How does DNA fingerprinting works? DNA fingerprinting is a reliable method for identifying people. How DNA fingerprinting works as to do with something called the HLA system (human leukocyte antigen system). The HLA is a system that codes for proteins on the surfaces of many cells, including white blood cells. HLA genotyping is used in transplants. With this system, people could match transplant genetically, so that a transplant from one person to another wouldn’t be rejected by the recipient.
There are four different HLA genes, labeled nicely A, B, C and D. HLA A has 23 alleles. HLA B has 47. HLA C has 8 and D has 23. A person could be, for example, A11, B16, C5 and D11. With more alleles is more likely that people would be different from one another, and that parents and children can be matched better.
There are a couple of problems with the HLA system, however. First, you need well preserved tissue or blood. That’s a little difficult sometimes. Second, HLA proteins are not always present in our cells. Third, a lot of mixtures of these genes go on when gametes are produced. Fourth, there are pretty common HLA alleles, and some extremely rare ones.
The Short Tandem Repeats
Human genome sequencing has revealed that the genome contains short sequences that are repeated many times in tandem. These are appropriately called Short Tandem Repeats (STR). For example, let’s consider the DNA sequence TCAT. Looking through the whole genome, there are different Short Tandem Repeats, and the repeat numbers are inherited. You might inherit one chromosome that has TCAT repeated five times, and the chromosome from the other parent might have TCAT repeated seven times.
You might ask how this block repeat happens. Molecular biologists, believe it or not, say that it is not clear how it happens. They have some ideas, though, but it is not clear. There are 10000 of STR’s scattered throughout the genome, but for DNA fingerprinting purposes, we use typically 13 of them.
These 13 repeated sequences are polymorphic. This means that there is more than one type of repeats. I might inherit five repeats of TCAT at a certain location, and seven from my other parent. If we were all the same for this repeat number, they wouldn’t do any good. These different numbers of repeats are what set us apart.
To analyze DNA this way, however, we need first to make a population survey. We need to know the frequencies of the alleles. For example, five TCAT are present 50% of the time in the population, and seven is present 50% also. If somebody comes across and has ten would be a totally different individual.
Supposing we are dealing with two of these 13 short tandem repeat chains, and that they have three alleles: A, B and C. Let’s say that the A allele is frequent in one person in a hundred. The B allele is one in five. The C allele is the more common, four in five. For the second short tandem repeat: A allele one in ten, B one in two, C two in five. A, B and C are just the number of repeats. A for example might be five, and B seven repeats.
So, let’s review:
Short Tandem Repeat 1:
A: one in a hundred
B: one in five
C: four in five
Short Tandem Repeat 2:
A: one in ten
B: one in two
C: two in five
Here is the key argument for doing DNA identification in this way. It comes from Mendel and probability. For a person to be carrying both the A and B alleles of STR number 1, the combined probability is the product of the two probabilities. The combined probability of A(1/100) and B(1/5) is:
The probability for STR number 2 A(one in ten) and B(one in two) is:
So, what is the probability of having both of them at once? Yes! It is the product of their probabilities:
We’re now getting a pretty low probability. One in ten thousand! This is the probability of carrying the four alleles: A and B of STR 1, A and B of STR 2. Think about it. We have 13 different systems for identifying people. If we’ve got these different alleles, the probability of two people having identical alleles is vanishingly low. It turns out that we’re all virtually unique in these sequences. That’s why DNA fingerprinting is so useful in identifying people.
Monday, March 1, 2010
Risks of Genetic Engineering
What are the risks of genetic engineering? The revolution that genetic engineering caused was profound. There was initially great concern about genetic engineering. The concerns centered on several aspects of this work. First, the bacteria used in these experiments were E. coli. This bacterium commonly lives on our intestines. People were worried about what will happen if this laboratory organism got out into our gut. Could the bacteria lead to cancer? This fear led almost to hysteria. Municipalities passed laws banning all genetic engineering work. A very famous scientist arrived to his laboratory one day to find the police out front, saying “you’ve broken our municipal ordinance against doing any gene swapping”. Doom scenarios were all over the place.
In 1975, a conference was held in California which brought together scientists, ethicists, physicians and lawyers to deal with this situation. This was a unique event in the history of science and government relations. The meeting was called by the scientists who were doing the work. They wanted some sort of feedback on what they were doing, because they were worried about the possible risks of genetic engineering.
At this meeting, after several days of heated discussions, they decided to do a moratorium on certain types of experiments. For example, until they knew what they were doing, they weren’t allowed to put cancer genes into bacteria to study them. They imposed extreme safety precautions on all of their types of experiments. Government agencies and institutional boards at research universities were set up to oversee this.
Scientists really asked for this oversight, which is very unusual, because scientists usually are of the type “just let us do our work and leave us alone, we would never harm you”. In this case, scientists were quite worried because this was so profound a change in biological manipulation.
In retrospect, these concerns were overblown, and no dangerous events have really occurred with genetic engineering. In fact, experiments that required severe precautions in 1975 are now done in high-school science labs. This doesn’t mean that we don’t need to constantly monitor this research. If we are dealing with harmful genes we must take extreme precautions.
In 1975, a conference was held in California which brought together scientists, ethicists, physicians and lawyers to deal with this situation. This was a unique event in the history of science and government relations. The meeting was called by the scientists who were doing the work. They wanted some sort of feedback on what they were doing, because they were worried about the possible risks of genetic engineering.
