Gene Mapping by In Situ Hybridization

Gene Mapping by In Situ Hybridization

The previous mapping methods are indirect in that they provide information on the physical location of a gene on a particular chromosome but without actually visualizing the gene's map position. A more direct approach is in situ hybridization, which involves hybridizing DNA (or RNA) probes directly to metaphase chromosomes spread on a slide and visualizing the hybridization signal (and thus the location of the gene to which the probe hybridizes) under a microscope.

The DNA in metaphase chromosomes is denatured in place (hence, in situ) on the slide, and hybridization of a labeled probe is allowed to proceed. Methods for mapping single-copy gene sequences by in situ hybridization originally were laborious and slow, requiring long exposures of the slides under photographic emulsion to detect the location of hybridized probe that had been labeled with low-level isotopes, such as tritium. Mapping with confidence required analysis of many metaphase spreads to distinguish the real hybridization signal from background radioactivity. However, more sensitive techniques have now been developed that enable rapid detection of hybridized probes labeled non radioactively with compounds that can be visualized by fluorescence microscopy (Fig). Even in a single metaphase spread, one can easily see the position of the gene being mapped.

In combination with banding methods for chromosome identification, fluorescence in situ hybridization can be used to map genes to within 1 to 2 million base pairs (1000 to 2000 kb) along a metaphase chromosome. Although this degree of resolution is a considerable improvement over other methods, it is still substantially larger than the size of most individual genes.

Figure: Gene mapping by in situ hybridization of a biotin-labeled DNA probe for the human muscle glycogen phosphorylase gene (MGP) to a spread of human metaphase chromosomes. Location of the MGP gene is indicated by the bright spots seen over each chromatid at the site of the gene in band q13 of chromosome 11. The mapping of MGP to 11q13 also assigns the locus for McArdle disease, an autosomal recessive myoglobinuria caused by deficiency of MGP. (Photograph courtesy of Peter Lichter, Yale University)

Celera Genomics HGP

Celera Genomics & HGP

In 1998, an identical, privately funded quest was launched by the American researcher Craig Venter and his firm Celera Genomics. The $300 million Celera effort was intended to proceed at a faster pace and at a fraction of the cost of the roughly $3 billion publicly-funded project.Celera Genomics was established in May 1998 by the Perkin-Elmer Corporation (and was later purchased by Applera Corporation), with Dr. J. Craig Venter from The Institute for Genomic Research (TIGR) as its first president. While at TIGR, Venter and Hamilton Smith led the first successful effort to sequence an entire organism's genome, that of the Haemophilus influenzae bacterium. Celera was formed for the purpose of generating and commercializing genomic information to accelerate the understanding of biological processes.
The rise and fall of Celera as an ambitious competitor of the Human Genome Project is the main subject of the book The Genome War by James Shreeve, who takes a strong pro-Venter point of view. (He followed Venter around for two years in the process of writing the book.) A view from the public effort's side is that of Nobel laureate Sir John Sulston in his book The Common Thread: A Story of Science, Politics, Ethics and the Human Genome.Celera used a newer, riskier technique called whole genome shotgun sequencing, which had been used to sequence bacterial genomes up to 6 million base pairs in length, but not for anything nearly as large as the 3 billion base pair human genome.Celera initially announced that it would seek patent protection on "only 200-300" genes, but later amended this to seeking "intellectual property protection" on "fully-characterized important structures" amounting to 100-300 targets. Contrary to its public promises, the firm eventually filed patent applications on 6,500 whole or partial genes.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 90% of the genome, with much of the remaining 10% filled in later. 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 again in 2005, filling in roughly 8% of the remaining sequence.
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 2005, 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.

RNA genes

RNA genes

RNA genes (sometimes referred to as non-coding RNA or small RNA) are genes that encode RNA that is not translated into a protein. The most prominent examples of RNA genes are transfer RNA (tRNA) and ribosomal RNA (rRNA), both of which are involved in the process of translation. However, since the late 1990s, many new RNA genes have been found, and thus RNA genes may play a much more significant role than previously thought. In the late 1990s and early 2000, there has been persistent evidence of more complex transcription occurring in mammalian cells (and possibly others). This could point towards a more widespread use of RNA in biology, particularly in gene regulation. A particular class of non-coding RNA, micro RNA, has been found in many metazoans (from Caenorhabditis elegans to Homo sapiens) and clearly plays an important role in regulating other genes. First proposed in 2004 by Rassoulzadegan and published in Nature 2006.

RNA is implicated as being part of the germline. If confirmed, this result would significantly alter the present understanding of genetics and lead to many question on DNA-RNA roles and interactions.RNA Deatiles,ScienceRibonucleic acid (RNA) is a nucleic acid polymer consisting of nucleotide monomers, that acts as a messenger between DNA and ribosomes, and that is also responsible for making proteins out of amino acids. RNA polynucleotides contain ribose sugars and predominantly uracil unlike deoxyribonucleic acid (DNA), which contains deoxyribose and predominantly thymine. It is transcribed (synthesized) from DNA by enzymes called RNA polymerases and further processed by other enzymes.

RNA serves as the template for translation of genes into proteins, transferring amino acids to the ribosome to form proteins, and also translating the transcript into proteins. Nucleic acids were discovered in 1868 (some sources indicate 1869) by Johann Friedrich Miescher (1844-1895), who called the material 'nuclein' since it was found in the nucleus. It was later discovered that prokaryotic cells, which do not have a nucleus, also contain nucleic acids. The role of RNA in protein synthesis had been suspected since 1939, based on experiments carried out by Torbjörn Caspersson, Jean Brachet and Jack Schultz. Hubert Chantrenne elucidated the messenger role played by RNA in the synthesis of proteins in ribosome.

The sequence of the 77 nucleotides of a yeast RNA was found by Robert W. Holley in 1964, winning Holley the 1968 Nobel Prize for Medicine. In 1976, Walter Fiers and his team at the University of Ghent determined the complete nucleotide sequenceDNA Bases Bio TechnologyDeoxyribonucleic acid, or DNA is a nucleic acid molecule that contains the genetic instructions used in the development and functioning of all living organisms. The main role of DNA is the long-term storage of information and it is often compared to a set of blueprints, since DNA contains the instructions needed to construct other components of cells, such as proteins and RNA molecules.
The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information. Chemically, DNA is a long polymer of simple units called nucleotides, which are held together by a backbone made of alternating sugars and phosphate groups. Attached to each sugar is one of four types of molecules called bases. It is the sequence of these four bases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription. Most of these RNA molecules are used to synthesize proteins, but others are used directly in structures such as ribosomes and spliceosomes.
Within cells, DNA is organized into structures called chromosomes and the set of chromosomes within a cell make up a genome. These chromosomes are duplicated before cells divide, in a process called DNA replication. Eukaryotic organisms such as animals, plants, and fungi store their DNA inside the cell nucleus, while in prokaryotes such as bacteria it is found in the cell's cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA, which helps control its interactions with other proteins and thereby control which genes are transcribed Biotechnology Indroduction. The convention recognized for the first time in international law that the conservation of biological diversity is "a common concern of humankind" and is an integral part of the development process.

The agreement covers all ecosystems, species, and genetic resources. It links traditional conservation efforts to the economic goal of using biological resources sustainably. It sets principles for the fair and equitable sharing of the benefits arising from the use of genetic resources, notably those destined for commercial use. It also covers the rapidly expanding field of biotechnology through its Cartagena Protocol on Biosafety, addressing technology development and transfer, benefit-sharing and biosafety issues. Importantly, the Convention is legally binding; countries that join it('Parties') are obliged to implement its provisions .

Apply Bio Technology Science The convention reminds decision-makers that natural resources are not infinite and sets out a philosophy of sustainable use. While past conservation efforts were aimed at protecting particular species and habitats, the Convention recognizes that ecosystems, species and genes must be used for the benefit of humans. However, this should be done in a way and at a rate that does not lead to the long-term decline of biological diversity The convention also offers decision-makers guidance based on the precautionary principle that where there is a threat of significant reduction or loss of biological diversity, lack of full scientific certainty should not be used as a reason for postponing measures to avoid or minimize such a threat. The Convention acknowledges that substantial investments are required to conserve biological diversity. It argues, however, that conservation will bring us significant environmental, economic and social benefits in return.In this situation, your range of choices is very broad and many packages will meet these limited.

