On 2001 September 11, the world experienced four unprecedented events of terror; the crash of four hijacked commercial jets into the Pentagon in Washington, D.C., a farming field in Pennsylvania, and two into the World Trade Centre in New York City, NY. Never has an event like this shaken the whole world. Classed as an act of terrorism, many of the previous devastating acts of rebellion or aggression were by convention means; that is, shootings, bombings, arson, etc… The events of September 11, or what is now commonly referred to as ‘9-11’, have raised the world’s comprehension of conceivable terrorist acts to a whole new level. Now, the terrorists are resorting to collaborating the innocent lives of those under siege (e.g. hijacking or kidnapping) to afflict further damage onto the property and other people elsewhere.
With this event, it is now conceivable that the most devastating weapon known to mankind may soon be around the corner; nuclear attack, chemical warfare, and biological warfare. A nuclear attack is the most destructive and devastating weapon to exist due to the high amount of damage afflicted on living organisms and physical structures over a wide range of land, but it is also the most difficult to afford, attain and deploy. Chemical warfare are relative easy to attain and inexpensive, but it is a complex weapon to handle and deploy. Biological threats are the most affordable, easy to handle, transport and deploy.
Characteristics of Biological Warfare
The characteristics of a biological war are:
Its potential for massive numbers of casualties
Ability to produce lengthy illnesses requiring prolonged and intensive care
Ability of certain agents to spread via contagion
Paucity of adequate detection systems
Diminished role for self-aid and buddy aid, thereby increasing sense of helplessness
Presence of an incubation period, enabling victims to disperse widely
Ability to produce non-specific symptoms, complicating diagnosis
Ability to mimic endemic infectious diseases, further complicating diagnosis (influenza)
Cost effective, easily obtainable
This paper is intended to describe the bio-terrorist threat, the methods of deployment, how it can be detected, methods of cleansing or quarantining the biological agent, and the environment impacts of this threat.
What is Bio-Terrorism?
Bio-terrorism is defined as the use or threatened use of a biological agent to promote fear, death and intimidation on a person, group of people, or a nation.
Risks of Bioterrorism
There are many risks in developing biologic warfare agent. There are many risks for both the bioterrorist and the victims of the bioterrorism. The bioterrorist cannot fully control the dispersion on the agent, and not risk infecting their own people. The biological agents will show no mercy to anyone of the people that it come in contact with, therefore if the biological agent is produced and not properly controlled then a full fledge epidemic can break out.
Impacts of Bioterrorism
There are several types of impact of bio-terrorism:
How long the agent will survive in the environment?
Other, social political, economic
a. Biological Agent (BA). The NATO definition of a biological agent is: a microorganism (or a toxin derived from it) which causes disease in man, plants or animals or which causes the deterioration of material.
b. Biological Defence (BD). Biological defence comprises the methods, plans and procedures involved in establishing and executing defensive measures against biological attack. (Procedures, equipment and training would be encompassed in this definition.)
c. Biological Warfare (BW). Biological warfare is the employment of biological agents to produce casualties in man or animals and damage to plants or material. The NATO definition then continues, to include, "or defence against such employment."
d. Biological Weapon. A biological weapon is an item of material, which projects, disperses, or disseminates a biological agent; including arthropod vectors.
e. Toxin. A poisonous substance produced or derived from living plants, animals, or microorganisms; some toxins may also be produced or altered by chemical means. Compared with microorganisms, toxins have a relatively simple biochemical l composition and are not able to reproduce themselves. In many aspects, they are comparable to chemical agents.
Two Categories of Biological Agents
Biological Agents can be broken into two (2) categories:
Category A Agents
easily disseminated or transmitted person to person
high mortality, with potential for public health impact
Category B Agents
moderately easy to disseminate
What is Anthrax?
Anthrax is the name given to an infectious disease caused by bacteria, Bacillus anthracis. And the Bacillus anthracis can be found in all parts of the world. Anthrax is known for infecting domesticated animals, such as, pigs, goats, sheep, etc.
