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INTRODUCTION Biotechnology refers to technologies utilizing or based on biology – a formal definition from the United Nations Convention on Biological Diversity states that biotechnology is “any technological application that uses biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific use.” Biotechnology is used in a variety of fields, including agriculture, food science and medicine and is often associated with genetic manipulations. This chapter will provide some background information on genetics, will apply that information to the techniques of cloning and will end with a discussion of a hot topic in the world of biotechnology – stem cells. GENETICS You have probably heard the expression, “it runs in the family”, but have you ever wondered what exactly that means? Or why you have the same bright red hair as your dad? Or why all of your uncles are bald? A lot of questions like these can be answered by genetics. Genetics refers to the study of genes, or DNA. DNA stands for deoxyribonucleic acid and it acts as a sort of instruction manual for every living thing. DNA is found in almost all cells and is very, very small! Despite the fact that DNA is so small, it is really important! The structure of DNA DNA looks like a ladder that has been twisted, a spiral staircase of sorts – this twisted shape is called a helix. (You will often hear of DNA referred to as the double helix because it has two interwoven helical strands). Even though DNA looks like a ladder, it behaves more like a zipper. Picture the two sides of a ladder or a zipper. Figure 1: Deoxyribonucleic acid (DNA) contains the “recipe” for making organisms. Source: http://en.wikipedia.org/wi ki/Image:DNA-structureand-bases.png 1 5’ 3’ AT CG TA Sugar deoxyribose & phosphate phosphate backbone backbone GC GC AT 3’ 5’ nucleic acid Figure 2: When DNA is unfolded from its helical structure, it looks like a ladder, with the base pairs as the rungs and the deoxyribose and phosphate as the sides These two parts are the backbone of DNA and are made up of a type of sugar molecule called deoxyribose that is joined together with phosphate bonds. These “backbones” have different ends, called the 3’ (pronounced “3 prime”) and 5’ (“5 prime”) ends. Since one side runs 3’5’ and the other runs 5’3’, we call the strands antiparallel. The teeth of the zipper (or the rungs of the ladder) are made of nucleic acids. There are four types of nucleic acids in DNA: A (for adenine), G (for guanine), C (for cytosine) and T (for tyrosine). A can only pair with T and G can only pair with C. An A-T link is held together by two bonds (bonding is the linking of chemical structures to each other) while a G-C link is held together by three bonds. This makes G-C bonds stronger. This model for DNA is called the Watson and Crick model, named after James D. Watson and Francis Crick who received the Nobel Prize for their model in 1962. Another researcher, Rosalyn Franklin was also very important in figuring out the double helix shape of DNA. What does DNA do? Okay, I bet you’re thinking, how do these nucleic acids turn into a blueprint for making people? There are around 3 billion pairs of Gs, Cs, Ts and As in humans that are arranged in a pattern, which is called the DNA sequence. Different combinations of these nucleic acids mean different things. Think of how many combinations can be made with 6 billion G, C, T and As! It’s just like a code; in fact it’s actually called the genetic code. Important parts of the DNA sequence are called genes. They code for specific things like hair colour, for example. If you think of how many ways that every person is the same, it makes sense that most of your DNA is exactly like your mom’s, or your best friend’s or the Queen of England’s. In fact, your DNA is even 99% the same as a mouse’s DNA! Even though each person has very similar DNA sequences, there are some small differences that make each person’s DNA unique. 2 How do those CSI guys tell people apart by their DNA? Since every person’s DNA is a little bit different, we can use DNA to distinguish one person from another. Solving crimes using DNA evidence is part of the field of forensic biology. Basically, after DNA evidence like hair, blood or skin has been collected from a crime scene, DNA is extracted, or removed, from the cells. Then, a few steps are followed using special machines. What you end up with is a way to compare different people. Here’s how it works: All of the The DNA gets cut up by special scissors!!! STEP 1. Special proteins, called restriction enzymes, act like scissors and cut up the DNA. These enzymes are specific, so that a certain restriction enzyme can only cut a particular sequence cutof up pieces sizes. A, C, ofGDNA andareT.different For