils and monocytes, and toxin B degrades the colonic epithelial cells, both leading to colitis, pseudomembrane formation, and watery diarrhea. Produces entertoxins that damage the intestine and can cause the "pseudomembrane" development. Major symptom is severe diarrhea with cramps and possible fever. Colon perforation and death are possible. Highest risk patients are those on broad spectrum antibiotics for an extended time period (nursing home patients #1). Treatment by removing the antibiotics in weak cases, using a strong antibiotic targeted to anaerobes is possible, probiotics and even fecal transplantation to restore normal flora.

Otitis Media Video

Caused when other infections spread to the middle ear. More common in children. 75% of children experience an episode by their 3rd birthday. More common in kids because they have trouble fighting infections with a developing immune system. Breastfeed children have fewer episodes. Symptoms are unusual irritability, difficulty sleeping, tugging at one or both ears, fever, fluid draining from ear, loss of balance, unresponsiveness to quiet sounds. Eustachian tube in children is shorter and straighter than adults, leading to fluid accumulation and difficulty draining. Adenoids (composed of lymphocytes) are larger in children, due to their larger size, may become infected or get in the way of the eustachian tube opening; the infection may spread to the eustachian tube. Can cause trouble hearing or severe ear pain if it continues; untreated can cause permanent hearing impairment.

Campylobacter jejuni

Causes bacterial gastroenteritis. Transmitted by food (raw poultry and unpasteurized dairy). Adheres to intestine, burrows through the mucus and multiplies, secretes C. jujuni enterotoxin which causes watery/bloody diarrhea, headache, fever, abdominal pain, and possible vomiting. Usually self limiting within a week. Often undiagnosed and untreated, possibly most common food infection, cross contamination with just one drop of raw chicken juice is so common. Very rare to have complications, if there are any, it's a high risk group and antibiotics and rehydration therapy can help fix.

Blastomyces Dermatitidis

Causes blastomycosis. Thermally dimorphic. Free-living species distributed in soil and rotting wood of a large section of the midwestern and southeastern US. Inhaled 10-100 conidia convert to yeasts and multiply in lungs. Symptoms include cough and fever. Specifically causes North America Blastomycosis. Fungal pneumonia similar to histoplasmosis but not as common. Can disseminate into skin and bones. Broad-based budding, thick wall, characteristic "figure 8" appearance.

Enteropathogenic E Coli (EPEC)

Causes chronic diarrhea and infantile diarrhea in developing countries (though rotavirus is more common). Attachment and subsequent injections of proteins directly into small intestine epithelia leads to small intestine microvilli damage and surface effacement, causing watery diarrhea.

Coccidioides Immitis

Causes coccidioidomycosis. Lives in alkaline soils in semiarid, hot climates, and is endemic to southwestern USA. Distinctive morphology; block-like arthroconidia in free-living stage. Arthrospores inhaled from dust, creates spherules containing endospores in lungs; dirt-biking in desert, farming, and construction sites.

Corynebacterium Diphtheriae

Corynebacterium diphtheriae is a Gram + bacillus that tends to form an arrangement called "palisades" where the bacteria line up next to one another like a picket fence. C. diphtheriae is also known for having metachromatic granules that they use to store excess phosphate and you can often see these metachromatic granules in a stain done with methylene blue because the granules look iridescent red. Therefore, simple stains of C. diphtheriae can be very distinctive with the side by side palisades and metachromatic granules.

Listeria Monocytogenes

Causes listeriosis upon ingestion of contaminated foods which starts with diarrhea and can progress to septicemia and meningitis by entering lymph then bloodstream, particularly in high risk groups like pregnant women, immunocompromised adults and the elderly. Non-spore-forming, gram + bacillus. Resistant to cold, heat, salt, pH extremes, and bile. Primary reservoir is soil and water, contaminates produce and dairy products. Variety in bacillus structure. Results in food poisoning particularly after refrigeration of unpasteurized dairy products, poultry and prepared foods. Outbreaks have been traced to contaminated foods such as produce, deli meats, soft cheeses, and other dairy products. Individual cases arise from the organism growing in the fridge. Treat with antibiotics. High risk groups need careful monitoring because complications and death are possible.

Vibrio Cholera

Causes the disease cholera resulting in rice-water stools when the bacteria is ingested in contaminated water or from fecal contamination from infected people. Comma-shaped bacterium that causes cholera. In some humid environments and infected people are the reservoirs. Ingested with food or water or contact with feces of someone suffering from cholera. Attaches to intestinal cells. Infects surface of small intestine, noninvasive. Cholera toxin causes electrolyte and water loss through secretory diarrhea, resulting dehydration leads to muscle, circulatory, and neurological symptoms. Can lose as much as one liter of fluid per hour, many patients die from dehydration. Rice water stools, bits of intestinal mucosa coming off with diarrhea.

Influenza Transmission and Control

Causes varying degrees of respiratory illness (possibly deadly pneumonia) 1918 Spanish Flu H1N1 (killed many young healthy adults, 20 million in 2 years) 1968 Honk Kong Flu H3N2 2005 Bird Fly H5N1 (high death rate in kids, only went bird to human, not human to human) 2009 Swine Flu H1N1 (enough antigenic drift in Hs and Ns that the high death rates of spanish flu did not appear again) Currently see H1N1 and H3N2 Treatment: Anti-virals and supportive care. No aspirin, can cause Reye's syndrome which is a viral infection complication that can cause encephalitis. Yearly flu vaccine.

Adenovirus Serotypes 40-42

Classified as the enteric adenoviruses because they primarily infect the gastrointestinal tract. Infection by these serotypes can be attributed to 5-20% of hospitalizations for childhood diarrhea worldwide, but they can infect any age group. Adenoviruses 40-42 are the only DNA viruses that cause viral gastroenteritis. Symptoms last 7 to 8 days and include diarrhea, vomiting, and fever. Transmission is thought to be contact with contaminated food, water, or surfaces.

Clostridium Perfringens Exotoxin

Clostridium perfringens as being the causative agent of gas gangrene, but the endospores of this gram positive bacillus can also contaminate many kinds of foods. The foods most likely to cause food intoxication from this organism are meat dishes, stews and gravies that are improperly reheated. When these foods are cooled, kept only warm for long periods of time, or left unrefrigerated, spores can germinate and the cells begin to multiply. If the food is eaten without adequate reheating, C. perfringens enters the small intestines and releases exotoxin. The C. perfringens exotoxin is an enterotoxin that acts upon the epithelial cells of the small intestines, causing watery diarrhea, nausea (usually without vomiting), and severe abdominal cramping and pain. Symptoms begins to arrive in 8 to 16 hours post-ingestion of contaminated food. The recovery is rapid and no treatment is required as deaths are extremely rare.

Transmission of Cold Viruses

Coughing (small droplets) or sneezing (large droplets). Most common means through transmission from contaminated fingers/hands to mucous membranes of nose or eye. Practically everyone gets colds fairly frequently. People can acquire some degree of immunity to a cold virus that they have encountered before but minimal overall protection because of sheer number of cold viruses. Children get it 5-7 times, adults get it 2-3.

Dental Caries

Dental caries is considered the most common infectious disease of humans. Over time, oral microbes found living in dental plaque can destroy enamel and cause infection in the deeper layers of teeth containing soft tissue, called the pulp. The pulp contains blood vessels and nerves and infections in this region lead to pain, referred to as a "toothache." The main cause of dental caries are oral alpha-hemolytic viridans streptococci such as Streptococcus mutans. The best way to prevent dental caries is through dietary restriction of sucrose and regular brushing and flossing to remove plaque from teeth. In the United States, fluoride is added to water to increase tooth hardness by remineralizing teeth that may have begun to demineralize because of plaque buildup. New strategies of prevention include the use of probiotics which introduce a mix of bacteria found in healthy mouths. These have been shown to reduce the levels of S. mutans and other bacteria associated with periodontal disease. Several vaccines are in development that aim to prevent dental caries by producing antibodies that bind and block the proteins bacteria use to attach to teeth.

Fermentation Identification

During the unknown identification lab project many of you will chose to use carbohydrate fermentation media to see if your unknown can ferment a particular sugar. This broth has the sugar you are investigating (glucose, sucrose, lactose, etc.) along with a pH indicator that is red at neutral pH and turns yellow in acid. When you inoculate this media and allow it to grow the bacteria may or may not ferment the sugar provided. If the sugar is fermented, the media turns yellow from the acid released during fermentation. There is also a little upside down tube in the medium that will catch bubbles of gas if gas is released during fermentation. So the possible results would be: 1) Yellow with a gas bubble meaning the sugar was fermented and gas was produced (left picture) 2) Yellow without a gas bubble meaning the sugar was fermented without any gas (middle picture) 3) Red meaning the sugar was not fermented (right picture)

The Enterics: Gram Negative Bacilli causing Acute Diarrhea

Enterobacteriaceae family. All small, gram - rods. Facultative anaerobes. Ferment glucose, reduce nitrates to nitrites, oxidase negative, and catalase positive. Many inhabit soil and water and some are common occupants of the large intestine. Enteric pathogens are most frequent cause of diarrheal illnesses through action of enterotoxins. Divided into fecal coliforms (lactose fermenters and non-coliforms (non-lactose fermenters). MacConkey Agar is selective (only gram -) and differential (lactose fermenting or not) media for distinguishing between lactose and nonlactose fermenting Enterobacteriaceae. Classified by 2 surface antigens; O - cell wall antigen, H - flagella antigen, and K - capsule/fimbrial antigen. Virulence factors; fimbriae (for adherence), endotoxin (LPS), exotoxins (mostly enterotoxins causing gastroenteritis. Escherichia coli (coliform) Salmonella (non-coliform) Shigella (non-coliform)

Excision Repair of Mutations

Enzymes that cut out mutated pieces of DNA. DNA polymerase 1 then fills in with new DNA and ligase seals up the gaps. Happens at all points in lifetime of our cells.