Figure 1.1, This is a picture of the Anthrax spore. The nucleoid, plasma membrane, prondoglycan, s-layer and capsule are labelled. This picture was taken from the Internet. Reference: No author (2001) Supercourse on Anthrax. Retrieved November 29, 2001 from the Internet: http://www.pighealth.com/Scourse/anthrax.htm
Figure 1.2, This is a picture of the Anthrax gram stain. This is how anthrax looks under a microscope. This picture was taken from the Internet. Reference: No author (2001) Supercourse on Anthrax. Retrieved November 29, 2001 from the Internet: http://www.pighealth.com/Scourse/anthrax.htm
Figure 1.3, This is a picture of the Anthrax gram stain. This is how anthrax looks under a microscope. This picture was taken from the Internet. Reference: No author (2001) Supercourse on Anthrax. Retrieved November 29, 2001 from the Internet: http://www.pighealth.com/Scourse/anthrax.htm
Where does it come from?
The original biological agents that are used are found in the natural world, with an exception to small pox. Most of these biological agents are harmless, or very weak, and not capable of killing people unless there is constant contact with a reservoir of the biological agent. So most of the biological agents can be found in the natural world.
This means that anthrax can be found in the world, and that the anthrax is not strong enough to do any real damage to the human population.
However, the weapon used in bioterrorism, is not found in the natural world. This is because the biological agents that are found in the natural world are not lethal enough, and do not have the capabilities to become a weapon, therefore the terrorist would have to take the biological agent and enhance the biological agent ability to infect humans, and resist vaccines and antibodies. After the terrorist has done that then the biological agent becomes a weapon, and the weapon is found and made from the hands of the terrorist.
So the bioterrorist can find anthrax and can change it from the form it is found in the natural world, and make it a lethal weapon.
How does it get to people?
There are many ways for the biological agent to reach the human. The three more common methods for biological agents to enter the body:
The first one is
Through cuts and breaks in the skin: This is when the anthrax spores enter the body through a cut or break in the skin.
The second one is:
Inhalation: This is when the anthrax spores are inhaled and enter into the body through the lung.
The third one is:
Consuming contaminated food: This is when the anthrax is consumed when the person is eating a piece of meat that is contaminated with anthrax
These methods of entering the human body are all very applicable in the natural world, for instance if you were a farmer and worked with domesticated animals everyday of your life, and the animals that you worked with had come in contact with anthrax, and since you work with those animals everyday, you are bound to come in contact with the anthrax, and the three methods mentioned above are the three main ways that you could get anthrax. However this project is about bioterrorism and there are many different ways for the anthrax to reach you as a human.
When the terrorist get hold of the anthrax that is found in the natural world it is not ready for the mass destruction that they would like to use the anthrax, so first they have to alter the anthrax to suit their purposes. And then there are many methods for the terrorist to change the anthrax to suit their purposes, for instance the terrorist may want to make the anthrax into an aerosol spray, and want to spray the anthrax over a city or something like that. Then the terrorist could also want to put the anthrax in to a powder form and hope that people either inhale the anthrax or hope that they come in contact with it and hope that they either eat or come into contact with the anthrax.
Therefore there are two main methods for the terrorist to expose the people to anthrax.
The first method is turning the anthrax into a spray and spraying the anthrax over a population. The second method is turning the anthrax into a powder and either sending it to the people or leave it somewhere to have the people come in contact with the anthrax.
Figure 1.6, This is a picture of anthrax under a microscope. This picture was found on the Internet. Reference: Kenneth Todar University of Wisconsin Department of Bacteriology (2001) Retrieved December 12, 2001 from the Internet: http://www.bact.wisc.edu/Bact330/lectureanthrax
How does it affect the person that comes in contact with it?
When a person comes in contact with the anthrax the symptoms are divided into three different types.
First there is the inhalation:
The signs that anthrax has been inhaled are:
Fever, cough, chest discomfort, and breathing problems
Inhalation of the anthrax very hard to get because it requires the inhalation of many spores, however if enough of the spores are inhaled then it is very dangerous for the person that inhaled the anthrax. It is very rare that a person could naturally get anthrax through inhalation because a normal average healthy person can resist up to 2000 spores daily. Inhalation anthrax is the most dangerous and most highly effective way of dying from anthrax. This is because of two reasons. The first reason is when the spores are inhaled and there is a sufficient amount of the spores are inhaled, then the spores grow and there is lesion in the lungs. When the lung stops the bodies dies, and it is almost impossible to get antibiotics into the lungs to fight the anthrax. The second reason that inhalation anthrax is dangerous is because the initial symptoms resemble the symptoms of a common cold. And the person that is infected may try to pass off the symptoms as a cold, because they may not be expecting to be infected with anthrax. This is a major concern because the only way to have anthrax cured is if the detection of the infection is early, and not much damage has been done to the body, but if the infected person does not realize that they are infected with anthrax then when the person is finally diagnosed with anthrax then it is too late to save the person.