example, one Figure 3: Restriction enzymes (represented by the scissors) cut DNA at specific sequences. enzyme called HpaII will only cut when it sees the sequence CCGG. Another restriction enzyme is the BamHI, which recognizes this sequence: 5’GGATTC-3’ and cut between the two guanines (G). Figure 4: After being cut up by restriction enzymes, you end up with different sized pieces of DNA. In Figure 3, imagine that the green scissors are HpaII. They can only cut CCGG, represented here by the green bar. When the enzymes cut up the DNA, it ends up in many pieces, of many different sizes (Figure 4). A special machine sorts the DNA by size. Step 2. All of the cut up pieces are placed in a machine that will sort the pieces by size. That machine is called a gel electrophoresis machine. How it works is that when the pieces of DNA get put in the gel, they move from the top to the bottom. The thing is, different sized pieces move at different speeds. Little pieces are speedy and move quickly through the gel, while large pieces are slow and stay close to the top of the gel. (Little pieces are fast, so they move faster to the bottom.) BIG TOP LITTLE BOTTOM Figure 5: Gel electrophoresis lets you separate pieces of DNA based on their size 3 WANT TO KNOW MORE? If you noticed, the word electrophoresis sounds a lot like electricity. That is because the machine uses electricity to get the pieces to move. Have you ever played with magnets? If you had a bar magnet then one side would be negative and one side would be positive. If you tried to bring the two negative ends together, they would repel each other. DNA has a negative charge. So if you make the gel have a negative charge at the top and a positive charge at the bottom, the negative pieces of DNA will try to get away from the negative charge in the gel. That’s why the pieces of DNA move! So, now that you understand how these gels work, but I bet you want to know how exactlyWe you two people apart. Well, remember how everyone’s DNA is a arecan ALLtell a little bit different! little bit different? Each person’s DNA will be a little bit different at those cut sites too. In Figure 6, can Uncle Norm of Õs DNA Queen England BIG you see how the green cut site is LITTLE large for the Queen of England but small for Uncle Norm? Well, when PrimeUncle MinisterNorm Harper Õs DNA these two people’s DNA is all cut up, it will make different sized pieces. Figure 6: Pieces of DNA from the Queen of When those pieces are run on the gel, England and from Uncle Norm. Note how there they will each make a different are some differences. pattern. Our DNA has different sizes of pieces so it makes a different pattern when it ’s all cut up. Queen of England Uncle NormÕ s DNA Here is an example of what two different people’s gels could look like (Figure 7). (Remember, they wouldn’t actually be different colours!) You can see that you can tell the difference between the Queen of England and Uncle Norm by the pattern the pieces of DNA make. Uncle Norm Prime Minister HarperÕ s DNA Figure 7: Gel electrophoresis of DNA from the Queen of England and from Uncle Norm. 4 Here is an example of what it can look like for real: 1 piece of DNA another piece of DNA Six different people Figure 8: A real picture of a gel electrophoresis of DNA from six different people. Picture courtesy of Karla Bretherick from UBC. Why do people say that I have my mum’s nose and my dad’s chin? In Figure 9, you see a very simple version of what is known as a pedigree. In this pedigree Mr. & Mrs. Smith have three children. Mr. Smith Mrs. Smith Jane has her dad’s eyes and nose, but her mum’s mouth. Peter has his mum’s nose and eyes but his dad’s mouth. Sue has her mum’s eyes and her dad’s nose and mouth. It seems like all three children are a Sue Jane Peter mixture of mum and dad. This is ene pretty much what happens in Figure 9: A pedigree of the Smith family. humans! (There isn’t a single “nose” gene or “mouth” gene – instead there are many, many genes that, together, result in a given trait). The DNA that carries all this information gets handed down from parents in packages called chromosomes. This is known as inheritance. Humans have a total of 46 chromosomes, half from each parent. 