Fermentation

Fermentation

The word fermentation is derived from a latin verb ‘fervere’ which means to boil. However, events of boiling came into existence from the fact that during alcoholic fermentation, the bubbles of gas (CO2) burst at the surface of a boiling liquid and give the warty appearance. The conventional definition of fermentation is the breakdown (metabolism) of larger molecules. For example, carbohydrates, into simple ones under the influence of micro-organism for their enzymes. This definition of fermentation had little meaning until the metabolic process were known. In a micro-biological way, fermentation is defined as “any process for the production of useful products through mass culture of micro-organism” wheteras, in a biochemical sense, this word means the numerous oxidation – reduction reactions in which organic compounds, used as source of carbon and energy, act as acceptors of donors of hydrogen ions. The organic compounds used as substrate give rise to various products of fermentation which accumulate in the growth medium (Riviere, 1977)

Almost in all organism metabolic pathways generating energy are fundamentally similar. In autophototrophs, (e.g. some bacteria, cyanobacteria and higher plants) ATP is generated as a result of photosynthesis electron transport mechanisms, whereas in chemotrophs the source of ATP is oxidation of organic compounds in the growth substrates. The oxidation reaction may be accomplished in the presence of oxygen (in aerobes) or in absence of oxygen (in anaerobes). Thus, in aerobic microorganism the process in ATP generation is referred to as cellular respiration whereas in anaerobes or aerobes functioning under anaerobic condition, it is known as anaerobic respiration or fermentation.

Although, fermentation (e.g. brewing and wine production) was done for many hundred years, yet during the end of 15th century, brewing became partially industrialized in Britain. Antony van Leeuwenhoek (1632-1723) developed method to observe yeasts and other micro-organism under the microscope but this study could not be further strengthened. By early 19th century Cagniard-Latour and Schwann reported that the fermentation of wine and beer is accomplished by yeast cells. It was L. Pasteur who observed microorganism associated with fermentation and causing many diseases in human beings. Detailed studies on fermentation products, culture improvement, recovery, and scale up of products were made after the world war I.

The Human Genome Projects - Benefits

The Human Genome Projects - 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 search to a particular gene. By visiting the human genome database on the worldwide 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 the theory 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, 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.

What's Turning Genomics Vision Into Reality

In "A Vision for the Future of Genomics Research," published in the April 24, 2003 issue of the journal Nature, the National Human Genome Research Institute (NHGRI) details a myriad of research opportunities in the genome era. This backgrounder describes a few of the more visible, large-scale opportunities.

The International HapMap Project

Launched in October 2002 by NHGRI and its partners, the International HapMap Project has enlisted a worldwide consortium of scientists with the goal of producing the "next-generation" map of the human genome to speed the discovery of genes related to common illnesses such as asthma, cancer, diabetes and heart disease.Expected to take three years to complete, the "HapMap" will chart genetic variation within the human genome at an unprecedented level of precision. By comparing genetic differences among individuals and identifying those specifically associated with a condition, consortium members believe they can create a tool to help researchers detect the genetic contributions to many diseases. Whereas the Human Genome Project provided the foundation on which researchers are making dramatic genetic discoveries, the HapMap will begin building the framework to make the results of genomic research applicable to individuals.

ENCyclopedia Of DNA Elements (ENCODE)

This NHGRI-led project is designed to develop efficient ways of identifying and precisely locating all of the protein-coding genes, non-protein-coding genes and other sequence-based, functional elements contained in the human DNA sequence. Creating this monumental reference work will help scientists mine and fully utilize the human sequence, gain a deeper understanding of human biology, predict potential disease risk, and develop new strategies for the prevention and treatment of disease.The ENCODE project will begin as a pilot, in which participating research teams will work cooperatively to develop efficient, high-throughput methods for rigorously and fully analyzing a defined set of target regions comprising approximately 1 percent of the human genome. Analysis of this first 30 megabases (Mb) of human genome sequence will allow the project participants to test and compare a variety of existing and new technologies to find the functional elements in human DNA.

Chemical Genomics

NHGRI is exploring the acquisition and/or creation of publicly available libraries of organic chemical compounds, also referred to as small molecules, for use by basic scientists in their efforts to chart biological pathways. Such compounds have a number of attractive features for genome analysis, including their wide structural diversity, which mirrors the diversity of the genome; their ability in many cases to enter cells readily; and the fact that they can often serve as starting points for drug development. The use of these chemical compounds to probe gene function will complement more conventional nucleic acid approaches.This initiative offers enormous potential. However, it is a fundamentally new approach to genomics, and largely new to basic biomedical research as a whole. As a result, substantial investments in physical and human capital will be needed. NHGRI is currently planning for these needs, which will include large libraries of chemical compounds (500,000 - 1,000,000 total); capacity for robotic-enabled, high-throughput screening; and medicinal chemistry to convert compounds identified through such screening into useful biological tools.

Genomes to Life
The Department of Energy's "Genomes to Life" program focuses on single-cell organisms, or microbes. The fundamental goal is to understand the intricate details of the life processes of microbes so well that computational models can be developed to accurately describe and predict their responses to changes in their environment."Genomes to Life" aims to understand the activities of single-cell organisms on three levels: the proteins and multi-molecular machines that perform most of the cell's work; the gene regulatory networks that control these processes; and microbial associations or communities in which groups of different microbes carry out fundamental functions in nature. Once researchers understand how life functions at the microbial level, they hope to use the capabilities of these organisms to help meet many of our national challenges in energy and the environment.

Structural Genomics Consortium

Structural genomics is the systematic, high-throughput generation of the three-dimensional structure of proteins. The ultimate goal for studying the structural genomics of any organism is the complete structural description of all proteins encoded by the genome of that organism. Such three-dimensional structures will be crucial for rational drug design, for diagnosis and treatment of disease, and for advancing our understanding of basic biology. A broad collection of structures will provide valuable biological information beyond that which can be obtained from individual structures.

A Possible Cure for HIV

A Possible Cure for HIV 

 

Patients who have recently been able to clear or control their acquired immune deficiency syndrome (AIDS) have renewed the interest of scientists in finding a cure for the human immunodeficiency virus (HIV) and subsequently, AIDS. The newest ideas to help generate a cure include transplants of naturally resistant stem cells or the genetic modification of immune cells to render them immune to the virus (Pollack 2011). Since people with HIV are required to take antiviral drugs to control the infection for the rest of their lives the discovery of a cure would improve countless lives and solve one of the world’s foremost health issues.

HIV is a retrovirus which attacks the cells of the human immune system, causing their inability to function. As the HIV infection advances, the immune system of the person gradually weakens, making them more vulnerable to other illnesses. The last stage of the HIV infection, AIDS, usually takes 10-15 years to reach and antiviral drugs can slow the development down even further (World Health Organisation 2012).
In the first patient, a man seemingly cleared his HIV infection through numerous bone-marrow transplants he received as leukemia treatment. The donor was one of the 1% of Northern Europeans that lack a protein, CCR5, rendering him naturally resistant to HIV. Due to the bone-marrow (stem cell) implant the patient is able to produce a resistant immune system and has been free of the virus for four years (CBS News 2011). However, this approach for a cure is unlikely due to the difficulties of finding a matching donor as well as the transplant procedure being risky and expensive. In addition, donors would be unethically ‘farmed’ for bone-marrow. Therefore this approach for a cure is highly improbable.

Scientists attempted to modify the immune cells of the second patient, eliminating the CCR5 protein, in order to make them resistant to HIV. White blood cells were removed from the body of the patient and put through gene therapy which modified the cells to produce another protein which disrupted the CCR5 protein. The treated cells were replaced into the man’s body and a month later the man stopped taking antiviral drugs as part of the experiment. Initially, the amount of HIV rose sharply, as expected, but then dropped to an undetectable level gradually while immune cell counts rose. However, the gene therapy did not work as well in 5 other patients (Pollack 2011). This approach to a cure is unproven through these patients but is still being developed, moving onto further clinical trials earlier this year (Instinct Staff 2012). This idea presents numerous problems, the main one being that each individual would have to undergo the procedure making this cure implausible at this point.

Although there is great need of a cure for HIV, with the current methods and ideas involving stem cell transplants and gene modifications, it is doubtful that a functional cure that can be used on a wide scale will be found in the near future.

Gene Therapy Restores Vision

Gene therapy is an exciting treatment option that is starting to take off in the field of treating genetic diseases. Three women in the United States, who had previously been treated for genetic blindness with gene therapy in one eye, have been treated in the second eye, and the results are looking promising (http://www.bbc.co.uk/news/health-16942795). Gene therapy is still only in its early stages as a treatment option, but the promise of recent studies into its success in treating genetic eye diseases mean this technology is on the rise and could soon become a widespread treatment option throughout the world.