Third there is anthrax entering the body through a cut or break in the skin.
The signs of anthrax entering the body through a cut or break in the skin:
Painful swelling of a black circle that if filled with dead tissue.
Figure 1.4, This is a picture of a cutaneous anthrax infection. The infection is found on the middle finger of the hand shown in the picture. The infection is identifiable because of thee black lesion that is just under the knuckle of the middle finger. This picture was taken from the Internet. Reference: Terry, T.(2001) Biology 102: Lecture Notes: Bioterrorism. Retrieved December 5, 2001 from the Internet: http://www.sp.uconn.edu/~bi102vc/102f01/terry/bioterrorism.html
What are consequences of short-term exposure? Long-term exposure?
The consequences of short-term exposure to anthrax are very minor, assuming that short-term exposure means minimal contact with the anthrax spores. Many sources say that a large quantity of anthrax spores needs to enter the body before any type of infection would occur, and that short-term exposure to the biological agent anthrax should not cause the person that is harmed too much pain.
Long-term exposure however needs to be taken seriously. This depends on the severity of the infection and it also depends on if the disease was diagnosed and whether or not the person knows its anthrax of not, however if nothing is done then the regular result is death.
How much does it take?
There are many sources out there that say that it takes about 10,000 spores to enter the body, before any type of infection that can occur that the person that is affected needs to worry about, however there are other sources that say that anthrax can start infecting after even 100 spores, however each sources agrees that it is not that the method of the anthrax entering the body plays a large role in how deadly anthrax is.
Figure 1.4, This is a picture of a cutaneous anthrax infection. The infection is on the cheek of the person that is infected with cutaneous anthrax. This picture was taken from the Internet. Reference: Terry, T.(2001) Biology 102: Lecture Notes: Bioterrorism. Retrieved December 5, 2001 from the Internet: http://www.sp.uconn.edu/~bi102vc/102f01/terry/bioterrorism.html
How does it destroy, or assist in destroying the body?
When anthrax enters the body, there are three different methods for the anthrax to enter; however when the anthrax enters and starts infecting the person, it destroys the body in the same manner. First when the spores enter the body, the anthrax leaves its dormant stage, and starts to germinate, and grow. Then after the bacterium is formed the bacterium releases 3 proteins that cooperate to kill the body. The first protein is called the Protective Antigen (PA) and this protein is the most important protein because it is the protein that provides a method of entering the cells of the body. Then the second protein that I released is called the Lethal Factor (LF) and this protein goes into the cell and disrupts the cells activity and kills the cells. Then the third and last protein that is released is called the Edema Factor (EF), and this protein stops the flow of ions from cells to cells, and that causes fluid to build and collect (known as edema). These three proteins are the reason that anthrax can kill; they play the most important part in killing the body.
Figure 1.5, This is a diagram of the method that anthrax uses to enter the human body, and how it kills the infected person. It shows all three of the methods of infection. This picture was taken from the Internet. Reference: Terry, T.(2001) Biology 102: Lecture Notes: Bioterrorism. Retrieved December 5, 2001 from the Internet: http://www.sp.uconn.edu/~bi102vc/102f01/terry/bioterrorism.html
Figure 1.7, This is a picture of how anthrax kills a cell. This diagram shows the three proteins that anthrax expels to kill the cell. It shows the protective antigen, the lethal factor and the edema factor. This diagram was found on the Internet. Referenced: Tenenbaum, D. (2001) Key Anthrax ‘Door’ Found Retrieved December 17, 2001 from the Internet:http://whyfiles.org/shorties/089anthrax_receptor/index.html
How can it be cured?
So far there is no cure for anthrax, however anthrax is susceptible to penicillin and other antibiotics, however the antibiotics need to be taken early on in the infection or the will not provide enough help for curing the anthrax disease. There is a vaccine for it, and the vaccine works by having the first protein that the bacteria releases destroyed so that the other proteins cannot enter the cell and to their damage.
What is small pox?
Smallpox is the name given to an infectious disease caused by bacteria, Variola virus. Smallpox is a viral disease that is unique to humans. The virus is transmitted from one human to another. There are two forms of the variola virus; there is the variola major and the variola minor. Variola minor is a more minor and less deadly form. Another two forms of smallpox are the hemorrhagic and the malignant forms. Hemorrhagic is 100% fatal and the malignant form is frequently fatal.
Where does it come from?
