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BioTechnology Resources
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BioTechnology Resources

AgBiotechNet - Abstracts Database
http://www.agbiotechnet.com/

Applied Biochemistry and Biotechnology
http://www.springer.com/humana+press/biotechnology/journal/12010

Baylor College of Medicine Genome Center
http://gc.bcm.tmc.edu:8088/

BIO - Biotechnology Industry Organization
http://www.bio.org/

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http://www.bio.com/

BioABACUS - Searchable Database of Abbreviations and Acronyms in Biotechnology
http://darwin.nmsu.edu/~molbio/bioABACUShome.htm

Biobased USA - Gateway to the Biobased World
http://www.biobased.us/

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Biotechnology Australia
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Biotechnology Information Directory
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BioTrack
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Conversations About Plant Biotechnology
http://www.monsanto.com/biotech-gmo/index.htm

Council For Biotechnology Information
http://www.whybiotech.com/

eBioinfogen.com: A Biological Web Resources Navigator
http://www.ebioinfogen.com/

Electronic Journal of Biotechnology
http://www.ejbiotechnology.info/

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http://www.genscript.com/

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http://www.informatik.uni-rostock.de/HUM-MOLGEN/hum-mol.html

International Journal of Agricultural and Biological Engineering (IJABE)
http://www.ijabe.org/index.php/ijabe

International Journal of Biotechnology (IJBT)
http://www.inderscience.com/ijbt

Journal of Biotechnology
http://www.sciencedirect.com/science/journal/01681656

Journal of Plant Biochemistry and Biotechnology
http://www.iospress.nl/html/09717811.php

Microbial Biotechnology
http://www.blackwellpublishing.com/mbt_enhanced/

NCBI Medline Searches of Biotechnology Subjects
http://atlas.nlm.nih.gov:5700/Entrez/index.html

NanoBioTechnology
http://www.springerlink.com/content/120565/

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https://www.nanohub.org/

National Agricultural Library - Research and Technology - Biotechnology
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Nest Group Molecular Biology WWW Resources
http://world.std.com/~nestgrp/molbiol.html

New Biotechnology
http://www.elsevier.com/wps/product/cws_home/713354

Open Source Biotechnology by Janet Hope
http://opensource.mit.edu/papers/hope.pdf

The Center for Integrated BioSystems at Utah State University
http://www.biosystems.usu.edu/

World Wide Web Virtual Library: Biotechnology
http://www.cato.com/interweb/cato/biotech/



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What factors have kept gene therapy from becoming an effective treatment for genetic disease?
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What factors have kept gene therapy from becoming an effective treatment for genetic disease?

* Short-lived nature of gene therapy - Before gene therapy can become a permanent cure for any condition, the therapeutic DNA introduced into target cells must remain functional and the cells containing the therapeutic DNA must be long-lived and stable. Problems with integrating therapeutic DNA into the genome and the rapidly dividing nature of many cells prevent gene therapy from achieving any long-term benefits. Patients will have to undergo multiple rounds of gene therapy.

* Immune response - Anytime a foreign object is introduced into human tissues, the immune system is designed to attack the invader. The risk of stimulating the immune system in a way that reduces gene therapy effectiveness is always a potential risk. Furthermore, the immune system's enhanced response to invaders it has seen before makes it difficult for gene therapy to be repeated in patients.

* Problems with viral vectors - Viruses, while the carrier of choice in most gene therapy studies, present a variety of potential problems to the patient --toxicity, immune and inflammatory responses, and gene control and targeting issues. In addition, there is always the fear that the viral vector, once inside the patient, may recover its ability to cause disease.

* Multigene disorders - Conditions or disorders that arise from mutations in a single gene are the best candidates for gene therapy. Unfortunately, some the most commonly occurring disorders, such as heart disease, high blood pressure, Alzheimer's disease, arthritis, and diabetes, are caused by the combined effects of variations in many genes. Multigene or multifactorial disorders such as these would be especially difficult to treat effectively using gene therapy. For more information on different types of genetic disease, see Genetic Disease Information.

Posted on: 2009/12/25 16:51
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What is the current status of gene therapy research?
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What is the current status of gene therapy research?