At this meeting, after several days of heated discussions, they decided to do a moratorium on certain types of experiments. For example, until they knew what they were doing, they weren’t allowed to put cancer genes into bacteria to study them. They imposed extreme safety precautions on all of their types of experiments. Government agencies and institutional boards at research universities were set up to oversee this.
Scientists really asked for this oversight, which is very unusual, because scientists usually are of the type “just let us do our work and leave us alone, we would never harm you”. In this case, scientists were quite worried because this was so profound a change in biological manipulation.
In retrospect, these concerns were overblown, and no dangerous events have really occurred with genetic engineering. In fact, experiments that required severe precautions in 1975 are now done in high-school science labs. This doesn’t mean that we don’t need to constantly monitor this research. If we are dealing with harmful genes we must take extreme precautions.
Good Things About Genetic Engineering
Here I want to talk about one of the good things about genetic engineering: using it to clean up the environment. I’ve already written about the benefits of genetic engineering in medicine and agriculture; let’s turn to the good things about genetic engineering regarding the environment. We can use bacteria as nature’s recyclers. Bacteria thrive on all sorts of nutrients, including things that we refer to as waste. There are species of bacteria that have the genetic capacity to produce enzymes that humans don’t. Composting uses bacteria to break down the carbon rich stores such as cellulose, which are the indigestible parts of wood chips, paper or straw. Also, they break down nitrogen rich sources, such as protein wastes and coffee grounds. When the bacteria work on these things, they produce four things: carbon dioxide, water, heat and humus.
Waste water treatment uses bacteria to act on human waste, paper products and household chemicals. The liquids and solids are treated differently. There is one group of bacteria that digest harmful substances in the solids of our wastes. Some of these bacteria, by the way, make a gas called methane as a byproduct, which is used for energy. Liquid wastes are digested by other bacteria. There is a whole series of bacteria that will digest different substances that are in things we call waste.
We’re still discovering more efficient and better ways to use bacteria for our purposes. This is called bioremediation.
Bacteria and plants have or can be given genes that remove pollutants. In addition to being nature’s recyclers, bacteria break down many human-made pollutants. How do we know this? We take soil with water, and we take that pollutant, oil for example. Then we look and see whether any of it gets broken down. We grow up the bacteria that thrive on the pollutant and use it.
In 1989, the oil tanker Exxon Valdez ran aground near the Alaskan shore, releasing 11 million gallons of crude oil over a thousand miles of shoreline. This was an environmental disaster of major proportions. Cleanup by physical methods was used first and the result was a dispersion of two thirds of the oil. Genetically engineered bacteria did the rest by bioremediation. Genetic strains of bacteria that can eat up oil were used. This process is ongoing.
The government of Kuwait is using bioremediation to try to clean up 150 million gallons of oil that was spilled probably deliberately by exploding oil wells during the Gulf War of 1991. This is probably the largest single remediation project in the world, and it is going on as I write. This is maybe one of the most useful of the good things about genetic engineering.
Good Things About Genetic Engineering? Environmental Cleanup
There is a type of bacteria called extremophiles. They have many genes that are useful in bioremediation. Extremophiles are bacteria that love the extremes of nature. They are kind of the ultimate athletes of the biological world. They can live in very hot places or icy places like Antarctica, or deep in the ocean, or very salty environments like the Dead Sea. These organisms form a separate group from bacteria called the archaea. They are called archaea because they resemble the organisms that are believed were the first living cells.
The archaea genomes have been sequenced and half of the genes of the archaea do not resemble anything in any types of bacteria or eukaryotes. Some of them have genes that use carbon dioxide, just like plants do, not to make sugars but to make methane gas. Archaea are by far the major producers of this gas.
The granddaddy of all archaea is called Deinococcus radiodurans. This organism lives in probably the most dangerous environment on Earth: ones with extremely high levels of radiation. Normally, radiation kills cells by damaging DNA. When DNA in any cell is damaged by radiation, we can repair it thanks to a system that we have. Large amounts of radiation, however, overwhelm that, and you get permanent mutations and cancers as a result.
Deinococcus radiodurans gets around this by having the most efficient and sensitive radiation repair system in nature. It is a phenomenally good system. This wonderful organism is responsible by one of the good things about genetic engineering. Genes from other extremophiles are being engineered into Deinococcus radiodurans. People call this new organism Conan the Bacterium. It is used to clean up the most toxic sites we know of. For example, in America there are sites extremely contaminated with extremely bad stuff. These Deinococcus radiodurans are being used there.
Plants can be genetically engineered for environmental cleanup. For instance, bacterial genes that allow environmental cleanup can be put into transgenic plants to break down oil. There are plants that would convert solid mercury into harmless substances. They might ask why use plants when microbes are available. The issue is that you want to get the microbe out of the soil when you don’t need it anymore. You don’t want extra microbes. Getting bacteria out of the soil is quite difficult. Plants are easy to take out. You plant it, it does its thing, and you take it out. This might be a better way of doing bioremediation in some cases.
Waste water treatment uses bacteria to act on human waste, paper products and household chemicals. The liquids and solids are treated differently. There is one group of bacteria that digest harmful substances in the solids of our wastes. Some of these bacteria, by the way, make a gas called methane as a byproduct, which is used for energy. Liquid wastes are digested by other bacteria. There is a whole series of bacteria that will digest different substances that are in things we call waste.