Originally smallpox was also found in the natural world, however the World Heath Organization (WHO) noticed the impact that the disease had on the people around the world. And they mutually decided that smallpox should be eradicated from the natural world. And in 1977 the world was eradicated of smallpox, however smallpox was not eradicated from the science world. Strains of the variola virus were kept in labs around the world for research purposes and the producing vaccines. However the threat of bioterrorism was becoming a problem for the world, therefore the World Heat Organization also wanted to rid the world of smallpox, they wanted to have all the strains destroyed, and all the vaccines destroyed, and anything that had any piece of the smallpox virus in it to be destroyed. There was a deadline set for this to be done, however scientists around the world argued that they needed more time to study smallpox and understand how it works. So the date was postponed, and after the new date was about to be reached, the scientists again argued that they did not fully understand smallpox yet, therefore the date was postponed again. This happened many times, and smallpox is still found in some of the high security labs in the United States, and Russia. There are probably many other ‘secret’ laboratories around the world, where the countries are secretly doing tests and such with the smallpox virus, however the WHO does not have the power to infiltrate all these labs and ensure the destruction of the virus, therefore the power countries such as the US and Russia, can say that since they cannot completely ensure that all strains of the virus was destroyed, they need to keep strains of the virus too, so they can produce vaccines and do tests for defense against a possible bioterrorist attack with smallpox as its weapon.
Smallpox is a disease that is specific to humans, and the only way for a person to get smallpox is to come in contact with another person that has the smallpox virus. The virus is passed through the saliva of the infected person. When the infected person releases water droplets into the air and a healthy person inhales the air droplets with the variola virus in it, and then the healthy person then becomes infected too. This is the natural way for a person to get the smallpox virus. However there is another way for the normal healthy average person to come in contact with the smallpox virus. This alternate method is caused by bioterrorist.
Bioterrorist can use the smallpox virus (variola) and produce it and make the virus into a liquid and then make it into an aerosol form, and spray the virus over a population. This is very achievable because the smallpox virus can be placed into a liquid and then the liquid can be made to be placed into an aerosol. And since the biological agent that causes smallpox is a virus, it has a more contagious effect. The virus is very easily passed on to another human when the infected does not realize that they have the virus. So the bioterrorist can access the methods and technology to mass produce the virus and spread the virus over a city, or group of people through the method of using aerosol sprays to spray the virus over the people. The bioterrorist can also infect individuals in the population without them knowing and hope that the virus would spread through the population that way.
One of the main reasons that the bioterrorist may choose smallpox is because the smallpox virus is easily vaccinated, there is an effective vaccine that is available, and the bioterrorist only needs to vaccinate their ‘group’ members and then when they release the virus into the human population they do not need to fear the virus.
How does it affect the person that comes in contact with it?
There are various symptoms when the person is infected with the variola virus. In all the different ways that the smallpox virus gets into the body, the virus affects the body in the same manner. Most of the symptoms resemble the symptoms of the chicken pox. The first signs of the smallpox infection normally take about 12 days to appear, and the first thing that shows up is fever, headache, and malaise. Then the symptoms that appear next is a red rash that appears on the throat and the face, then later on the rash spreads to the arms, legs and torso. The dangerous thing is in the beginning the rash looks like regular chicken pox, however a couple days later the rash develops into pocks (bullet like, puss filled blisters). When the pocks develop the person that is infected has been highly contagious for a couple days already, and everyone that has come in contact with the person has a highly chance of also developing smallpox. Only when the scabs of the pocks all fall off is the person not contagious anymore, however the scabs still contain the variola virus, but they are not as contagious as the saliva. The only way to tell the difference between chicken pox and the beginning rash of smallpox, is the chicken pox are more dense and chicken pox is never found on the soles of feet or palms of hands.
What are consequences of short-term exposure? Long-term exposure?
The consequences for short-term and long-term exposure are the same. As long as the person is infected with the variola virus the same things will happen. As long as the virus gets into your body you are infected, unless you are the lucky person that has an amazing immune system, and can withstand a brief exposure to the virus.
How much does it take to infect the person?
The amount of the variola virus it takes to get infected is unknown to the medical world, however it is speculated that it may only take a few virons (single viruses).
How does it destroy, or assist in destroying the body?