Haemophilus Influenza Type B

Especially notorious for causing epiglottitis (inflammation of the epiglottis). The epiglottis is a flap in the throat that prevents food from going down the trachea. Because of its location in the airways, inflammation of the epiglottis can interfere with breathing and is life-threatening. Shown in the image below is an inflammed epiglottis that appears cherry red in color. Children with epiglottitis have difficulty and painful swallowing and they are often seen drooling heavily to avoid swallowing at all. Other symptoms include fever, hoarseness of voice and wheezing due to airway obstruction. Epiglottitis can lead to a surgical emergency if the inflammation is too severe. Fortunately, with the introduction of the Hib vaccine, the incidence of epiglottitis has decreased dramatically.

Surveillance and Preparation for Influenza

Essential; scientists observe bird and pig populations to try and reduce transmission to humans. Make a best guess for flu vaccines. Winter infection unless they live near the equator; belief is that the cold in other areas keeps you indoors closer to others, rather than the weather actually affecting anything.

Bacterial Infections with Acute Diarrhea and Vomitting

Food poisoning, also called foodborne illness, refers to symptoms in the gastrointestinal tract that are caused by a preformed exotoxin produced by a pathogen. Symptoms include severe nausea, frequent vomiting accompanied by diarrhea, and abdominal cramping. Three bacteria in particular cause acute diarrhea and vomiting. By acute we mean symptoms present within one to a few hours post-ingestion of the contaminated food. These bacteria include: Staphylococcus aureus Bacillus cereus Clostridium perfringens

Vibrio Vulnificus

Gastroenteritis from raw oysters, cutting yourself opening up an oyster. If it gets into the skin, can cause a necrotizing fasciitis. Watery diarrhea.

Vibrio Parahaemolyticus

Gastroenteritis from raw seafood. Watery diarrhea.

Influenza Genetic Shifts

Genome constantly changes; antigenic shift (mixing up of two viruses to create a new combination of virus caused by segmented genome) and antigenic drift (low level mutation rate but higher in prokaryotes since they don't have enzymes removing mutations). Constantly have "new" flu strains occurring. Immunity to 1 strain doesn't protect against other strains.

Fermentation Strategy

Glycolysis Pathway: Uses 1 glucose to yield 2 pyruvate, 2 ATP, and 2 NADH. Fermentation Pathway: Uses pyruvate and NADH to yield NAD+, acids, or alcohols and sometimes gas. Produces only 2 ATP per glucose along with the acid/alcohol and sometimes, gas.

Hepatitis A Virus (HAV)

HAV is a nonenveloped, single-stranded RNA enterovirus that belongs to the Picornavirus family. Remember that many viruses from this family can result in viral meningitis and we will see that other enteroviruses can cause gastroenteritis. Infection by HAV is quite mild compared to many of the other Hepatitis viruses. Patients are likely to experience "fluish" symptoms possibly accompanied by nausea and vomiting. In severe cases you might see jaundice and abdominal tenderness (from the inflamed liver) but that is pretty rare in this mild and self-limiting infection.

Hepatitis B Virus (HBV)

HBV is an enveloped DNA virus from the family Hepadnaviridae. Interestingly, the DNA of this virus is partly single-stranded and partly double-stranded. HBV is often called a "Dane Particle" and can be identified in serological tests by looking for a protein in it's envelope called it's "Surface Antigen". HBV is a more severe infection than HAV. Patients usually experience fever, chills, malaise, anorexia, abdominal pain, diarrhea and nausea. In addition to commonly seeing jaundice in HBV patients, you might also see a rash and/or arthritis. HBV is a very serious infection and can be life-threatening. Most patients will recover fully after an acute case of HBV but for some patients, HBV becomes chronic and that long-term infection can result in liver cirrhosis (permanent scarring to the liver tissue). These chronic HBV patients also have a substantially higher risk for liver cancers. Some patients become latent carriers of HBV after recovering from the infection and continue to be infectious to others even after they have fully recovered. Although HBV is growing in the liver, it releases active virus into the blood which makes it easily transmissible through small amounts of blood and other body fluids including semen. This makes HBV a highly infectious disease through sexual contact, mother to baby during birth, sharing needles, tattooing, even sharing things that have trace amounts of blood or fluid like utensils and razors. It is a major concern for healthcare workers because of the risk of needle sticks and their likelihood to encounter patient body fluids. There is an effective HBV vaccine that is recommended by the CDC for all children and those adults that may not have received it and are considered high risk (healthcare workers, partners of HBV patients, homosexual men, injection drug users, etc.)

Hepatitis C Virus (HCV)

HCV is an RNA virus from the flavivirus group and is sometimes referred to "non-A non-B" hepatitis in the medical setting because it was identified as an infection before the actual virus was isolated and identified. Unfortunately HCV infection is often subclinical for months or years before the patient begins to experience symptoms of liver damage: jaundice, malaise, abdominal pain, etc. Since most HCV infections do become chronic, this leads to long term damage and even death in the patient. In fact, chronic HCV infection is the most common cause for a liver transplant in the US. HCV is infectious through blood contact and too a lesser degree, sexual contact. This unfortunately means that patients are infectious for months or years while their infection is subclinical and they have no idea they are infected. By far, the most common transmission for HCV is sharing needles with injection drug use but it is also possible to transmit the virus via sexual contact and of course, healthcare workers have some risk with their patient contact. We don't currently have a vaccine for HCV so prevention and screening are the best options.

Hepatitis D Virus (HDV)

HDV is a weird one. It can only infect as a co-infection with HBV because it is an incomplete virus particle on it's own. It appears that the presence of HDV along with HBV causes a more severe form of HBV infection. Although we don't have a vaccine specific for HDV, the HBV vaccine protects against both.

Hepatitis E Virus (HEV)

HEV is a relatively mild infection rarely seen in the US. It is transmitted through fecal-oral route and is usually associated with contaminated water supplies in countries without good sewage treatment protocols. HEV is a self limiting disease and there is no vaccine available for HEV.

URI Prevention

Handwashing Cover cough/sneeze Flu shots / vaccines

Sin Nombre Hantavirus

Hantaviruses are enveloped, RNA viruses that belong to the Bunyaviridae family. In the U.S., the only hantavirus is the Sin Nombre virus. The Sin Nombre hantavirus is carried in the gastrointestinal tract of wild rodents in the southwest and is transmitted via inhalation of dried rodent urine/feces in dust. In fact, it was breathing in rodent wastes from cabins in Yosemite that sparked the outbreak of acute respiratory distress syndrome in that famous national park. The Sin Nombre virus is now considered an emerging virus in the United States ever since it was first isolated in 1993 from rodents collected near the home of one of the initial patients with hantavirus pulmonary syndrome in the Four Corner region of the western United States (Utah, Colorado, Arizona, and New Mexico). A higher than normal rainfall (caused by El Niño) resulted in a bumper crop of piñon nuts, a favorite food of deer mice. Mouse populations increased, as did contact with humans. The Sin Nombre virus causes Hantavirus Pulmonary Syndrome (HPS) - initial symptoms are fever, chills and myalgia (muscle pain). Rapidly followed by a dry cough, shortness of breath, pulmonary edema, acute respiratory failure and death within days. HPS has a ~50% mortality rate.

Gastrointestinal Helminths

Helminths are parasitic worms that are covered in the parasitology branch of microbiology. These organisms may be large enough to be seen with the naked eye, ranging from tapeworms that can grow up to 50 feet long, to small roundworms that are less than 1 mm in length. Yet, we still include them in microbiology because they are pathogenic to humans and because microscopes are necessary to identify their microscopic eggs and larval stages.

Central Dogma of Biology

How we get proteins from DNA; transcription and translation.

Helicobacter Pylori Transmission

Humans are the only reservoir of this pathogen and to date, the transmission of Helicobacter pylori still remains a mystery. The current consensus is that the bacterium is spread through the oral-oral or fecal-oral route. Once in the host, the primary habitat is the harsh human stomach! Approximately two-thirds of the world's population are infected with H. pylori, occurring in the stomachs of 25% of healthy middle-age adults and in more than 60% of adults 60 years of age or older.

Gastrointestinal System

If you think about the structure of the digestive tract, it is really a long tube with openings on both ends (from mouth to anus), that is exposed to the outside environment. Therefore, most parts of the digestive tract have a rich mix of normal microflora that assist in digestion, protect against pathogenic infections and produce vitamins. The gastrointestinal flora are essential to the overall health of our bodies and patients that lose their flora have persistent symptoms until they are recolonized.

Laryngitis

Inflammation of the larynx/voice box.