We’re still discovering more efficient and better ways to use bacteria for our purposes. This is called bioremediation.
Bacteria and plants have or can be given genes that remove pollutants. In addition to being nature’s recyclers, bacteria break down many human-made pollutants. How do we know this? We take soil with water, and we take that pollutant, oil for example. Then we look and see whether any of it gets broken down. We grow up the bacteria that thrive on the pollutant and use it.
In 1989, the oil tanker Exxon Valdez ran aground near the Alaskan shore, releasing 11 million gallons of crude oil over a thousand miles of shoreline. This was an environmental disaster of major proportions. Cleanup by physical methods was used first and the result was a dispersion of two thirds of the oil. Genetically engineered bacteria did the rest by bioremediation. Genetic strains of bacteria that can eat up oil were used. This process is ongoing.
The government of Kuwait is using bioremediation to try to clean up 150 million gallons of oil that was spilled probably deliberately by exploding oil wells during the Gulf War of 1991. This is probably the largest single remediation project in the world, and it is going on as I write. This is maybe one of the most useful of the good things about genetic engineering.
Good Things About Genetic Engineering? Environmental Cleanup
There is a type of bacteria called extremophiles. They have many genes that are useful in bioremediation. Extremophiles are bacteria that love the extremes of nature. They are kind of the ultimate athletes of the biological world. They can live in very hot places or icy places like Antarctica, or deep in the ocean, or very salty environments like the Dead Sea. These organisms form a separate group from bacteria called the archaea. They are called archaea because they resemble the organisms that are believed were the first living cells.
The archaea genomes have been sequenced and half of the genes of the archaea do not resemble anything in any types of bacteria or eukaryotes. Some of them have genes that use carbon dioxide, just like plants do, not to make sugars but to make methane gas. Archaea are by far the major producers of this gas.
The granddaddy of all archaea is called Deinococcus radiodurans. This organism lives in probably the most dangerous environment on Earth: ones with extremely high levels of radiation. Normally, radiation kills cells by damaging DNA. When DNA in any cell is damaged by radiation, we can repair it thanks to a system that we have. Large amounts of radiation, however, overwhelm that, and you get permanent mutations and cancers as a result.
Deinococcus radiodurans gets around this by having the most efficient and sensitive radiation repair system in nature. It is a phenomenally good system. This wonderful organism is responsible by one of the good things about genetic engineering. Genes from other extremophiles are being engineered into Deinococcus radiodurans. People call this new organism Conan the Bacterium. It is used to clean up the most toxic sites we know of. For example, in America there are sites extremely contaminated with extremely bad stuff. These Deinococcus radiodurans are being used there.
Plants can be genetically engineered for environmental cleanup. For instance, bacterial genes that allow environmental cleanup can be put into transgenic plants to break down oil. There are plants that would convert solid mercury into harmless substances. They might ask why use plants when microbes are available. The issue is that you want to get the microbe out of the soil when you don’t need it anymore. You don’t want extra microbes. Getting bacteria out of the soil is quite difficult. Plants are easy to take out. You plant it, it does its thing, and you take it out. This might be a better way of doing bioremediation in some cases.
Stem Cell Research
Stem cell research is in our news all the time, both from a scientific point of view and a political point of view. Today we’re on the threshold of stealing a power from the gods, the power to regenerate human organs and make life much longer. There are some people who fear retribution from the gods, but I know we’re going to do this anyway. Our scientists, no matter what the political climate is, are going to learn how to use stem cells to regenerate organs.
What are Stem Cells?
Stem cells are unspecialized cells in the body that constantly divide to form a pool of cells that can then specialize when they are needed. The ultimate stem cells are embryonic stem cells. They are totipotent. They can become any cell in the organism. In laboratory experiments on animals, these embryonic stem cells can be induced to form many different cell types. In animals, these cell types coming from embryonic stem cells have cured brain damage, heart damage, muscle damage, etc. This has generated great excitement for stem cell research.
The proposal is to use laboratory grown stem cells as a supply. You don’t need a lot of embryos to do this. The problem is that if I get some stem cells from someone else, they’re not mine. Those cells going into my heart would do the work, but then my immune system would ultimately reject them.
What is the advantage of stem cell research?
There is a need for new cells in medicine to replace cells that are damaged. For example, in a heart attack, the heart muscle is damaged, and it is usually permanent damage. How are you going to replace that tissue? In the brain, Parkinson’s disease and others result from a lack of functional cells. Diabetes, specially type 1, the pancreas is damaged. Let’s get new cells to replace these!
Stem cell transplants are already performed every day. Bone marrow gets damaged when cancer is treated with radiation therapy and chemotherapy. All the cells, including the stem cells inside the bone marrow, are damaged. A person who is treated with radiation and chemotherapy for cancer is going to be severely anemic and immune-compromised; because their immune system would not be working (white blood cells would not be produced in sufficient numbers).
What are Stem Cells?
Stem cells are unspecialized cells in the body that constantly divide to form a pool of cells that can then specialize when they are needed. The ultimate stem cells are embryonic stem cells. They are totipotent. They can become any cell in the organism. In laboratory experiments on animals, these embryonic stem cells can be induced to form many different cell types. In animals, these cell types coming from embryonic stem cells have cured brain damage, heart damage, muscle damage, etc. This has generated great excitement for stem cell research.