5 So Jane, Peter and Sue got 23 chromosomes from their dad and 23 from their mum. The chromosomes from Mr. Smith pair up with the same chromosomes that came from Mrs. Smith making 23 pairs. A picture of the set of chromosomes that a person has is called a karyotype. While paired together some parts of the chromosomes swap places making the chromosomes that the children have a chromosome slightly different from Mr. & Mrs. Smith’s chromosomes (a process called recombination). So what’s the biggest difference between Peter and his two sisters Jane and Sue? Well he’s a boy, which means he has a Y-chromosome. Ychromosomes are special because only boys have them and getting a Ychromosome is what makes boys, well boys. But… don’t get too excited boys, the Y chromosome is WAY tinier and has less genetic material than the X Figure 10: A karyotype is a picture of the set chromosome So Peter’s last pair of of chromosomes belonging to a person. Source: chromosomes is made of an Xhttp://www.genome.gov/Pages/Hyperion/DIR/VIP/Glossa chromosome, which he got from his mum, ry/Illustration/karyotype.cfm?key=karyotype and a Y-chromosome, which he got from his dad. Both his sisters got 1 X-chromosome from each parent for a total of 2. Why is it important to know about pedigrees and karyotypes? So, in the pedigree Jane has the genes from Mr. Smith that say “brown eyes” and “round nose”, she may also have genes that say “high blood pressure” inherited from her dad. Her dad may have received this gene from his dad, and Jane may pass this gene to her children when she’s older. So just by looking at the pedigree you can follow the gene. In medicine today special doctors, called medical geneticists, do this all the time so that people know much more about the chances of getting a “bad” gene. 6 Want to know more? Here is a karyotype that is different from normal. Can you spot what is different in this karyotype? Figure 11: Can you spot the abnormality in this karyotype? Karyotype courtesy of Snezana Arsovska In this karyotype there is an extra chromosome 21. When a person has an extra copy of any chromosome this is called trisomy. Trisomy 21 causes a specific disease that you may have heard of called Down Syndrome. CLONING The word “clone” indicates two things that are genetically identical. This means that you can have cloned molecules of DNA, cloned cells that contain the same DNA, and cloned organisms (e.g., animals). DNA cloning is used all the time to study genes of interest. Cell cloning is very important to study cellular function and development. Animal cloning is more controversial, but could offer many benefits to scientific research. In this section, cellbased cloning of a DNA molecule, cell-free cloning of a DNA molecule, and organism cloning will be discussed. Figure 12: “Cloning” means to make two things that are genetically identical. This can be cloned DNA, cloned cells or even cloned organisms! 7 Cell-based cloning of a DNA molecule Often researchers want to clone a specific “gene of interest” to study gene function (i.e., what it does), structure (i.e., what it looks like), or sequence (i.e., the number and order of A, C, G and T’s). The techniques used might differ depending on what organism the gene came from, where it will end up, and the type of gene (e.g., large or small, or complex structures). There are four major components of cell-based DNA cloning: 1. Making a recombinant DNA molecule by ligation reactions, 2. Transformation, 3. Selection and propagation of transformed cell clones, and 4. Isolation of recombinant DNA. Let’s look at each step in more detail! 1. Making recombinant ligation reactions DNA molecules by A recombinant DNA molecule is a piece of DNA that has been linked to another piece of foreign DNA. If we want to clone a gene, we need to link the gene of interest to another piece of DNA such as a vector. A vector is also made of DNA and can be transferred between different organisms. So, if you link your gene of interest to a vector, it acts like a “vehicle” to transfer your gene to a simpler organism where it can be copied rapidly. Figure 13: Plasmid molecules. An illustration of what plasmids look like in nature. Plasmids are DNA molecules that can contain genes of antibiotic resistance. Source: http://universe-review.ca/I1071-plasmid.jpg. A plasmid is a type of vector (Figure 13). A plasmid is a circular piece of DNA. Bacteria often have plasmids present in their cells and use them in the case of “emergencies”. For example, plasmids commonly carry genes for antibiotic resistance. These are genes that wouldn’t be required under normal growing conditions but are very helpful in the presence of an antibiotic, such as penicillin, ampicillin, erythromycin, etc., which normally will kill the cell. Scientists can use antibiotic resistance to figure out which bacteria contain the plasmid and which don’t. More about this later! In order to insert the gene of interest (to be cloned) into the plasmid, the plasmid must be opened. Remember the restriction enzymes we learned about in the 8 Genetics section? Well, in addition to being used to cut up DNA for gel electrophoresis, they are also used to open up plasmids! Cutting with a restriction enzyme leaves what is called an overhang. This is a sequence of nucleotides that remain “dangling” beyond the edge of the complementary strand. If the gene of interest