H. Pylori Stomach Issues

Immune responses cause inflammation of the stomach (gastritis), and subsequent infiltration of white blood cells lead to deeper erosion of the stomach epithelium and more ulcers. H. pylori and the host immune response against it are a major factor in the development of stomach cancer. Patients with ulcers and those suffering from sharp or burning pains emanating from the abdomen as a result from gastritis can prevent symptoms by limiting spicy foods or whichever food aggravate the condition and by taking over-the-counter remedies like Pepto-Bismol. Now that we know H. pylori is the responsible agent causing peptic ulcers, the best treatment is a course of antibiotics.

Operons in Eukaryotes

In Eukaryotes, each gene has it's own promoter meaning each one has to be transcribed individually. This is part of why bacteria can make proteins faster, they can transcribe all the enzymes needed for a function at the same time.

Inducible Operons

In an inducible operon the repressor protein is made in it's active form which means the repressor is binding to the operator. When the repressor binds to the operator it blocks RNA Polymerase which blocks transcription. In other words: active repressor = repressor bound to the operator = RNA polymerase is blocked = no transcription happening from that operon. So in an inducible operon, the default situation is transcription is blocked because of that active repressor. Inducible operons have to be able to respond to their environment and start transcription. They do this through a substance called the INDUCER. An inducer is something that will bind to the repressor and inactivate that repressor protein. When the repressor is no longer active, it falls off of the operator and allows transcription to start again.

Streptococcus pyogenes and Strep Throat

It is a Gram + coccus in strepto chainsIt is normal flora for 15% of humans but can be transmitted through respiratory droplets and direct contact to those that don't have it in their flora. It has quite a few virulence factors including: C-carbohydrate and M-protein for attachment and phagocytosis defense, hemolysin toxins that cause beta hemolysis, and the Erythrogenic toxin that causes a bright red rash and fever but is only released by lysogenic strains of S. pyogenes.

Common Cold Prevalence

In the course of a year, people in the U.S. suffer from about 1 billion colds. Many people have several episodes a year with children usually having 5-7 colds per year and adults having 2-3 per year. Colds cause a lot of people to stay home. The CDC says 22 million school days are lost each year in the U.S. because of them. Although a fairly innocuous infection, it is estimated that the common cold costs the U.S. $40 billion a year in trips to the doctors, medications, and lost work time.

Treatment of Otitis Media and Sinusitis

Include broad-spectrum antibiotics when infections are of bacterial origin.

Types of Operons

Inducible and Repressible

Lac Operon

Inducible operon. Structural genes contain the enzymes needed to catabolize lactose. Normally transcription if off but can be induced if lactose appears. Lac repressor is synthesized in its active form. Lactose (inducer) inactivates the repressor and turns transcription of lac on.

Rhinitis

Infection/inflammation of nasal cavity.

Sinusitis Animation

Interconnected hollow spaces in skull with mucous membranes helping drain from nose. Can be inflamed, preventing draining and causing pressure and pain. Acute comes quickly and leaves but chronic stays often. Severe sinusitis can require surgical opening of passageways to remove bone and tissue blocking drainage. Balloon sinoplasty uses a balloon catheter to the blocked passageway and is inflated, to widen the passageway and help with drainage and relief.

Nematodes (Roundworms)

Intestinal nematodes mature in small intestine. Adults attach to the intestinal wall via anterior oral hooks or cutting plates. Examples of intestinal nematodes include the giant intestinal roundworm, hookworms, and pinworms.

Enteroinvasive E Coli (EIEC)

Invades intestinal wall and causes inflammatory disease of the large intestine leading to bloody diarrhea and pus. virulence due to invasion of intestinal epithelium (via invasion proteins). Transmission may be associated with contaminated food.

Lactose

Lactose is a type of carbohydrate called a disaccharide because it contains two simple sugars bound to each other. The bond between the two sugars must be broken using enzymes before you, as the E. coli cell, can use it.

Human Hookworms - Necator Americanus (New World) and Ancylostoma Duodenale (Old World)

Larvae hatch from eggs in human feces and contaminate soil, larvae penetrate skin (usually between toes of bare feet) and cause ground itch. Larvae enter the circulation and perform a liver-lung migration similar to Ascaris. Adults mature in small intestine with females releasing 20,000 eggs per day. Diagnose by stool examination looking for eggs. Infections cause chronic anemia; hookworms hang onto intestinal mucosa with teeth, secrete anticoagulant, and suck the host's blood. Loss of blood leads to the chronic anemia and severity is proportion to worm burden. Severe infections lead to weight loss and fatigue, particularly if nutrition is poor. Infection in young children may lead to developmental delays.

Anaerobic Respiration

Less common than it's oxygen rich counterpart. Only some prokaryotes can do anaerobic respiration and no eukaryotes do it. Anaerobic respiration starts out just like aerobic respiration, it uses glycolysis and the TCA cycle identically. The difference between anaerobic and aerobic respiration happens in the electron transport system. In aerobic respiration the final electron acceptor is oxygen but in anaerobic respiration the final electron acceptor is some sort of inorganic salt. Common salts to use are sulfate, nitrate, nitrite, fumarate, etc. The amount of the ATP that is made differs depending on what salt is used as the final electron acceptor but it's never as high as with oxygen in aerobic respiration. The ATP yield for anaerobic respiration is usually somewhere between 10-24 ATP/glucose. Uses glycolysis, TCA cycle, and ETS. Final oxygen acceptor is an inorganic salt instead of O2 (NO3, NO2, SO4, etc.) Amount of ATP depends on salt being used.

Aerobic Respiration Step 1: Glycolysis

Location: Glycolysis happens in the cytoplasm of a prokaryote or a eukaryote. We are going to learn glycolysis from what is called the "black box approach" which means you need to know what goes in and what comes out but you won't need to know all of the reactions that make up glycolysis. That said, I want you to know that the term glycolysis describes a whole group of reactions that work together in the cytoplasm to turn glucose into pyruvate. There are many enzymes working in concert to comprise "glycolysis". Black Box Approach: One molecule of glucose (a 6 carbon sugar) enters glycolysis and it gets broken down into 2 pyruvate molecules (a 3 carbon sugar). The early steps of glycolysis require 2 ATP and the later steps yield 4 ATP so the net yield is 2ATP per glucose. You also have 2 NAD+molecules entering into glycolysis and coming out as 2 NADH.

Scarlet Fever

Lysogenic S. pyogenes makes the erythrogenic toxin that results in a bright red rash and high fever. The classic symptoms would be strep throat along with a bumpy red rash that feels like sandpaper and high fever. Sometimes you can see the rash on the tongue when it turns dark red with white bumps and this is commonly called "strawberry tongue". Scarlet fever can be dangerous if it doesn't get treated quickly.

Differences in Prokaryotes and Eukaryotes in Transcription and Translation

Main difference in structure of cell, prokaryotes don't have nucleus where DNA is. Transcription and translation therefore both happen in cytoplasm, and can happen at the same time; however, in eukaryotes, translation is in the nucleus with transcription in the cytoplasm, so they can't happen at once. Another difference is eukaryotes have introns (non-coding sections of DNA). Introns are spliced out and exons are glued together before the mRNA can leave the nucleus, so they have one more processing step before translation, slowing the process. Prokaryotes don't have this step. Only prokaryotes have operons. All reasons why eukaryotes are slower at protein production and why they respond to the environment slower.

URI Treatment for Virus

Mainly wait it out for your immune system to kill it, but can perform supportive actions. Hydrate to urinate often and release wastes. Symptom relief; suck on a lozenge or use an over the counter nasal decongestant or antipyretic (fever reducer). Rest.

Enterotoxigenic E Coli (ETEC)

Major cause of traveler's diarrhea and infant diarrhea in developing countries, both are watery diarrheas. Non-invasive (stays outside cell) and causes severe diarrhea due to heat-labile toxin and heat-stable toxin (which enter small intestines)- stimulate secretion and fluid loss. Transmitted in developing countries through poor sanitation and use of human feces as fertilizer on food crops.

Why not always make the enzymes needed for digesting lactose?

Making enzymes requires energy and resources, it would be a giant waste to make enzymes that you don't need. You want to be able to do is to keep a close eye on your environment and make only those enzymes that you can use and if your environment changes, you want to be able to change your enzyme expression quickly. Bacteria do that by using operons.

Other Common Causes of Acute Otitis Media

Moraxella catarrhalis (3rd most common cause) - a gram negative diplococcus Staphylococcus aureus Streptococus pyogenes

Rhinitis or Common Cold

Many viruses (200+) can cause rhinitis.

Pneumonia Infections

Means inflammatory fluids in the alveoli, there are multiple microbes that can result in pneumonia. Lobar pneumonia = one lobe infected. Bronchopneumonia = many areas of both lungs. Symptoms are difficulty breathing, chest pain, coughing, fever and chills, confusion, headache, muscle pain and fatigue. Can lead to respiratory failure (can't breathe on your own, need a ventilator), bacteremia (bacteria in lungs travels to bloodstream to affect other areas), abscess (collection of fluid and pus in lungs, if around outside is empyema). Treatments are antibiotics (for bacteria or parasite), antivirals (if flu virus), anti fungal medication (for fungus), rest and fluids, over the counter anti-fever and pain medications, or intravenous antibiotics and oxygen if severe. Major players (all with different pathology/transmission): Streptococcus pneumoniae Legionella pneumophila Respiratory Syncytial Virus Influenza

MERS - Middle Eastern Respiratory Syndrome

More recently, a new strain of Coronavirus called MERS-CoV has emerged in the Middle East. Most people infected with MERS-CoV develop severe acute respiratory illness, including fever, cough, and shortness of breath. Like SARS, this novel coronavirus had proved just as deadly. Causes death in about half of cases. Severe cases can cause pneumonia, diarrhea, kidney failure, and death. New to humans.

