#1 “Anthrax Genome Spills its Deadly
Secrets” Scientific American, 5/1/03
Due to the deadly nature of anthrax and its role in the bio-weapons arsenal of the world, much research as been aimed at understanding the molecular workings of this bacterium. Just recently, scientists have used basic genetic techniques to sequence the bacterium’s genetic sequence and
compare it to its two closest relatives, which are not as toxic and dangerous to human beings. By looking at the genetic sequence of the bacterium responsible for anthrax and comparing it to its genetic ancestors, scientists are able to understand how this bacterium has evolved in virulence. This would hopefully one-day lead to a better defense against this potential, devastating bacteria. In addition, by understanding how this bacterium functions will hopefully also lead to better vaccines and cures against B. anthracis.
Previous research had been done to determine most of B. anthracis’s genome. The scientists found out that the main difference between B. anthracis and its related soil bacteria is from two plasmids. It is these plasmids that carry the genes responsible for the toxicity caused to animals and humans. The scientists must have conducted some sort of basic bacterial transformation to discover that the toxicity was found in the two plasmids. What they might have done was to take the B. anthracis bacteria and infected a mouse with it. The mouse should have died of anthrax. Then they would take the harmless soil bacteria and infect the mouse and the mouse would have been fine. Then they would have introduced the B. anthracis to the harmless soil bacteria, allowing the plasmid from the anthrax bacterium to be taken up by the harmless soil bacterium. Then take the soil bacterium and infect a mouse with it. If the mouse dies (which it should), then the harmful genes must have been in the plasmids, the vector that got transformed from one bacterium to another.
Now, scientists at the Institute for Genomic Research have sequenced the 5 million DNA bases that are on the B. anthracis chromosome. Though it is not stated in the article, most likely, this high-tech genetics company uses the more rapid method of PCR. Sequence maps were probably created using fast computer technology that sequences the DNA base by base by using fluorescent markers. The scientists then compared the DNA sequence to the genes of B. thuringiensis (bacteria that is used as a pesticide) and B. cereus (bacteria that can cause food poisoning). The scientists only found 150 significant differences, and, once again, complex computer programs must have been used to compare the sequence of DNA that can distinguish between DNA variable regions that are significant or natural variance.
The scientists speculate that these changes in the DNA came about from horizontal gene exchanges rather than mutations. Horizontal gene transfer is when bacterial exchange genetic information through the process of transformation, conjugation, or transduction. The receiving bacteria take up entire chucks of genetic information. With such large changes in the DNA, it makes sense that the DNA mutations did not happen spontaneously all at once, but that there were chunks of DNA being exchanged from one bacteria to another that proved to be beneficial.
Another scientist at Integrated Genomics compared the anthrax organism to B. cerus. After this comparison, it was determined that it is likely that the bacteria originated from ancestral bacterial that was once a parasite or an organism that consumed dead flesh. To determine this relationship, the scientists probably used some sort of genetic phylogenic tree, which can be created through the use of different computer programs. After comparing all three of these organisms, it is obvious that they are all very similar. Their genetic code shares many commonalities, therefore, it must be somewhere in how these genes are regulated that determine the difference between a killer bacterial, a food poisoning bacteria, and a pesticide. Different techniques could be used to understand how these genes are regulated. Analysis of the products of each of these genes such as protein analysis through gel electrophoresis or protein sequencing techniques could be used to understand which combination of genes are being expressed. Mutations could be made and knock out organisms could be made to determine what happens when a gene fails to function. There are many ways to induce mutations at different points in the DNA of bacteria and the outcome can then be studied. By understanding which genes are being turned on and off, how they are regulated, and which sequences are responsible for regulating the genes, research can continue to come up with ways of disrupting this bacteria and providing methods of faster detection, better vaccines, and better cures.
#2 Transgenic
Foods
In the last few years, many headlines have been seen in newspapers, magazines, and on television regarding the production and distribution of genetically modified (GM) foods. A debate has emerged regarding these products and whether or not they should be made available for public consumption. While proponents argue that these foods could help end world hunger and provide the world with superior quality foods, opponents raise the question about the risks to human health and the environmental.
