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DNA FINGERPRINTING

DNA

DNA (Deoxyribonucleic acid) is a chemical structure that forms chromosomes. A piece of a chromosome that dictates a particular trait is called a gene.

Structurally, DNA is a double helix: two strands of genetic material spiraled around each other. Each strand contains a sequence of bases (also called nucleotides). A base is one of four chemicals (adenine, guanine, cytosine and thymine).

The two strands of DNA are connected at each base. Each base will only bond with one other base, as follows: Adenine (A) will only bond with thymine (T), and guanine (G) will only bond with cytosine (C).

What is DNA Fingerprinting?

The chemical structure of everyone’s DNA is the same. The only difference between people (or any animal) is the order of the base pairs. There are so many millions of base pairs in each person’s DNA that every person has a different sequence.

Using these sequences, every person could be identified solely by the sequence of their base pairs. However, because there are so many millions of base pairs, the task would be very time-consuming. Instead, scientists are able to use a shorter method, because of repeating patterns in DNA.

These patterns do not, however, give an individual “fingerprint,” but they are able to determine whether two DNA samples are from the same person, related people, or non-related people. Scientists use a small number of sequences of DNA that are known to vary among individuals a great deal, and analyze those to get a certain probability of a match.

Applications

1. Paternity and Maternity

Because a person inherits his or her VNTRs from his or her parents, VNTR patterns can be used to establish paternity and maternity. The patterns are so specific that a parental VNTR pattern can be reconstructed even if only the children’s VNTR patterns are known (the more children produced, the more reliable the reconstruction). Parent-child VNTR pattern analysis has been used to solve standard father-identification cases as well as more complicated cases of confirming legal nationality and, in instances of adoption, biological parenthood.

2. Criminal Identification and Forensics

DNA isolated from blood, hair, skin cells, or other genetic evidence left at the scene of a crime can be compared, through VNTR patterns, with the DNA of a criminal suspect to determine guilt or innocence. VNTR patterns are also useful in establishing the identity of a homicide victim, either from DNA found as evidence or from the body itself.

3. Personal Identification

The notion of using DNA fingerprints as a sort of genetic bar code to identify individuals has been discussed, but this is not likely to happen anytime in the foreseeable future. The technology required to isolate, keep on file, and then analyze millions of very specified VNTR patterns is both expensive and impractical. Social security numbers, picture ID, and other more mundane methods are much more likely to remain the prevalent ways to establish personal identification.

PROCESS

1. Isolating the DNA in question from the rest of the cellular material in the nucleus. This can be done either chemically, by using a detergent to wash the extra material from the DNA,or mechanically, by applying a large amount of pressure in order to “squeeze out” the DNA.

2. Cutting the DNA into several pieces of different sizes. This is done using one or more restriction enzymes.

3. Sorting the DNA pieces by size. The process by which the size separation, “size fractionation,” is done is called gel electrophoresis. The DNA is poured into a gel, such as agarose, and an electrical charge is applied to the gel, with the positive charge at the bottom and the negative charge at the top. Because DNA has a slightly negative charge, the pieces of DNA will be attracted towards the bottom of the gel; the smaller pieces, however, will be able to move more quickly and thus further towards the bottom than the larger pieces. The different-sized pieces of DNA will therefore be separated by size, with the smaller pieces towards the bottom and the larger pieces towards the top.

4. Denaturing the DNA, so that all of the DNA is rendered single-stranded. This can be done either by heating or chemically treating the DNA in the gel.

5. Blotting the DNA. The gel with the size-fractionated DNA is applied to a sheet of nitrocellulose paper, and then baked to permanently attach the DNA to the sheet. The Southern Blot is now ready to be analyzed.

In order to analyze a Southern Blot, a radioactive genetic probe is used in a hybridization reaction with the DNA in question. If an X-ray is taken of the Southern Blot after a radioactive probe has been allowed to bond with the denatured DNA on the paper, only the areas where the radioactive probe binds [red] will show up on the film. This allows researchers to identify, in a particular person’s DNA, the occurrence and frequency of the particular genetic pattern contained in the probe.

