Case Study 1 Perspectives
Plankton is the assemblage of living organisms floating with currents in upper regions of aquatic environments such as lakes and oceans. In addition to the bacteria (called bacterioplankton) targeted by the study, plankton contains microscopic algae, which are termed phytoplankton, and protozoa and tiny animals, which make up the zooplankton. One would also expect to find some archaea and viruses. Microscopic fungi such as molds and yeasts are less likely to occur in the planktonic community.
Other specialists that could be involved in further studies of the plankton are marine ecologists, molecular biologists, biochemists, geomicrobiologists, taxonomists, bacteriologists, algologists, protozoologists, virologists, geneticists, and microbiologists with expertise in specific groups or species of microorganisms.
The ocean makes up three-fourths of the earth’s surface area, and it extends down several miles into a giant basin carved out of the earth’s crust. The existence of vast areas that have yet to be searched and sampled means that many unknown life forms are yet to be discovered. Very recently microbiologists identified species of amoebas living in the ocean that harbored the largest viruses ever discovered. These unusual viruses have a structure that is not typical of known viruses and yet they are not cells. A number of virologists are postulating that they could constitute a new, fourth domain. It will take hundreds of years of scientific exploration to reveal all of the hidden secrets of planet earth.
This ambitious undertaking was just the beginning. It was followed by additional voyages by Sorcerer II and a team from the Marine Biological Institute in Woods Hole, Massachusetts, and it is continuing today all over the globe. Dr. Venter plans to use his findings to explore potential applications for microorganisms, including developing synthetic bacteria for creating new chemical products, bioremediation of wastes, and developing alternative forms of energy.
Case Study 2 Perspectives
Water is composed of two hydrogens covalently bonded to a single oxygen. The nature of the bonding makes water molecules polar, that is, having ends with opposite charges. In its liquid form, its polarity makes it an excellent solvent for dissolving ions and numerous biological compounds. Cells require molecules dissolved in solution for most chemical reactions, which are involved in membrane function, digestion, synthesis, and other metabolic activities.
It is now clear that Mars has abundant water, but mainly in the ice and vapor form. A major unknown is whether any significant liquid water currently exists. There are surface features that point to a past history of liquid water, but right now it appears that the ice converts directly into water vapor when exposed to increasing temperatures. Some locations on the planet may have “hot spots” deeper in the crust where liquid water exists part of the time. It is here that any remnants of life are most likely to occur.
Carbon is a versatile element that can make four bonds with numerous other atoms, including other carbon atoms. It forms compounds with elongate chains, side chains, and rings that make it possible to construct the complex macromolecules like protein and DNA that are so crucial to functions and structures in cells.
It is clear that inorganic carbon in the form of carbon dioxide occur in places in the solar system that could not support life. So, even though inorganic carbon may be involved in cellular reactions like photosynthesis and respiration, non-living processes may also create them. With organic compounds, something as simple as methane may also be produced by non-living reactions, and it is not a firm indicator of life. More complex compounds such as sugars and amino acids tend to be associated with life functions and are more reliable evidence. The discovery of intact proteins or nucleic acids would be a chemical signature that truly points to life. These complex macromolecules must be synthesized, and would not ordinarily arise by random chemical reactions.
Other elements that would ordinarily be involved in the chemistry of biological forms are oxygen gas, phosphorus, sulfur, nitrogen gas, magnesium, iron (iron oxide is the reason Mars has a red color), sodium, potassium, calcium, and chloride. All of these have been tested for and found to be present in the atmosphere or soil. So, chemically at least, the major participants for life as we know it exist on Mars.
Case Study 3 Perspectives
Signs and symptoms are noticeable manifestations in a patient that can help direct diagnosis of a disease and help pinpoint which anatomical sites are affected. A sign is an objective observation that is measurable, like a fever or white blood cell count. A symptom is a subjective reportrelated to something a patient feels, for instance, a headache or pain. The most important initial diagnostic signs of infection in this case are an elevated white blood cell count, cloudy spinal fluid, and splotches on the legs. The most important symptoms are headache, stiff neck, and mental confusion.
Monitoring the cerebrospinal fluid or CSF provides a means to quickly assess the presence of infectious agents in the spinal column and the brain. The CSF bathes the brain, spinal cord and membranes and is ordinarily completely free of microbes, or sterile. If it is cloudy macroscopically, this could indicate growth of bacteria or other infectious agents. A microscopic inspection can provide immediate feedback as to a possible cause of the cloudy CSF.