Streptococcus Pneumoniae

Most common cause of acute otitis media. Endogenous pneumococcus can gain access to the chamber of the middle ear by way of the eustachian tube thanks in part to the fluid build up and inflammation caused by a concurrent viral infection. When the pneumococcus encounters the mucus and fluid in the middle ear, it multiplies rapidly, leading to an increased inflammatory response and pus production. As the fluid and pressure increase in the middle ear, symptoms develop that include sensation of fullness or pain the ear and loss of hearing.

Tooth Decay Video

Most common disease in the world. Plaque bacteria turn sugars into acid which eat at our tooth enamel but our spit is full of minerals that replace those the acids destroy. If more minerals are eaten than replaced, you get a cavity. When decay hits pulp area, you get a tooth ache. Avoid this with less sugary snacks, flossing, and brushing.

Pinworm aka Enterobius Vermicularis

Most common helminth infection in the USA and affects 200 million worldwide. Infection most prevalent among small children (infects 20% of all school children) and institutionalized persons. Seldom produce serious disease but may cause considerable discomfort. At night female pinworms deposit eggs on anal canal. Eggs ingested in household dust, from contaminated clothing or bedding. Eggs hatch in small intestines; larvae mature in large intestines. Adult females migrate out of rectum to deposit eggs. Infective eggs can spread to the same person (auto infection or others by putting contaminated fingers into their mouths. Infection known as enterobiasis; the most typical symptom is intense parietal itching (pruritus). Anal pruritus in small children leads to loss of sleep, irritability, and frequent scratching of anal and vulval areas. Diagnosis by sample perianal skin for eggs using scotch tape early in the morning. Microscopically check for eggs on tape.

Giant Intestinal Roundworm aka Ascaris Lumbricoides

Most common helminth infection worldwide, 2nd highest in USA. Transmission is via ingestion of eggs (5 F's - feces, food, flies, fingers, fomites). Low workloads are well tolerated but a large workload can cause serious illness. Larvae hatch in small intestine, exit the intestinal wall, and migrate through the vasculature into the liver, heart, and lungs (liver to lung migration). In lungs: larvae burst through the alveoli, crawl up trachea/pharynx where they are coughed up and swallowed, going back to the GI tract where they mature to adults. Females release eggs in stool (up to 200,000 eggs per day). Infection is called ascariasis, adults stay in intestines; low worm burdens are often asymptomatic. Heavy worm burden leads to tangled mass, abdominal pain and intestinal obstruction. Adults may move to other parts. In developing nations, cause malnourishment, physical and mental damage by starving host.

Causative Agents of Common Cold

Most common: Rhinovirus, coronavirus, parainfluenza virus. Other Causes: Influenza, respiratory syncytial virus, and adenoviruses.

DNA Mutations

Mutations are changes in genetic material. Spontaneous mutations occur constantly in all organism's DNA. Mutagens drastically increase frequency of mutations; i.e. chemicals, UV light and radiation. Not dangerous to DNA, but that information is used to make proteins, which may cause changes in protein shape and function. Substitution mutations; one nucleotide is switched; can cause missense mutation if one amino acid is changed (maybe catastrophic maybe not), can cause nonsense mutation if creates stop codon and cuts off protein creation (can be really bad if early on in protein read). Frameshift mutations; insertion or deletion of nucleotide, particularly dangerous since it changes one or more nucleotides after. Insertion if added, deletion if removed.

Regulatory Gene

NOT AN ACTUAL PART OF THE OPERON BUT IS ESSENTIAL TO ITS FUNCTION It is a gene somewhere else in the DNA and it has it's own promoter and termination sequence. The regulatory gene is constantly expressed and it produces a protein called the REPRESSOR protein. So, that Repressor protein is constantly made and floating around in the cell. When the repressor is active, it will bind to the operator to block transcription and when the repressor is inactive it does not bind to the operator.

Salmonella

Non-coliform member. Highly motile, encapsulated organisms. Over 1700 serotypes. Of all serotypes, salmonella typhi is unique in having no nonhuman animal reservoirs, only human to human. Produces hydrogen sulfide, H2S (how it is differentiated from shigella). Salmonella Typhi is the most serious pathogen, etiological agent of typhoid fever, humans are only host and reservoir. Fecal-oral transmission. Some people are permanent carriers, i.e. Typhoid Mary, a cook who infected 51 people, 3 died. Infections are uncommon in developed countries (about 500 cases yearly in the USA), versus underdeveloped world (17 million cases/year with 600,000 deaths). Feces-contaminated food or water is ingested and motile bacilli attaches to intestinal cells. Gradual onset of headache, loss of appetite, lethargy, fever, abdominal pain, followed by few short bouts of diarrhea after second week. Disease varies from prolonged, mild, self-resolving fever, but can lead to perforations in small intestine leading to death. Salmonella enteritidis has about 1700 serotypes (including S. typhimurium). Normal animal intestinal flora (cows, chickens, rodents, reptiles). Transmission mainly from raw poultry or eggs, reptilian pets, or raw milk. One of the leading causes of gastroenteritis and acute diarrhea. Bacteria is ingested and they invade small intestine epithelial cells. Usually self-limiting in the healthy, causing fever and an inflammatory but watery diarrhea with abdominal pain, nausea, and vomiting.

Shigella

Non-motile gram - rods. Do not produce H2S. Etiological agent of bactillary dysentery, a disease marked by crippling abdominal cramps and frequent diarrhea with mucus and blood. Important species are S. dysenteriae (severest form), S. boydii and both S. sonnei and S. flexneri (found in US) Only found in human and ape gastrointestinal tract. Transmission through fecal-oral spread. Feces-contaminted food or water is ingested and the non-motile shigella is phagocytosed into the large intestines where they survive in the phagosome and multiply. They are invasive and spread to adjacent cells and stimulate an inflammatory immune response that causes extensive tissue destruction. Also release endotoxin and exotoxin (shiga toxin). Shiga toxin cleaves the 60S ribosome, inhibiting protein synthesis. Shigellosis symptoms vary widely, depending on the patient's nutritional status and age, the infective strain, and dose.

