Biochemistry

1) Set-up the following Pre-Hybridisation solution in a Coplin Jar and incubate at65°C during the labeling incubation period to equilibrate. 20X SSC 8.75 ml 20% SDS 0.25 ml BSA (100 mg/ml) 5.0 ml H2O to 50.0 ml

2) Label control and test genomic DNA as follows:- CONTROL TEST Genomic DNA ˜ 2 mg ˜ 2 mg Random Hexamers (3 mg/ml) 1 ml 1 ml H2O to 41.5 ml to 41.5 ml Heat at 95ºC for 5 minutes. Snap cool on ice and briefly centrifuge. 10X buffer 5 ml 5 ml dNTP's (5mM each dATP, dGTP & dTTP, 2mM dCTP) 1 ml 1 ml Cy-labelled dCTP 1.5 ml (Cy3) 1.5 ml (Cy5) Klenow fragment (10U/ml) 1 ml 1 ml Incubate at 37°C for 90 minutes.

3) Incubate the microarray slide(s) in the Pre-Hybridisation solution for 20 minutes at65°C, beginning just before the end of the labelling reactions incubation time at37°C.

4) Combine the control and test reactions and purify using the Qiagen MinElute PCR Purification kit, using a two step wash stage using 500 ml then 250 ml volumes of Buffer PE and eluting the labeled cDNA from the MinElute column with 14 ml H2O. The columns retain approximately 1 ml, so the final eluted volume will be 13 ml.

5) Rinse the pre-hybridised microarray slides in H2O for 1 minute, then in isopropanol for 1 minute. Spin at 1500 rpm for 5 minutes to dry slides. Keep in covered slide box. 1 NICK DORRELL - LAST UPDATE FEBRUARY 2004

6) Prepare the Hybridisation solution as follows: - Sample 13 ml H2O 26 ml 20X SSC 12 ml 2% SDS 9 ml Heat at 95ºC for 2 minutes. Allow to cool slowly at room temperature and centrifuge for 30 seconds. Add 2 x 20 ml H2O to the corners of the hybridisation chamber. Place a slide into the chamber. Place a LifterSlip™ glass coverslip (22 mm x 25 mm) over the array section on the slide using tweezers. Pipette the Hybridisation solution onto the slide at the top of the coverslip. Seal the chamber and incubate in a water bath at 65°C overnight.

7) Prepare Wash solutions as follows: - Wash A (1X SSC 0.5% SDS) Wash B (0.06X SSC) 20X SSC 20 ml 2.4 ml 20% SDS 1 ml H2O to 400 ml to 800 ml Incubate Wash A solution at 65ºC overnight. Dispense 400 ml volumes into three glass slide washing dishes. Remove slide(s) from the hybridisation chambers and gently remove coverslip(s) by rinsing in Wash A. Place slide(s) in a slide rack and rinse with agitation for 5 minutes. Transfer slide(s) to a clean slide rack and rinse with agitation in Wash B(i) for 2 minutes, then in Wash B (ii) for a further 2 minutes. Spin at 1500 rpm for 5 minutes to dry slide(s).

8) Scan slide(s) using Affymetrix 418 scanner and analyse data

（NICK DORRELL - LAST UPDATE FEBRUARY 2004）

Thursday, June 30, 2011

Cloning Fact Sheet: questions and answers (2)

What animals have been cloned?

Scientists have been cloning animals for many years. In 1952, the first animal, a tadpole, was cloned. Before the creation of Dolly, the first mammal cloned from the cell of an adult animal, clones were created from embryonic cells. Since Dolly, researchers have cloned a number of large and small animals including sheep, goats, cows, mice, pigs, cats, rabbits, and a gaur. All these clones were created using nuclear transfer technology.

Hundreds of cloned animals exist today, but the number of different species is limited. Attempts at cloning certain species have been unsuccessful. Some species may be more resistant to somatic cell nuclear transfer than others. The process of stripping the nucleus from an egg cell and replacing it with the nucleus of a donor cell is a traumatic one, and improvements in cloning technologies may be needed before many species can be cloned successfully.

Can organs be cloned for use in transplants?

Scientists hope that one day therapeutic cloning can be used to generate tissues and organs for transplants. To do this, DNA would be extracted from the person in need of a transplant and inserted into an enucleated egg. After the egg containing the patient's DNA starts to divide, embryonic stem cells that can be transformed into any type of tissue would be harvested. The stem cells would be used to generate an organ or tissue that is a genetic match to the recipient. In theory, the cloned organ could then be transplanted into the patient without the risk of tissue rejection. If organs could be generated from cloned human embryos, the need for organ donation could be significantly reduced.