VNTRS

Every strand of DNA has pieces that contain genetic information which informs an organism’s development (exons) and pieces that, apparently, supply no relevant genetic information at all (introns). Although the introns may seem useless, it has been found that they contain repeated sequences of base pairs. These sequences, called Variable Number Tandem Repeats (VNTRs), can contain anywhere from twenty to one hundred base pairs.

Every human being has some VNTRs. To determine if a person has a particular VNTR, a Southern Blot is performed, and then the Southern Blot is probed, through a hybridization reaction, with a radioactive version of the VNTR in question. The pattern which results from this process is what is often referred to as a DNA fingerprint.

A given person’s VNTRs come from the genetic information donated by his or her parents; he or she could have VNTRs inherited from his or her mother or father, or a combination, but never a VNTR either of his or her parents do not have. Shown below are the VNTR patterns for Mrs. Nguyen [blue], Mr. Nguyen [yellow], and their four children: D1 (the Nguyens’ biological daughter), D2 (Mr. Nguyen’s step-daughter, child of Mrs. Nguyen and her former husband [red]), S1 (the Nguyens’ biological son), and S2 (the Nguyens’ adopted son, not biologically related [his parents are light and dark green]).

Because VNTR patterns are inherited genetically, a given person’s VNTR pattern is more or less unique. The more VNTR probes used to analyze a person’s VNTR pattern, the more distinctive and individualized that pattern, or DNA fingerprint, will be.

Problems In DNA Fingerprinting

Like nearly everything else in the scientific world, nothing about DNA fingerprinting is 100% assured. The term DNA fingerprint is, in one sense, a misnomer: it implies that, like a fingerprint, the VNTR pattern for a given person is utterly and completely unique to that person. Actually, all that a VNTR pattern can do is present a probability that the person in question is indeed the person to whom the VNTR pattern (of the child, the criminal evidence, or whatever else) belongs. Given, that probability might be 1 in 20 billion, which would indicate that the person can be reasonably matched with the DNA fingerprint; then again, that probability might only be 1 in 20, leaving a large amount of doubt regarding the specific identity of the VNTR pattern’s owner.

1. Generating a High Probability

The probability of a DNA fingerprint belonging to a specific person needs to be reasonably high–especially in criminal cases, where the association helps establish a suspect’s guilt or innocence. Using certain rare VNTRs or combinations of VNTRs to create the VNTR pattern increases the probability that the two DNA samples do indeed match (as opposed to look alike, but not actually come from the same person) or correlate (in the case of parents and children).

2. Problems with Determining Probability

A. Population Genetics

VNTRs, because they are results of genetic inheritance, are not distributed evenly across all of human population. A given VNTR cannot, therefore, have a stable probability of occurrence; it will vary depending on an individual’s genetic background. The difference in probabilities is particularly visible across racial lines. Some VNTRs that occur very frequently among Hispanics will occur very rarely among Caucasians or African-Americans. Currently, not enough is known about the VNTR frequency distributions among ethnic groups to determine accurate probabilities for individuals within those groups; the heterogeneous genetic composition of interracial individuals, who are growing in number, presents an entirely new set of questions. Further experimentation in this area, known as population genetics, has been surrounded with and hindered by controversy, because the idea of identifying people through genetic anomalies along racial lines comes alarmingly close to the eugenics and ethnic purification movements of the recent past, and, some argue, could provide a scientific basis for racial discrimination.