Urinary Tract Infections

One of the most common bacterial infections in humans. By the age of 30, at least 20% of all women have experienced an episode of UTI, and over 50% have one or more lifetime UTIs. The greater frequency of UTI in women is attributable to a shorter urethra compared to males, and a closer proximity of the urethra to the anus, where fecal material harboring enteric bacteria can contaminate the urethral opening. A shorter urethra makes it more likely that bacteria can quickly make its way to the bladder, resulting in a urinary tract infection. A lower urinary tract infection is an infection or the urethra, bladder, or both. Bladder infection leads to burning sensation, pressure, frequent urination, and unpleasant smelling urine that may have blood; most common cause is bacteria. Colds can't cause bladder infections. Antibiotics can help speed up getting better. To prevent infections, drink 2 liters daily, urinate frequently, and don't resist the urge to go to bathroom, always completely empty all urine, and urinate after sex. Causes are not enough fluid intake, sexual intercourse, bad hygiene, bladder or kidney stones, pregnancy, menopause, diabetes mellitus, a catheter, birth defects, and chemicals. Urinary tract infections usually occur when normal flora in the gastrointestinal tract ascend up the urethra into the bladder. Normally, the flushing action of urine helps to keep infections at bay but if urine flow is reduced or bacteria are introduced into the bladder, a bladder infection (known as cystitis) can occur. If the infection then spreads to the kidneys it is called pyelonephritis. Signs and symptoms of cystitis include burning pain upon urination (dysuria), frequent urges to urinate even when the bladder is empty, pain in the pubic area, fever and nausea. Cloudy urine is indicative of the presence of bacteria and white blood cells, and an orange or red tinge from the presence of red blood cells (hematuria) may be found in the urine. If back pain is present, this is a sign that the kidneys are now involved in the infection (pyelonephritis). The main causes of bacterial UTIs (which combined account for 95% of all cystitis and pyelonephritis cases) are the following opportunistic normal flora: Escherichia coli - Escherichia coli (a gram negative bacillus) is by far the most common cause of urinary tract infection, accounting for 80-85% of acute cystitis. The species of E. coli that cause UTIs are different from those that cause diarrhea and are known as UPEC - Uropathogenic E. coli. UPEC strains do exist as normal flora in the GI tract and they have a variety of virulence factors that facilitates their infection in the urinary tract. These include: 1) numerous fimbriae with adhesins that specifically attach to the epithelial cells lining the urinary tract, and 2) motility that is adapted to allow UPEC to ascend the urinary system quickly. Other factors promoting UTI with E. coli include sexual intercourse and urinary catheters, the latter accounting for UTIs being the most common of nosocomial infections. Staphylococcus saprophyticus - Staphylococcus saprophyticus is an opportunistic gram positive staphylococci that is responsible for 5-15% of acute cystitis. S. saprophyticus can be a resident of the skin, gastrointestinal tract, and vagina. UTIs caused by this organism is found almost exclusively in sexually active young woman and is the second most common cause of urinary infections in this age group. Cultures of S. saprophyticus can be differentiated from Staphylococcus aureus because they lack Coagulase (thus referred to as Coagulase-negative staphylococci) and S. saprophyticusis Novobiocin resistant, unlike S. aureus which is sensitive to Novobiocin. Proteus mirabilis - Proteus mirabilis is a gram (-) bacillus and an opportunistic non-coliform enteric that can also cause urinary infection. P. mirabilis is of particular importance because it can lead to the formation of kidney stones in patients through its production of urease. Urease is an enzyme that catalyzes urea (a major solute in urine) into CO2 and ammonia. Proteus can grow well in urine and its urease activity causes an increase in ammonia which in turn increases the urine pH (alkaline). Ammonia and the alkaline environment are factors in the formation of kidney stones. Has fimbriae for attachment to epithelial cells of the urinary tract and is highly motile, especially when hyperflagellated. P. mirabilis can swarm on the surface of moist agar and create distinguishing concentric rings which can be used for laboratory identification. Proteus can also be identified by testing positive for urease and H2S(hydrogen sulfide) production. All UTIs are treated with antibiotics and prevention comes by way of basic practices such as emptying the bladder frequently and (especially for females) wiping from front to back after a bowel movement. Scientific studies have found that components in cranberry juice discourage attachment of UPEC to the urinary tract, hence drinking cranberry juice is encouraged for people who are predisposed to UTIs. Another bacterium that we are including in this UTI section is Leptospira interrogans, a spirochete with very tight coils and characteristic hooked ends. An infection with this organism is known as Leptospirosis. Leptospirosis is a zoonotic infection (primarily an animal disease accidentally transmitted to humans) that is transmitted to humans via contact with contaminated animal urine. L. interrogans can affect the kidneys, along with the liver, brain, and eyes. In infected domesticated or wild animals, Leptospira interrogans invades and grows inside the kidney. Animals shed the spirochete in their urine and contaminate water (rivers, streams, swimming pools). Once in the water, humans can come in contact with Leptospira interrogans through broken skin or the mucous membranes. Leptospirosis is an occupational hazard of sewer workers, rice farmers, slaughterhouse workers, veterinarians, dairy farmers and military personnel. There has even been a case of athletes competing in the swimming phase of a triathlon contracting leptospirosis from the water. The incidence of Leptospirosis increases in times of natural disasters like hurricanes and floods where humans and animals are wading in water. Leptospirosis has two phases: 1) an early phase where L. interrogans can be found in the blood and CSF. Symptoms include fever, headache, muscle aches, conjunctivitis and vomiting; 2) the immune phase which causes meningitis, and Weil's Syndrome, a condition characterized by kidney invasion, liver disease, jaundice, anemia, and neurological disturbances. Death can result if left untreated due to severe kidney and liver damage. Leptospirosis can be treated with antibiotics, the sooner the better. Prevention includes a vaccine only made available for military personnel who train in jungle regions and animal care and livestock workers. For the general population, the best prevention is wearing protective clothing and avoid swimming and wading in natural water sources that are frequented by livestock.

Influenza Virus

One of the most prevalent viral infections that varies dramatically in severity and transmission from one strain to another. Seasonal epidemic the last few winters. The CDC keeps track of influenza diagnoses and when they hit a certain level, an epidemic is declared. Since children generally have the most severe influenza cases, it's no surprise to see a similar pattern with influenza-associated pediatric death rates and of course, rates were higher this past winter than they have been in awhile. The particular strains identified by the CDC are also constantly monitored, here is the data from last winter. When we have an early and intense flu epidemic by Influenza A there is often a second wave of Influenza B infections later in the winter.

Common Cold Virus

Only replicate in living cells. Simple and consist of genetic material, protein coat, and sometimes a lipid envelope. Common causes are adenovirus, rhinovirus (most), influenza, and coronavirus. Bind to ICAM-1 Receptor on epithelial cells to allow virus DNA into host cell, it then takes over machinery to make more of itself, then it bursts to release more of itself. Symptoms caused by immune system reaction to virus invasion. When cells are infected by viruses, they release chemokine and cytokine to start defending; causing cold symptoms. Common medicines limit symptoms and often cause the cold to last longer, since it eliminates the body's defense systems. Best way is by own immune system, rest, hydration, zinc, and prevention.

Influenza Video

Orthomyxovirus; enveloped, (4-8 segments) segmented ssRNA genome. Types A, B, and C. Causes influenza / "flu". 2 important envelope glycoprotein spikes; hemagglutinin (HA) - binds to host cell receptors of respiratory mucosa, neuraminidase (NA) - assist in viral bussing and release / breaks down mucous so hemagglutinin can attach easier. Different types of HA, NA, and these help give influenza their name. H1N1 is HA type 1, NA type 1.

Helmiths

Parasitic worms causing infection in humans. Multicellular animals with organs for reproduction, digestion, movement, and protection. About 50 species parasitize humans. Distributed worldwide; some restricted to certain geographic regions with higher incidence in tropics. Acquired through ingestion of larvae or eggs in food; from soil or water, some are carried by insect vectors. Afflict billions of humans.

Helicobacter Pylori

Pathogen has made the harsh, acidic environment of the stomach its home. Curved, spiral-shaped, gram-negative bacilli with a lophotrichous flagellar arrangement. Helicobacter pylori is highly motile and quickly bores into the stomach epithelium where it binds to specific binding sites on these cells and entrenches itself. In fact, one specific receptor that Helicobacter binds to is the same molecule on RBCs that confers the O blood type, hence the higher rates of stomach ulcers caused by this pathogen in people with this blood type. To protect itself against stomach acids, Helicobacter pylori secrete urease which hydrolyzes stomach urea to produce an alkaline ammonia cloud. This cloud neutralizes stomach acid and protects the pathogen as it makes its way through the stomach. Helicobacter pylori is Implicated in 90% of stomach and duodenal ulcers (also called peptic ulcers). Before this bacterium was discovered, it was believed that spicy foods and stress caused these ulcers, but now it appears that these factors merely aggravate the ulcers caused by the pathogen. The notion that a bacteria was the cause of ulcers was so controversial at the time that the researcher who introduced this idea drank broth with Helicobacter to prove his theory to a skeptical scientific community. Sure enough, he developed gastritis and went on to win the Nobel prize.

Periodontal Disease

Periodontal disease is one of the most common human infections with nearly 100% of the population developing some form of this disease by age 45. Like dental caries, the causative agent of periodontal disease is not attributed to a single organism, but to a community of oral biota. When plaque biofilms consist of the right combination of bacteria, such as the anaerobes Fusobacterium and Porphyromonas gingivalis, the periodontal destruction process begins. These bacteria are obligate anaerobes that are gram negative rods. These organisms naturally produce metabolic byproducts that are foul-smelling and are the cause of bad breath in individuals. The initial stage of periodontal disease is gingivitis, inflammation of the gingiva (gums) that causes swelling, redness, and bleeding of the gums. This is reversible if the plaque is removed with proper toothbrushing. If untreated, the receding gums can expose pockets of varying depths alongside the teeth, causing the inflammation to spread to bone and other deeper tissues, leading to periodontitis. The deeper the pockets, the more likely teeth can become loosened and fall off. Other signs of periodontal disease are the formation and buildup of calculus(plaque that has become calcified to produce a hard and porous substance). The presence of calculus leads to inflammation and bacterial disease progression. In the picture below, calculus can be seen in the tartar region. Regular brushing and flossing is the best form of prevention to remove plaque buildup. This reduces both caries and calculus production. Once calculus has formed on teeth, it can not be removed by brushing but by special mechanical procedures in the dentist office. Periodontal disease is treated by removing calculus and plaque and maintaining good oral hygiene. Dental surgery can be performed to reduce the depth of periodontal pockets.

Parts of an Operon

Promoter: The region of the DNA where RNA polymerase will bind. It marks the start of gene, but does NOT contain DNA that is expressed. Operator: The DNA sequence right after the promoter that controls whether or not RNA polymerase can bind to promoter. It does not contain DNA that is expressed. Structural Genes: The actual genes involved in the function of the operon (in our example these are the enzymes needed to digest lactose.) These genes are all together in a straight line and they are the DNA that IS expressed. Termination Sequence (or Terminator): The sequence where RNA polymerase disconnects from the DNA and stops transcription. It marks the end of the transcribed gene, but does NOT contain DNA that is expressed.

RNA vs DNA

RNA (ribonucleic acid) is different from DNA (deoxy ribonucleic acid). Remember that DNA is made of building blocks called nucleotides and those nucleotides are made of a sugar (deoxy ribose), a phosphate group, and a nitrogenous base (Adenine, Thymine, Guanine or Cytosine). The nucleotides are assembled into strands and two strands come together to form the DNA double helix. RNA is also a nucleic acid that is made of nucleotides. The RNA nucleotides are made of the sugar ribose, a phosphate group and a nitrogenous base. There is a change in the nitrogenous bases because we don't have Thymine in RNA, instead we have Uracil. So the base pair rules for RNA would be: C-G and A-U. RNA is a single stranded molecule so you don't have the same helix structure.

Transcription

RNA polymerase binds to the promoter. RNA polymerase adds nucleotides complementary to the template strand of DNA in the antiparallel 5' to 3' direction. Uracil is used in place of Thymine. RNA polymerase falls off the DNA and stops transcription at the termination signal (terminator).