Smallpox is a virus, and all viruses destroy bodies in the same relative manner. The small poxvirus enters the body through the respiratory system. When the virus successfully enters the body, it can start to replicate itself and then leave the host body to find another organism to infect. The first stage of the infection occurs in the respiratory tract. This includes the respiratory mucosa, and the lymph nodes. In the end of the first stage of the infection the virus starts to spread and the virus reaches the spleen and the bone marrow. This is after third or fourth day. Then after eight days the second stage of the infection occurs and the virus spreads to the leukocytes and the blood vessels of the dermis and beneath the oral and pharyngeal mucosa. After about 12 days the virus spreads to the skin and the lesions start to appear.
At a more detail level the smallpox virus acts like all normal viruses. The virus is not able to reproduce on their own because they lack the enzymes needed for replication. However the smallpox virus is a double stranded DNA and when it enters the body it attaches itself to cells. The receptors of the virus recognize the cell membrane and penetrate the cell membrane allowing the virus to inject its nuclear material (DNA). Then as the nucleic material enters cell the virus uses the cells enzymes to either produce enzymes that the virus needs, or use the cells enzymes to replicate. As the virus uses the cell for replication the cell is destroyed and the virus reorganizes itself and builds a cell membrane for itself, then the virus leaves the dead cell and goes searching for another cell in the host body to use for replication. After many cells have been killed the patient has no cells left to survive, or many vital cells needed for life have been destroyed, thus killing the infected individual.
How can it be cured?
There is no accepted cure for smallpox however there is a vaccine that is available. And the vaccine contains the vaccinia virus. The origin of the vaccinia virus is unknown however from modern technology and DNA sequencing the scientist can determine that the vaccinia virus is a hybrid of the cowpox virus and the smallpox virus (variola). The vaccine is a live vaccine, meaning that the vaccinia virus that is found in the vaccine is alive. The vaccine causes one single lesion to appear on the site that the vaccine was inoculated. The pockmark dries up and the scab falls off after ten days. However, even though vaccine for smallpox is effective, there is a limited supply of the vaccine.
Dispersion and Routes of Delivery of Biological Agents
A variety of possible systems exist for the dispersion of biological agents. For humans and animals these range from the use of live vectors (e.g. insects and rodents) to aerosol sprays of dried spores and infective powders or direct contamination of consumables (food, water, medication).
Weapons previously designed for biowarfare have included spray-tanks, bombs, cluster bombs and bomblet dispensers (explosive methods can destroy the organism), however unsophisticated deployment devices such as crop duster airplanes or small perfumed atomisers are also effective methods of delivery.
Ingestion, inhalation and direct cutaneous contact are all routes by which biological agents could be administered to target populations. Intact skin provides and excellent barrier to most, but not all, biological agents, with mucous membranes and damages in the dermal layer providing breaches in this barrier through which agents may pass. Delivery of agents via the ingestive route can occur in two ways; direct contamination of food and water supplies or secondary contamination after an aerosol attack.
Dispersion of low altitude aerosol clouds is potentially the most lethal way of delivering biological agents as the process of breathing causes a continual influx of biological agent into the exposed individual. The easiest way to produce organisms for weaponisation in this form is to produce a liquid 'slurry'
Powders have the advantage of remaining suspended in the air for a longer period of time, but their production requires more advanced techniques.
Aerosol delivery systems aim to generate invisible clouds of particles/droplets between 0.5 and 10 microns in diameter, as these can remain suspended for long periods and once inhaled can enter the lower respiratory tract and gain direct access to the bloodstream.
Therefore there are two main methods for the terrorist to expose the people to anthrax:
Turning the anthrax into a spray and spraying the anthrax over a population; and,
Turning the anthrax into a powder and either sending it to the people or leave it somewhere to have the people come in contact with the anthrax.
Table 1 - Anthrax (release of 50 kg agent by aircraft along a 2 km line upwind of a population centre of 500,000
Downwind Reach, km
Rift Valley Fever
How is a biological agent detected?
Anthrax is a powdery white substance in the solid form.
Symptoms – Pulmonary Anthrax
Symptoms of pulmonary anthrax are very similar to the flu, which can make an initial diagnosis somewhat difficult. However, in light of recent events many doctors have a heightened awareness of the possibility.
Symptoms of the disease vary depending on how the disease was contracted, but usually occur within seven days. Officials at the Centres for Disease Control list the following:
Cutaneous: Most (about 95 percent) anthrax infections occur when the bacterium enters a cut or abrasion on the skin, such as when handling contaminated wool, hides, leather or hair products (especially goat hair) of infected animals. Skin infection begins as a raised itchy bump that is dark in color and resembles an insect bite but within 1-2 days develops into a vesicle and then a painless ulcer, usually 1-3 centimeters in diameter, with a characteristic black area in the center. Lymph glands in the adjacent area may swell. About 20 percent of untreated cases of cutaneous anthrax will result in death. Deaths are rare with appropriate therapy.