The Food and Drug Administration (FDA) has not yet approved any human gene therapy product for sale. Current gene therapy is experimental and has not proven very successful in clinical trials. Little progress has been made since the first gene therapy clinical trial began in 1990. In 1999, gene therapy suffered a major setback with the death of 18-year-old Jesse Gelsinger. Jesse was participating in a gene therapy trial for ornithine transcarboxylase deficiency (OTCD). He died from multiple organ failures 4 days after starting the treatment. His death is believed to have been triggered by a severe immune response to the adenovirus carrier.

Another major blow came in January 2003, when the FDA placed a temporary halt on all gene therapy trials using retroviral vectors in blood stem cells. FDA took this action after it learned that a second child treated in a French gene therapy trial had developed a leukemia-like condition. Both this child and another who had developed a similar condition in August 2002 had been successfully treated by gene therapy for X-linked severe combined immunodeficiency disease (X-SCID), also known as "bubble baby syndrome."

FDA's Biological Response Modifiers Advisory Committee (BRMAC) met at the end of February 2003 to discuss possible measures that could allow a number of retroviral gene therapy trials for treatment of life-threatening diseases to proceed with appropriate safeguards. In April of 2003 the FDA eased the ban on gene therapy trials using retroviral vectors in blood stem cells.

Posted on: 2009/12/18 16:08
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How does gene therapy work?
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How does gene therapy work?

In most gene therapy studies, a "normal" gene is inserted into the genome to replace an "abnormal," disease-causing gene. A carrier molecule called a vector must be used to deliver the therapeutic gene to the patient's target cells. Currently, the most common vector is a virus that has been genetically altered to carry normal human DNA. Viruses have evolved a way of encapsulating and delivering their genes to human cells in a pathogenic manner. Scientists have tried to take advantage of this capability and manipulate the virus genome to remove disease-causing genes and insert therapeutic genes.

Target cells such as the patient's liver or lung cells are infected with the viral vector. The vector then unloads its genetic material containing the therapeutic human gene into the target cell. The generation of a functional protein product from the therapeutic gene restores the target cell to a normal state. See a diagram depicting this process.

Some of the different types of viruses used as gene therapy vectors:

* Retroviruses - A class of viruses that can create double-stranded DNA copies of their RNA genomes. These copies of its genome can be integrated into the chromosomes of host cells. Human immunodeficiency virus (HIV) is a retrovirus.

* Adenoviruses - A class of viruses with double-stranded DNA genomes that cause respiratory, intestinal, and eye infections in humans. The virus that causes the common cold is an adenovirus.

* Adeno-associated viruses - A class of small, single-stranded DNA viruses that can insert their genetic material at a specific site on chromosome 19.

* Herpes simplex viruses - A class of double-stranded DNA viruses that infect a particular cell type, neurons. Herpes simplex virus type 1 is a common human pathogen that causes cold sores.

Besides virus-mediated gene-delivery systems, there are several nonviral options for gene delivery. The simplest method is the direct introduction of therapeutic DNA into target cells. This approach is limited in its application because it can be used only with certain tissues and requires large amounts of DNA.

Another nonviral approach involves the creation of an artificial lipid sphere with an aqueous core. This liposome, which carries the therapeutic DNA, is capable of passing the DNA through the target cell's membrane.

Therapeutic DNA also can get inside target cells by chemically linking the DNA to a molecule that will bind to special cell receptors. Once bound to these receptors, the therapeutic DNA constructs are engulfed by the cell membrane and passed into the interior of the target cell. This delivery system tends to be less effective than other options.

Researchers also are experimenting with introducing a 47th (artificial human) chromosome into target cells. This chromosome would exist autonomously alongside the standard 46 --not affecting their workings or causing any mutations. It would be a large vector capable of carrying substantial amounts of genetic code, and scientists anticipate that, because of its construction and autonomy, the body's immune systems would not attack it. A problem with this potential method is the difficulty in delivering such a large molecule to the nucleus of a target cell.

Posted on: 2009/12/11 16:16
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What is gene therapy?
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What is gene therapy?


Genes, which are carried on chromosomes, are the basic physical and functional units of heredity. Genes are specific sequences of bases that encode instructions on how to make proteins. Although genes get a lot of attention, it’s the proteins that perform most life functions and even make up the majority of cellular structures. When genes are altered so that the encoded proteins are unable to carry out their normal functions, genetic disorders can result.

Gene therapy is a technique for correcting defective genes responsible for disease development. Researchers may use one of several approaches for correcting faulty genes:

* A normal gene may be inserted into a nonspecific location within the genome to replace a nonfunctional gene. This approach is most common.

