Monday, March 21, 2011


Medical research

Biomedical research (or experimental medicine), in general simply known as medical research, is the basic research, applied research, or translational research conducted to aid and support the body of knowledge in the field of medicine. Medical research can be divided into two general categories: the evaluation of new treatments for both safety and efficacy in what are termed clinical trials, and all other research that contributes to the development of new treatments. The latter is termed preclinical research if its goal is specifically to elaborate knowledge for the development of new therapeutic strategies. A new paradigm to biomedical research is being termed translational research, which focuses on iterative feedback loops between the basic and clinical research domains to accelerate knowledge translation from the bedside to the bench, and back again

What Is the Procedure for DNA Testing?

There are various ways to test DNA. One very common method used in various settings, including forensic and paternity testing labs, is polyermase chain reaction, or PCR. Using this method, DNA is extracted from sample cells and primers are used to locate the sequence of interest on the DNA strand. This sequence is then amplified to create many million and even billions of copies, according to University of Washington professor Donald E. Riley. 

In the case of paternity testing, somatic, or body, cells from the possible father are obtained by taking a swab of the inner lining of the suspected father's mouth. The DNA is extracted from the cells and is then amplified, creating many copies. 

These copies are then compared to those of the offspring to see whether there is a close match, according to one Buzzle writer. As stated by professor Riley, although PCR is less time-consuming and cheaper than another method called RFLP, it is very susceptible to contamination and care must be exercised during the entire testing process. 

In RFLP, or Restriction Fragment Length Polymorphism, a restriction enzyme is used. Obtained by bacteria that can "cut" DNA at a particular location, restriction enzymes cut many copies of the DNA sequence of interest. The sequence is then separated according to size using gel electrophoresis. Next, "blotting" is performed in which a film is applied to the gel and stained allowing the different bars, representing different sequences, to be seen. This prevents any further migration of the DNA sequences in the gel. A DNA probe is then attached to the sequence of interest. 

As in PCR, the DNA copies are compared to others in the population to determine if there is a "match." Rather than just one person's DNA, in the case of paternity testing, DNA from a large population needs to be used in order to effectively compare the lab sample to those in the population. This, along with the increased cost and time required, is the reason that RFLP is no longer widely used as it had been.

DNA profiles for forensic use

Each of the chromosomes in your cells contains sections of non-coding DNA — DNA that does not code for a protein. Non-coding DNA contains areas called short tandem repeats (STRs), made up of repeats of short base sequences, such as CATG in the sequence CATGCATGCATG. 

If the DNA of two people was analysed for 10 different STRs on different chromosomes, there is only one chance in a million that they would have the same number of repeats in all of these STRs. Identical twins are the only exception — they have identical DNA and identical STRs.

If a crime suspect's DNA profile for 10 STRs matches the STR profile of a sample found at the crime scene, there is a very high probability that both lots of DNA are from the same person. However, if the profiles differ for even one STR, this cannot be assumed. 

DNA is used as evidence in court, but it is considered ‘circumstantial' evidence, and can only be used as proof with other supporting evidence. However, it has proven useful in establishing the innocence of suspects.

What is a gene?


A gene is the basic physical and functional unit of heredity. Genes, which are made up of DNA, act as instructions to make molecules called proteins. In humans, genes vary in size from a few hundred DNA bases to more than 2 million bases. The Human Genome Project has estimated that humans have between 20,000 and 25,000 genes.

Every person has two copies of each gene, one inherited from each parent. Most genes are the same in all people, but a small number of genes (less than 1 percent of the total) are slightly different between people. Alleles are forms of the same gene with small differences in their sequence of DNA bases. These small differences contribute to each person’s unique physical features.

What is Genetic Engineering?

We find it mixed in our food on the shelves in the supermarket--genetically engineered soybeans and maize. We find it growing in a plot down the lane, test field release sites with genetically engineered rape seed, sugar beet, wheat, potato, strawberries and more. There has been no warning and no consultation. 

It is variously known as genetic engineering, genetic modification or genetic manipulation. All three terms mean the same thing, the reshuffling of genes usually from one species to another; existing examples include: from fish to tomato or from human to pig. Genetic engineering (GE) comes under the broad heading of biotechnology. 

But how does it work? If you want to understand genetic engineering it is best to start with some basic biology. 

What is a cell? A cell is the smallest living unit, the basic structural and functional unit of all living matter, whether that is a plant, an animal or a fungus.Some organisms such as amoebae, bacteria, some algae and fungi are single-celled - the entire organism is contained in just one cell. Humans are quite different and are made up of approximately 3 million cells -(3,000,000,000,000 cells). Cells can take many shapes depending on their function, but commonly they will look like a brick with rounded comers or an angular blob - a building block.Cells are stacked together to make up tissues, organs or structures (brain, liver, bones, skin, leaves, fruit etc.). 