is cut on either end (at the 5’ and 3’ end) with the same enzyme, it will have complementary overhangs (i.e., the pieces will match and so they can be joined together), also known as “sticky ends”. The overhangs of the cut plasmid can then be ligated (i.e., joined) to the overhangs of the cut gene because they are complementary. Another enzyme, DNA ligase, is needed to ligate the pieces of DNA together. This is how we can insert a gene of interest into a plasmid (Figure 14). Once the gene is in the plasmid, it’s ready to be cloned! Figure 14. Ligation of a gene of interest into a plasmid. Both the plasmid and the gene are digested with the same restriction enzyme. The overhanging regions created by the digestion are complementary, therefore the gene will bind to the cut plasmid (with the help of ligase). 2. Transformation Plasmids are a vector to aid in the cloning of a gene. However, a plasmid can’t clone a gene on its own – it needs a host system to make copies of the plasmid (and therefore, make copies of your gene of interest). The most efficient copying host is bacteria, specifically E. coli (Escherichia coli). This is because E. coli divide and grow very rapidly. A culture consisting of one cell can grow and divide into billions of cells in just 24 hours! If E. coli are carrying the plasmid with your gene of 9 interest, every time the bacteria duplicates it will also duplicate the plasmid. Therefore, with an overnight growth period you could potentially have billions of copies (clones) of your gene! How can we alter E. coli so they carry a plasmid? Many types of bacteria will naturally take up DNA molecules from their environment. In addition, E. coli can be treated with chemicals to make them more competent (make it easier) to take up DNA. You can then incubate the treated cells with a mixture of your plasmid and salt. The osmotic pressure (i.e., high salt concentration on the outside of the cells, lower salt concentration inside the cells) created and the presence of the plasmid DNA causes a flow into the cells (Figure 15). Figure 15. Transformation and selection of transformed cells for cloning. A. Bacterial cells are transformed with plasmid DNA. B. Transformed bacteria are selected based on antibiotic resistance. Resistant lines can then be grown up to harvest large concentrations of the cloned plasmid. 3. Selection and propagation of transformed cell clones So how do we know which bacteria picked up the plasmids (with the gene we are trying to clone) and which didn’t? 10 Well, when we grow the bacteria, we do so in the –presence of an antibiotic. Remember how the plasmids carry cool genes that give antibiotic resistance to bacteria? Bacteria WITH plasmids will be able to live and grow on the Petri dish with antibiotics. Bacteria WITHOUT plasmids will die. So we know that all the bacteria that are living, growing and duplicating contain the plasmid -- and therefore the gene we are trying to clone! This is called antibiotic selection. Once you have selected a colony of bacteria that are carrying the plasmid you can grow the bacteria to clone billions of copies of your gene. (Figure 3B). 4. Isolation of recombinant DNA The final step is to harvest the high concentration of your plasmid (and therefore, the gene) from the bacteria. To do this, the bacteria will be lysed (the cell membrane is broken open) and the plasmid DNA will be separated from the bacterial DNA and RNA. This is done using a high salt and low pH solution (because plasmid DNA can withstand these conditions but regular DNA and RNA cannot). Once the cells are lysed and the solutions have been added, the plasmid can be separated using centrifugation (spinning at high speed). Presto! You now have a whole bunch of copies of that specific gene you are cloning! Organism cloning Organism cloning is the production of two individuals (the same organism) that have identical DNA. Identical twins are a natural example of human clones. Their DNA, therefore, are exact copies. Techniques have been developed that allow researchers to take the nucleus (which contains DNA) from one cell and put it into another cell from which the nucleus has been removed. This is called nuclear transfer technology because you are transferring the nucleus from one cell to another. This technique can be used to create cells that are clones of each other, because they carry the same DNA. In the case of animal cloning, the cloned cell can be an oocyte (an egg cell from a female), which can then be implanted into a female and could grow into an embryo, and eventually a cloned individual organism (Figure 4). This is how the first cloned sheep (Dolly) was created. 