Genetic disorders are caused by the malfunctioning of one or more of our genes, which prevent the proteins in our body, which are instructed by the genes, from fulfilling their normal functions (http://www.ornl.gov/sci/techresources/Human_Genome/medicine/genetherapy.shtml). In gene therapy, the malfunctioning gene is replaced by a new, better-functioning gene, which is inserted into the area of the body where the faulty gene is located (http://www.scientificamerican.com/article.cfm?id=experts-gene-therapy). If we do not replace this malfunctioning gene, it can be the cause of disease within in the body. Gene therapy was first tested for treating genetic blindness back in 2008, when a research team at Moorfields Eye Hospital’s NIHR Biomedical Research Centre in the UK used gene therapy successfully on the eyes of human patients, proving it was safe and helped to improve their sight (http://www.ornl.gov/sci/techresources/Human_Genome/medicine/genetherapy.shtml).

In early 2012, three women in the US were treated with a second round of gene therapy to relieve their genetic blindness, caused by an inherited condition known as Leber’s Congenital Amaurosis (LCA). LCA is a very rare disease, appearing just after birth, and occurring as cells from the retina, the “light-sensitive layer of cells at the back of the eye” (Briggs 2012), progressively die out over time, degrading the vision of the sufferer. It is caused by a faulty gene in the cells of the retina, RPE65, and gene therapy aims to fix this by injecting a virus containing a functioning version of the gene into the eye. Dr Jean Bennett, of the University of Pennsylvania’s Mahoney Institute of Neurological Sciences, first treated the three women with this method back in 2008. At the time, twelve people suffering from LCA were injected in just one eye, recovering some vision in the injected eye, and in early 2012, the three women were chosen out of the twelve to have the procedure repeated in the second eye, showing a notable improvement in the vision quality in both eyes. Information regarding Dr Bennett’s most recent results in this area can be found in the February 8th edition of Science Translational Medicine (http://stm.sciencemag.org/content/4/120/120ra15.full.html 2012).

It is evident that, in the last few years, gene therapy has started to emerge as a potentially successful treatment for genetic diseases, in particular those involving genetic blindness. Recent studies, such as the ones referred to above, have demonstrated gene therapy to be successful in improving vision quality for those suffering from inherited eye diseases, such as LCA, and have provided evidence that it is a safe treatment option. It is hoped that these discoveries will lead to more widespread use of gene therapy as a valid treatment for genetic blindness, and will improve the quality of life of those suffering from poor vision quality as a result of inherited eye conditions.

Genetics and Bacterial Resistance

Genetics and Bacterial Resistance

Bacteria have many mechanisms for adapting to their environment and they certainly use them when responding to adverse conditions. In particular, bacteria such as Eschericha coli go through many genetic mutations when building resistance to various antibiotics (Toprak et al. 2012). A team of scientists at Harvard have developed a method for recording and understanding these mutations in an experiment which could have future implications on the way we approach bacterial infections (stealth tactics of bacteria revealed, 2012).

aims to not only record, but understand precisely how bacteria forms a resistance to antibiotics. In order to control the present antibiotic, the concentration of that drug and to record how the bacterium responds, they created the ‘morbidostat’ (stealth tactics of bacteria revealed, 2012). Results have been obtained from E. coli as it was monitored about how it responded to controlled doses of various antibiotics.

The results showed that the bacteria developed resistance to all three of the introduced antibiotics (stealth tactics of bacteria revealed, 2012). Some antibiotics can be faulted by a single gene change, although in this case, like many others, a number of genetic mutations had to occur to obtain the desired phenotype (Toprak et al. 2012). The group of genetic mutations that occurred in this case targeted the bacteria’s susceptibility to each of the antibiotics. The way in which the bacteria responded to the three test drugs separately was a testament to the variability bacteria is capable of. Achaean organisms are widely recognized for their adaptive abilities, which stem from their methods of reproduction. High generational rates are achieved by the ability of the organisms to use binary fission.  Also, plasmids play a role in increasing the genetic material available to the bacteria (Campbell et al. 2009). These mechanisms give reason for the successful rapid mutation of genes measured within the experiment.

The mutations occurring within the bacteria differed between the types of antibiotic it was exposed to (Toprak et al. 2012). The differences between these changes can be applied to the way the bacteria’s resistance developed. But perhaps the most useful data that resulted from this experiment was the congruency between separated test populations.  The genomes of bacteria responding to the same drug, which were measured throughout the test, concluded that “parallel populations evolved similar mutations and acquired them in a similar order.” (Toprak et al. 2012, p101). The patterns that were observed suggests that there are specific pathways of mutation, along which bacteria moved to achieve a goal; antibiotic resistance (Toprak et al. 2012). Now that these genetic pathways have been measured, a more complex set of knowledge can be applied to improving antibiotics and increasing their effectiveness in the future.

A greater understanding of bacteria and it’s mechanisms for coping with its environment is being achieved through many studies being conducted, genetic resistance is a particularly relevant topic and developing improved ways of treating bacterial infections in humans is highly beneficial. The measurement of the response of bacteria to antibiotics has resulted in evidence of mutational pathways for bacteria gaining resistance (Toprak et al. 2012). These results are of great significance to the notions of improving the antibiotic method and overcoming bacterial resistance.

Finding the source of Individuality

Finding the source of Individuality

Have you ever wondered at the uniqueness of every individual around you? Including yourself. Even identical twins that have the same set of genes and have grown up together differ in some of their characteristics and personality. This brings up the old question of nature/ nurture. Recent research findings show that the answer may lie in certain type of DNA within a class called Mobile Genetic Elements (MGE). More specifically, the ones found moving in the brain are called Retratransposons.

Retratransposons like the Long Interspersed Element (L1) for example, follow a copy and paste method to move itself around. It is able to do this because it is thought that L1 retratransposons encode for all the ‘machinery’ it requires to move itself.  The original L1 segment of DNA first transcribes itself into its RNA form following which, the RNA strand moves out of the nucleus to synthesize the proteins in its code. This RNA strand and protein complex then re-enter the nucleus where one of the proteins, endonuclease creates nicks in the existing DNA. At this point, the RNA is retranscribed by the endonuclease into a double stranded DNA which is then inserted into the nicked area.

Transposon events cause the mosaicism
 seen in the color of corn kernels.

This was seen as fascinating because such an explicit change of the DNA within humans is not seen in any other cell excepting immune cells where it is necessary to help churn out new antibodies to fight new diseases.  Although mobile elements were discovered in the 1940’s by Barbara McClintock which resulted in the famous ‘multi-coloured’ corn, its presence and activity in human cells has been a recent discovery. Working with mice and post-mortem samples of the human brain, Professor Fred H. Gage and colleagues discovered that these mobile elements are ‘switched off’ in most human somatic cells except in the hippocampus in the brain from where new neurons are ‘born’. It was found that these mobile elements are extraordinarily active within the neural progenitor cells in the hippocampus with an average of 80-100 L1 jumps per cell. This find is particularly interesting due to the consequences of each jump.

neuron
During the early stages of human nervous system development LINE-1 elements become active (indicated by green flourescence) possibly affecting neuronal function.

When a L1 DNA segment inserts itself into a new area in the genome, it can have several different effects depending on insertion site. On occasion, the new DNA may not have any effect whatsoever. However, the other effects can either be good or bad. If the L1 insertion site is within a DNA segment coding for a protein, the insertion may disrupt the code thus preventing any protein being made or may produce a new variant of the protein. On the other hand, the L1 DNA can act as a promoter if it inserts itself just outside a coding segment in the DNA. This means that it can either ‘turn off’ or ‘turn on’ that segment resulting in the inhibition or production of a certain protein. On a wide scale, this leads to a huge amount of diversity between cells in the brain. As Gage says, “This is a potential mechanism to create the neural diversity that makes each person unique." Thus, this also makes humans “true chimeras”.


Retratransposons have garnered increased interest due to research showing that L1 insertions play a part in neurological and psychiatric conditions. Although further research is required to be carried out, this is a field that holds many promises and discoveries especially since up to 50% of the human DNA is made up of Mobile Elements.