* An abnormal gene could be swapped for a normal gene through homologous recombination.

* The abnormal gene could be repaired through selective reverse mutation, which returns the gene to its normal function.

* The regulation (the degree to which a gene is turned on or off) of a particular gene could be altered.

Posted on: 2009/12/4 18:55
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What is a transgenic organism?
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What is a transgenic organism?



1. Of, relating to, or being an organism whose genome has been altered by the transfer of a gene or genes from another species or breed: transgenic mice; transgenic plants.
2. Of or relating to the study of transgenic organisms: transgenic research.

Posted on: 2009/11/27 15:26
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What is a recombinant DNA organism?
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What is a recombinant DNA organism?

Recombinant Antibody
The term recombinant and especially recombinant DNA regards to an artificial methods of producing DNA (synthetic DNA and proteins).

The manufacturing technique make use of bacterias, these bacterias are genetically modified in such a way that a specific DNA segment (gene) is artificially combined with their original DNA. After this insertion of DNA segment. The bacterias are nourished and kept in ideal conditions for reproduction and after a relative short period of time, after the reproduction, these specific segment of DNA is extracted out of the original DNA bacterias.

In short a segment of DNA is recombined (recombinant) with the original DNA of the bacteria, these genetically modified bacterias are rapidly reproduce and by that reproduce the DNA segment that was recombined with the original genome.

Antibodies are protein molecules produced by our immune system, the shape of an antibody is similar to a Y shape. The role of the antibodies to keep our health is crucial, their task is to recognize and attack foreign bacterias and viruses in our body.

There are many types of antibodies, each type can recognize unique antigen, the antibody Y tips has a unique molecular structure (keys) that combines with the targeted antigen. This attachment of many antibodies to a foreign objects (bacteria or virus) ultimately brings to its destruction.

Using recombinant antibody has significant advantages compared with the conventional antibody and there for its use becoming more popular now days. The fact that no animals are needed in the manufacturing procedure of the recombinant antibodies, in addition, the manufacturing time is relatively short compared with the conventional method. Moreover, the quality of the final product is higher that these of the non recombinant method.

Posted on: 2009/11/20 14:13
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What is cloning? And how did recombinant DNA make cloning possible?
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What is cloning? And how did recombinant DNA make cloning possible?

Recombinant DNA

Recombinant DNA technology emerged as a response to the need for specific DNA segments in amounts sufficient for biochemical analysis. The method entails clipping the desired segment out of the surrounding DNA and copying it millions of times. The success of recombinant DNA technology, by which microbial cells can be engineered to produce foreign proteins, relies on the faithful reading of the corresponding genes by bacterial cell machinery, and has fueled most of the recent advances in modern molecular biology. During the last twenty years, studies of cloned DNA sequences have given us a detailed knowledge of gene structure and organization, and have provided clues to the regulatory pathways by which the cell controls gene expression in the multiple cell types comprising the basic vertebrate body plan. Genetic engineering, by which an organism can be modified to include new genes designed with desired characteristics, is now routine practice in basic research laboratories. It has provided the means to produce large amounts of highly purified normal and mutant proteins for detailed analysis of their function in the organism.

Recent advances in this technology have also changed the course of medical research. Exciting new approaches are being developed to exploit the enormous potential of recombinant DNA research in the analysis of genetic disorders. The new ability to manipulate human genetic material has opened radically new avenues for diagnosis and treatment, and has far-reaching consequences for the future of medicine. Yet the basic principles of recombinant DNA, like the structure of DNA itself, are surprisingly simple.

Cloning DNA

Molecular cloning provides a means to exploit the rapid growth of bacterial cells for producing large amounts of identical DNA fragments, which alone have no capacity to reproduce themselves. The fragment of DNA to be amplified is first inserted into a cloning vector. The most popular vectors currently in use consist of either small circular DNA molecules (plasmids) or bacterial viruses (phage). The vectors contain genetic information that allows bacterial DNA replication machinery to copy them. After insertion of the foreign DNA, the plasmid or phage vector is re-introduced into a bacterial cell. The growing bacterial culture replicates the foreign DNA, along with the vector, in hundreds of copies per cell. This process yields multiple, identical clones of the original recombinant molecule. It is easy to harvest vectors from the bacterial culture, and release the amplified foreign DNA fragments with the same restriction enzyme used to insert the original DNA fragment into the vector (Figure 4, top). The power of molecular cloning is remarkable: a liter of bacterial cells engineered to amplify a single fragment of clones human DNA can produce about ten times the amount of a specific DNA segment than could be purified from the total cellular content of the entire human body.

