HIV Genome = Revealed!

Researchers from North Carolina, USA, have decoded the genome structure of the Human Immunodeficiency Virus (HIV), the virus that causes AIDS. The genome, which carries its information as RNA, is composed of two separate strands, of nearly 10,000 nucleotides each. On top of this, the intricate structures that these strands form are often difficult and painstaking to analyze. In fact, up until now they have only ever been partially modeled, and always in small regions. Now that this has changed, it could well represent a change in the ability of modern medicine to fight and possibility to control viruses as dangerous as HIV.

The RNA structure has been found to influence many important steps in the infectivity cycle of HIV. Such information can be used to help scientists understand how the human host is tricked into ignoring the presence of the virus, which can make early detection and medication possible. An understanding of exactly what we are dealing with can also lead to scientists modifying the sequence of the virus, and seeing what changes affect its growth. This can help to ascertain what segments of the genome are the most important to the virus, which can give us an indication of possible weaknesses.

These results will have considerable implications for the understanding of human viruses, and are expected to accelerate further research into the development of future antiviral drugs.

Lonsdale - 42060228

Reference:
http://www.sciencedaily.com/releases/2009/08/090805133015.htm

Wolf is Responsible for Our Short Legs

Have you ever wondered why dog breeds such as dachshunds and basset hounds have legs that are noticeably short and stubby? Recently, US and British researchers have investigated on this matter and found out that it was due to the mutation of a single gene. This mutation occurred in the early evolution of dogs and the mutated gene is a slightly altered copy of a gene called fibroblast growth factor 4, also known as FGF4. Short-legged dogs have this mutated gene as their second growth-related gene whereas most dogs only have one growth-related gene.

So, where does this retrogene of FGF4 came from? The researchers examined the genes and brought up a conclusion that it seems to be a copy of a wolf gene. This can be quite possible as some modern dog breeds diverged from wolves. This means that a physical trait of quite a few dog breeds were caused by one retrogene being inserted at some point within the evolution. Therefore, the researchers are looking forward to see these retrogenes playing larger role in evolution.

posted by: Anna Won-Kyung Jang (42042372)

Original Artical:
http://www.abc.net.au/science/articles/2009/07/17/2629078.htm?

DNA Sketch Artists

Have you ever wondered why detectives don’t use DNA to construct an image of what the suspect may look like, rather than just comparing DNA to a crime database? Well Christopher Phillips, a forensic geneticist at the University of Santiago de Compostela in Galicia, Spain, certainly has and for very good reason.

The idea certainly makes sense; by constructing a virtual image of a suspect it would be possible to compare the features of the person to a much larger array of people than just those who have committed a crime. For ex ample, in 2007 a judge ordered that DNA from a bombing in Spain be determined to be European or North African. The reason for this is that two groups were suspected of being behind the attacks: The Basque separatist group ETA and Islamic Militants. Members of the ETA would most likely be of European descent, whereas Islamic militants would almost certainly be of North African descent. By making the distinction of which ancestry the DNA from the bombing site was linked to detectives were able to hone in their search into more refined areas.

The current method of determining a suspect’s ancestry is through use of Y-chromosome and mitochondrial DNA; however this method becomes inaccurate when interbreeding between two different races occurs. However, Phillips’ team at the University of Santiago de Compostela have managed to discern that the DNA collected from a toothbrush of the bombing site in Spain was of North African ancestry by genotyping 34 single DNA letter differences in the chromosomes from the unidentified samples still connected to the bombing. This result was later confirmed when the DNA was later linked to Daoud Ouhnane, a suspect in the case and is still at large. Interestingly the findings were in conflict with that obtained from Y-chromosome and mitochondrial sequences.

Despite the excellent results, it is unlikely that this method of genetic profiling will become widely used for quite some time. There are fears that genetic profiling may be construed as prejudiced to certain ethnic groups. Until such fears can be abated in the general public genetic profiling will remain in the world of high profile cases such as the Madrid bombings. It is, however, an exciting prospect that we can hope to look forward to.