Inheritance of Male Pattern Baldness

Inheritance of Male Pattern Baldness

The Genetics of Baldness - Stephen Connor (s4291526)
What is Male Pattern Baldness (MPB)?
Male pattern baldness (MPB) is a condition which most men (and some women) will face during their lives. MPB causes in people a receding hair line and their hair will become a lot thinner. In the later stages of MPB complete baldness around the crown and possibly the middle section of the top of the head can occur. But what causes male pattern baldness?

What causes MPB?
Testosterone is a steroid hormone that affects many different areas of the body and their functions, however it is not often realized that testosterone is also the cause of hair loss. When testosterone is in the presence of an enzyme called 5-alpha-reductase, the enzyme will break down testosterone into dihydrotestosterone, which is often referred to as DHT.

Male pattern baldness occurs as a result of hair follicles being sensitive to DHT. If a hair follicle is sensitive to DHT it will miniaturize and eventually no hair will grow where that hair follicle grew. It can be seen that through the process of miniaturizing and loss of hair how the symptoms of MPB are so (Receding hair line, thinning of hair). (WebMD 2010)

How does a person’s genetics affect their chance of having MPB?
In 2005, German researches discovered a gene on the X-chromosome that affects baldness (Dr Barry Starr 2006). This gene (androgen-receptor gene, AR) instructs the making of androgen-receptors (also known as dihydrotestosterone receptors).   If the AR gene allows too many androgen-receptors to be made in the scalp or in hair follicles it can result in more testosterone being on the scalp. This in turn results in the creation of more dihydrotestosterone which then leads to greater loss of hair.
Some people who have MPB have an AR gene that performs normally. This means the AR gene is not the only factor that influences the development of MPB. Two independent studies were conducted to discover a common factor that people with MPB had that people without MPB did not have. Both studies came to the conclusion that people suffering with MPB have changes on their chromosome 20 compared to those without MPB.
Everyone has two chromosome 20s, one from each parent. This allows for one chromosome 20 to be unchanged even though the other is changed. This shows that there are three different combinations of chromosome 20s a person can have (and therefore three different likelihoods of having MPB):

1.       Two unchanged chromosome 20s (0 times more likely to develop MPB)
2.       One unchanged and one changed chromosome 20 (3.7 times more likely to develop MPB)
3.       Two changed chromosome 20s (6.1 times more likely to develop MPB)
(Melinda Beck 2008)

Not just one factor affects the likeliness of developing male pattern baldness.  An AR gene that allows for too many androgen-receptors to be in the scalp or hair follicles will increase the chances of developing MPB dramatically. Certain variations to the chromosome 20 also increase the probability of having MPB. Variations on one chromosome 20 will increase the chance of having MPB by 3.7 times and having variations on both chromosome 20s will increase the chance by 6.1 times.

Designer Babies Preimplantation Genetic Diagnosis

Designer Babies – Preimplantation Genetic Diagnosis

Inheriting genes of unfavourable nature has plagued humanity since the dawn of time. And it was long before Gregor Mendel’s discovery of how our physical and behavioural traits are inherited, that humans had already established a desire for the customization of our off springs characterized by disease-free-inheritance matched by superior physical and behavioural genes such as good looks, intelligence and athleticism.  It was not until the beginning of the 21st century that scientists started making advances in this sensitive area of eugenics, colloquially termed designer baby – “a baby whose genetic make-up has been modified in order to eradicate a particular defect, or to ensure that a particular gene is present.”   In spite of the ethical concerns, scientists continue to put preimplantation genetic diagnosis (PGD) into practice, involving in vitro fertilization (IVF) to examine chromosomal abnormalities and perform procedures on the embryo’s DNA before implantation.
The biological causes of genetic variation is at the heart of what PGD aims to eliminate. The three most common mechanisms that arise from sexual reproduction are independent assortment of chromosomes, crossing over and random fertilization. Mendel’s Law of Independent Assortment tells us that during meiosis each pair of alleles segregates independently of each other pair of alleles. And thus, each sperm cell carries chromosomes with a unique combination of the male’s genes and it is by chance that any one of the sperm cells will fertilize the female’s egg – the random nature of fertilization. Finally, the crossing over of alleles results in recombinant chromosomes the uniquely combined DNA from both parents. A fourth less common mechanism, Mutations can also develop whereby DNA replication encompasses an error either during meiosis or mitosis in a zygote.   How can PGD reverse this variance at a cellular level?

PGD was originally developed to eradicate life-threatening diseases in unborn babies and to instill a sense of security in the mother, yet in more recent times it has gone one step further to enhance superficial features. PGD, first of all involves the fusion of gametes in the lab. Mitotic divisions form a cluster of embryo cells.  An incision is made through the membrane using acid and cells are removed. Each cell undergoes genetic analysis biopsy using Fluorescent in-situ Hybridization (FISH). Chemicals are used to illuminate chromosomes to correspond to a particular colour. A DNA probe is used to visualize the cell for genetic analysis. This process is repeated until a cell of favourable genes is found, which is implanted into the mother’s womb. All other cells are discarded, which brings up ethical concerns.

Figure 3: Unnatural Selection using PGD                                                            

Perhaps the practicality of PGD can be improved by maximizing its benefits while minimizing harm. Chromosomal analysis is quite often essential in couples, who carry balanced translocations, in advanced age women and women with previous children who have abnormal chromosome numbers. In addition, women experiencing recurrent pregnancy loss, recurring poor quality embryos or repeated IVF failures could also benefit from the PGD procedure to select healthy embryos. PGD can be arguably unethical due to its superficial and selective nature but its benefits looms large for those in need. 

Fattened monkeys as a proxito human obesity

Fattened monkeys as a "proxi" to human obesity?

BEYOND. In today's edition of The New York Times (cover page) was published an article about using monkeys in different primate research centers to study obesity in humans. The main centers are the Oregon National Primate Research Center and the Southwest National Primate Research Center in San Antonio, Texas. Some studies are reporting results on how high fructose corn syrup appears to accelerate the development of obesity and diabetes. While these results sound promising, we should ask if this animal model (closer to us than rats) and the treatment applied (specific diet and intake) is a real "proxi" to human diet / lifestyle and human reaction to that particular experimental conditions. Monkeys (macaques and baboons) are pushed to changed their diets and lifestyles (wild vs. cage) in a short (really short) period of time; while humans are dealing with lifestyle and diet changes since the agriculture revolution (approximately 12,000 ya). In my graduate class (last Fall) about human evolution in health and disease (ANTH 650), and a recent seminar in a colleague's class (ANTH 612) we discussed human obesity taking into consideration the evolutionary perspective, where not only today's diet and lifestyle must be analyzed but past environments and habits must be included in the discussion.
I was happy when reading in the same article (NYT) a colleague's comment where he points out that he "prefers animals that become naturally obese with age, just as many humans do".

Types of Gene therapy and general strategies

Types of Gene therapy and general strategies

Gene therapy may be classified into two types

1) Germ line gene therapy

2) Somatic cell gene therapy

a) Incase of germ line gene therapy germ cells that is sperms or eggs are modified by the introduction of functional genes, which are ordinarily integrated into their genomes.


Therefore the change due to therapy is heritable and passed onto the later generations. This approach, heretically, is highly effective in counteracting the genetic disorders. However this option is not consider, at least for the present for application in human beings for a variety of technical and ethical reasons.

b) In the case of somatic cell gene therapy the gene is introduced only in somatic cells, especially of those tissues in which expression of the concerned gene is critical for health. Expression of the introduced gene relieves symptoms of the disorder, but this effect is not heritable, as it does not involve the germ line. It is the only feasible option, and clinical trials have already started mostly for the treatment of cancer and blood disorders.

GENERAL GENE THERAPY STRATEGIES

1) Gene augmentation therapy (GAT): -

It is done by simple addition of functional alleles has been used to treat several inherited disorders caused by genetic deficiency of a gene product. It is also involved in transfer to cells of genes encoding toxic compounds (suicide genes) or prodrugs (reagents which confer sensitivity to subsequent treatment with a drug). It has been particularly applied to autosomal recessive disorders where even modest expression levels of an introduced gene may make a substantial difference.

2) Targeted killing of specific cells: -

Artificial cell killing and immune system assisted cell killing have been popular in the treatment of cancers. It can be done by two ways.

a) Direct cell killing: - it is possible if the inserted genes are expressed to produce a lethal toxin (suicide genes), or a gene encoding a prodrug is inserted, conferring susceptibility to killing by a subsequently administered drug. Alternatively selectively lytic viruses can be used.

b) Indirect cell killing: - It uses immunostimulatory genes to provoke or enhance an immune response against the target cell.