The proposal is to use laboratory grown stem cells as a supply. You don’t need a lot of embryos to do this. The problem is that if I get some stem cells from someone else, they’re not mine. Those cells going into my heart would do the work, but then my immune system would ultimately reject them.
What is the advantage of stem cell research?
There is a need for new cells in medicine to replace cells that are damaged. For example, in a heart attack, the heart muscle is damaged, and it is usually permanent damage. How are you going to replace that tissue? In the brain, Parkinson’s disease and others result from a lack of functional cells. Diabetes, specially type 1, the pancreas is damaged. Let’s get new cells to replace these!
Stem cell transplants are already performed every day. Bone marrow gets damaged when cancer is treated with radiation therapy and chemotherapy. All the cells, including the stem cells inside the bone marrow, are damaged. A person who is treated with radiation and chemotherapy for cancer is going to be severely anemic and immune-compromised; because their immune system would not be working (white blood cells would not be produced in sufficient numbers).
Cancer Prevention
Let’s talk about cancer prevention. What can we do to prevent it? Cancer is the second leading cause of death in the United States, and the most feared diagnosis. Although heart disease is the number one killer of Americans, the diagnosis of cancer is the most terrifying. Clearly we have much to do in the prevention of cancer. Poor diet is estimated to account for 30% to 35% of the cancers. Therefore, we can do something to modify our risk. Please keep in mind that modification of risk does not preclude the need for early detection and diagnosis. Although you might do everything possible in terms of diet and exercise, make sure you keep up with diagnostic testing.
Outside of diet, there are other lifestyle risk factors: tobacco use, alcohol consumption and lack of exercise. These can increase the overall risk of almost all cancers.
Here I want to talk about the dietary strategies and lifestyle modifications needed to reduce cancer risk.
Both tobacco and alcohol initiate and promote cancer development. Not only they cause cell damage, they also promote cancer development.
The American Cancer Society suggests that 1 million skin cancers could be prevented by eliminating sun exposure. This is a double edged sword. We know that the sun is a great source of vitamin D. By eliminating sun exposure, you can also eliminate one of your major sources of vitamin D. Sun screen can be very effective for preventing skin cancer, but it must be applied in an appropriate way. The higher the Sun Protection Factor (SPF), the better.
Exposure to UV light in tanning salons can be just as dangerous as exposure to the sun itself.
Some of the most exciting things in terms of cancer development is that we now know that certain viruses have been implicated in cervical cancer and possibly others as well. New vaccines can be given to prevent certain forms but not all of cervical cancer.
The current thinking is that nutrition can either act as a cancer promoter or a cancer-cell killer. According to the American Cancer society, diet and weight management can aid in the prevention of cancer. If you’re struggling with weight management and exercise, you might want to think about this as your deposit in the cancer prevention account.
There appears to be a dose-related response to exercise. That means that 30 minutes of exercise is good, but an hour would be better. Human bodies evolved to move. Apparently, in this case, what is happening is that individuals who do not exercise become resistant to insulin. They make of it, and the more you make, more you promote cancer development.
Simple Recommendations
What do you think of a plant-based diet? The more of your plate is occupied by vegetables, the better. Think about having a meat-less Monday, were your main dish might be vegetarian.
A recent study that included more than half a million subjects (this is a lot!!) suggest that those who consume the highest amount of red meat have a higher mortality rate. This study is known as the NIH-AARP Diet and Health Study. Mortality rates from both heart disease and cancer were increased with increasing red meat consumption.
What are some big recommendations from this study? Reduce the meat and avoid grilling. Grilling can increase the charring of that meat. It is the charred meat that can increase the risk of cancer.
Well, suppose you’re invited over somebody’s house and they are not really great with their grilling skills and you’ve got everything that’s significantly blackened. Trim off as much of that as you can and maybe flavor it up with a bit of barbecue sauce.
Regarding alcohol use in cancer prevention, the best approach is no alcohol. Keep in mind that alcohol minimally is going to serve as an initiating event. If you do drink alcohol, the recommendation is to limit your intake to one drink per day for women and two for men.
Avoid cured meats. These are processed meats, such as bacon, ham and hot dogs. Individuals are trying to get away from beef and pork, we now have cured turkey products. We have now turkey hot dogs and everyone believes that’s better for them. The problem is the curing of the meat. Cancer-causing compounds are formed when meats are cured.
Well, here I ended talking more about what we should avoid to prevent cancer. In my next post I’ll talk about a healthy diet and lifestyle that would help in cancer prevention.
Outside of diet, there are other lifestyle risk factors: tobacco use, alcohol consumption and lack of exercise. These can increase the overall risk of almost all cancers.
Here I want to talk about the dietary strategies and lifestyle modifications needed to reduce cancer risk.
Both tobacco and alcohol initiate and promote cancer development. Not only they cause cell damage, they also promote cancer development.
The American Cancer Society suggests that 1 million skin cancers could be prevented by eliminating sun exposure. This is a double edged sword. We know that the sun is a great source of vitamin D. By eliminating sun exposure, you can also eliminate one of your major sources of vitamin D. Sun screen can be very effective for preventing skin cancer, but it must be applied in an appropriate way. The higher the Sun Protection Factor (SPF), the better.
Exposure to UV light in tanning salons can be just as dangerous as exposure to the sun itself.