Posted by Alistair Lavers - 42048468

Original Article:

Newscientist Magazine, 'DNA mugshots' narrow search for Madrid bombers, http://www.newscientist.com/article/dn17630-dna-mugshots-narrow-search-for-madrid-bombers.html, 18^th August 2009

Hunting for Disease

With new DNA sequencing methods being constantly discovered and improved, studying the genetics of an individual has never been so quick and affordable. With these developments fast nearing the world at large, the scientific community is beginning to see new ways to utilise this technology. A common suggestion is to use this technology to identify the specific gene mutations, which cause genetic diseases; such as Sickle cell anemia or Cystic fibrosis. However, because of the complexity of the human genome, tracking down the specific mutation which is causing the disease could still be very difficult and costly.

A research team from the University of Washington has developed a cheap and fast way of tracking down disease causing genetic mutations. How? They compared the genetics of 4 people who were unrelated (ie. Having no family ties), in order to track down the genetic cause of Freeman-Sheldon Syndrome. They narrowed down their search to the 1% of the genome which codes for protein synthesis (exomes). After comparing their DNA, they discovered a mutation at a single gene: MYH3 which was the likely cause of the disease.

The identification of this disease causing mutation took the research team approximately 3 months to complete. They believe with newer and faster genome sequencing techniques, this process could take as little as a few weeks. Now all we need to discover is a cure...


Post by Robert Wu (42051217)

Article Link: http://www.medicalnewstoday.com/articles/161000.php

Viral-Mediated Gene Therapy - A Cure for Muscular Dystrophy?

Muscular dystrophy is a heterogeneous muscular degenerative disease characterised by weakening of the skeletal muscle, poor balance and in extreme, but common circumstances, the loss of a person’s ability to move. At present there is no known cure for this genetic disorder however recent research has given sufferers hope. Studies conducted by Odom et al, have shown that viral mediated gene therapy can halt the progression of muscular dystrophy, in particular the use of adeno-associated viruses have delivered encouraging results. The attractive feature of using adeno-associated viruses(AAV) is the small size of the virus. AAVs immediate very low immunogenicity, seemingly confined to the generation of neutralizing antibodies, while they cause no clearly-defined cytotoxic response. This feature, along with the ability to infect both dividing and non-dividing cells, presents their dominance as use in vectors for muscular dystrophy treatment.

There are however disadvantages to using AAV’s. Tests carried out by Odom et al, suggest some therapeutic genes that are used to treat muscular dystrophy, require the complete transcription onto the virus’s 4.8 kilobase genome. Currently due to their limited vector capacity, this cannot be done. The scientists are therefore researching ways of expanding the limited coding capacity of the AAV’s. One option suggested by the study is the idea of forming the inverted terminal repeats of the AAV’s to form head to tail concatamers, which would result in almost doubling the capacity of the vector. As advocated by Odom et al, more research is essential in order to overcome the disadvantages of using AAV’s in muscular dystrophy treatment, before they can be used clinically as a treatment.


Source of Article : http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1894910&blobtype=pdf&tool=pmcentrez

New Breed of GM Rice Combats Common Allergies

GM crops were first produced to combat food shortages caused by rising fuel prices and diversion of land to grow biofuel instead of food crops as well as droughts in Australia, one of the world's main producers of wheat. These genetically modified plants were more pest-resistant and offered higher yields than their natural counterparts. The introduction of these transgenic plants was expected to increase the overall yield per acre of farmed land.

A new batch of genetically modified rice developed by Japanese scientists to combat cedar pollen allergies is currently under development. Cedar pollen allergy is a common ailment which affects over 20 percent of the Japanese population. However, unlike the GM products introduced previously, this 'new generation' of GM food, such as the anti-allergy rice mentioned before carries a more direct effect on human health. Examples of these transgenic foods include vegetables and grains that produce higher levels of nutrients, such as vitamins and minerals. As groundbreaking as this may seem however, this anti-allergy rice still has to undergo more research and testing before finding its way into the global market.

Though the advantages of GM food are obvious, many in the general population are still sceptical as the long-term effects of consuming GM products are still unknown.

Posted by Jonathan Ting (42019767)
Original article: http://www.livescience.com/health/090627-gm-rice.html

Genes in Brain Disorder Diagnosis: What methods should researchers be using?