3) Targeted mutation correction: -

The repair of a genetic defect to restore a functional allele, is the exception, technical difficulties have meant that it is not sufficiently reliable to warrant clinical trails.

4) Targeted inhibition of gene expression: -

It is suitable for treating infectious diseases and some cancers. If disease cells display a novel gene product or inappropriate expression of a gene a variety of different systems can be used specifically to block the expression of a single gene at the DNA, RNA or Protein levels.
REFERENCE

1) Tom strachan and Andrew P. Read, Human Molecular Genetics, Second edition.

2) T.A. Brown, Gene Cloning an introduction, Third Edition.

3) S.N. Jogdand, Gene Biotechnology.

4) B.D Singh, Biotechnology.

Human Gene Therapy

Human Gene Therapy
Human beings suffer from more than 5000 different diseases caused by single gene mutations, e.g., cystic fibrosis acatalasis, hunting tons chorea, tay sachs disease, lisch nyhan syndrome, sickle cell anemia, mitral stenosis, hunter's syndrome, haemophilia, several forms of muscular dystrophy etc. In addition, many common disorders like cancer, hypertension, atherosclerosis and mental illness seem to have genetic components.

The term gene therapy can be defined as introduction of a normal functional gene into cells, which contain the defective allele of concerned gene with the objective of correcting a genetic disorder or an acquired disorder.
The first approach in gene therapy is: -

a) Identification of the gene that plays the key role in the development of a genetic disorder.

b) Determination of the role of its product in health and disease.

c) Isolation and cloning of the gene.

d) Development of an approach for gene therapy.

The genetic material may be transferred directly into cells within a patient, which is referred as in vivo gene therapy or else cells may be removed from the patient and the genetic material inserted into them, which is referred as invitro gene therapy. Apart from the two methods mentioned above there is one more method that is ex-vivo gene therapy in which genetic material is inserted into the cells just prior to transplanting the modified cells back into the patient.

Major disease classes under gene therapy include: -

a) Infectious diseases: - infection by a virus or bacterial pathogen

b) Cancers: - uncontrolled and enormous cell division and cell proliferation as a result of activation of an oncogene or inactivation of a tumors suppressor gene or an apoptosis gene.

c) Inherited disorders: - genetic deficiency of an individual gene product or genetically determined in appropriate expression of a gene.

d) Immune system disorders: - includes allergies, inflammation and also autoimmune diseases in which immune system cells appropriately destroy body cells.

Telomerase: A Cancer Therapeutic Target

Telomerase: A Cancer Therapeutic Target


Although Elizabeth Blackburn had identified telomerase in 1980, it took 29 years for her work to be truly recognised. In 2009, Blackburn and her esteemed colleagues were awarded the Nobel Prize in Physiology or Medicine based on the successful ‘discovery of how chromosomes are protected by telomeres and the enzyme telomerase’ (Nobelprize.org, 2012).


As a result of this initial discovery, many scientific studies and research projects have aimed to further understand telomerase and the way in which it is related to degenerative diseases, aging and cancer (Reece, 2011). One such study was conducted by Jian Hu from the Dana-Farber Cancer Institute, Boston, USA. Titled ‘Antitelomerase Therapy Provokes ALT and Mitochondrial Adaptive Mechanisms in Cancer’, the study looked at modeling telomerase reactivation through the use of an inducible telomerase reverse transcriptase allele (Hu, 2012).

The starting point for a mutation has been found to be related to a problem which can arise during cell division if the subject (mouse) has levels of the enzyme which are low or nonexistent. When this factor is married with conventional DNA polymerases exhibiting an end-replication problem a normal or premalignant cell can lose the essential telomere sequences and uncapping can occur (Hu, 2012). This leads to the activation of cellular checkpoints not unlike those caused by DNA double-stranded breaks and ultimately results in telomere dysfunction (Hu, 2012). Flow on effects of dysfunction can be seen with records of induced p53 (tumor suppressor protein), cellular senescence and apoptosis (Children’s Medical Research Institute, 2006). Mutational inactivation of the p53 protein allows for cell cycling to continue and provides a procarcinogenic mutator mechanism for cells with telomere dysfunction via translocations, amplification and deletions (Hu, 2012). However, continual dysfunction and uncontrolled chromosomal instability can restrict full malignant progression.

As a result, clinically derived inhibitors with oligonucleotide changes enable maintenance of telomeres through homologous recombination. The alternative lengthening of telomeres (ALT) mechanism is one such inhibitor. By engineering an allele, TERT (a reverse transcriptase catalytic subunit) which can be inserted into the genome, and using mice mutant for Atm, the development of high penetrance and T cell lymphomas was able to be modeled. Results showed that mice from either the parental or first generation with the allele 4-Hydroxytamoxifen (4-OHT)-inducible Telomerase Reverse Transcriptase-Estrogen Receptor (TERTER) developed T cell lymphomas at synonymous penetrance and latencies. In comparison, the third and fourth generation mice presented lymphomas with lower penetrance and longer latency (Hu, 2012), refer to Figure 2.

Several key genes including those that were regulated from a master regulator possessed deviant expression in relation to oxidative and mitochondria pathways. The PGC-1ß, believed to control mitochondrial oxidative energy metabolism by activating specific target transcription factors including estrogen-related receptors (Sonoda, 2007), was found to be a major driver of the adaptive response to telomere dysfunction (Hu, 2012), refer to Figure 3.


The pressure for a cell to maintain mitochondrial function is directly relatable to the ROS (reactive oxygen species) levels and may be of great importance to telomeres due to ROS destroying telomeric G-rich sequences. Thus confirming the PGC link (refer to Figure 4) between mitochondria, telomeres and carcinogenic cells (Hu, 2012).


Furthermore, rendering genetic modelling crucial in the desire to understand tumor cell response, and quite possibly providing the answer to curing cancer.

Genetic Testing

Genetic Testing

This last century has seen an escalation in advancement of technology. In about one hundred years, man has gone from the horse and buggy to super sonic flight. These advancements have also been implanted in the health industry as seen in the almost doubling of the life expectancy of man.It also appears as though this escalation will only continue. One field where these advancements are moving at a very high speed is the field of genetics and biotechnology. The last ten years have seen some of the greatest landmarks in genetic genealogy research. The pattern in this field indicates that the discoveries and applications of those discoveries will continue to grow at an exponential rate.

With the increase in genetic knowledge there has also been an increase in the variety and ease of genetic testing available. Genetic testing refers to any sort of test which involves the study of the genome. When genetics was in its infancy, tests were expensive and took a long period of time to perform. Recent advances have significantly decreased the costs and time needed to perform genetic testing. This decrease in cost and time has made genetic testing available to more of the general public.

Genetic testing has also been used for determining family relationships. The simplest relationship to determine with a genetic test is a paternal or a maternal relationship. Today, genetic testing can also be used to determine other, more distant relationships. Genetic testing is available for full siblings, half siblings, grandparents and cousins. This allows family relationships to be determined even if one or more of the family members is deceased. As research continues, the ability to dive deeper into your family tree is becoming possible. With the use of Y-chromosome and mtDNA (mitochondrial DNA) testing more can be learned. The use of these genetic tests has allowed genealogists to verify their family trees and in some cases discover new branches that were not previously known. Genetic testing is even being used to understand the roots of family trees. This includes the use of genetic tests to look for Native American ancestry, and ancestry from different parts of Europe and Asia.

As knowledge and research in the area of genetics and biotechnology continue to advance, genetic testing will become even more accessible. This increase in use of genetic tests will give people more access to information. This information can be used to help solve crimes, increase the quality of health care, and provide information into your personal or family history.

Gene Therapy - Viral Vectors

Gene Therapy - Viral Vectors

In both types of therapy, scientists need something to transport either the entire gene or a recombinant DNA to the cell's nucleus, where the chromosomes and DNA reside. In essence, vectors are molecular delivery trucks. One of the first and most popular vectors developed were viruses because they invade cells as part of the natural infection process. Viruses have the potential to be excellent vectors because they have a specific relationship with the host in that they colonize certain cell types and tissues in specific organs. As a result, vectors are chosen according to their attraction to certain cells and areas of the body.

One of the first vectors used was retroviruses. Because these viruses are easily cloned (artificially reproduced) in the laboratory, scientists have studied them extensively and learned a great deal about their biological action. They also have learned how to remove the genetic information that governs viral replication, thus reducing the chances of infection.