Some of the most exciting things in terms of cancer development is that we now know that certain viruses have been implicated in cervical cancer and possibly others as well. New vaccines can be given to prevent certain forms but not all of cervical cancer.
The current thinking is that nutrition can either act as a cancer promoter or a cancer-cell killer. According to the American Cancer society, diet and weight management can aid in the prevention of cancer. If you’re struggling with weight management and exercise, you might want to think about this as your deposit in the cancer prevention account.
There appears to be a dose-related response to exercise. That means that 30 minutes of exercise is good, but an hour would be better. Human bodies evolved to move. Apparently, in this case, what is happening is that individuals who do not exercise become resistant to insulin. They make of it, and the more you make, more you promote cancer development.
Simple Recommendations
What do you think of a plant-based diet? The more of your plate is occupied by vegetables, the better. Think about having a meat-less Monday, were your main dish might be vegetarian.
A recent study that included more than half a million subjects (this is a lot!!) suggest that those who consume the highest amount of red meat have a higher mortality rate. This study is known as the NIH-AARP Diet and Health Study. Mortality rates from both heart disease and cancer were increased with increasing red meat consumption.
What are some big recommendations from this study? Reduce the meat and avoid grilling. Grilling can increase the charring of that meat. It is the charred meat that can increase the risk of cancer.
Well, suppose you’re invited over somebody’s house and they are not really great with their grilling skills and you’ve got everything that’s significantly blackened. Trim off as much of that as you can and maybe flavor it up with a bit of barbecue sauce.
Regarding alcohol use in cancer prevention, the best approach is no alcohol. Keep in mind that alcohol minimally is going to serve as an initiating event. If you do drink alcohol, the recommendation is to limit your intake to one drink per day for women and two for men.
Avoid cured meats. These are processed meats, such as bacon, ham and hot dogs. Individuals are trying to get away from beef and pork, we now have cured turkey products. We have now turkey hot dogs and everyone believes that’s better for them. The problem is the curing of the meat. Cancer-causing compounds are formed when meats are cured.
Well, here I ended talking more about what we should avoid to prevent cancer. In my next post I’ll talk about a healthy diet and lifestyle that would help in cancer prevention.
Genetic Engineering
Genetic Engineering is the manipulation of microbes, plants and animals to make products that are useful to people. As such, this technology is not new. It began a long time ago. I would say that biotechnology began with agriculture.
What is Genetic Engineering?
Estimates are that agriculture probably began about 10000 years ago, in what is now the region near Iraq. We have evidence that Sumerians living there at the time learned that barley plants growing around their homes made seeds that could be used to make bear and bread. They started growing these seeds near their settlements. They would use some of the seeds to make bear and bread, and then they would grow the rest of the seeds nearby. This was the first biotechnology.
A History of Genetic Engineering
Werner Arber was born in 1929. As a graduate student at the University of Geneva in the 1950’s, he studied with a physics professor who converted from doing pure physics to biophysics. Arber’s PhD thesis was on the phenomenon of bacteriophages restriction. He didn’t even suspect that his research would begin a revolution.
In 1973, scientists had taken two chromosomes, cut them open, put them back together, and showed that they were functional in a cell. They had created genetically functional recombinant DNA. It was a revolutionary discovery.
Review the timeline of genetic engineering.
Benefits of Genetic Engineering
The first major product of biotechnology was human insulin. This type of insulin is now used to treat type 1 diabetics. Another example is the blood-clotting protein that is missing in hemophilia.
There is a protein called Erythropoietin (EPO). EPO is a hormone-like substance made by the kidneys. The gene coding for EPO was isolated, EPO was made by recombinant DNA technology, and this is now widely used for people who are undergoing kidney dialysis and also people who are being treated with cancer chemotherapy.
There are a significant number of humans that lack adequate amounts of growth hormone. These people are very short in stature. The growth hormone is a protein. So, again, we got to get it through recombinant DNA technology.
We can use biotechnology to have a plant make a vaccine. You could become immune to a disease simply by eating a fruit. Pretty nice, eh?
These are just a few benefits of this new technology.
Genetic Engineering in Agriculture
According to UN estimates, human population will level off at about 10 billion people. Can biotechnology help solve this issue? A real problem in agriculture that existed for millennia is that most plants cannot grow in salty soils. Salt-tolerant transgenic plants may make deserts bloom again.
Other applications of biotechnology in agricultura are:
Plants That Make Their Own Insecticide
Plants Resistant to Herbicides
Nutritionally Rich Crops
Problems with Genetic Engineering
The first supposed problem is that genetic manipulation is an unnatural manipulation of nature. This is what philosophers call the “yuck factor”. According to this argument, eating food from a plant that has genes from bacteria is just “going too far”. There is no real response to this emotional argument.
The second of the supposed problems is that genetically modified foods might be unsafe to eat. It turns out that most genetically modified plants grown today are not altered in the food part of the plant. We’ve got to be careful with allergies, however.
The third of the risks is that genetically modified plants may be dangerous to the environment. This is maybe a real risk, but not a really serious one.
What is Genetic Engineering?
Estimates are that agriculture probably began about 10000 years ago, in what is now the region near Iraq. We have evidence that Sumerians living there at the time learned that barley plants growing around their homes made seeds that could be used to make bear and bread. They started growing these seeds near their settlements. They would use some of the seeds to make bear and bread, and then they would grow the rest of the seeds nearby. This was the first biotechnology.