For analysis of long stretches of DNA, eukaryotic vectors that can grow in yeast have been developed which can hold megabases of foreign DNA. These vectors mimic yeast chromosomal structure, so that they are replicated along with the native yeast chromosomes every time a yeast cell divides. Yeast Artifical Chromosomes, or YACs, are often the only way to clone extremely large genes including huge introns all in one continuous piece. YACs also provide a way to propagate DNA in a eukaryotic cell, where DNA modification, an important part of the eukaryotic genetic regulatory machinery, is more likely to be retained (more on this later). YACs are increasingly useful in the many Genome Projects underway, as we aim to understand the metastructure of chromosomes, where the placement and arrangement of genes within the "junk" DNA surrounding them may hold as yet undiscovered regulatory information for packaging and accessibility.

Amplification of Recombinant DNA

The DNA segment to be amplified is separated from surrounding genomic DNA by restriction enzyme cleavage, which often produces staggered or sticky ends. In the example illustrated here, the restriction enzyme EcoRI recognizes the palindromic sequence GAATTC, and cuts on each strand between G and A (the two strands of the genomic DNA are green and purple). The plasmid vector (brown) is prepared to accept the isolated genomic DNA fragment by cutting the circular plasmid DNA at a single site with the same restriction enzyme, generating sticky ends which are complementary to the sticky ends of the genomic DNA fragment. The cut genomic DNA and the linearized plasmid are mixed together in the presence of a ligase enzyme, which rejoins the bonds in the DNA backbone on each side of the plasmid-genomic DNA junction. This recombinant DNA molecule is then introduced into bacteria which are able to take up plasmid DNA, and then replicate the plasmid as the culture grows.

Posted on: 2009/11/13 13:38
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How was able to make a recombinant DNA?
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How was able to make a recombinant DNA?

Making Recombinant DNA

How does recombinant DNA technology work? The organism under study, which will be used to donate DNA for the analysis, is called the donor organism. The basic procedure is to extract and cut up DNA from a donor genome into fragments containing from one to several genes and allow these fragments to insert themselves individually into opened-up small autonomously replicating DNA molecules such as bacterial plasmids. These small circular molecules act as carriers, or vectors, for the DNA fragments. The vector molecules with their inserts are called recombinant DNA because they consist of novel combinations of DNA from the donor genome (which can be from any organism) with vector DNA from a completely different source (generally a bacterial plasmid or a virus). The recombinant DNA mixture is then used to transform bacterial cells, and it is common for single recombinant vector molecules to find their way into individual bacterial cells. Bacterial cells are plated and allowed to grow into colonies. An individual transformed cell with a single recombinant vector will divide into a colony with millions of cells, all carrying the same recombinant vector. Therefore an individual colony contains a very large population of identical DNA inserts, and this population is called a DNA clone. A great deal of the analysis of the cloned DNA fragment can be performed at the stage when it is in the bacterial host. Later, however, it is often desirable to reintroduce the cloned DNA back into cells of the original donor organism to carry out specific manipulations of genome structure and function. Hence the protocol is often as follows:

http://www.ncbi.nlm.nih.gov/books/bookres.fcgi/mga/ch10e1.gif


Inasmuch as the donor DNA was cut into many different fragments, most colonies will carry a different recombinant DNA (that is, a different cloned insert). Therefore, the next step is to find a way to select the clone with the insert containing the specific gene in which we are interested. When this clone has been obtained, the DNA is isolated in bulk and the cloned gene of interest can be subjected to a variety of analyses, which we shall consider later in the chapter. Notice that the cloning method works because individual recombinant DNA molecules enter individual bacterial host cells, and then these cells do the job of amplifying the single molecules into large populations of molecules that can be treated like chemical reagents. Figure 10-1 on the following page gives a general outline of the approach.