Retroviruses work best in actively dividing cells, but cells in the body are relatively stable and do not divide often. As a result, these cells are used primarily for ex vivo (outside the body) manipulation. First, the cells are removed from the patient's body, and the virus, or vector, carrying the gene is inserted into them. Next, the cells are placed into a nutrient culture where they grow and replicate. Once enough cells are gathered, they are returned to the body, usually by injection into the blood stream. Theoretically, as long as these cells survive, they will provide the desired therapy.

Another class of viruses, called the adenoviruses, also may prove to be good gene vectors. These viruses can effectively infect nondividing cells in the body, where the desired gene product then is expressed naturally. In addition to being a more efficient approach to gene transportation, these viruses, which cause respiratory infections, are more easily purified and made stable than retroviruses, resulting in less chance of an unwanted viral infection. However, these viruses live for several days in the body, and some concern surrounds the possibility of infecting others with the viruses through sneezing or coughing. Other viral vectors include influenza viruses, Sindbis virus, and a herpes virus that infects nerve cells.

Scientists also have delved into nonviral vectors. These vectors rely on the natural biological process in which cells uptake (or gather) macromolecules. One approach is to use liposomes, globules of fat produced by the body and taken up by cells. Scientists also are investigating the introduction of raw recombinant DNA by injecting it into the bloodstream or placing it on microscopic beads of gold shot into the skin with a "gene-gun." Another possible vector under development is based on dendrimer molecules. A class of polymers (naturally occurring or artificial substances that have a high molecular weight and formed by smaller molecules of the same or similar substances), is "constructed" in the laboratory by combining these smaller molecules. They have been used in manufacturing Styrofoam, polyethylene cartons, and Plexiglass. In the laboratory, dendrimers have shown the ability to transport genetic material into human cells. They also can be designed to form an affinity for particular cell membranes by attaching to certain sugars and protein groups.

Early migration of modern humans into Arabia.....but from where?

Early migration of modern humans into Arabia.....but from where?

TOOLS. Stone tools (hand axes) were unearthed in the Arabian peninsula in a rock shelter called Jebel Faya. These tools were dated as old as 127,000 years as it was presented in Science last January. The authors suggest that this early expansion of anatomically modern humans took place from Africa and then added that "It is likely that populations expanded and moved through the interior of Arabia, as well as via the coastline, and used adaptive strategies incorporating terrestrial resources" But, other researchers do not share this idea. John Shea of Stony Brook University in New York pointed out that "stone points from Jebel Faya are shorter, thicker and less pointy than those found throughout Africa beginning 100,000 years ago" Moreover, he proposes that the stone tools similarities of Jebel Faya to Indian finds could reflect a different migration, one that came from Asia. Now the debate is open and waiting for more evidence.

Creative Explosion: European caves or South African Caves?

Creative Explosion: European caves or South African Caves?

TOOLS and BEYOND. Back again and trying to catch up with some news. An article published in the August issue of Scientific American magazine presents a general review from the work conducted in the last two decades by archaeologist Curtis Marean and his team on coastal South African sites. His main findings challenge the previous hypothesis that suggests that earliest modern human behaviors were all found in Europe around 40,000 years ago (and suggesting that this was the departure "place"). The authors wrote that at Pinnacle Point they found evidence that supports the idea that modern humans (at Pinnacle Point) "may be very well the ancestors of everyone in the planet". Marean an colleagues published similar findings in other South African sites such as Blombos Cave suggesting that modern human behaviors emerged earlier that previously accepted. Maybe we must recognize that the "creative explosion" leading to modern human behavior happened at different times in different regions....(by the way, what's the meaning of "modern human behavior?)
If you want to learn more about Pinnacle Point, and the findings presented by Marean and colleagues, you can check a very entertaining link created by Scientific American.

The biological basis of gene therapy

The biological basis of gene therapy
Gene therapy is a rapidly growing field of medicine in which genes are introduced into the body to treat diseases. Genes control heredity and provide the basic biological code for determining a cell's specific functions. Gene therapy seeks to provide genes that correct or supplant the disease-controlling functions of cells that are not, in essence, doing their job. Somatic gene therapy introduces therapeutic genes at the tissue or cellular level to treat a specific individual. Germ-line gene therapy inserts genes into reproductive cells or possibly into embryos to correct genetic defects that could be passed on to future generations. Initially conceived as an approach for treating inherited diseases, like cystic fibrosis and Huntington's disease, the scope of potential gene therapies has grown to include treatments for cancers, arthritis, and infectious diseases. Although gene therapy testing in humans has advanced rapidly, many questions surround its use. For example, some scientists are concerned that the therapeutic genes themselves may cause disease. Others fear that germ-line gene therapy may be used to control human development in ways not connected with disease, like intelligence or appearance.

The biological basis of gene therapy

Gene therapy has grown out of the science of genetics or how heredity works. Scientists know that life begins in a cell, the basic building block of all multicellular organisms. Humans, for instance, are made up of trillions of cells, each performing a specific function. Within the cell's nucleus (the center part of a cell that regulates its chemical functions) are pairs of chromosomes. These threadlike structures are made up of a single molecule of DNA (deoxyribonucleic acid), which carries the blueprint of life in the form of codes, or genes, that determine inherited characteristics.

A DNA molecule looks like two ladders with one of the sides taken off both and then twisted around each other. The rungs of these ladders meet (resulting in a spiral staircase-like structure) and are called base pairs. Base pairs are made up of nitrogen molecules and arranged in specific sequences. Millions of these base pairs, or sequences, can make up a single gene, specifically defined as a segment of the chromosome and DNA that contains certain hereditary information. The gene, or combination of genes formed by these base pairs ultimately direct an organism's growth and characteristics through the production of certain chemicals, primarily proteins, which carry out most of the body's chemical functions and biological reactions.

Scientists have long known that alterations in genes present within cells can cause inherited diseases like cystic fibrosis, sickle-cell anemia, and hemophilia. Similarly, errors in the total number of chromosomes can cause conditions such as Down syndrome or Turner's syndrome. As the study of genetics advanced, however, scientists learned that an altered genetic sequence also can make people more susceptible to diseases, like atherosclerosis, cancer, and even schizophrenia. These diseases have a genetic component, but also are influenced by environmental factors (like diet and lifestyle). The objective of gene therapy is to treat diseases by introducing functional genes into the body to alter the cells involved in the disease process by either replacing missing genes or providing copies of functioning genes to replace nonfunctioning ones. The inserted genes can be naturally-occurring genes that produce the desired effect or may be genetically engineered (or altered) genes.

Scientists have known how to manipulate a gene's structure in the laboratory since the early 1970s through a process called gene splicing. The process involves removing a fragment of DNA containing the specific genetic sequence desired, then inserting it into the DNA of another gene. The resultant product is called recombinant DNA and the process is genetic engineering.

There are basically two types of gene therapy. Germ-line gene therapy introduces genes into reproductive cells (sperm and eggs) or someday possibly into embryos in hopes of correcting genetic abnormalities that could be passed on to future generations. Most of the current work in applying gene therapy, however, has been in the realm of somatic gene therapy. In this type of gene therapy, therapeutic genes are inserted into tissue or cells to produce a naturally occurring protein or substance that is lacking or not functioning correctly in an individual patient.

BIOTECHNOLOGY AND ENVIRONMENTAL BIOSAFETY

BIOTECHNOLOGY AND ENVIRONMENTAL BIOSAFETY

Genetical modification of Agricultural Seeds- cotton, soya, maize, potato, rice and trees in the forest.

Prologue

The all encompassing big macabre issue discussed world wide today is the invasion of the good science, ‘biotechnology’ to virtually every nook and corner of the biosphere and practically turned to the bad science, ‘thanotechnology’ for every living element of concern and speeding up the rate to total annihilation of the biosphere.It all began with a little known episode in 1980, that is the US Supreme Court decision in the case, Diamond vrs. Chakrabarty, where the highest US court decided that biological life was legally patentable.

History

Anand Mohan Chakrabraty a microbiologist and employee of General Electric Company (GE) developed a type of bacteria that could ingest oil from oil spills. GE rushed for a patent in 1971 which was turned down as life forms were not patentable. GE sued and won. In 1985 the US Patent and Trademark Office (PTO) ruled that the Chakrabraty ruling could be further extended to all plants, seeds and plant tissues or to the entire plant kingdom.