Inhalation: Initial symptoms may resemble a common cold. These symptoms may actually then retreat for a short period. But after several days, the symptoms progress to severe breathing problems and shock. Inhalation anthrax is usually fatal.
Intestinal: The intestinal disease form of anthrax may follow the consumption of contaminated meat and is characterized by an acute inflammation of the intestinal tract. Initial signs of nausea, loss of appetite, vomiting, fever are followed by abdominal pain, vomiting of blood, and severe diarrhea. Intestinal anthrax results in death in 25 percent to 60 percent of cases.
How is anthrax infection diagnosed?
For people with suspected anthrax disease, the CDC lists a number of laboratory testing that can identify the disease. Tests can include:
Taking cultures of blood and spinal fluid to detect antibodies to the disease. These tests should be done before antibiotic treatment has been initiated.
Cultures of tissue or fluids from affected areas, which could include fluid from a skin sore or sputum coughed up from the lungs.
A PCR (polymerase chain reaction) test that amplifies trace amounts of DNA to detect if the anthrax bacteria are present.
Real Time PCR vs. Conventional PCR
Although there are numerous tests that can detect if a certain biological agent is present, real time PCR is the preferred test. The conventional way of testing for the presence of a biological agent would include growing cultures etc. This process is very time consuming, as it takes 5 times longer than that of real time PCR. Real time PCR only takes 1 hour to complete the testing. Time is the main issue for anyone who might be suspected of being exposed to a biological agent. Therefore, it is essential to have a testing method that is quick and accurate.
How is anthrax exposure detected?
The most common way to detect anthrax exposure is to take samples swabbed from the nose to detect any anthrax spores present there. The CDC emphasizes, however, that nasal swabs cannot rule out exposure but are helpful because they can provide clues to help investigators assess where spores may have traveled.
Polymerase Chain Reaction (PCR)
Polymerase Chain Reaction (PCR), is a technique in molecular biology that amplifies a specific region of deoxyribonucleic acid (DNA). This specific region of DNA can be rapidly cloned, or duplicated, to produce multiple DNA copies. This enables scientists to make billions of copies of a DNA molecule in a very short time. PCR allows scientists to adequately test the DNA to detect:
Diagnose genetic diseases
Carry out DNA fingerprinting (identify individuals)
Bacteria or viruses
Research human evolution
PCR was the first nucleic acid amplification method to be produced. This technique was conceived in 1985 by an intellectual maverick, American biochemist Kary B. Mullis (bachelor’s degree in Chemistry and a Ph.D. in Biochemistry). Mullis and his associate Fred A. Faloona at the Cetus Corporation in Emeryville, California later developed PCR in 1983. When PCR was first developed, it was not immediately recognized. However, in 1991, PCR was renowned for its capabilities as it was now used widespread. In 1993, Mullis was named a co winner of the 1993 Nobel Prize in chemistry for his work with PCR.
PCR goes through a 3-phase process, which proceeds in a series of cycles, or rounds. The DNA fragment is duplicated after one successive cycle. Thus, more than 1 billion copies of a single DNA fragment can be made in just a few hours. The technique of PCR is very straightforward that scientists with little training in molecular biology can use it. The use of PCR has a very high probability achievement. The supplies necessary for carrying out PCR are available in a kit form manufactured by Roche and Cepheid. This kit is used in such varied settings as crime laboratories and clinical diagnostic laboratories.
How PCR Works
In nature, most organisms copy their DNA in the same way. The PCR mimics this process, only it occurs in a test tube. Most DNA is double-stranded, apart from the exception of some viruses. Each strand of DNA is paired with a complementary strand. DNA consists of 4 different components (nitrogen bases) that have a precise order. The 4 components are Adenine, Thymidine, Cytosine and Guanine. They are abbreviated respectively as A, T, C, and G. This is respectively the 4-letter alphabet. The arrangement of letters creates a “sentence” (a gene sequence). The number of letters in a sentence may vary in length depending on the gene. These two strands have a particular pattern it must stick to. The A on one strand always pairs with the T on the other, whereas C always pairs with G. The two strands are said to be complementary to each other.
When any cell divides, enzymes called polymerases make a copy of the entire DNA in each chromosome.