In an organism, cells depend on each other to perform various functions and tasks; some cells will produce enzymes, others will store sugars or fat; different cells again will build the skeleton or be in charge of communication like nerve cells; others are there for defence, such as white blood cells or stinging cells in jelly fish and plants. In order to be a fully functional part of the whole, most cells have got the same information and resources and the same basic equipment. 

A cell belonging to higher organisms (e.g. plant or animal) is composed of: 
• a cell MEMBRANE enclosing the whole cell. (Plant cells have an additional cell wall for structural reinforcement.) 
• many ORGANELLES, which are functional components equivalent to the organs in the body of an animal e.g. for digestion, storage, excretion. 
• a NUCLEUS, the command centre of the cell. It contains all the vital information needed by the cell or the whole organism to function, grow and reproduce. This information is stored in the form of a genetic code on the chromosomes, which are situated inside the nucleus. 

Proteins are the basic building materials of a cell, made by the cell itself. Looking at them in close-up they consist of a chain of amino-acids, small specific building blocks that easily link up. Though the basic structure of proteins is linear, they are usually folded and folded again into complex structures. Different proteins have different functions. They can be transport molecules (e.g. oxygen binding haemoglobin of the red blood cells); they can be antibodies, messengers, enzymes (e.g. digestion enzymes) or hormones (e.g. growth hormones or insulin). Another group is the structural proteins that form boundaries and provide movement, elasticity and the ability to contract. Muscle fibres, for example, are mainly made of proteins. Proteins are thus crucial in the formation of cells and in giving cells the capacity to function properly. 

Chromosomes means "coloured bodies" (they can be seen under the light microscope, using a particular stain). They look like bundled up knots and loops of a long thin thread. Chromosomes are the storage place for all genetic - that is hereditary - information. This information is written along the thin thread, called DNA. "DNA" is an abbreviation for deoxyribo nucleic acid, a specific acidic material that can be found in the nucleus. The genetic information is written in the form of a code, almost like a music tape. To ensure the thread and the information are stable and safe, a twisted double stranded thread is used - the famous double helix. When a cell multiplies it will also copy all the DNA and pass it on to the daughter cell. 

The totality of the genetic information of an organism is called genome. Cells of humans, for example, possess two sets of 23 different chromosomes, one set from the mother and the other from -the father. The DNA of each human cell corresponds to 2 meters of DNA if it is stretched out and it is thus crucial to organise the DNA in chromosomes, so as to avoid knots, tangles and breakages. The length of DNA contained in the human body is approximately 60,000,000,000 kilometres. This is equivalent to the distance to the moon and back 8000 times! 

The information contained on the chromo-somes in the DNA is written and coded in such a way that it can be understood by almost all living species on earth. It is thus termed the universal code of life. In this coding system, cells need only four symbols (called nucleotides) to spell out all the instructions of how to make any protein. Nucleotides are the units DNA is composed of and their individual names are commonly abbreviated to the letters A, C G and T These letters are arranged in 3-letter words which in turn code for a particular amino acid - as shown in the flow diagram 1. The information for how any cell is structured or how it functions is all encoded in single and distinct genes. A Gene is a certain segment (length) of DNA with specific instructions for the production of commonly one specific protein. The coding sequence of a gene is, on average about 1000 letters long. Genes code for example for insulin, digestive enzymes, blood clotting proteins, or pigments.

How does a cell know when to produce which protein and how much of it? In front of each gene there is a stretch of DNA that contains the regulatory elements for that specific gene, most of which is known as the promoter. It functions like a "control tower," constantly holding a "flag" up for the gene it controls. Take insulin production (which we produce to enable the burning of the blood sugar). When a message arrives in the form of a molecule that says, 'more insulin", the insulin control tower will signal the location of the insulin gene and say "over here". The message molecule will "dock in" and thus activate a "switch" to start the whole process of gene expression. 

How does the information contained in the DNA get turned into a protein at the right time? As shown in picture 2, each gene consists of 3 main components: a "control tower" (promoter), an information block and a polyA signal element. If there is not enough of a specific protein present in the cell, a message will be sent into the nucleus to find the relevant gene. If the control tower recognises the message as valid it will open the "gate" to the information block. Immediately the information is copied - or transcribed - into a threadlike molecule, called RNA. RNA is very similar to DNA, except it is single stranded. After the copy is made, a string of up to 200 "A"-type nucleotides - a polyA tail - is added to its end (picture 2). This process is called poly-adenylation and is initiated by a polyA signal located towards the end of the gene. A polyA tail is thought to stabilise the RNA message against degradation for a limited time. Now the RNA copies of the gene leave the nucleus and get distributed within the cell to little work units that translate the information into proteins. 

No cell will ever make use of all the information coded in its DNA. Cells divide the work up amongst one other - they specialise. Brain cells will not produce insulin, liver cells will not produce saliva, nor will skin cells start producing bone. If they did, our bodies could be chaos! 