Strep Throat Diagnosis

Rapid Strep Test for streptococcus pyogenes antigen in patient swab. Other swab for confirmatory diagnosis and culturing on blood agar to look for beta hemolysis. Better to treat, but 99% of the time fine without treatment, you just get better faster. Rare to have strep under 1-2 years old.

Thioglycolate Results Interpretation

Reducing medium - contains a substance that absorbs oxygen or slows penetration of oxygen into medium. Aerobe: Must only be able to do aerobic respiration since it can only grow where there is oxygen available. Anaerobe: Must only be able to do anaerobic respiration. It can't be doing aerobic respiration since there is no growth in oxygen and it can't be doing fermentation since ALL fermentors can also do aerobic respiration. Facultative Anaerobe: Must be doing aerobic respiration at the top of the tube and able to do either anaerobic respiration and/or fermentation at the bottom of the tube. It's possible this organism can do all 3 modes of catabolism (like E. coli can).

Common URI Viruses

Rhinovirus - common cold. Influenza Coronavirus Adenovirus URIs are usually viral.

Ribosome Binding Site of Translation

Ribosome has small and large subunit that assembles around the mRNA, there are two major tRNA binding sites; the A site (first site for tRNA) and P site. Exit site allows tRNA to leave the ribosome quickly. All activity starts at start codon, then first tRNA anticodon binds to mRNA codon, then brings the first amino acid (methionine). The second tRNA then comes into the A site and binds its anticodon to the second codon of the mRNA to bring the second amino acid. The two amino acids form a peptide bond, and the first tRNA is kicked as the ribosome moves. Second tRNA ends up in P site, and new tRNA enters A site to bind to the third codon. Another peptide bond forms and the ribosome moves one codon further and the empty tRNA is kicked by the exit site. Translation works as the ribosome moves along the mRNA one codon at a time, the tRNA bringing the amino acids one at a time. This process continues until there is a stop codon, and all the pieces fly apart (two pieces of ribosome, tRNAs, and new protein released). Process can be very efficient, with transcription and translation happening at the same time.

Pertussis Video

Rod shaped bacteria infecting respiratory tract. Highly contagious and travels by mucus being coughed or sneezed into the air, can also be transferred by shared surfaces. Clinical timeline is 12 weeks, no clinical symptoms for about 12 weeks; 3 stages: onset of symptoms for about 2 weeks is catarrhal stage. Catarrhal stage is inflammation of respiratory tract with increased secretions, runny nose with sneezing, small cough, and low grade fever. Most contagious stage because the bacteria has not been killed yet by the immune system so it is dividing in high numbers and each sneeze expels it into the air, the onset of symptoms, a patient should stay away from others for around 21 days. By then the body has created antibodies against pertussis, which tag it as a foreign invader needing to be killed by the immune system. The next 2-8 weeks is the paroxysmal stage, most bacteria is dead so not as contagious, but damage and inflammation caused leading till now can cause coughing fits and whooping noises. Paroxysm is a fit or reoccurrence of a symptom; here it's coughing and the coughing fits are exhausting and followed by vomiting and other problems by forcefulness of cough. Last stage is convalescent stage, weeks 8-12. Convalescense means recovery, and that's what the body is doing now that the infection is gone. Over time, frequency and intensity of cough goes away but it takes a while which is why it's called the 100 day cough. Stages can be harder to decipher based on a few modifying factors; anything that changes the length or severity of disease; i.e. age, immunization status,

SARS - Severe Acute Respiratory Syndrome

SARS is a viral respiratory illness caused by a Coronavirus. It is often referred to as the SARS-associated Coronavirus (SARS-CoV). SARS was first reported in Asia in February 2003. The illness spread to more than two dozen countries in North America, South America, Europe, and Asia before the SARS global outbreak of 2003 was contained. The SARS-coronavirus originated in bats and previously infected only palm civets and ferret badgers. Consumption of civets by humans in China selected for mutations that expanded the virus host range and facilitated human transmission. From there, the virus was able to be transmitted through droplet or direct contact from human to human. Symptoms of SARS included fever, body ache, and malaise. Patients may or may not experience respiratory symptoms with breathing problems but severe cases could result in respiratory distress and death.

SARS-CoV-2 and COVID-19

SARS-CoV-2 is a coronavirus and very closely related to the SARS virus. This virus is likely to have spilled over from bats around Wuhan China since nearly identical strains have been isolated in wild bat populations in the area. It is possible that there was an intermediary host between bats and humans but we don't know that yet. One thing that does seem to be clear is that this newer coronavirus is very contagious and more easily transmitted between humans than it's closest known relative. On average, each person to have the virus infects 5-6 others. People can pass the infection before showing symptoms, i.e. presymptomatic transmission. Also asymptomatic transmission, passing the disease without ever being sick themselves. Older diseases needed more large droplets of fluid like coughing or sneezing, but covid-19 works by smaller droplets or a more infectious dose (more virus per droplet). Enter body via ACE2 enzyme found in human respiratory system that lowers blood pressure. Spike protein grabs onto ACE2; the covid-19 spike protein is 10x better at binding than SARS-2. The better at binding, the less viruses you need to infect a cell, so it's infectious dose may be lower than SARS and other respiratory viruses. There may even be an extra chunk of the spike protein that makes it stronger at infecting. Hijacks endocytosis to enter cells, instead of being digested it breaks out, covid may be able to do this more efficiently than other viruses. Is also better at evading the immune system. People with covid-19 can have huge viral loads even when not too sick. Peak viral load for covid can be really early on before symptoms even appear. As the number of Covid-19 cases continue to increase, new nucleic acid vaccine is in phase III clinical trial. It has been shown to be 90% effective in preventing the disease in more than 40.000 participants but it is not known whether is can prevent severe cases of Covid-19. We will know more about its efficacy as the scientists continue to collect data about the trial participants.

Complications of Strep Throat

Scarlet Fever Rheumatic Fever Glomerulonephritis

Coronaviruses

Second most common cause of common cold. Relatively large RNA viruses with distinctively spaced spikes on their envelopes. Common in domesticated animals. Grow best at 33-35 degrees celsius. Infections peak around winter and spring (colder months). Symptoms similar to rhinovirus but with greater nasal discharge.

Haemophilus Influenza

Second most common cause of otitis media. Similar to the pneumococcus, it predominantly causes ear infection in young children and it may arise from endogenous infection following a viral upper respiratory tract infection.

Pharyngitis

Sore throat, varied pain.Many sore throats are side effects from other respiratory infections that have multiple symptoms (like a cold with sneezing or the flu with intense fever and congestion.) 3 pathogens specifically affecting the throat; adenovirus (serotypes 1-7), Corynebacterium diphtheriae and Diptheria, and Streptococcus pyogenes.

Respiratory System

Split into upper respiratory tract ; which includes the mouth, nose, nasal cavity, and sinuses, the throat (pharynx), the epiglottis, and larynx (or voice box). Also the lower respiratory tract; which begins with the trachea and also includes the bronchi, bronchioles, and the lungs.

Staphylococcus aureus Enterotoxin

Staphylococcus aureus is responsible for numerous infections throughout the human body. S. aureus is also one of the most common causes of acute food poisoning, especially from eating foods that are rich in carbohydrates such as custards, cream pastries, and especially potato salad. It is also associated with processed meats, chicken salad, and ham (recall that Staphylococcus are halotolerant). Staph food poisoning is caused by release of an enterotoxin. Enterotoxins are a type of exotoxin that act upon the gastrointestinal tract of humans which induce nausea, vomiting, and diarrhea. The illness does not require the actual bacteria to be present or alive in the contaminated food as the toxin alone is sufficient for causing symptoms. If the bacterium is allowed to multiply in the food, it produces its toxin. Even if the bacteria are subsequently destroyed by heating or reheating, the preformed toxin will act quickly once it is ingested. The Staph enterotoxin is heat-stable; inactivation requires 100 degrees C for at least 30 minutes. As a result, heating food after toxin production may not prevent disease. Ingestion of the enterotoxin causes acute symptoms of vomiting, diarrhea and abdominal cramping within 1-6 hours post-ingestion. Recovery is also rapid, usually within 24 hours. Often, a single food source will cause disease in several people, leading to a mini-outbreak. Prevention comes from proper food handling which includes washing hands, fruits and vegetables, and keeping cooked hot foods hot [140°F (60°C) or above] and cold foods cold [40°F (4°C) or below].

Tryptophan Operon

Structural genes contain the enzymes needed to synthesize tryptophan. Normally transcription is on. Tryptophan turns transcription of the operon off. Tryptophan operon is repressible. Try repressor is synthesized in its inactive form. Default is transcription is on.

DTaP Vaccine

The DTaP vaccine is a combination toxoid vaccine for diptheria ("D"), tetanus ("T") and pertussis which is also called whooping cough ("aP"). While diptheria rates have dropped significantly with vaccination we have seen outbreaks when herd immunity is lost. Interestingly, when they screened seemingly healthy people several years ago they still found C. diptheriae amongst them indicating that the vaccine is still necessary to prevent outbreaks of diptheria even here in the US!