US company W.R. Grace was granted 50 US patents on the Indian Neem tree which even included patenting indigenous knowledge of medicinal use of the Neem products (since been leveled ‘biopiracy’). In 1988 PTO issued patent on animal to Harvard Professors, Philip Lader and Timothy A. Stewart who had created a transgenic mouse having genes of the chicken and human being. In 1991, PTO granted patent to human stem cells and later to human genes. Biocyte was awarded European patent on all umbilical cord cells from foetuses and new born babies even without the permission of the ‘donors’. European Patents Office (EPO) received applications from Baylor University for the patenting of women who had been genetically altered to produce GE proteins in their mammary glands.

Baylor University essentially sought monopoly rights over the use of human mammary glands to manufacture pharmaceuticals. Attempts also were made to patent blood cells of indigenous people of Panama, the Solomon Islands and Papua New Guinea. Within a decade the ‘Chakrabarty ruling’ of the US Supreme Court revolutionised the research and developments in biotechnology involving microbes to human beings which led it to be branded as bad science, “thanotechnology” in the following decade and hated world wide. biotech companies engaged in biotech pharmaceuticals quickly moved to agriculture, obtained patents on seeds, buying up small seed companies, destroying their seed stocks and replacing the same with GE seeds. In the last decade several companies have gained monopoly control over such seeds world wide as soy, corn and cotton ( used in processed foods via cotton seed oil). As a result, nearly 2/3 rd. of such processed foods showed some GM ingredient in them.

However, even without any labelings, the concerned US consumers were aware of such pervasive food products of biotech companies. Immediately the companies knew that aware citizen kept away from GM foods and they organized to convince the regulators not to require such labelings. Somewhat shockingly the bureaucratic risk evaluators in the US turned a blind eye towards the ill motives of the bio-tech companies.

The point of concern

All genetical modifications are based on recombinant DNA technology. The present society is faced with unprecedented problems not only in the history of science, but of all life on earth. The GE technology enables the profit oriented biotech companies the capacity to redesign the living organisms, the products of three billion years of evolution. In the words of Dr. George Wald, Nobel Laureate in Medicine (1967), Higgins Professor of Biology at the Harvard University, “potentially it could breed new animal and plant diseases, new sources of cancer and novel epidemics”.

On Record

In 1989, dozens of Americans died and over several thousands were afflicted and impaired owing to the ingestion of a genetically altered version of food supplement L – tryptophan. A settlement of $ 2 billion was paid by Showa Denko, Japan’s 3rd. largest chemical company (Mayeno and Gleich, 1994)

In 1996, pioneer Hi-Bred spliced Brazil nut genes into soy beans. Some individuals are so allergic to this nut that they go into apoplectic shock which can cause death. Animal tests confirmed the peril and the product was soon removed from the market before any fatalities occurred. In the words of Marion Nestle, HOD Nutrition, New York University, “the next case could be less than ideal and public less fortunate.”

In 1994 US Food and Drug Administration approved Monsanto's r-BGH, a GE growth hormone, for injecting the dairy cows to enhance their milk yield in spite of experts warning that the resultant increase of IGF-1, a potent chemical hormone, linked to 400 – 500 % higher risks of human breast, prostrate and colon cancer. According to Dr. Samuel Epstein of University of Chicago, “ it induces the malignant transformation of human breast epithelial cells.” Studies on Rats confirmed the suspicion and showed damage to internal organs with r-BGH ingestion. Even FDA’s own tests showed a spleen mass increase by 46%, a state that is a prelude to ‘leukemia’. The argument that the substance get damaged by pasteurization was nullified by 2 of Monsanto’s own scientists, Ted Elasser and Brian Mc Bride who found only 19% of the hormone get destroyed after 30 minutes of boiling (pasteurization takes only 30 seconds). Inspite of Canada, EU, Australia, New Zealand and even the UN’s Codex Alimentarius refusing to endorse the GE hormone, the same is freely marketed in the US by Monsanto. It was found out that 2 US bureaucrats namely, Margaret Miller and Micheal Taylor in the US FDA who helped Monsanto’s r-BGH pass the risk factor barrier were in fact earlier Monsanto employees.

Several other GM products approved by US FDA involve herbicides that are commonly known as ‘carcinogenic’, viz – ‘bromoxiny’l used on Bt. Cotton and Monsanto's ‘round-up’ or Glufosinate used on GM soy, corn and canola. Sharyn Martin, a researcher, has opined that a number of auto- immune diseases are enhanced by foreign DNA fragments which come with G M food that are not fully digested in the human stomach and intestine. These DNA fragments absorbed into the blood stream mix with normal DNA through recombination and are, hence, unpredictable. Such DNA fragments have been found to be in GM soy and other GM products available in the market.

The fear factor

Professor Joe Cummins, Professor Emeritus of Genetics, University of Western Ontario said, ‘ Virus resistant crops are becoming the mainstay of biotech industries. These crops carry foreign virus genes which are genetically engineered to empower the plants to resist virus attacks. Most of the fruits, vegetables and baby food marketed in the US are of this category. Lab. experiments have shown that ‘the GE viral genes in food potentially give rise to new viruses – deadlier than the viruses that the crops are being protected from’, a fact that is quite alarming.
In 1986, it was reported that GE plants having TMV genes delayed the development of the disease and this report opened the flood gates to create resistance to a range of other viruses. But the fact is that viral coat protein production in GE crop does not block the virus entering into the plant cell rather the transgene is exposed to the nucleic acids of many viruses that are brought to the plant by insect vectors. A number of study results are there to show that plant viruses can acquire a variety of viral genes from GE plants through recombination.

For examples-
* Defective Red Color Mosaic Virus lacks the gene enabling it to move from cell to cell and hence is not infectious ,but recombined with a copy of that gene in GE Nicotina benthamiana plants, regenerated the infectious RCMVirus.
* GE Brassica napus and Nicotiana bigelovii containing “ gene- vi ”, a
translational activator from the Cauliflower Mosaic Virus (CaMV) which
recombined with the complementary part of a virus missing that gene, and
produced new infectious virus in all GE plants.
* N. benthamiana expressing a segment of the Cowpea Chlorotic Mottle Virus (CCMV) coat protein gene recombined more frequently with the defective virus missing that gene.
* N. benthamiana was transformed with 3 different constructs containing coat protein coding sequence of African Cassava Mosaic Virus (ACMV). The transformed plants were inoculated with a coat protein deletion mutant of ACMV that induces mild systemic symptoms in control plants. Several such inoculated plants of the transgenic lines developed severe systemic symptoms typical of ACMV confirming recombination had occurred between mutant viral DNA and the integrated construct DNA resulting in the production of recombined viral progeny with ‘ wild type ’ virulency.

The CaMV recombination, when and where ?

CaMV 35 s promoter gene, is the ubiquitous viral sequence in all the transgenic (GM) plants which are either already commercially released in the market or undergoing field trials. This gene is needed by all GM plant producers because it drives the production of gene messages from the genes inserted to provide herbicide tolerance, insect- pest resistance, antibiotic resistance and a range of other functions deemed to improve the commercial quality of the crop plant. In the absence of this ‘promoter gene’, the ‘inserted gene’ remains inactive, while in its presence the gene activity is maintained at a high level in all of the plant tissues irrespective of the changing environmental conditions which drastically affect the activity of ‘promoters’ native to the crop plant.

The 2 events which occurred in 1999 provoked Professor Cummins and other independent scientists to draw global attention to such alarming industrial scientific maladies that may have disastrous consequences. In fact Professor Cummins had in 1994 questioned the environmental safety of the release of CaMV 35 s promoter gene through the GM plants. Experimental evidences available indicated that the frequency of genetic recombination of CaMV 35 s promoter gene was much higher than those of other viruses. When recombinant CCMV was recovered from 3% of transgenic N. benthamiana containing CCMV sequences, recombinant CaMV was recovered from 36% of transgenic N. begelovii.

Event -1. Scientists of John Innes Research Institute published a paper showing that the CaMV 35 s promoter has a recombination ‘hot spot’ meaning it is prone to break and reassociate with other pieces of genetic material, may be of other viruses.

Event- 2. Dr. Arpad Pusztai, a senior scientist working in the UK govt. funded Rowett Institute in Scotland was sacked from his job because he revealed the results of feeding experiments suggesting that transgenic potatoes were unsafe. The lab. Rats fed with GM food showed increased lymphocytes in gut lining indicating damage to intestine from non specific viral infection.