B. Technical Difficulties


Errors in the hybridization and probing process must also be figured into the probability, and often the idea of error is simply not acceptable. Most people will agree that an innocent person should not be sent to jail, a guilty person allowed to walk free, or a biological mother denied her legal right to custody of her children, simply because a lab technician did not conduct an experiment accurately. When the DNA sample available is minuscule, this is an important consideration, because there is not much room for error, especially if the analysis of the DNA sample involves amplification of the sample (creating a much larger sample of genetically identical DNA from what little material is available), because if the wrong DNA is amplified (i.e. a skin cell from the lab technician) the consequences can be profoundly detrimental. Until recently, the standards for determining DNA fingerprinting matches, and for laboratory security and accuracy which would minimize error, were neither stringent nor universally codified, causing a great deal of public outcry.



 
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Posted by on April 21, 2011 in Science

 

Human Genome Project

The Human Genome Project (HGP) is an international scientific research project with a primary goal of determining the sequence of chemical base pairs which make up DNA and to identify and map the approximately 20,000–25,000 genes of the human genome from both a physical and functional standpoint.

The project began in 1990 and was initially headed by  head of the Office of Biological and Environmental Research in the U.S. Department of Energy’s Office of Science. A working draft of the genome was announced in 2000 and a complete one in 2003, with further, more detailed analysis still being published. The mapping of human genes is an important step in the development of medicines and other aspects of health care.

While the objective of the Human Genome Project is to understand the genetic makeup of the human species, the project has also focused on several other nonhuman organisms such as E. coli, the fruit fly, and the laboratory mouse. It remains one of the largest single investigative projects in modern science.

The Human Genome Project originally aimed to map the nucleotides contained in a human haploid reference genome (more than three billion).

The “genome” of any given individual (except for identical twins and cloned organisms) is unique; mapping “the human genome” involves sequencing multiple variations of each gene.The project did not study the entire DNA found in human cells; some heterochromatic areas (about 8% of the total genome) remain un-sequenced.

Project History

The project began with the culmination of several years of work supported by the United States Department of Energy, in particular workshops in 1984  and 1986 and a subsequent initiative of the US Department of Energy. This 1987 report stated boldly, “The ultimate goal of this initiative is to understand the human genome” and “knowledge of the human as necessary to the continuing progress of medicine and other health sciences as knowledge of human anatomy has been for the present state of medicine.” Candidate technologies were already being considered for the proposed undertaking at least as early as 1985.

The $3-billion project was formally founded in 1990 by the United States Department of Energy and the U.S. National Institutes of Health, and was expected to take 15 years. In addition to the United States, the international consortium comprised geneticists in the United Kingdom, France, Germany, Japan, China, and India.

Due to widespread international cooperation and advances in the field of genomics (especially in sequence analysis), as well as major advances in computing technology, a ‘rough draft’ of the genome was finished in 2000 (announced jointly by then US president Bill Clinton and the British Prime Minister Tony Blair on June 26, 2000). This first available rough draft assembly of the genome was completed by the UCSC Genome Bioinformatics Group, primarily led by then graduate student Jim Kent. Ongoing sequencing led to the announcement of the essentially complete genome in April 2003, 2 years earlier than planned. In May 2006, another milestone was passed on the way to completion of the project, when the sequence of the last chromosome was published in the journal Nature.

State of completion

There are multiple definitions of the “complete sequence of the human genome”. According to some of these definitions, the genome has already been completely sequenced, and according to other definitions, the genome has yet to be completely sequenced. There have been multiple popular press articles reporting that the genome was “complete.” The genome has been completely sequenced using the definition employed by the International Human Genome Project. A graphical history of the human genome project shows that most of the human genome was complete by the end of 2003. However, there are a number of regions of the human genome that can be considered unfinished:

  • First, the central regions of each chromosome, known as centromeres, are highly repetitive DNA sequences that are difficult to sequence using current technology. The centromeres are millions (possibly tens of millions) of base pairs long, and for the most part these are entirely un-sequenced.
  • Second, the ends of the chromosomes, called telomeres, are also highly repetitive, and for most of the 46 chromosome ends these too are incomplete. It is not known precisely how much sequence remains before the telomeres of each chromosome are reached, but as with the centromeres, current technological restraints are prohibitive.
  • Third, there are several loci in each individual’s genome that contain members of multigene families that are difficult to disentangle with shotgun sequencing methods – these multigene families often encode proteins important for immune functions.
  • Other than these regions, there remain a few dozen gaps scattered around the genome, some of them rather large, but there is hope that all these will be closed in the next couple of years.