A History of Genetic Engineering
Werner Arber was born in 1929. As a graduate student at the University of Geneva in the 1950’s, he studied with a physics professor who converted from doing pure physics to biophysics. Arber’s PhD thesis was on the phenomenon of bacteriophages restriction. He didn’t even suspect that his research would begin a revolution.
In 1973, scientists had taken two chromosomes, cut them open, put them back together, and showed that they were functional in a cell. They had created genetically functional recombinant DNA. It was a revolutionary discovery.
Review the timeline of genetic engineering.
Benefits of Genetic Engineering
The first major product of biotechnology was human insulin. This type of insulin is now used to treat type 1 diabetics. Another example is the blood-clotting protein that is missing in hemophilia.
There is a protein called Erythropoietin (EPO). EPO is a hormone-like substance made by the kidneys. The gene coding for EPO was isolated, EPO was made by recombinant DNA technology, and this is now widely used for people who are undergoing kidney dialysis and also people who are being treated with cancer chemotherapy.
There are a significant number of humans that lack adequate amounts of growth hormone. These people are very short in stature. The growth hormone is a protein. So, again, we got to get it through recombinant DNA technology.
We can use biotechnology to have a plant make a vaccine. You could become immune to a disease simply by eating a fruit. Pretty nice, eh?
These are just a few benefits of this new technology.
Genetic Engineering in Agriculture
According to UN estimates, human population will level off at about 10 billion people. Can biotechnology help solve this issue? A real problem in agriculture that existed for millennia is that most plants cannot grow in salty soils. Salt-tolerant transgenic plants may make deserts bloom again.
Other applications of biotechnology in agricultura are:
Plants That Make Their Own Insecticide
Plants Resistant to Herbicides
Nutritionally Rich Crops
Problems with Genetic Engineering
The first supposed problem is that genetic manipulation is an unnatural manipulation of nature. This is what philosophers call the “yuck factor”. According to this argument, eating food from a plant that has genes from bacteria is just “going too far”. There is no real response to this emotional argument.
The second of the supposed problems is that genetically modified foods might be unsafe to eat. It turns out that most genetically modified plants grown today are not altered in the food part of the plant. We’ve got to be careful with allergies, however.
The third of the risks is that genetically modified plants may be dangerous to the environment. This is maybe a real risk, but not a really serious one.
Cell culture H1N1 vacc could be ready in 3 months
industry response to the h1n1 pandemic suggests that cell culture vaccine production is about to come of age with two firms that use the technique, novartis and baxter, claiming it will cut development and manufacturing timelines by months.
Margaret Chan officially declared the pandemic explaining that H1N1 infections worldwide can no longer be traced and that “further spread is considered inevitable.” She asked drugmakers to begin preparing for large-scale H1N1 vaccine production when manufacture of seasonal stocks is completed, prompting a flurry of industry updates from vaccine producers.
Baxter and Novartis aim for early availability
The most eye-catching of these responses came from US drugmaker Baxter which announced it has completed testing of its Celvapan H1N1 vaccine and is “now in full-scale production,” and is working to deliver it as early as next month. Traditionally, seasonal influenza vaccines are mass produced using the albumin found in fertilised hens eggs as a growth media.
Swiss drug major Novartis made similar claims for its cell culture developed vaccine, although it was more measured about its timelines.
Novartis said it completed making the first batch of a H1N1 vaccine weeks ahead of expectations, explaining that its culture system allows production to begin “without the need to adapt the virus strain to grow in eggs, as with traditional…technologies.”
The firm, which claims to have been asked to supply vaccine ingredients by more than 30 countries, said it will begin trials of its product next month and expects to obtain regulatory approval for the vaccine in the autumn.
In a follow up statement reported by London’s Financial Times yesterday, Novartis said that it “will not give free vaccines against H1N1 flu to poor countries, though it will consider discounts.”
GSK, Sanofi and CSL
The response of companies that use egg-based production methods was more uniform, with almost all saying that large-scale manufacture will begin by September at the earliest.
Initial media reports suggested that Australia’s CSL will finish making the first batch of its vaccine ahead of producers like GlaxoSmithKline (GSK) and Sanofi Aventis, although this was later denied by company spokesperson Rachel Davis.
Margaret Chan officially declared the pandemic explaining that H1N1 infections worldwide can no longer be traced and that “further spread is considered inevitable.” She asked drugmakers to begin preparing for large-scale H1N1 vaccine production when manufacture of seasonal stocks is completed, prompting a flurry of industry updates from vaccine producers.
Baxter and Novartis aim for early availability
The most eye-catching of these responses came from US drugmaker Baxter which announced it has completed testing of its Celvapan H1N1 vaccine and is “now in full-scale production,” and is working to deliver it as early as next month. Traditionally, seasonal influenza vaccines are mass produced using the albumin found in fertilised hens eggs as a growth media.
Swiss drug major Novartis made similar claims for its cell culture developed vaccine, although it was more measured about its timelines.
Novartis said it completed making the first batch of a H1N1 vaccine weeks ahead of expectations, explaining that its culture system allows production to begin “without the need to adapt the virus strain to grow in eggs, as with traditional…technologies.”
The firm, which claims to have been asked to supply vaccine ingredients by more than 30 countries, said it will begin trials of its product next month and expects to obtain regulatory approval for the vaccine in the autumn.