A Gram stain is one of the key tests for getting quick feedback on the kind of microbes that might be present in a sample. It is routine in meningitis because it can differentiate among several types of bacteria and detect certain other infectious agents, but it will not detect viruses. Within moments, a lab technician can tell if there are bacterial cells, and they can identify their gram reaction and shape. For example, in this case the result showed gram-negative cocci, but meningitis is also commonly caused by Streptococcus pneumoniae, which would stain as gram-positive cocci, and Haemophilus influenzae, which would appear as gram-negative rods. An early clue to the microorganism also helps to instruct the types of drugs that will be given. Since meningitis can cause death in 5% to 10% of people in a few hours, early drug treatment is critical.
Neisseria meningitidis is routinely isolated and grown on blood agar, chocolate agar, and Thayer Martin medium. Its identity can be confirmed by a series of biochemical tests that differentiate it from close relatives that may look microscopically similar. See figure 3.13 for an example.
Case Study 4 Perspectives
All of the symptoms and signs in this case can be linked to endocarditis, but most of them are too non-specific to be helpful in diagnosis. The most important considerations are the constant fever, the history of a replacement heart valve, and the respiratory and circulatory symptoms. A fever of unknown origin (FUO) is often traced to a chronic infection. The artificial heart valve provides an opportunity for microorganisms to grow in the body because it readily supports a biofilm that will not be protected by the immune system. The dysfunctional valve causes blood to back up in the heart, leading to respiratory distress and abnormal heart function.
The reason that Mr. Jones throat cultures were negative was because his throat was not the source of the pathogen. It was a blood-borne infection, also known as septicemia. The patient might have survived if the attending physician had known about the heart valve and a prior infection early on. If he had taken blood cultures earlier, the infectious agent could have been isolated and identified and the correct treatment started.
Staphylococcus aureus is the most common cause of endocarditis, especially associated with artificial heart valves. MRSA stands for methicillin-resistant Staphylococcus aureus, which is a shorthand way of saying that the microbe is resistant to numerous drugs used in treatment. The reason that the penicillin Mr. Jones was given to take at home would not have worked is that most strains of S. aureus are resistant to it. Treatment with a mixture of drugs is indicated, but it needs to start early in the infection. MRSA is an emerging pathogen that started as a problem in the hospital, but is now prominent in non-hospital settings as well.
Case Study 5 Perspectives
Parasitology is the study of eukaryotic organisms called parasites that invade the body and cause disease. It includes two major groups: the protozoans--primarily single-celled microorganisms, and the helminth worms-- multicellular invertebrate animals that may or may not be microscopic. Parasitologists study the morphology, life cycles, epidemiology, and pathology of these parasites. A list of the most common parasitic diseases in humans would total around 35, distributed all around the globe.
Dr. Hotez’ quote about the estimated worldwide case rate is meant to emphasize the enormity of the situation. In those regions where neglected tropical parasites prevail, the populationscould be suffering from several different NTDs simultaneously, so the actual disease burden could easily top 3 or 4 billion cases overall.
A vector is any animal that passes an infectious agent to humans. Vectors may be invertebrates or vertebrates. The most common vectors are arthropods such as insects (mosquitoes, fleas, bugs, biting flies) and arachnids (ticks and mites). Vectors of this type usually have a unique relationship with their parasite, serving as an alternate host that supports a different phase of development for the vector. Many vectors infect humans by taking a blood meal, thereby providing a route of entry for the parasite.
Dr. Hotez has been deeply involved in educating about and finding solutions for the terrible legacy of these diseases of poverty. He has partnered with the Gates Foundation to develop a vaccine for hookworm and written dozens of articles and a book on the subject. Recently Global Networkin partnership with END7 has developed programs to oversee the world funding for 7 of these diseases with the goal of eradicating them by the year 2020. These organizations support the “Just 50 cents” campaign, which advocates that a donation of only 50 cents will provide the necessary medication to save a child’s life.
Case Study 6 Perspectives
Viruses must attach to their host cells by their receptor molecules before they can enter the cells and complete their infection cycle. The shape of these receptors is complementary to specific molecules on the host cell. This specificity of attachment limits the kinds of cells they can invade. Once they are bound, viruses go to the next phase, which is their entry into the interior of the cell and production of new viruses. The flu virus attaches by its H receptors to the epithelial cells of the upper respiratory tract. From here it is poised to fuse with the cell and continue its path into the cell. N receptors have the important functions of helping the virus to penetrate the respiratory mucosa and facilitating the release of new viruses from infected cells.
Even though influenza virus has host specificity, infection does not require that all of its receptors be specific to its primary host. For example,a swine virus could have half of its hemagglutinin receptors specific to swine, but the other half could be specific to humans. As a result it can infect both species. The same would be true with bird influenza viruses. The underlying mechanism comes down to viral genetics. If a virus has developed mutated genes that give rise to receptors that fit another host, then that other host will be susceptible to infection.