In summary: the best estimates of total genome size indicate that about 92.3% of the genome has been completed and it is likely that the centromeres and telomeres will remain un-sequenced until new technology is developed that facilitates their sequencing. Most of the remaining DNA is highly repetitive and unlikely to contain genes, but it cannot be truly known until it is entirely sequenced. Understanding the functions of all the genes and their regulation is far from complete. The roles of junk DNA, the evolution of the genome, the differences between individuals, and many other questions are still the subject of intense interest by laboratories all over the world.

Goals

The sequence of the human DNA is stored in databases available to anyone on the Internet. The U.S. National Center for Biotechnology Information (and sister organizations in Europe and Japan) house the gene sequence in a database known as GenBank, along with sequences of known and hypothetical genes and proteins. Computer programs have been developed to analyze the data, because the data itself is difficult to interpret without such programs.

The process of identifying the boundaries between genes and other features in a raw DNA sequence is called genome annotation and is the domain of bioinformatics. While expert biologists make the best annotators, their work proceeds slowly, and computer programs are increasingly used to meet the high-throughput demands of genome sequencing projects. The best current technologies for annotation make use of statistical models that take advantage of parallels between DNA sequences and human language, using concepts from computer science such as formal grammars.

Another, often overlooked, goal of the HGP is the study of its ethical, legal, and social implications. It is important to research these issues and find the most appropriate solutions before they become large dilemmas whose effect will manifest in the form of major political concerns.

All humans have unique gene sequences. Therefore the data published by the HGP does not represent the exact sequence of each and every individual’s genome. It is the combined “reference genome” of a small number of anonymous donors. The HGP genome is a scaffold for future work in identifying differences among individuals. Most of the current effort in identifying differences among individuals involves single-nucleotide polymorphisms and the Hap Map.

Findings

Key findings of the draft (2001) and complete (2004) genome sequences include

1. There are approximately 20,500 genes in human beings, the same range as in mice and twice that of roundworms. Understanding how these genes express themselves will provide clues to how diseases are caused.

2. Between 1.1% to 1.4% of the genome’s sequence codes for proteins

3. The human genome has significantly more segmental duplications (nearly identical, repeated sections of DNA) than other mammalian genomes. These sections may underlie the creation of new primate-specific genes

4. At the time when the draft sequence was published less than 7% of protein families appeared to be vertebrate specific

5. The first printout of the human genome to be presented as a series of books, displayed at the Wellcome Collection, London

6. The Human Genome Project is considered a Mega Project because the human genome has approximately 3.3 billion base-pairs.

If the sequence obtained was to be stored in book form, and if each page contained 1000 base-pairs recorded and each book contained 1000 pages, then 3300 such books would be needed in order to store the complete genome. However, if expressed in units of computer data storage, 3.3 billion base-pairs recorded at 2 bits per pair would equal 786 megabytes of raw data. This is comparable to a fully data loaded CD.

Although the working draft was announced in June 2000, it was not until February 2001 that Celera and the HGP scientists published details of their drafts. Special issues of Nature (which published the publicly funded project’s scientific paper) and Science (which published Celera’s paper) described the methods used to produce the draft sequence and offered analysis of the sequence. These drafts covered about 83% of the genome (90% of the euchromatic regions with 150,000 gaps and the order and orientation of many segments not yet established). In February 2001, at the time of the joint publications, press releases announced that the project had been completed by both groups. Improved drafts were announced in 2003 and 2005, filling in to ≈92% of the sequence currently.