Electron Transport System (ETS)

The ETS is located in the inner membrane of the mitochondria for an eukaryote and the ETS is in the cell membrane of a prokaryote. The ETS is made of several membrane bound proteins that will transfer the electrons from NADH and FADH2 down the line of proteins through a series of redox reactions and finally onto oxygen making oxygen the final electron acceptor. During all of this action, H+ will be pumped across the inner membrane of the mitochondria and get trapped between the 2 membranes. Over time, a large concentration difference of H+ develops across the inner mitochondrial membrane where there are a lot of H+ trapped between the mitochondrial membranes and very little H+ left inside the mitochondrial matrix. This form of potential energy is called proton motive force (pmf). The pmf then pushes H+ through ATP synthase back into the mitochondria matrix and as protons move through ATP synthase, it makes ATP from ADP. When NADH drops off it's electrons onto the ETS it makes enough pmf to produce 3 ATP and each FADH2 makes enough pmf to produce 2 ATP. Since glycolysis and the TCA cycle gave us 10 NADH and 2 FADH2, that makes a whooping 34 ATP that are made during the ETS.

Mumps

The Mumps virus is a Paramyxovirus that belongs to the same family of viruses which include measles and parainfluenza. All members of the Paramyxoviruses are RNA, enveloped viruses. The mumps virus targets the salivary glands (shown above). Humans are the only reservoir and transmission is via salivary and respiratory secretions. Symptoms of a mumps infection includes fever, malaise, and inflammation of the salivary glands (especially the parotid glands - Parotitis). The best form of prevention against Mumps is through the live, attenuated MMR vaccine. Recall that Mumps infection can often lead to meningitis and possible neurological damage so vaccination is highly recommended.

Fermentation

The last catabolic strategy is fermentation. Fermentation is done by some prokaryotes and some eukaryotes but only if those cells find themselves without access to oxygen. There are a lot of different ways fermentation can happen but they generally fall into 2 categories: alcohol fermentation pathways and acid fermentation pathways. In either case, organisms doing this process first start with glycolysis and it's the same glycolysis that we've seen before, 1 glucose going in and yielding 2 pyruvate, 2 NADH and 2 ATP. Now, the pyruvate enters into a fermentation pathway where it gets broken down into an acid or an alcohol. Sometimes some carbon dioxide gas is released during fermentation but there is never more ATP made beyond the 2 in glycolysis. Without a doubt, the most important part of fermentation is that it oxidizes the NADH back to NAD+. This is absolutely essential because if NADH isn't oxidized, glycolysis will stop! There are lots of different versions of fermentation and some organisms can do multiple kinds of fermentation releasing a mixture of acids and/or alcohols during fermentation. Some of these fermentation products are interesting and helpful in food production. Yeasts fermenting to produce alcohol is essential for the production of beer, wine and spirits. Yeast fermentation also causes bread to rise in baking. Lactobacillus fermentation of milk to produce lactic acid causes the milk proteins to curdle which is the first step in yogurt and cheese making. Propionibacteriumfermentation releases propionic acid which causes the mild acid taste of swiss cheese. Propionibacterium fermentation also releases some carbon dioxide gas which causes the hole in swiss cheese. Gluconobacter and Acetobacterium ferment to produce acetic acid which is the beginning of making vinegar.

Protein Expression

The making of proteins. Central dogma of biology. 2 steps are transcription and translation.

Viridans Streptococci

The most numerous and widespread residents of the oral cavity, nasopharynx, genital tract, and skin. At least 24 species have been identified and have been divided into 5 groups. Some other examples include Streptococcus sobrinus, Streptococcus mitis, Streptococcus salivarius, and Streptococcus sanguinis. In the presence of sucrose and other sugary substances, these bacteria produce sticky polymers of glucose called fructans and glucans. These polymers initiate the formation of plaque biofilm. If these biofilms are not removed through good dental hygiene practices, the streptococci and other oral bacteria begin to produce acid as they ferment the carbohydrates and start to erode away at teeth.

Infection of Salivary Glands

The oral cavity contains 3 pairs of salivary glands, and during certain infections, these can become inflammed.

Repressible Operons

The other kind of operon is a repressible operon. In a repressible operon the repressor protein is made in it's inactive form which means the repressor is not binding to the operator so transcription is happening. In other words: inactive repressor = repressor not bound to the operator = RNA polymerase is able to bind to the promoter = transcription is happening. So in a repressible operon, the default situation is transcription on. Repressible operons have to be able to respond to their environment and stop transcription. They do this through a substance called the COREPRESSOR. A corepressor is something that will bind to the repressor and activate that repressor protein. When the repressor is active, it binds to the operator and stops transcription.

Influenza Lifecycles

The segmented genome complicates the packaging of new viruses. If more than 1 flu virus infects the cell, the genome segments could get mixed up during packaging, called antigenic shift (mixing up of two viruses to create a new combination of virus).

Microbial Metabolism

The term "metabolism" often gets used incorrectly.... People often talk about their "metabolism" as how fast their body breaks down the food that they eat. While metabolism does include these degradation pathways, it also includes lots more biochemical reactions. Metabolism is the term to describe all of the chemical reactions and physical processes occurring in a cell. So everything from breaking down the sandwich you ate for lunch to making new cellular membrane would be part of "metabolism". Metabolic processes are often sorted into 2 groups: Catabolism are the degradation pathways that break down large macromolecules into smaller molecules. Catabolic processes release energy. Anabolism are the biosynthetic pathways that use small molecules to build larger ones. Anabolic processes require some energy input. The cell stores the energy released during catabolism as ATP and then uses the ATP to drive anabolism.

Aerobic Respiration Step 2: Tricarboxylic Acid Cycle

The tricarboxylic acid cycle (TCA) is known by 2 other names: Kreb's cycle and citric acid cycle. Isn't it fun when scientists use 3 names for the very same thing?!?! Location: The TCA cycle happens in the cytoplasm of prokaryotes and in the mitochondria matrix of the eukaryote (the matrix is the very center of the mitochondria.) Black Box Approach: After the pyruvate leaves glycolysis it heads to the TCA cycle. There is a little processing step that happens turning the pyruvate into acetyl coA and then it enters into the TCA cycle where it gets broken down into carbon dioxide. A couple more ATP are made during the TCA cycle and we also get some more NADH and some FADH2. Counts: For each pyruvate that heads to the TCA cycle, you yield 1 ATP, 4 NADH and 1 FADH2along with 3 CO2. Usually, however, these numbers are expressed per glucose and since 1 glucose made 2 pyruvates during glycolysis, the per glucose values for the TCA cycle are double: 2 ATP, 8 NADH, 2 FADH2 and 6CO2.

Adenovirus (Serotypes 1-7)

There are over 30 serotypes of Adenoviruses that can infect humans through the respiratory mucosa, gastrointestinal epithelia and/or conjunctiva of the eye. Serotypes 1-7 are specifically involved in the upper respiratory tract and conjunctiva so they can cause colds, pharyngitis, conjunctivitis and combinations of these (ever had a sore throat with irritated, watery eyes?) Therefore, the common symptoms for Adenovirus 1-7 would be fever, sore throat, red inflamed throat and/or conjunctiva and possible photophobia. While there are treatments to ease discomfort (like eye drops and throat lozenges), we can't cure the infection since it is viral. The good news, however, is that this is a relatively mild infection for most patients and is self limiting. Most patients will fully recover on their own within 1-2 weeks.

Protistan Infections That Can Cause Diarrhea

These protistan infections that can also impact the GI tract. These protists are from different supergroups, but share the distinction of causing diarrhea and the most common route of infection is via fecally-contaminated water. Cryptosporidium spp. Entamoeba histolytica Giardia intestinalis

Legionella Pneumophila

This Gram negative bacillus is a strict aerobe that grows in close association with an amoeba in lots of fresh water environments including ponds, pools, cooling towers and air conditioning units. When aerosolized droplets of contaminated water are inhaled, it can result in Legionnaires' disease which presents with a high fever, cough, chills, respiratory infections, diarrhea, abdominal pain and possibly, pneumonia (mainly in the elderly and debilitated patients who are diabetic or alcoholics). There have been several outbreaks of Legionnaires' disease and a more mild reaction, Pontiac Fever, that is caused by the same pathogen but rarely moves into the lungs. Outbreaks have been associated with air conditioning units, misters, hot tubs, etc. Perhaps the last pathogen you would worry about at the Playboy mansion, Legionella was isolated from fog machines and the famous "Grotto" after an outbreak was traced back to a party at the mansion. Legionella pneumophila is a pretty unusual organism when it comes to lung infections because it is acquired through the inhalation of contaminated water droplets. During an outbreak of Legionnaires' disease it is often suspected based on epidemiological information. If, for example, you have a group of people that work in the same building coming down with pneumonia but none of their family members got sick....sounds like contamination from the building and all possible water sources should be tested and thoroughly cleaned.

Inner Lining of the Respiratory Tract

To defend against dust, debris, and microorganisms that are always found in the large volumes of air we breathe, this lining contains mucus that acts as a natural trap for invading microbes and ciliated epithelial cells that propel these particles stuck to the mucus upward and out of the respiratory tract. The cough and sneeze reflexes help to expel these invaders completely.