A pandemic is generally defined as an epidemic that spreads across continents. Health officials consider influenza at pandemic levels when a new virus emerges that many people are susceptible to, when there is sustained human to human transmission, and when infection becomes widespread globally. The rapid spread of this pandemic can be attributed to factors such as its prevalence and rate of travel, the ready spread of the virus through the air by means of respiratory secretions, and the lack of prior exposure and immunity in a large number of people.
One benefit of prior influenza infections is that a person usually develops long term immunity to that strain of virus. Older members of the population are likely to have encountered viruses in the past that were similar enough to 2009 H1N1 that protective immunities from the earlier infection also worked to counteract the new virus. Thus a person with prior immunities will be able to inactivate the virus before it can get a foothold. This is the same idea behind the flu vaccines--they prevent the infection by getting the immune system ready to respond to the virus in the future.
Case Study 7 Perspectives
Extremophiles that can survive the toxic conditions of the pit are representedby all microbial groups. In all, 130 unique species of microorganisms have been identified so far. They include prokaryotes—the archaea and bacteria, which are best known for their capacity to adapt to extremes, but algae, protozoa, and fungi have also been found in abundance. Though it is true that animals and plants cannot adapt rapidly to such toxic conditions, many types of single celled microorganisms can alter their metabolism in a relatively short time; this coupled with their short generation times—hours vs years—they are much better at adapting to extreme conditions.
In being photosynthetic, the algae are a prolific source of oxygen gas that promotes survival and growth of aerobic organisms--namely, fungi, protozoa, and many types of bacteria. In addition, algae play an important role in the biogeochemical cycling of several elements-- nitrogen, phosphorus, sulfur, and carbon--that all organisms use in metabolism. Algae also add carbonates to the water which in time could buffer the pH and reduce its acidity.
Bioremediation is the introduction of microbes into polluted environments to reduce or degrade the toxic chemicals present there. Some microbes absorb heavy metals and others help to precipitate them into insoluble compounds which could be more readily removed. Since the organisms that naturally detoxify the pit ecosystem seem to be already present, a viable solution would be to enrich the water with extra inorganic nutrients such as nitrates and phosphates that favor algal growth. It is expected that the increased population of algae would absorb the toxic metals and concentrate them in the sediments at the bottom of the pit, where they would be less accessible and less likely to leak out.
Case Study 8 Perspectives
Biochemically, fermentation is the partial breakdown of simple carbohydrates that does not involve oxygen as a final electron acceptor, and that releases a wide variety of products along with a small amount of energy (ATP). The term is also used collectively in a later chapter (27) to define any large scale industrial processes for synthesizing commercial products such as drugs, foods, and other organic chemicals.
Fermentations begin with a usable substrate such as simple sugars (glucose), amino acids, or other small organic compounds. The process requires microbeswith the necessary metabolic pathways and enzymes tocarry out a particular type of fermentation. Fermentation proceeds under anaerobic conditions in a medium that contains additional essentialnutrients for growth (all major bioelements) and appropriate conditions of pH and temperature. Depending on the starting substrates and the type of microbes, thousands of different types of products can result. Generally, they fall into the categories of acids, alcohols, gases, and a wide variety of organic compounds. Alcoholic fermentation of the type carried out by yeasts yields primarily ethyl alcohol and carbon dioxide. A different fermentation pathway in Clostridium botulinumyields complex proteins such as botulinum toxin.
First, it must be emphasized that there is no way to simply look at or smell a food product and be able to tell if it contains toxins or other dangerous byproducts. They can only be detected by specialized testing. Some food that smells or tastes disagreeable or unpleasant (for example, limburger cheese) may be perfectly harmless and safe, and food that is contaminated or toxic often smells and tastes normal. The bubbles of carbon dioxide coming off the fermenting wine are an expected product of fermentation and harmless. Consequently, the inmates could not have known the wine contained something toxic until someone drank it.In a way, they were serving as guinea pigs for their crude chemistry experiment.
The antitoxin is an antidote consisting of macromolecules called antibodies that bind specifically to the toxin, an action which neutralizes or inactivates the toxin and prevents it from attaching to the receptor on its target cells (the myoneural junction). If the toxin has already reached its target and bound, the antitoxin is ineffective and the toxin will still have its full effect. So, the antitoxin must already be in the bloodstreamwhile the toxin is still circulating, which is within the first few hours of ingestion. After a day or two, most toxin molecules will have bound to and entered the cells. There is also the effect of quantity—it takes only a tiny dose of botulinum toxin to cause the disease, and the greater the amount ingested the less effective the antitoxin will be.