In a follow up statement reported by London’s Financial Times yesterday, Novartis said that it “will not give free vaccines against H1N1 flu to poor countries, though it will consider discounts.”
GSK, Sanofi and CSL
The response of companies that use egg-based production methods was more uniform, with almost all saying that large-scale manufacture will begin by September at the earliest.
Initial media reports suggested that Australia’s CSL will finish making the first batch of its vaccine ahead of producers like GlaxoSmithKline (GSK) and Sanofi Aventis, although this was later denied by company spokesperson Rachel Davis.
New Microarray Technology
Moxtek, a nano-photonics company, today announced that it has reached a collaboration agreement with Philips Research to develop a new wire grid microarray chip (WGM) that has been designed to offer ultra-high surface specificity and excellent suppression of background signals. The WGM is based on a wire grid pattern on a glass substrate.
The WGM technology provides the potential for rapid quantitative detection with improved accuracy, of biomolecules such as proteins and nucleic acids. In addition, the technology promises to significantly simplify the work flow and improve the reproducibility for such tests by removing the washing step and performing hybridization and detection in parallel. These strengths match with the needs for advanced microarray technology in life sciences research. Rapid molecular detection for life sciences research is a fast-growing market, and could revolutionize healthcare research.
The WGM is based on illumination of a grid of metal nanowires with polarized excitation light and detecting the fluorescence generated by fluorescently labeled target molecules bound to capture probes on the substrate between the metal nanowires. The detection volume is limited to ~20 nm above the surface, and can be controlled via the dimensions of the nanowires and the excitation wavelength. The surface specific detection of the WGM provides a significant reduction in microarray workflow by making redundant the chip washing step; moreover, it has been shown to allow monitoring the binding of bio-molecules to the substrate in real-time.
Control of the polarization state enables using the wire grid microarray concept for both highly surface specific measurements and “conventional” measurements where the measurement volume is determined by the optical set-up rather than the geometry of the wire grid. This versatile technique has been designed to be compatible with commercial optical microarray readers currently available on the market.
The WGM technology provides the potential for rapid quantitative detection with improved accuracy, of biomolecules such as proteins and nucleic acids. In addition, the technology promises to significantly simplify the work flow and improve the reproducibility for such tests by removing the washing step and performing hybridization and detection in parallel. These strengths match with the needs for advanced microarray technology in life sciences research. Rapid molecular detection for life sciences research is a fast-growing market, and could revolutionize healthcare research.
The WGM is based on illumination of a grid of metal nanowires with polarized excitation light and detecting the fluorescence generated by fluorescently labeled target molecules bound to capture probes on the substrate between the metal nanowires. The detection volume is limited to ~20 nm above the surface, and can be controlled via the dimensions of the nanowires and the excitation wavelength. The surface specific detection of the WGM provides a significant reduction in microarray workflow by making redundant the chip washing step; moreover, it has been shown to allow monitoring the binding of bio-molecules to the substrate in real-time.
Control of the polarization state enables using the wire grid microarray concept for both highly surface specific measurements and “conventional” measurements where the measurement volume is determined by the optical set-up rather than the geometry of the wire grid. This versatile technique has been designed to be compatible with commercial optical microarray readers currently available on the market.
The good news in our DNA: Defects you can fix with vitamins and minerals
As the cost of sequencing a single human genome drops rapidly, with one company predicting a price of $100 per person in five years, soon the only reason not to look at your "personal genome" will be fear of what bad news lies in your genes.
University of California, Berkeley, scientists, however, have found a welcome reason to delve into your genetic heritage: to find the slight genetic flaws that can be fixed with remedies as simple as vitamin or mineral supplements.
"There are over 600 human enzymes that use vitamins or minerals as cofactors, and this study reports just what we found by studying one of them," Rine said. "What this means is that, even if the odds of an individual having a defect in one gene is low, with 600 genes, we are all likely to have some mutations that limit one or more of our enzymes."
The subtle effects of variation in enzyme activity may well account for conflicting results of some clinical trials, including the confusing data on the effect of vitamin supplements, he noted. In the future, the enzyme profile of research subjects will have to be taken into account in analyzing the outcome of clinical trials.
If one considers not just vitamin-dependent enzymes but all the 30,000 human proteins in the genome, "every individual would harbor approximately 250 deleterious substitutions considering only the low-frequency variants. These numbers suggest that the aggregate incidence of low-frequency variants could have a significant physiological impact," the researchers wrote in their paper.
University of California, Berkeley, scientists, however, have found a welcome reason to delve into your genetic heritage: to find the slight genetic flaws that can be fixed with remedies as simple as vitamin or mineral supplements.
"There are over 600 human enzymes that use vitamins or minerals as cofactors, and this study reports just what we found by studying one of them," Rine said. "What this means is that, even if the odds of an individual having a defect in one gene is low, with 600 genes, we are all likely to have some mutations that limit one or more of our enzymes."
The subtle effects of variation in enzyme activity may well account for conflicting results of some clinical trials, including the confusing data on the effect of vitamin supplements, he noted. In the future, the enzyme profile of research subjects will have to be taken into account in analyzing the outcome of clinical trials.
If one considers not just vitamin-dependent enzymes but all the 30,000 human proteins in the genome, "every individual would harbor approximately 250 deleterious substitutions considering only the low-frequency variants. These numbers suggest that the aggregate incidence of low-frequency variants could have a significant physiological impact," the researchers wrote in their paper.