For year farmers have relied on the process of selection and cross breeding to create improved species of crops. In fact, in nature, plants and animals selectively breed in order to ensure an optimal gene pool to produce the best possible offspring. However, these traditional breeding methods are slow and often very labor intense. In order to obtain a crop that is as useful and productive as possible, breeders are required to assemble a combination of genes. However, achieving this is often very difficult because traditional breeding is limited to artificially crossing plants within the same species to bring different genes together. Transgenic technology, however, enables breeders to cross plants of different species and even different organisms. Thus, in one plant, they are able to bring together useful genes from a wide variety of sources. Technology has also provided breeders with a means of identifying and isolating specific characteristics in one organism that would enhance a different crop. This enables organisms to acquire one specific gene or a few genes together within a single generation through genetic modification.1 They would also not receive any unwanted traits.
The process of genetically modifying foods is accomplished through introducing genes via DNA into an organism’s cells and chromosomes. The biggest problem in the transgenic process is identifying and isolating genes. Many times, identifying a single gene involved with a trait is not sufficient enough to affect an organism’s phenotype. In order to successfully incorporate a new gene into an organism’s genetic code, scientists must understand how the gene is regulated, what effects it has on the plant, and how it interacts with other genes. Private research and new technological advances have enabled scientists to determine the function of genes and have thus resulted in the identification of a number of genes potentially useful in producing transgenic varieties.
Once a gene has been isolated and cloned, many modifications must take
place before it can be inserted into the plant. For a gene to be expressed properly, a
promoter sequence must be attached to it.
Most promoters used in transgenic crops are constitutive, which means
they cause gene expression throughout the life cycle of the plant’s
tissues. The gene can then be
modified to achieve greater expression or to give the plant defense against
bacteria or other organisms.
Finally, a marker is added to the gene construct so that the transgene
can be identified in plant cells that have successfully integrated the
transgene. One example of a marker
could be resistance to agents such as antibiotics or herbicides which are
normally toxic to plants. Only the
plant cells that have successfully acquired the transgene will be able to grow
on a medium that contains antibiotics or herbicides.1
After creating the transgene construct the process of transformation begins. Transformation is defined as an acquired change in a cell or organism due to the uptake of foreign DNA. There are two main methods of transformation used in creating transgenic crops. The first is the “Gene Gun” method in which cells are placed in a cylindrical enclosure and are held on a platform by a mesh covering. The cells are then bombarded with particles that are directed towards the cell in a helium flow. The particles are coated with a plasmid containing the transgenic DNA that is to be inserted into the cells. The particles hit the cells at such a speed that the plasmid is transferred and incorporated into the plant’s genome, while the uncoated particle and helium pass through the cell.1 The second type of procedure is the Agrobacterium method. This is the preferred technique because it has a greater frequency of single entry sites which makes tranformation easier to monitor. The Agrobacterium method employs a special soil-dwelling bacteria which has the ability to infect plant cells with a piece of its DNA, known as T-DNA. In this method, the T-DNA is copied and the desired product is attached, to act as a leader strand. Proteins, for example ones that might transmit resistance, can then be added along the length of the T-DNA. A channel is then opened in the bacterial cell’s membrane and the T-DNA passes through and enters the plant cell through a wound.1 Following the gene insertion process, successfully transformed cell tissues are selected. After all the transformation embryo cells for different traits have been collected, a completely transgenic plant can be regenerated if the cells are grown under controlled conditions with hormones and nutrients.
While the production of better quality crops that contain resistance to herbicides, insect infestation and other environmental factors seem advantageous to farmers, the debate arises over whether or not these transgenic plants may be hazardous to the environment. In order to understand each position clearly, we must look at the pros and cons to genetically modified foods.