11 Figure 16. Nuclear transfer technology to create a clone. The DNA in the cloned cell will be identical to that of the donor, therefore a nuclear DNA clone. INTRODUCTION TO STEM CELLS What is a “stem cell?” Most of us have heard the term “stem cell” from newspapers and TV news reports. Stem cells were not this popular until 10 years ago and have become a popular as well as an important field of scientific research. So…exactly what is a stem cell and why is it important? In general, a stem cell is defined as an unspecialized (with no specific function) cell type that can self-renew (make copies of itself) and differentiate (make cells that do have a specific function). Cells in our body usually get old, die, and then are replaced by new cells. Some cells die fast and are replaced fast, which means they have a high turnover (like skin cells). Other cells are slower in this process and hence have a low turnover (like muscle cells or T cells). But in the end, most of the cells die and are replaced. As a whole population, stem cells have a ridiculously low turnover because they possess the ability to “self-renew” – this 12 means they can make daughter cells that are also stem cells. This allows them to go on making specialized/differentiated cells with some of their progeny and while also saving some cells to make keep the numbers of stem cells up. Taken together, the special properties of stem cells make it possible to generate different types of cells such as blood cells, neural cells, muscle cells, and many more using just one single stem cell. There are two types of stem cells: embryonic stem cells (also called ES cells) and adult stem cells. ES cells are the most most powerful type of stem cell and can make all the other types of adult stem cells, while adult stem cells can typically only make the cells in a given tissue type (i.e.: blood stem cells make T cells, B cells, red blood cells, etc) Embryonic Stem Cells Before knowing what an embryonic stem cell is, we have to start from where WE came from: a fertilized egg. During the process of fertilization, a sperm from male and an egg from female come together to generate a fertilized egg, or zygote. A zygote is a single cell that will continue to develop, dividing into a cluster of cells, at which stage it is called a blastomere. A blastomere divides into 2, 4, 8 blastomeres (the cluster of blastomeres is called morula), and eventually form a blastocyst with a hollow centre (Figure 17). A blastocyst has the ability to implant itself in the uterus of a female (the process is called implantation), and then grow into fetus, and eventually become an individual. Embryonic stem cells come from the inner cell mass of blastocyst. These cells can generate any cell type in our body (except the cell types that grow outside of the embryo (extra-embryonic) – which are still required for the embryo to grow!) , which is very amazing if you think about it!! This characteristic is called pluripotency (pluri: several, just think plural; potency: potential). 13 Inner Mass (Embryonic Stem Cell) First Division Sperm and egg Second Division 2 Fertilized Blastomere blastomeres egg Third Division 4 blastomeres After many Divisions 8 blastomeres Blastocyst Figure 17: Development of embryo from fertilized egg Adult Stem Cells Adult stem cells are quite a bit different from embryonic stem cells. The best-known example of an adult stem cell is the blood stem cell (called hematopoietic which comes from the Latin “hemato” (iron/blood) and “poiesy” (the verb “to make” – also the root of poetry), although much is known about adult stem cells in other organ systems too. It has been shown that adult stem cells can be found in the liver, pancreas, skin, muscle, and possibly more! A hematopoietic stem cell can generate red blood cells, platelets, and various types of white blood cells (Figure 18). In this case, the adult stem cells can only generate a specific set of cells (i.e., blood cells) but not every cell in a body, and therefore they are called multipotent instead of pluripotent. Compared to embryonic stem cells, adult stem cells are even more limited in the cell types they can make (Table 1). 14 B-lymphocyte Lymphoid Progenitor Cells Hematopoietic Stem Cells T-lymphocyte Natural Killer Cells Red blood cells Platelet Myeloid Progenitor Cells Basophil Neutrophil Eosinophil Macrophage Figure 18 Various types of hematopoietic cells generated from hematopoietic stem cells Table 1 Comparing embryonic stem cells with adult stem cells Embryonic Stem Cells The kind of cells they can All cells in a body except generate extra-embryonic tissue Plasticity Pluripotent Source Embryo (inner cell mass of blastocyst) Adult Stem Cells A limited set of cells, usually in the same system Multipotent Adult tissue Stem Cells And Our Society Why Are Stem Cells Important? The study of embryonic stem cells has become very popular because of two major reasons. First of