Scientists Mae- Wan Ho and Angel Ryan published a paper in October 1999 issue of Journal of Microbial Ecology in Health and Disease warning that the CaMV 35 s promoter is interchangeable with promoters of other plant and animal virus and is promiscuous and functions efficiently in all plants, green algae, yeast and E. coli. Its recombination hot spot is flanked by multiple motifs and is similar to other recombination hot spots such as that of the Agrobacterium –T DNA vector, the other most commonly used gene, in making transgenic plants. They also claimed to have demonstrated in the lab. of the recombination between viral transgenes and infecting viruses.

In an article published in the online journal of European Food Research and Technology (2006) authors ( Marit R. Myhre, et. al. ) claimed to have constructed expression vectors with CaMV 35 s promoter inserted in front of 2 ‘reporter genes’ encoding firefly luciferase and green fluorescent protein (GFP), respectively and performed transient transfection experiments in the human enterocyte – like cell line, Caco - 2 and found that the CaMV 35 s promoter genes drive the expressions of both the ‘reporter genes’ to significant levels.

A Major development into the cause of Brain Cancer in children

A Major development into the cause of Brain Cancer in children

A recent breakthrough from a study on paediatric brain cancer, may be the key to finding a cure, or at least much more effective treatment. The study, spearheaded by the Research Institute of the McGill University Health revealed a significant genetic difference between this type of cancer and the adult equivalent (Jeremy Schwartzentruber, 2012). Brain cancer is one of the deadliest of cancers in children, and the most common form of brain cancer, GBM multiforme has an average survival of only 12-17 months even with aggressive treatment. 

 As you may already know, cancer is a disease, which stems from damaged DNA, leading to uncontrolled cell division, and then tumours. Tumours, however, are not always cancerous, and are only malignant if they “invade nearby tissues and spread to other parts of the body” and may return even after being removed through surgical methods. (National Institutes of Health, 2012). Brain cancer is particularly life threatening as it is located in an essential organ of the body, which has limited space. The tumour in the brain may increase the intracranial pressure, which leads to headaches, vomiting, comas, and in children; large bulges in the fontanelles (soft spots which allow the skull flexibility to fit through the birth canal). Other symptoms of brain tumours include many neural dysfunctions ranging from impaired senses to changes in personality to epileptic seizures, which sadly can be explained by many other diseases, and brain cancer can be overlooked. (Charles Patrick Davis, 2012)

 This study sequenced the exomes of 48 children who had GBM and found two genetic mutations which accounted for up to 40% of the GBM in the sample (Science Daily, 2012). An exome is a specific area of the entire genome which are important the creation of particular types of proteins. This method is more efficient, as there are over 180,000 exons in the entire genome, and the “relevant” exons can be sequenced much faster and can detect variations or mutations much more successfully (Sarah B. Ng, 2009).


 Figure 1 MRI of a Glioblastoma multiforme (Eric M. Thompson, 2011)
 The two genetic mutations were:
1.     “Somatic mutations in the H3.3-ATRX-DAXX chromatin remodelling pathway in 44% of the tumours” (Jeremy Schwartzentruber, 2012)
2.     “Recurrent mutations in H3F3A, which lead to amino acid substitutions in critical parts of the histone tail in 31% of tumours” (Jeremy Schwartzentruber, 2012)

 According to Dr Jabado of the MUHC, it was not known why children and adolescent GBM patients did not respond to treatments as well as adult patients. The commonplace treatments of chemotherapy and radiotherapy had inexplicably been resisted by tumours in children, which were revealed by this study to be caused by the mutations preventing the treatments to properly target and differentiate cancerous cells from healthy cells. He continued to say that this results “(are) significant here … (as) the first time in humans we have identified a mutation in one of the most important genes that regulates and protects our genetic information. This is the irrefutable proof that our genome, if modified, can lead to cancer and probably other diseases.” (Science Daily, 2012)

This genetic mutation has been detected in other forms of cancer, and the researchers from MUHC are hopeful that this breakthrough will lead to new treatments for cancer in specific patients with these mutations (Hazell, 2012). Continued developments such as these will lead to the future of patient care, which will utilise personalised genome mapping and treatment plans based on the individual.

Genetics in Cancer

Genetics in Cancer

Hello, everyone. Today, I shall discuss the topic of cancer or, more accurately, a recent advance in genetics that should assist us greatly in the fight against cancer. Cancer currently afflicts 112,300 Australians, and causes 39,000 deaths every year (Australian Institute of Health and Welfare 2008). You can see that this is quite an intolerably large figure. Luckily, scientists are becoming able to identify the specific genetic mutations that lead to individual malignant neoplasms (that’s just the smart-people name for cancerous tumours). This innovation lets us give more effective treatment, and undergo greater in-depth analysis of the origins of a cancer.


The University of Colorado

This technique is still in the early stages of development, so scientists are not even close to identifying all of the genetic mutations that cause all types of cancer. However, researchers at the University of Colorado Cancer Centre performed a clinical trial in 2010 in which they did actually manage to link genetic anomalies to cancer. In this case, they studied a particular rearrangement of genes inside the cancer cells of thirteen different lung cancer patients. The study involved testing a drug designed to target this ‘gene rearrangement’ (Camidge 2010).

Diagram of human lungs containing a tumour

These researches managed to show that the identification of genetic mutations in cancer cells allows cancer to be treated very effectively. To see just how effective it is, you can look at the results of the trial for one of its patients, 60-year-old Ellen Pulhamus. Before the study, she had five malignant tumours, which shrunk by 62 percent after just six weeks! In addition to that, another round of treatment brought down their size by a further 50 percent! (Brown 2010) Results as fantastic as these mean that oncologists should soon be able to move on from prescribing drugs that will only work for about one in ten cancer patients, and charge forward to the stage where they can determine exactly which patients will benefit from which treatments, by looking at the genes of their tumours (Brown 2010).


Tumours in a lung


Another goal of the researchers in this field is to try to use gene identification to trace cancer cell mutation back to its origins. This could allow the primary prevention of some cancers by exposing the kinds of lifestyles and environmental conditions that lead to them (Brown 2010). It may even provide current cancer patients with some peace of mind, in that they could find out the reason or reasons behind them being so sick.




Cancer is a tragedy that most of us will have to experience at some point in our lives, whether it be through having to endure it ourselves or witness it in someone close to us. The work done by researchers like those at the University of Colorado Cancer Centre will allow us to extend, or even save, a considerable number of lives, from within our species and perhaps outside it. With cancer being the prevalent calamity that it is, such an achievement will have far-reaching positive consequences for our entire race.

Alcoholism - Is it a Genetic Mutation?

Alcoholism - Is it a Genetic Mutation?


Alcohol dependence, also known as alcoholism, is considered medically as a disease. Its symptoms, as listed by the American Association for Clinical Chemistry (2010), include increased tolerance, cravings, loss of control and physical dependence. For decades, sufferers of the disease have not only experienced its harsh physical and psychological effects, but also discrimination and stereotypes created by society. In recent years, however, scientific research has revealed that the likelihood of developing alcoholism is increased by the possession of variations in certain genes (Arbor 2011). When variation occurs in two specific genes, unc-79 and GABRA2, it is thought that it influences alcohol sensitivity (O’brien 2010) and impulsive behaviours (Arbor 2011).

 Gene mutations are permanent alterations to sequences of DNA sections of chromosomes (U.S. National Library of Medicine 2012). When mutations occur in genes, it can affect the cell or organism’s ability to function normal, therefore promoting alcoholism in humans.

The gene unc-79 in mice, as well as the human version of the gene, is a poorly understood gene thought to interact with a neuron called NALCN (O’Brien 2010). In studies with mice, the mice that possessed mutated unc-79 genes voluntarily chose alcohol over water when offered the two. The mutant mice also were highly more sensitive to the alcohol. When injected with pure ethanol, the mice blacked out for much longer than the non-mutant mice. These observations in mice are thought to arise from the unc-79 gene mutation, dubbed as Lightweight, altering the neuronal responses to alcohol governed by NALCN (O’Brien 2010).



The GABRA2 gene is responsible for the functioning of receptors in part of the mammalian brain called the insula (Arbor 2011). In a recent study, those with the variant GABRA2 gene demonstrated higher levels of impulsiveness when under distress, with high activation in the insula. This links to the idea humans, particularly females, turn to alcohol to relieve distress and anxiety (Arbor 2011).

Both unc-79 and GABRA2 gene variants are just some of the genes that contribute to the symptoms of alcoholism, but do not directly cause it. However, as alcoholics, their families and researchers attempt to discover its medical foundations, the discoveries of mutations in genes as alcoholism contributors is extremely significant for prevention, treatment and understanding of alcohol dependence.