GM supporters believe that while initial cost of planting transgenic foods is expensive, over all farmers will garner larger profits. This is because plants can be modified for increased productivity, to be more weather tolerant, have a shorter seed maturation cycle, and to be pest and herbicide resistant which will reduce their annual season costs.3 The minimal use of herbicides and pesticides due to their genetic resistance will also be less harmful to the environment. These sprays when used in large amounts can be very detrimental because their toxins can leak into groundwater and thus contaminate it.2 Also, crops that genetically mature faster will have increased production, therefore more can be exported for profit. Furthermore, by maturing faster, farmers can have two growing seasons in the time that one would have normally taken. Therefore, less land would be used to create the same amount of crops, helping to ease the problem of overcrowding and less destruction of rain forests to provide for farmland.2 Scientists can also modify foods to be more nutritious, and to prevent/reduce disease. Some types of rice have been altered to include vitamin A and Iron. These two nutrients can help prevent blindness and death from malnutrition. Since the diet of many people living in third world countries is eighty percent rice, this can provide greater nutrition to the masses. Also, certain modified bananas and tomatoes contain a vaccine for hepatitis B thus reducing the cost of medicines and increasing the use of fruits and vegetables.2
In contrast to these benefits, opponents find that it is mostly the information we don’t know about GM foods which is potentially more harmful to humans and the environment. The genetic structure of an organism is very complex, as a result, it is hard to test all of the effects of introducing a foreign gene into such an intricate structure. For example, transgenic DNA is from a foreign organism, usually a bacteria or virus. Since whenever we eat a meal we consume this DNA and not all of it is broken down into macromolecules that our body can digest, one has to wonder where the undigested portions ends up. Viral and bacterial DNA not broke down can be absorbed into our blood stream, as a result, there is always the risk of toxins affecting our body year from now.1 Also, since modified foods sometimes use virus DNA, mutations may occur that make such viruses more potent and lead to serious health risks. Another unknown result of transgenic food can be the increase in the number of allergic reactions to foods. The genes acquired from other organisms that are inserted into GM foods may trigger new allergies. Two products, StarLink corn and a type of soybean, have booth been found to have a higher allergenicity than their conventional counterparts.1 Also, there is no evidence that clearly supports the reductions of pesticides on plants that have pesticide resistance. In studies there have been no clear reduction of pesticides associated with Roundup Ready soybeans, Bt corn, and herbicide tolerant cotton & corn. Therefore, the combination of the plan resistance with normal spraying could actually be more detrimental because of leakage of GM proteins into the soil.4
There is still a lot of information that scientists do know that is
equally as troubling. One of the
biggest problems with plants that have antibiotic resistance is the fear of
horizontal transfer to micro organisms.
The purpose of resistance to antibiotics is used in the laboratory as a
marker to see observable transformation.
Outside of the lab there is no practical use for such resistance. In the fields though, this resistance is
being transferred to micro organisms which normally inhabit our stomach and
intestines. As a result, these
micro organisms will be able to survive an oral does of antibiotic medicine
normally used to kill bacterial infections.1 Therefore, bacterial illness would be
hard to suppress with their new found resistance. Also, the hybridization crops with
nearby weeks could enable weeds to acquire certain traits such as herbicide
resistance. This would enable weeds
to survive spraying that would normally kill them off and thus hinder the
productivity of the crops. These
traits may also escape into wild populations. Since many transgenic plants have
compatible wild relatives with which they can hybridize, they can pass their
traits to normal commercial crops and infect the world’s food supply
adversely.1
In conclusion, while transgenic crops seem to provide many of the answers to the world’s short supply of food, the cost of such answers may be too great to risk. While the debate still ranges on there is one thing that’s for sure, whatever the decision it will no doubt be met with opposition and controversy.
Bibliography:
1. Colorado State University: Life Sciences and Department of Soil & Crop Sciences.
Transgenic Crops: An Introduction and Resource Guide. 2003. 1 May 2003.