HAV Transmission

Transmission of HAV is through the fecal-oral route meaning that you ingest something contaminated by feces from an infected person. This infection is more common in places suffering from poor hygiene and sewage treatment. In this country we see HAV usually as an outbreak associated with poor hygiene with food prep. The last multi-state outbreak of HAV in the US came from packaged pomegranate seeds sold by Costco stores in multiple states (including California). The CDC traced the cases and using epidemiological information, identified the cause and stopped the epidemic. There is a vaccine available for HAV that is recommended for children but most adults are unvaccinated. You can request the vaccine from a healthcare provider or the health department but since good hygiene can prevent this infection, most americans are at a small risk for this relatively mild infection by HAV.

Trematodes (Flukes)

Trematodes (or flukes) are flat, fleshy, nofsegmented flatworms with ovoid leaflike bodies. All trematodes have complex life cycles involving snails as their intermediate hosts and water (or aquatic animal or plant) transmission to humans. Trematodes that infect humans include intestinal live, lung, and blood flukes. Fasciolopsis buski is the largest fluke that can affect human beings. Exceptionally large parasitic fluke (7.5cm) and largest known to parasitize humans. Found in Asia and India. Larval form is ingested on water plants, especially water chestnuts and bamboo shoots. Strict vegetarians are susceptible. Most infections are mild and symptoms increase with fluke burden. Signs and symptoms are local inflammation, diarrhea, and anorexia. Diagnosis through eggs released into stool and used for diagnosis by fecal sample.

Histoplasmosis

Typically dimorphic. Distributed worldwide; most prevalent in eastern and central regions of USA. Grows in moist soil high in nitrogen content (bird and bat-droppings). Inhaled conidia produce primary pulmonary infection; cave dwelling (spelunking), demolition work, and cleaning old chicken coops.

Upper Respiratory Tract Infections

Upper respiratory tract infection (URI) represents the most common acute illness evaluated in the outpatient setting. URIs range from the common cold to pharyngitis that can predispose patients to life-threatening illnesses such as pneumonia.

Respiratory Syncytial Virus (RSV)

Usually causes colds (upper respiratory tract infection) in both children and adults but unfortunately in very young children (6 months and under) it can progress to the bronchi and lungs. RSV is an enveloped RNA virus that belongs in the same viral family as Measles, Mumps and Parainfluenza. RSV is the most common form of pneumonia in very young children. There is also some evidence that if a child has a lower respiratory tract infection by RSV, it may predispose the child to getting asthma later in life. The possible asthma link isn't fully understood but we see it based on epidemiology (statistical correlation identified between LRT infection by RSV and the development of asthma.) RSV infection is so common, they estimate that 100% of kids have had RSV by the time they reach 3 years old but most of those infections present like a cold. 25-30% will have wheezing and difficulty breathing, and have a higher risk of developing asthma. The highest risk group for LRT infections are babies and most especially, premature babies due to less lung development. RSV is highly contagious via respiratory droplets and fomites and outbreaks are common during the winter. While there is no vaccine for RSV, passive immunization is available for high-risk babies, like synagis vaccine, which is given once a month in high risk times like winter (isn't actually a vaccine, it's a dose of anti-RSV antibodies that give those recipients passive immunization against RSV).

Gram - Vibrios causing Acute Diarrhea

Vibrio cholera Vibrio parahaemolyticus andVibrio vulnificus Vibrio pathogens are salt-tolerant inhabitants of coastal waters, associate with marine invertebrates (warmer waters of the atlantic). Campylobacter jejuni Helicobacter pylori (close relative to campylobacter)

Otitis Media (Ear Infection)

Viral infections of the upper respiratory tract (colds, flu, pharyngitis) can lead to inflammation of the eustachian tubes and the buildup of fluid in the middle ear. When this happens, it can lead to bacterial multiplication in those fluids and hence an ear infection called acute otitis media.

Chemiosmosis

When ATP synthase uses proton motive force to make ATP. 3 ATP for each NADH and 2 ATP for every FADH2. 10 NADH -> 30 ATP and 2FADH2 -> 4 ATP. 34 ATP per glucose in electron transport system by itself. Glycolysis and TCA each only gave 2. Proton motive force between cell wall and membrane of prokaryote. Proton motive force pushes hydrogens through ATP synthase (chemiosmosis) then ATP synthase makes ATP from ADP.

Hepatitis

When a virus infects the liver tissue the result is hepatitis (an inflammatory disease of the liver that interferes with liver function.) One of the major symptoms of hepatitis is jaundice (a yellow coloring to the skin and eyes.) Jaundice results from the lack of liver function which means that old RBCs and their components are left in the blood and tissues. One of the components in these RBCs is bilirubin, a yellow pigment which deposits into the fat of the skin and the whites of the eyes when it's not properly processed and removed by the liver. In addition to the distinct yellowing of the skin, you can often see yellowing in the whites of the eyes. The whites of the eyes are sometimes the first place you notice the jaundice. Jaundice on it's own doesn't necessarily mean infection by a virus, jaundice is a sign that the liver is not functioning properly to clear away old RBCs. In previously healthy adults, jaundice is a cause for some testing to look for a liver infection, liver cancer, cirrhosis or other liver malfunction (can be brought on by chronic drug and alcohol use.) Premature newborns are the most common to develop jaundice for a completely different reason, mom's liver did the filtering in utero and it can take some time and food intake for their livers to get started. Phototherapy helps breakdown the bilirubin into molecules that can be processed and eliminated properly by their systems. There are a number of different viruses that can infect the liver and result in hepatitis. These viruses are quite different in their structure, transmission and severity but they are grouped together as "hepatitis viruses" simply because they infect the liver.

Strep Throat

When someone that does not carry S. pyogenes in their normal throat flora is exposed, it can result in Strep Throat which is known for causing extreme throat pain. Examination would show the back of the throat would be bright red with pusand often a foul smell.

Transcription

Where the enzyme RNA Polymerase copies a gene from the DNA and the copy is made of mRNA (messenger RNA). Transcription can make tRNA, mRNA, or rRNA. Enzyme is RNA polymerase; it reads DNA and synthesizes a complementary antiparallel strand of RNA. Promoter (sequence of DNA where RNA polymerase binds) is the start sight of transcription, it is upstream of the gene being transcribed. RNA polymerase adds nucleotides complementary to the template strand of DNA in the 5' to 3' direction. Uracil in place of thymine. RNA polymerase falls off the DNA and stops transcription at the termination signal. End of transcription is termination sequence.

Translation

Where the mRNA is used to make a protein. This happens on the ribosomes and relies on tRNAs (transfer RNAs) reading the mRNA and bringing in amino acids (the building blocks of proteins.) 3 nucleotides together form a codon and provide in formation for one amino acid. Major players are ribosome (sight of transcription), mRNA (which is read to make the protein), and tRNA (read the codon to find the amino acid). tRNA has anticodons that bind to the codons on the mRNA, bringing in the amino acid (i.e. first one methionine). The amino acid codes are universal among all lifeforms, reduncy in code (same amino acid made by different codes).

Whooping Cough

Whooping cough (aka pertussis) is a common early childhood infection caused by Bordetella pertussis, a small gram negative coccobacillus pictured below. B. pertussis produces fimbriaelike adhesion molecules that allow it to find and bind to the ciliated cells that line the upper respiratory tract. These ciliated cells are tasked with removing particles from the respiratory tract before they can enter (and possibly damage) delicate lung tissue. B. pertussis also produces exotoxins that destroy and remove the ciliated cells. Without these cells, mucus will build up in the lungs and block the airways. Although there is a vaccine available (the DTap vaccine), whooping cough infections have reached epidemic proportions in California twice in recent history (2010 and 2014). This is due to a combination of childhood vaccinations not lasting through adulthood and a low vaccination rate in general. Teenagers and adults should obtain a booster vaccination prior to contact with small children and pregnant women, as whooping cough in infants can be deadly. For example, infection in adulthood only requires hospitalization approximately 5% of the time, while infants and children up to age 4 will require hospitalization 50% of the time.

Testing Oxygen Requirements

You might need to know if your unknown organism is an aerobe, anaerobe or facultative anaerobe. To do that test you will need reducing medium that absorbs or slows the penetration of oxygen into the media meaning that the top of the broth will have oxygen in it but there will be no oxygen at the bottom of the tube. The reducing medium that we use (and is found in your lab manual) is called fluid thioglycolate. When you grow your unknown in the media there are 3 possible outcomes: Aerobes grow only at the top of the media where oxygen is present, anaerobes grow only at the bottom of the media where there is not oxygen present and facultative anaerobes grow both with and without access to oxygen.

Common Cold Symptoms

Young children with croup have a very distinct sounding cough described as a "seal bark cough". Rhinorrhea (runny nose), sneezing, coughing, scratchy throat, headache, malaise, and low grade fever. Start 2-3 days after infection and are rarely due to immune response to infection. Release lots of inflammatory mediators, can localized inflammation in nose and leakage of fluids from capillaries.

Aerobic Respiration

the most commonly used catabolic strategy since ALL eukaryotes and most prokaryotes do it. Aerobic respiration is sometimes called "cellular respiration" but this isn't a great term since there are prokaryotic cells that don't do it. The overall equation for aerobic respiration is 1 glucose plus 6 oxygen molecules yields 6 carbon dioxide and 6 waters. Aerobic respiration is made up of 3 distinct steps: glycolysis, the tricarboxylic acid cycle and the electron transport system and through the entire process the cell can make 38 ATP per glucose molecule.