Many challenges must be overcome before "cloned organ" transplants become reality. More effective technologies for creating human embryos, harvesting stem cells, and producing organs from stem cells would have to be developed. In 2001, scientists with the biotechnology company Advanced Cell Technology (ACT) reported that they had cloned the first human embryos; however, the only embryo to survive the cloning process stopped developing after dividing into six cells. In February 2002, scientists with the same biotech company reported that they had successfully transplanted kidney-like organs into cows. The team of researchers created a cloned cow embryo by removing the DNA from an egg cell and then injecting the DNA from the skin cell of the donor cow's ear. Since little is known about manipulating embryonic stem cells from cows, the scientists let the cloned embryos develop into fetuses. The scientists then harvested fetal tissue from the clones and transplanted it into the donor cow. In the three months of observation following the transplant, no sign of immune rejection was observed in the transplant recipient.

Another potential application of cloning to organ transplants is the creation of genetically modified pigs from which organs suitable for human transplants could be harvested . The transplant of organs and tissues from animals to humans is called xenotransplantation.

Why pigs? Primates would be a closer match genetically to humans, but they are more difficult to clone and have a much lower rate of reproduction. Of the animal species that have been cloned successfully, pig tissues and organs are more similar to those of humans. To create a "knock-out" pig, scientists must inactivate the genes that cause the human immune system to reject an implanted pig organ. The genes are knocked out in individual cells, which are then used to create clones from which organs can be harvested. In 2002, a British biotechnology company reported that it was the first to produce "double knock-out" pigs that have been genetically engineered to lack both copies of a gene involved in transplant rejection. More research is needed to study the transplantation of organs from "knock-out" pigs to other animals.

What are the risks of cloning?

Reproductive cloning is expensive and highly inefficient. More than 90% of cloning attempts fail to produce viable offspring. More than 100 nuclear transfer procedures could be required to produce one viable clone. In addition to low success rates, cloned animals tend to have more compromised immune function and higher rates of infection, tumor growth, and other disorders. Japanese studies have shown that cloned mice live in poor health and die early. About a third of the cloned calves born alive have died young, and many of them were abnormally large. Many cloned animals have not lived long enough to generate good data about how clones age. Appearing healthy at a young age unfortunately is not a good indicator of long-term survival. Clones have been known to die mysteriously. For example, Australia's first cloned sheep appeared healthy and energetic on the day she died, and the results from her autopsy failed to determine a cause of death.

In 2002, researchers at the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts, reported that the genomes of cloned mice are compromised. In analyzing more than 10,000 liver and placenta cells of cloned mice, they discovered that about 4% of genes function abnormally. The abnormalities do not arise from mutations in the genes but from changes in the normal activation or expression of certain genes.

Problems also may result from programming errors in the genetic material from a donor cell. When an embryo is created from the union of a sperm and an egg, the embryo receives copies of most genes from both parents. A process called "imprinting" chemically marks the DNA from the mother and father so that only one copy of a gene (either the maternal or paternal gene) is turned on. Defects in the genetic imprint of DNA from a single donor cell may lead to some of the developmental abnormalities of cloned embryos.

Should humans be cloned?

Physicians from the American Medical Association and scientists with the American Association for the Advancement of Science have issued formal public statements advising against human reproductive cloning. The U.S. Congress has considered the passage of legislation that could ban human cloning.

Due to the inefficiency of animal cloning (only about 1 or 2 viable offspring for every 100 experiments) and the lack of understanding about reproductive cloning, many scientists and physicians strongly believe that it would be unethical to attempt to clone humans. Not only do most attempts to clone mammals fail, about 30% of clones born alive are affected with "large-offspring syndrome" and other debilitating conditions. Several cloned animals have died prematurely from infections and other complications. The same problems would be expected in human cloning. In addition, scientists do not know how cloning could impact mental development. While factors such as intellect and mood may not be as important for a cow or a mouse, they are crucial for the development of healthy humans. With so many unknowns concerning reproductive cloning, the attempt to clone humans at this time is considered potentially dangerous and ethically irresponsible.

(Source: www.ornl.gov)

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Biochemistry

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Explanation of Biology Phrases

Biology Textbook online

Sunday, September 18, 2016

DNA microarray method

Thursday, June 30, 2011

Cloning Fact Sheet: questions and answers (2)

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