<http://www.colostate.edu/programs/lifesciences/TransgenicCrops/index.html>
2. Wong, Chris. “Pros for GMO’s” Human Security e-zines. 2002. 1 May 2003.
<http://www.youthlinks.org/articleInit.do?article_id=1004>
3. Sakko,Kemin. “The Debate Over Genetically Modified Foods.” Action Bioscience.
May 2002. 1 May 2003.
<http://www.actionbioscience.org/biotech/sakko.html>
4. Munkvold, Gary P. and Hellmich, Richard L. Apsnet Plant Pathology Online. 1999.
1 May 2003.
<http://www.apsnet.org/online/feature/Btcorn/Top.html>
#3 DNA In the World of
Forensics
Have you ever wondered how a crime would be solved if there was no witness or criminal present at the crime scene? What about no fingerprints or footprints? How about a sample of blood? In the world today, genetics has been a study that opened the door not only to forensics but many other topics as well. Every person, animal, plant and organism has its own and different genetic makeup, which allows scientists to discover many answers to some very difficult problems from forensics to the origin of life.
The topic of interest is forensics especially in reference to legal proceedings. In the past 150 years scientists developed ways of identifying people using three main samples: hair, bone and blood. Hair makes it possible to find one’s age, sex and even race with an error rate of only one in 4500. As for bones, age, sex and race can be found as well as medical history can be determined. But the best indicator in any investigation is blood. Blood carries four main groups of A, B, AB and O but also the sugar it carries, which are indicated by a plus or minus. Sometimes that is still not enough to find out what one needs, so DNA is used.
DNA allows us to distinguish an individual from one another living or dead. DNA can be retrieved through blood, semen, saliva, bone, teeth or even flecks of skin or other tissues. A cigarette butt has enough saliva as well as a postage stamp to obtain DNA of an individual for example. The FBI has recently launched a program called CODIS, which stands for Combined DNA Index System. This system contains the genetic description of 250,000 convicted felons and 4600 samples of DNA of unsolved crimes. This new resource is a powerful instrument in the war against crime and criminals and a refuge for the innocent when accused guilty.
DNA was first used in a court case in the year 1987 in Leicestershire England where a boy supposedly raped and murdered two girls. The seventeen-year-old boy was found innocent of the crime after a DNA analysis of all the men in the surround three villages found the suspect. Since this landmark case, thousands of convicted criminals were either given their freedom or put into their proper place, jail. The Innocence Project in New York is a group of individuals who use DNA to find the innocent. The project exonerated 35 people in New York between 1992 and 1998, which six of those people were on death row. This system not only freed the innocent but also identified the real perpetrator.
On the subject of identifying people, the military uses DNA to also identify soldiers who were unrecognizable. This technology identified victims of crimes, wars, plane crashes and even catastrophes. DNA samples of the victims were taken and matched up with their immediate family to see if there is a resemblance in the genetic code. The Department of Defense so far identified the remains of nearly 500 servicemen who died in the Vietnam War. These soldiers were listed as missing in action or marked as unknowns at the Arlington National Cemetery. Now, these names are known and the families can now be at rest.
A huge part of DNA analysis is used for the common man or women also in matters concerning the father of a child for instance. Samples from a child are taken and compared to a father and mother to see who are the actual parents. Another problem in paternity are hospital mix-up. DNA testing gave relief to parents to see which child is actually theirs. There even was a huge debate in the past about Thomas Jefferson who supposedly fathered a slave daughter by the name Sally Hemings. Tests showed that there was DNA present in Heming’s DNA from Jefferson but since we don’t have DNA from President Jefferson, one can’t prove this claim but it is known that it did come from one of his male relatives.