Invitrogen and Applied Biosystems to combine
Invitrogen Corporation and Applera Corporation today announced that their Boards of Directors have approved a definitive merger agreement, under which Invitrogen will acquire all of the outstanding shares of Applera's Applied Biosystems Group a cash and stock transaction valued at $6.7 billion.
This strategic combination will create a global leader in biotechnology reagents and systems generating approximately $3.5 billion in combined sales, with significant commercial, operational and technical scale, uniquely positioned to accelerate and drive new discoveries and commercial applications. The combined company will have a major presence in key growth markets and exceptional technical capabilities in the areas of genetic analysis, proteomics, cell biology and cell systems. Following the close of the transaction, the combined organization will be named Applied Biosystems, Inc. and will have its corporate headquarters in Carlsbad, California.
Under the terms of the merger agreement, Applera-Applied Biosystems shareholders will receive $38.00 for each share of Applera-Applied Biosystems stock they own in the form of Invitrogen common stock and cash. The expected split between cash and stock is 45% and 55%, respectively. Applera-Applied Biosystems shareholders will receive a value of $38.00 a share if the 20 day volume-weighted average price of Invitrogen common stock is in the range of $43.69 - $46.00 three business days prior to the close of the transaction. The total value per share will differ if Invitrogen's 20 day volume-weighted average price is above or below that range, measured shortly prior to the close of the transaction. The consideration represents a premium of 17% to Applied Biosystems's closing price on June 11, 2008, or 12% to Applied Biosystems's average closing price in the last 30 trading days. Applera-Applied Biosystems shareholders also will have the option to request all cash or all stock, subject to possible proration. Upon completion of the transaction, Invitrogen shareholders will own the majority of the company.
This strategic combination will create a global leader in biotechnology reagents and systems generating approximately $3.5 billion in combined sales, with significant commercial, operational and technical scale, uniquely positioned to accelerate and drive new discoveries and commercial applications. The combined company will have a major presence in key growth markets and exceptional technical capabilities in the areas of genetic analysis, proteomics, cell biology and cell systems. Following the close of the transaction, the combined organization will be named Applied Biosystems, Inc. and will have its corporate headquarters in Carlsbad, California.
Under the terms of the merger agreement, Applera-Applied Biosystems shareholders will receive $38.00 for each share of Applera-Applied Biosystems stock they own in the form of Invitrogen common stock and cash. The expected split between cash and stock is 45% and 55%, respectively. Applera-Applied Biosystems shareholders will receive a value of $38.00 a share if the 20 day volume-weighted average price of Invitrogen common stock is in the range of $43.69 - $46.00 three business days prior to the close of the transaction. The total value per share will differ if Invitrogen's 20 day volume-weighted average price is above or below that range, measured shortly prior to the close of the transaction. The consideration represents a premium of 17% to Applied Biosystems's closing price on June 11, 2008, or 12% to Applied Biosystems's average closing price in the last 30 trading days. Applera-Applied Biosystems shareholders also will have the option to request all cash or all stock, subject to possible proration. Upon completion of the transaction, Invitrogen shareholders will own the majority of the company.
DNA is clearly in the public consciousness
It is true that the DNA has become vernacular now, blogging previously on the Genome entering the drawing rooms in Dawn of the GATTACA era! found another cute, small and interesting article which relates to this interesting fact on how common a word is the "DNA" now When you care enough to send the very best DNA. After reading it i felt in days to come, well we might have MATTEL come out with a "Francis Crick DNA code-breaker toy" fighting and saving the world and a "Craig Venter" toy challenging him...
GNA-glycerol nucleic acid—a synthetic analog of DNA
Biodesign Institute colleague John Chaput is working to give researchers brand new materials to aid their designs. In an article recently published in the Journal of the American Chemical Society, Chaput and his research team have made the first self-assembled nanostructures composed entirely of glycerol nucleic acid (GNA)—a synthetic analog of DNA.
“Everyone in DNA nanotechnology is essentially limited by what they can buy off the shelf,” said Chaput, who is also an ASU assistant professor in the Department of Chemistry and Biochemistry. “We wanted to build synthetic molecules that assembled like DNA, but had additional properties not found in natural DNA.”
The DNA helix is made up of just three simple parts: a sugar and a phosphate molecule that form the backbone of the DNA ladder, and one of four nitrogenous bases that make up the rungs. The nitrogenous base pairing rules in the DNA chemical alphabet fold DNA into a variety of useful shapes for nanotechnology, given that "A" can only form a zipper-like chemical bond with "T" and "G" only pair with "C."
In the case of GNA, the sugar is the only difference with DNA. The five carbon sugar commonly found in DNA, called deoxyribose, is substituted by glycerol, which contains just three carbon atoms.
In nature, many molecules important to life like DNA and proteins have evolved to exist only as right-handed. The GNA structures, unlike DNA, turned out to be ‘enantiomeric’ molecules, which in chemical terms means both left and right-handed.
“Making GNA is not tricky, it’s just three steps, and with three carbon atoms, only one stereo center,” said Chaput. “It allows us to make these right and left-handed biomolecules. People have actually made left-handed DNA, but it is a synthetic nightmare. To use it for DNA nanotechnology could never work. It’s too high of a cost to make, so one could never get enough material.”
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