The competition proved to be very good for the project, spurring the public groups to modify their strategy in order to accelerate progress. The rivals at UC Santa Cruz initially agreed to pool their data, but the agreement fell apart when Celera refused to deposit its data in the unrestricted public database GenBank. Celera had incorporated the public data into their genome, but forbade the public effort to use Celera data.

HGP is the most well known of many international genome projects aimed at sequencing the DNA of a specific organism. While the human DNA sequence offers the most tangible benefits, important developments in biology and medicine are predicted as a result of the sequencing of model organisms, including mice, fruit flies, zebrafish, yeast, nematodes, plants, and many microbial organisms and parasites.

In 2004, researchers from the International Human Genome Sequencing Consortium (IHGSC) of the HGP announced a new estimate of 20,000 to 25,000 genes in the human genome. Previously 30,000 to 40,000 had been predicted, while estimates at the start of the project reached up to as high as 2,000,000. The number continues to fluctuate and it is now expected that it will take many years to agree on a precise value for the number of genes in the human genome.

This Mega Project is co-ordinated by the U.S. Department of Energy and the National Institute of Health. During the early years of the project, the Wellcome Trust (U.K.) became a major partner, other countries like Japan, Germany, China and France contributed significantly. Already the atlas has revealed some starting facts. The two factors that made this project a success are:

  1. Genetic Engineering Techniques, with which it is possible to isolate and clone any segment of DNA.
  2. Availability of simple and fast technologies, to determining the DNA sequences.

Methods

The IHGSC used pair-end sequencing plus whole-genome shotgun mapping of large (≈100 Kbp) plasmid clones and shotgun sequencing of smaller plasmid sub-clones plus a variety of other mapping data to orient and check the assembly of each human chromosome.

The Celera group emphasized the importance of the “whole-genome shotgun” sequencing method, relying on sequence information to orient and locate their fragments within the chromosome. However they used the publicly available data from HGP to assist in the assembly and orientation process, raising concerns that the Celera sequence was not independently derived.

Benefits

The work on interpretation of genome data is still in its initial stages. It is anticipated that detailed knowledge of the human genome will provide new avenues for advances in medicine and biotechnology. Clear practical results of the project emerged even before the work was finished. For example, a number of companies, such as Myriad Genetics started offering easy ways to administer genetic tests that can show predisposition to a variety of illnesses, including breast cancer, disorders of hemostasis, cystic fibrosis, liver diseases and many others. Also, the etiologies for cancers, Alzheimer’s disease and other areas of clinical interest are considered likely to benefit from genome information and possibly may lead in the long term to significant advances in their management.

There are also many tangible benefits for biological scientists. For example, a researcher investigating a certain form of cancer may have narrowed down his/her search to a particular gene. By visiting the human genome database on the World Wide Web, this researcher can examine what other scientists have written about this gene, including (potentially) the three-dimensional structure of its product, its function(s), its evolutionary relationships to other human genes, or to genes in mice or yeast or fruit flies, possible detrimental mutations, interactions with other genes, body tissues in which this gene is activated, diseases associated with this gene or other datatypes.

Further, deeper understanding of the disease processes at the level of molecular biology may determine new therapeutic procedures. Given the established importance of DNA in molecular biology and its central role in determining the fundamental operation of cellular processes, it is likely that expanded knowledge in this area will facilitate medical advances in numerous areas of clinical interest that may not have been possible without them.

The analysis of similarities between DNA sequences from different organisms is also opening new avenues in the study of evolution. In many cases, evolutionary questions can now be framed in terms of molecular biology; indeed, many major evolutionary milestones (the emergence of the ribosome and organelles, the development of embryos with body plans, the vertebrate immune system) can be related to the molecular level. Many questions about the similarities and differences between humans and our closest relatives (the primates, and indeed the other mammals) are expected to be illuminated by the data from this project.