DNA of any two humans is more than 99% identical but it is too expensive to look at all the DNA to find that 1% difference so scientists had to invent a way to develop a more efficient method. For unknown reasons, parts of the human DNA are made of short DNA patterns, which are repeated several times in a row. These repeats are called satellites. Scientists used this information about satellites and found out than many people have these repeats but there are many areas of satellite DNA scattered over the chromosomes in different places. This in turn, the chance that two people have the same repeats in the same area of chromosome is extremely small, about one in a trillion trillions. DNA cutting is also used to find differences in individuals DNA. Johns Hopkins scientist found an enzyme that actually cuts DNA. This enzyme is known as EcoR1 and it cuts DNA whenever it sees the base pairs GAATTC. No two people have their DNA cut into pieces of exactly the same length because there are too many variations in each person’s genes. Finally, southern blots are used also as a form to compare DNA of two or more individuals. Southern blots show the size of a person’s DNA pieces. By putting two southern blots next to each other shows at a glance whether they come from one, two or more people. One can see thickness differences in the pieces of DNA, which will either show a person is different or the same given a certain situation.
The future is bright for genetics and the use of DNA. It will soon be possible for crime scene experts to use portable credit-card-sized chips that allow them to process a DNA sample at the crime scene and get results within 10 minutes. It will also contain everything needed to cut, amplify, tag and analyze the DNA. In addition, it will be possible to develop a partial description of a suspect from the DNA left at a crime scene. Scientists are working on a way to determine hair color from DNA evidence as well as characteristics such as eye color, facial features and physical abnormalities.
As one can see, genetics is an important study in many aspects of life from criminal investigations to paternity tests. Technology is increasing everyday and we will soon see all the questions answered. Will we be able to actually find when the first human was evolved or even find Jimmy Hoffa’s body? Who knows but it is possible that such questions as these may soon be answered.
#4 Genetic Difference May
Cause Variation in Drug Reaction in Minorities
It has always been known that genetic variation causes different ethnic groups to develop difficulty in regards to diseases and reactions to environmental conditions that affect those diseases. Within the past year, it has been acknowledged that genetic differences might also cause variations in the responses to drugs and certain treatments among certain minority groups. Drug studies have shown that doctors must be more aware of ethnic backgrounds when prescribing drug regimens and of possible responses or side affects from medications in these minorities.
Drug therapy has often been depicted as a “one size fits all” regimen where not much is taken into account other than the nature of the illness and any allergies that the patient may have. Many health insurances that offer drug coverage may not cover all prescription medications, which may include drug choices that are better suited for some as a result of their genes. The problem with drugs is how they are transported across the cell membrane and then how they react with elements inside the cell. If genes are not properly coded, like the drug requires, then they will be ineffective in most cases or possibly over affective which maybe be more harmful than the previous case. In order to prevent over-dosing in some cases, we must be aware that genetics not only affect disease progress, but potential treatments as well.
First of all, dosing is the most important aspect that may be affected by genetics. A common drug, birth control, can be detrimentally affected by the expression of the genome. Many birth control pills are only effective up to a certain weight, yet dosage does not reflect these deviations within women, they only reflect the average amount of hormone needed to obtain a regular cycle. Another case is the administering of codeine to Caucasians and East Asians. East Asians metabolize certain pain medications at a higher rate than most people, which may require them to be given more than other patients require
A person’s metabolism may also cause complications if their genes cause over or under expression of metabolic functions. It is widely known that people of African American descent often retain salt more often then their Caucasian counterparts, which results in more cases of salt-sensitive high blood pressure. Therefore effective treatments for elevated blood pressure in the black community may not only include the typical medications but diuretics as well in an effort to reduce the amount of salt and water retained in the blood. Because of the chemical reactions that take place in the human body, drugs may react too fast or too slow to exert the desired effect, ultimately rendering them useless.
In addition to dosing or reaction times, drugs may have a completely adverse affect on the body. Ashkenazi Jews react very negatively to the drug clozapine, a common treatment for schizophrenia. When exposed to the drug, they develop a potentially life-threatening blood disease. If doctors are not aware of this obstacle or do not know enough about their patients background, it could crate more problems than it may solve.
So genes don’t only play a roll in disease development, but they can also affect how we treat diseases. If we are not careful in assessing the disease or the background of the patient, more harm that good may be done, negating any chance to cure. In order to prevent genetic differences from hindering treatments with certain medications, it would be beneficial to understand all possible reaction of medications with all potentially affect genes to ensure the best course of treatment for all patients.