all, because stem cells can produce an unlimited number of cells and can become many different cell types. They could possibly be used to replace cells, following damage or those lost when we are sick with certain medical 15 conditions. For example, type 1 diabetes is an illness when the insulin making cells inside the pancreas are dead and lost. People who have type 1 diabetes have no insulin, which is supposed to help those people to take glucose from the blood and store glucose in cells. Because of the lack of insulin, these patients have high blood glucose and suffer from its medical complications. If we can generate insulin-secreting cells using stem cells, then we can inject these cells into the patients to reverse their condition. Or, if we can find stem cells in the pancreas of these patients, we can stimulate those stem cells to increase the number of insulin secreting cells in the patient. A similar scenario can apply to many other diseases related to cell injury or cell death, including Alzheimer’s, Parkinson’s, Muscular Dystrophy, spinal cord injury, heart disease, and the list goes on. That’s why many scientists are trying to find ways to make more stem cells, and also make stem cells differentiate into the cell types they want. Another reason why stem cell research is so popular is because stem cells might be associated with certain types of cancer. Essentially, cancers result from the uncontrolled growth of cells which can cause many problems (for instance, leukemia makes too many white blood cells in the bone marrow and takes up all the space, which prohibits the production of other blood cell types used to carry nutrients around the body. Often, cancer can be controlled, either by chemotherapy (using chemicals to destroy the body’s cells, hoping that the cancer cells will die in the process) or surgery (to remove “cancerous growths” – this is limited to only some cancer types). But sometimes even though we think that all the cancerous cells have been removed, the condition relapses (comes back), more serious than before. Many scientists believe that it is because the cancerous cells removed are the downstream cells generated from stem cells. And if we just remove the cancerous cells but don’t do anything to the stem cells that they come from, the chance of relapse increases. By learning more about stem cells, we might be able to find better ways to stop cancer from spreading and to treat cancer more efficiently. Stem Cell Research: Ethical aspects So, even though it seems like stem cells might be used for treating many diseases, using them (especially using embryonic stem cells) has great concerns. This is mostly because embryonic stem cells are taken from the blastocyst, which (like it does in the real world) can implant in the uterus and develop into a being like you and me. Many groups, therefore, object to the use of embryonic stem cells for research despite the possible clinical use. Many ethical questions need to be addressed in this field – should embryos be considered as individuals? When does 16 life begin? Should scientists be able to generate embryos for research? What about if they are going to go to waste anyhow? Clearly, all scientists need to think about the implications of their work. Stem Cell Research: What the Future Holds Stem cells are an important key to future medical treatments. However, more research is needed before the stem cells are used for clinical treatment. We still need to know more about how stem cells differentiate and self-renew, how to target or isolate stem cells in adult tissue, and how to control stem cell differentiation. We also need to keep in mind that ethical issues need to be dealt with before we learn how practical stem cell research is for humans. There are many more questions to answer and hopefully one day we will see the implementation of stem cell therapy in medicine! 17 References Karp. G. Cell and molecular biology: Concepts and experiments. (3rd ed.) John Wiley & Sons, inc. 2002. Kimball's Biology Pages (Stem Cells): http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/S/Stem_Cells.html#Using _Stem_Cells_for_Human_Therapy_-_The_Problems Griffiths, Anthony J.F., Miller, Jeffrey H. Suzuki, David T, Lewontin, Richard C., and Gelbart, William M. An Introduction to Genetic Analysis Seventh Edition. 2000. W.H. Freeman & Company. New York, NY. Report on Stem cells: http://stemcells.nih.gov/info/scireport/ Stem Cell Information, the official National Institute of Health resource for stem cell research (USA): http://stemcells.nih.gov/index.asp Strachan, Tom, and Read, Andrew P. Human Molecular Genetics 2nd Edition. John Wiley & Sons Inc. Rexdale, ON. 1999. United Nations Convention on Biological Diversity http://www.biodiv.org/convention/articles.asp?lg=0&a=cbd-02 18