The Human Genome Diversity Project (HGDP), spin off research aimed at mapping the DNA that varies between human ethnic groups, which was rumored to have been halted, actually did continue and to date has yielded new conclusions. In the future, HGDP could possibly expose new data in disease surveillance, human development and anthropology. HGDP could unlock secrets behind and create new strategies for managing the vulnerability of ethnic groups to certain diseases (see race in biomedicine). It could also show how human populations have adapted to these vulnerabilities.

Advantages of Human Genome Project:

  1. Knowledge of the effects of variation of DNA among individuals can revolutionize the ways to diagnose, treat and even prevent a number of diseases that affects the human beings.
  2. It provides clues to the understanding of human biology.

Ethical, legal and social issues

The project’s goals included not only identifying all of the approximately 24,000 genes in the human genome, but also to address the ethical, legal, and social issues (ELSI) that might arise from the availability of genetic information. Five percent of the annual budget was allocated to address the ELSI arising from the project.

Debra Harry, Executive Director of the U.S group Indigenous Peoples Council on Biocolonialism (IPCB), says that despite a decade of ELSI funding, the burden of genetics education has fallen on the tribes themselves to understand the motives of Human genome project and its potential impacts on their lives. Meanwhile, the government has been busily funding projects studying indigenous groups without any meaningful consultation with the groups

The main criticism of ELSI is the failure to address the conditions raised by population-based research, especially with regard to unique processes for group decision-making and cultural worldviews. Genetic variation research such as HGP is group population research, but most ethical guidelines, according to Harry, focus on individual rights instead of group rights. She says the research represents a clash of culture: indigenous people’s life revolves around collectivity and group decision making whereas the Western culture promotes individuality. Harry suggests that one of the challenges of ethical research is to include respect for collective review and decision making, while also upholding the Western model of individual rights.

 
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Posted by on March 11, 2011 in Science

 

Stemcell Technology

Stem cells are biological cells found in all multi cellular organisms, that can divide through mitosis and differentiate into diverse specialized cell types. In mammals, there are two broad types of stem cells: embryonic stem cells that are isolated from the inner cell mass of blastocysts, and adult stem cells that are found in various tissues. In adult organisms, stem cells and progenitor cells act as a repair system for the body, replenished in adult tissues. In a developing embryo, stem cells can differentiate into all the specialized cells, but also maintain the normal turnover of regenerative organs, such as blood, skin, or intestinal tissues.

Stem cells can now be artificially grown and transformed into specialized cell types with characteristics consistent with cells of various tissues such as muscles or nerves through cell culture. Highly plastic adult stem cells are routinely used in medical therapies. Stem cells can be taken from a variety of sources, including umbilical cord blood and bone marrow. Embryonic cell lines and autologous embryonic stem cells generated through therapeutic cloning have also been proposed as promising candidates for future therapies.

Medical researchers believe that stem cell therapy has the potential to dramatically change the treatment of human disease. A number of adult stem cell therapies already exist, particularly bone marrow transplants that are used to treat leukemia. In the future, medical researchers anticipate being able to use technologies derived from stem cell research to treat a wider variety of diseases including cancer, Parkinson’s disease, spinal cord injuries, Amyotrophic lateral sclerosis, multiple sclerosis, and muscle damage, amongst a number of other impairments and conditions. However, there still exists a great deal of social and scientific uncertainty surrounding stem cell research, which could possibly be overcome through public debate and future research, and further education of the public.

One concern of treatment is the possible risk that transplanted stem cells could form tumors and have the possibility of becoming cancerous if cell division continues uncontrollably.

Stem cells, however, are already studied extensively. While some scientists are hesitant to associate the therapeutic potential of stem cells as the first goal of the research, they find the investigation of stem cells as a goal worthy in itself.

Contrarily, supporters of embryonic stem cell research argue that such research should be pursued because the resultant treatments could have significant medical potential. It is also noted that excess embryos created for in vitro fertilization could be donated with consent and used for the research.

 
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Posted by on February 25, 2011 in Science

 
 
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