The term recombinant DNA must be distinguished from the natural DNA recombinants that result from crossing-over between homologous chromosomes in both eukaryotes and prokaryotes. Recombinant DNA in the sense being used in this chapter is an unnatural union of DNAs from nonhomologous sources, usually from different organisms. Some geneticists prefer the alternative name chimeric DNA, after the mythological Greek monster Chimera. Down through the ages, the Chimera has stood as the symbol of an impossible biological union, a combination of parts of different animals. Likewise, recombinant DNA is a DNA chimera and would be impossible without the experimental manipulation that we call recombinant DNA technology.
Isolating DNA

The first step in making recombinant DNA is to isolate donor and vector DNA. General protocols for DNA isolation were available many decades before the advent of recombinant DNA technology. With the use of such methods, the bulk of DNA extracted from the donor will be nuclear genomic DNA in eukaryotes or the main genomic DNA in prokaryotes; these types are generally the ones required for analysis. The procedure used for obtaining vector DNA depends on the nature of the vector. Bacterial plasmids are commonly used vectors, and these plasmids must be purified away from the bacterial genomic DNA. A protocol for extracting plasmid DNA by ultracentrifugation is summarized in Figure 10-2 on page 303. Plasmid DNA forms a distinct band after ultracentrifugation in a cesium chloride density gradient containing ethidium bromide. The plasmid band is collected by punching a hole in the plastic centrifuge tube. Another protocol relies on the observation that, at a specific alkaline pH, bacterial genomic DNA denatures but plasmids do not. Subsequent neutralization precipitates the genomic DNA, but plasmids stay in solution. Phages such as λ also can be used as vectors for cloning DNA in bacterial systems. Phage DNA is isolated from a pure suspension of phages recovered from a phage lysate.top link
Cutting DNA

The breakthrough that made recombinant DNA technology possible was the discovery and characterization of restriction enzymes. Restriction enzymes are produced by bacteria as a defense mechanism against phages. The enzymes act like scissors, cutting up the DNA of the phage and thereby inactivating it. Importantly, restriction enzymes do not cut randomly; rather, they cut at specific DNA target sequences, which is one of the key features that make them suitable for DNA manipulation. Any DNA molecule, from viruses to humans, contains restriction-enzyme target sites purely by chance and therefore may be cut into defined fragments of size suitable for cloning. Restriction sites are not relevant to the function of the organism, nor would they be cut in vivo, because most organisms do not have restriction enzymes.

Let's look at an example: the restriction enzyme EcoRI (from E. coli) recognizes the following sixnucleotide-pair sequence in the DNA of any organism:

more detail : http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mga.section.1549

Posted on: 2009/11/6 15:51
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Is There a 'Bad Driver' Gene?
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Is There a 'Bad Driver' Gene?


Is There a 'Bad Driver' Gene?
1 in 3 people have DNA that may make things tougher behind the wheel, researchers say

In a small study, researchers found that people with a gene variation performed 20 percent worse on simulated driving tests and did as poorly a few days later. Almost one in three Americans have the variation, the team said.

"These people make more errors from the get-go, and they forget more of what they learned after time away," said Dr. Steven Cramer, neurology associate professor at the University of California at Irvine and senior author of a study published recently in the journal Cerebral Cortex, in a statement.

The study authors say the gene variation lowers available levels of a protein that boosts memory by helping brain cells talk to one another and work properly.

Earlier research has suggested people with the variation engage smaller areas of the brain when they take on tasks.

"We wanted to study motor behavior, something more complex than finger-tapping," said Stephanie McHughen, a graduate student and lead author of the study in a statement. "Driving seemed like a good choice because it has a learning curve, and it's something most people know how to do."

Twenty-nine people took a driving test on a simulator, including seven with the gene variation. They had to learn to "drive" on a track that included tough-to-navigate curves and turns. They came back four days later to retake the test.

Those with the variant did worse and failed to remember as much the second time around as the others. "Behavior derives from dozens and dozens of neurophysiologic events, so it's somewhat surprising this exercise bore fruit," Cramer said.

But don't be alarmed if you think you have this gene variation -- it has it's good side. The researcher say the gene also slows mental decline for people with conditions such as Parkinson's disease, Huntington's disease or multiple sclerosis.

"It's as if nature is trying to determine the best approach," Cramer said. "If you want to learn a new skill or have had a stroke and need to regenerate brain cells, there's evidence that having the variant is not good. But if you've got a disease that affects cognitive function, there's evidence it can act in your favor. The variant brings a different balance between flexibility and stability."

Posted on: 2009/10/30 17:59
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