The same is true for plants: root cells will not produce the green chlorophyll, nor will the leaves produce pollen or nectar. Furthermore, expression is age dependent: young shoots will not express any genes to do with fruit ripening, while old people will not usually start developing another set of teeth (exceptions have been known). 

All in all, gene regulation is very specific to the environment in which the cell finds itself and is also linked to the developmental stages of an organism. So f I want the leaves of poppy plants to produce the red colour of the flower petals I will not be able to do so by traditional breeding methods, despite the fact that leaf ells will have all the genetic information necessary. There is a block that prevents he leaves from going red. This block may be caused by two things: 
• The "red" gene has been permanently shut down and bundled up thoroughly in all leaf cells. Thus the information cannot be accessed any more. 
• The leaf cells do not need the colour red and thus do not request RNA copies of this information. Therefore no message molecule is docking at the "red" control tower to activate the gene. 

Of course - you might have guessed - there is a trick to fool the plant and make it turn red against its own will. We can bring the red gene in like a Trojan horse, hidden behind the control tower of a different gene. But for this we need to cut the genes up and glue them together in a different form. This is where breeding ends and genetic engineering begins. 

BREEDING is the natural process of sexual reproduction within the same species. The hereditary information of both parents is combined and passed on to the offspring. In this process the same sections of DNA can be exchanged between the same chromosomes, but genes will always remain at their very own and precise position and order on the chromosomes. A gene will thus always be surrounded by the same DNA unless mutations or accidents occur. Species that are closely related might be able to interbreed, like a donkey and a horse, but their offspring will usually be infertile (e.g. mule). This is a natural safety devise, preventing the mixing of genes that might not be compatible and to secure the survival of the species.

Genetic Engineering.


Genetic engineering (GE) is used to take genes and segments of DNA from one species, e.g. fish, and put them into another species, e.g. tomato. To do so, GE provides a set of techniques to cut DNA either randomly or at a number of specific sites. Once isolated one can study the different segments of DNA, multiply them up and splice them (stick them) next to any other DNA of another cell or organism. GE makes it possible to break through the species barrier and to shuffle information between completely unrelated species; for example, to splice the anti-freeze gene from flounder into tomatoes or strawberries, an insect-killing toxin gene from bacteria into maize, cotton or rape seed, or genes from humans into pig. 

Yet there is a problem - a fish gene will not work in tomato unless I give it a promoter with a "flag" the tomato cells will recognise. Such a control sequence should either be a tomato sequence or something similar. Most companies and scientists do a shortcut here and don't even bother to look for an appropriate tomato promoter as it would take years to understand how the cell's internal communication and regulation works. In order to avoid long testing and adjusting, most genetic engineering of plants is done with viral promoters. Viruses - as you will be aware - are very active. Nothing, or almost nothing, will stop them once they have found a new victim or rather host. They integrate their genetic information into the DNA of a host cell (such as one of your own), multiply, infect the next cells and multiply. This is possible because viruses have evolved very powerful promoters which command the host cell to constantly read the viral genes and produce viral proteins. Simply by taking a control element (promoter) from a plant virus and sticking it in front of the information block of the fish gene, you can get this combined virus/fish gene (known as a "construct') to work wherever and whenever you want in a plant. 

This might sound great, the drawback though is that it can't be stopped either, it can't be switched off. The plant no longer has a say in the expression of the new gene, even when the constant involuntary production of the "new" product is weakening the plant's defences or growth. 

And furthermore, the theory doesn't hold up with reality. Often, for no apparent reason, the new gene only works for a limited amount of time and then "falls silent". But there is no way to know in advance if this will happen. 

Though often hailed as a precise method, the final stage of placing the new gene into a receiving higher organism is rather crude, seriously lacking both precision and predictability. The "new" gene can end up anywhere, next to any 
gene or even within another gene, disturbing its function or regulation. If the "new" gene gets into the "quiet" non-expressed areas of the cell's DNA, it is likely to interfere with the regulation of gene expression of the whole region. It could potentially cause genes in the "quiet" DNA to become active. 

Often genetic engineering will not only use the information of one gene and put it behind the promoter of another gene, but will also take bits and pieces from other genes and other species. Although this is aimed to benefit the expression and function of the "new" gene it also causes more interference and enhances the risks of unpredictable effects.

How to get the gene into the other cell.

There are different ways to get a gene from A to B or to transform a plant with a "new" gene. A VECTOR is something that can carry the gene into the host, or rather into the nucleus of a host cell. Vectors are commonly bacterial plasmids (see below and next page) or viruses (a). Another method is the "SHOTGUN TECHNIQUE" also known as "bio-ballistics," which blindly shoots masses of tiny gold particles coated with the gene into a plate of plant cells, hoping to land a hit somewhere in the cell's DNA (b).