In order to use PCR, the exact sequences of the flanking region of the target DNA region must be known. The DNA sequence between the flanking regions does not need to be known for this technique. The flanking regions of many organisms are known and that the DNA of different organisms is different. Therefore, by identifying the genes, which are different, and therefore unique, one can use this information to identify an organism.
Would pair with:
In the above gene sequence, the “…” represents the DNA sequence between the flanking regions. Thus, the sequence of letters is the flanking region of the target DNA for the PCR. This flanking region in the above example is unique to particular organism’s DNA, and no other organism’s DNA.
How PCR is performed The first step in this process is to "unzip" the two DNA chains of the double helix at a high temperature (approximately 90-96oC). As the two strands separate, DNA polymerase makes a copy using each strand as a template.
During replication, the two strands of DNA separate and a specialized cell enzyme (a protein that initiates chemical reactions) called polymerase makes a copy of each strand, using the original strand as a template, or pattern. But the primers cannot bind to the DNA strands at such a high temperature, so the vial is cooled to 55oC. At this temperature, the primers bind or "anneal" to the ends of the DNA strands.
The final step of the reaction is to make a complete copy of the templates at 72oC.
We now have the enzyme producing new DNA of that particular region in opposite directions. After one cycle is completed, more primers and 4-letter mixtures can be added to continue the cycle. Each cycle results in a doubling of the target nucleic acid molecule and leads to the production of billions of copies of the DNA sequence. The reaction is usually completed in about 90 minutes.
The appearance of DNA by PCR will allow precise identification of the source of the amplified material.
Short oligonucleotide probe labelled with a reporter dye on the 5’ end and a quencher dye on the 3’ end.
Example: FAM (reporter) and TAMRA (quencher)
Probe hybridizes to target
Polymerase cleaves the hybridized probe
Reporter separated from quencher
Fluorescent signal increases (signal proportional to amount of amplicon)
Hairpin-shaped oligonucleotide molecule that has a fluorophore and a non-fluorescent quencher dye attached to the 3’ and 5’ ends.
Beacons hybridizes to the target
Reporter dye is separated from quencher
Fluorescence Resonance Energy Technology (FRET)
2 probes- one labelled with an acceptor dye and one labelled with a donor dye
Acceptor and donor dye spectrums must overlap
Both probes must hybridize to target head to tail within1-5 bases
Donor dye excited
Energy transferred to acceptor dye, when the two fluorescent dyes are in close proximity, which emits at longer wavelength
One fluorophore’s emission spectrum overlaps the other’s excitation spectrum
Donor’s absorbed energy is transferred to acceptor dye
Donor’s emission decreases while acceptor’s emission increases
How to Get Rid of the Biological Agent (Physics)
What is the Electron Beam used for?
The mailed anthrax to many news and government officials has forced the United States government to find an instrument that would kill the anthrax before it would be sent across the United States. The instrument the United States government implemented was the electron beam. The “Sure Beam” corporation supplies this type electron beam for the United States government.
What is an Electron Beam?
This type of electron beam uses electricity to generate a beam of accelerated electrons approaching the speed of light. This high-speed beam of electrons is scanned across a food product, and breaks the DNA chains of harmful bacteria either killing the bacteria or rendering it unable to produce. In the past gamma rays were used to sterilize medical equipment. Now the electron beam will kill the anthrax at a faster rate than any other type of beam.
What else is the Electron Beam Capable of?
Eighteen thousand kilograms of ground beef could be sterilized in seconds. The electron beam can also be used to disinfect fruits and vegetables of fruit flies and insects. It is also used to melt various metals such as titanium, zirconium, nickel, and cobalt. A less powerful electron beam is used as an electron microscope, which scans an object with electrons and shows a magnified image of the object. The electron beam can trap, and probe highly charged ions, which can be used for studying any element in the periodic table. Welding, laser drilling, cutting, and heart scans are other tasks the electron beam are capable of performing. This highly sophisticated machine will help rid anthrax sent through the mail and help calm the fears in United States citizens.
Deadly diseases such as anthrax don’t have to be sent through the mail to make it lethal. Shooting the bacteria by a missile or even just dropping it in a crowded city are just as deadly. But while shooting bacteria through a missile or dropping it in a crowded city, there are many calculations you will have to calculate to achieve your goal.
What Calculations are Necessary when Shooting a Missile Full of Bacteria or Virus?
When shooting a missile half way around the world, one needs to calculate many various factors. First you will need to calculate how much force you actually need for the missile to get off the ground. A general thrust equation can be used to calculate the amount of thrust need for your missile. Since force is the change in momentum in a given change of time, and momentum is the objects mass multiplied by its velocity. We can use the equation F = [(mv)2 – (mv)1 ] / (t2 – t1). Where F is the force required, m is the mass of the object, v is the desired velocity of the object, and t is the amount of time the object is in the air. Since the mass is kept constant, velocity can be changed. Then once the force is calculated the amount of fuel can be calculated. The amount of air resistance and friction must also be calculated so the missile doesn’t run out of fuel. The gravity is also a factor that is always missed. Since the force of gravity is pushing down on us, the net force of the missile will have top be greater than the force of gravity. Finding the shortest distance possible for the missile to travel may seem easy, but you have to remember that the earth is a spherical shape and going in a straight line may not be the shortest distance. A calculation of the curvature of the earth for the shortest distance possible is vital in launching a missile. The shape of the missile is extremely critical for maximum lift. A non-aerodynamic missile is not in your best interest.
What Calculations must be Necessary when Dropping Deadly Diseases?
When dropping deadly diseases in a crowded city, the wind is a big factor. If there were no wind, the bacteria or virus wouldn’t go anywhere. But if there is too much wind, the inhalation rate will be extremely low. A good wind is needed for the disease to spread quickly. The mass of the substance is also critical. If the bacteria or virus are too heavy then the wind will not be strong enough to carry the bacteria or virus. With an average wind speed a range can be calculated so an infection rate can be estimated. For both missile and dropping, an amount of bacteria or virus needed has to be calculated, because if an insufficient amount of bacteria or virus is used, the infection rate will be minimal. The growth rate of the bacteria must also be calculated.
What will happen in Real Life?
If given appropriate weather and wind conditions fifty kilograms of anthrax released from an aircraft along a two-kilometre strip could create a lethal cloud twenty kilometres downwind. Almost anyone in the vicinity would be infected. If a release of aerosolized anthrax upwind of a population of five million could lead to an estimated two hundred fifty thousand casualties and one hundred thousand of those casualties would die. If a release of one hundred kilograms of aerosolized anthrax was dropped over Washington, D.C, one hundred thirty thousand to three million deaths could occur, making it more lethal than a hydrogen bomb.
If ever a deadly biological agent, like anthrax or small pox, was ever found in an environment, and had already contaminated some of the organisms in that environment, then the organisms that feed on these organisms would start die as well. These organisms would die if they consumed an organism originally contaminated with anthrax. However the organism that is one trophic level lower then the contaminated organism is, it would increase in its population, since now there are less predators/consumers, given that they are all dying. Thus resulting in a very unbalanced environment, all the organisms that are in the higher trophic levels would soon disappear. Therefore only the lower trophic level organism can then be found in this once full of life, and various animal environment. The only possible way for these lost organism to return back into the environment would be after many decades, where the agent is now gone. Therefore allowing an existing organism in another environment to migrate to this environment. If these did not happen, the environment would continue to contain all the low trophic level organisms, thus creating a simple environment.
One type of biological agent that is known to infect domesticated animals such as, pigs, goats, and sheep is the bacterium Anthrax. Once these animals are inflected, the bacterium can spread easily among the animals if the animals were to have cuts, thus allowing the anthrax spores to get into the animal’s body. Another way would be if an animal were to consume another animal that had contained Anthrax in its body. Therefore, anthrax would be present in the consumer. Consequently, if one animal was infected with anthrax, then that animal should be put down right away before the anthrax has a chance to spread to other animals. However, the process must be done properly to prevent the spread of anthrax spores to the soil. If the anthrax spores were to end up in the soil, it could last there for decades. Thus the plants that grows there would then be contaminated by anthrax, and the organisms that feeds on these plants would too be contaminated, and so on.
Clean Up / Long-term Impact
The clean up for these biological agents must be done as soon as possible, before it can get into another organisms body, and spread. If the biological agent were to spread, tremendous deaths would arise. Therefore the long-term impact on the environment if the agent were not to be cleaned up, would be that there would be a possibility for the agent to spread. Thus, all organisms would start to die. Sooner or latter, these organisms would become extinct, if they are unable to reproduce faster then the death rate.
How long the agent will survive in the environment?
Most biological agents are found in the natural world, with the exception of smallpox. This shows that many biological agents can survive for years in the environment. For example, anthrax spores can survive for decades in soil.
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