The brain is the most important organ, the centre for all human function; therefore it would make sense that it is so widely studied. However, whilst being the most important, it is also highly complex, which makes it quite complicated in biomedical research. There is very little understanding of the functions of the brain, especially the genesis of the high order brain functions, which are central to brain disorders such as self-awareness, perception, thought and mood. Some researchers are sceptical about the use of genetics in the diagnosis pathway; however there is increasing evidence that genes are involved. There have been numerous amounts of gene studies conducted in relation to the brain, including many different approaches, old and new. Recent reviews have provided conflicting arguments, as to which approaches are favourable. A study which has been successful in identifying the genes related to Mental Retardation has been the study of balanced translocations and other chromosomal abnormalities. While these studies may not significantly contribute to brain disorders, studies of rare copying number variants (smaller chromosomal abnormalities) have increased the understanding of disease mechanisms for schizophrenia, autism, epilepsy, as well as mental retardation.

From numerous studies, it appears that for one disorder, numerous loci are involved which further complicates the understanding of the mechanisms. Due to the lack of specific information, researchers rely on candidate gene approach. However, with genome wide association (GWA) technology, the reliance of the approach has been diminished. It is expected that in the next few years, with advancement in gene sequencing, a further depletion in candidate gene approach will arise. GWA studies that use a larger sample should provide a better alternative for the candidate gene approach. There are several difficulties in the diagnosis of brain disorders, but recent reviews suggest that they can certainly be overcome. No single approach can be used for all brain disorders therefore it is important to employ all genetic tools, old and new. While there are still many gaps in the understanding of the brain, even partial glimpses of functions can amount to major advances on current pathophysiology knowledge, which in turn, can facilitate a higher standard of patient care.

Article Link: http://www.springerlink.com/content/g1070h252t881164/?p=c4bd58053de245c28128ddc3d13c8e3e&pi=0

Suggested Readings:
Craig I, Halton K (2009) Genetics of human aggressive behaviour.
Human Genet. doi:10.1007/s00439-009-0695-9

Franke B, Neale BM, Faraone SV (2009) Genome-wide association
studies in ADHD. Human Genet. doi:10.1007/s00439-009-0663-4

The genetics of addiction

Have you ever wondered whether the genes responsible for drug addiction, are the same or similar to those for an addiction to alcohol or other substances? Current research being undertaken could lead to a more effective treatments for various addictions. Take this link http://www.sciencedaily.com/releases/2009/03/090310142912.htm to read about progress being made in discovering the functional mechanisms of the genes thought to be involved in various addictions.

“It Could Kill You, But It Might Just Cure You.”

This is one little critter that you do not want to come near, as its sting could potentially put you in a dangerous situation, be it heart or lung failure. Like its “brother”, the vicious viper, or its “sister”, a pretty looking cone snail, the scorpion shares a similar characteristic among the two predators and that is they use their deadly toxin to capture and immobilize their prey.

Being lethal creatures, the toxins secreted by these organisms may contain biologically active compounds that could be of beneficial use for humans. The process of genetic engineering and the culturing of bacterial cells could be the key thing in extracting the active compounds and using them to create new drugs. These drugs could have the potential to be used to cure cancers, relieve pain or treat diseases.

One study has shown that the venom from a scorpion can have anti-cancerous effects. Once injected into a cancer-infected human brain, the venom destroys the glioma cells responsible for the brain cancer and leaves behind the surrounding healthy cells. Although a scorpion signifies a possible threat to humans, the use of knowledge and science can reverse that to something that will save many lives.

Another study has revealed that the conotoxin of cone snails has the potential to act as a painkiller. It is believed that the painkiller can be as much as 10,000 times stronger than many current anaesthetics and is not addictive compared to some of those currently in use. This painkiller could replace morphine, or other anaesthetics used in hospitals, in the years to come.

Innovative medical and biological research still continues today with anticipation to treat many disorders and diseases. However, with the continuing changes in the environment and the capabilities organisms have in creating new and unknown types of cancers or viruses, new cures need to be discovered in order to become immune to these bugs. Humans need to be “aware” of their surroundings as many species of organisms, whether abundant, endangered or still to be identified, could be lost through human activities, and the potential remedies and drugs that could have been discovered would be destroyed.

By Yungfu Phuong 42006879 (Thursday AM)

Source:
Koerth-Baker, M & Mills, L 2008, Deadly critters that might save your life, news, 8 April, CNN.com International, viewed 9 August 2009,
(http://edition.cnn.com/2008/LIVING/wayoflife/04/08/deadly.animals/index.html)

PCR! What can we do without you?!

The Polymerase Chain Reaction or PCR for short is a process which amplifies the gene of interest in vitro. This process was not possible in earlier times as there was no known enzyme that could survive the high temperature that is required in PCR, however it all changed when two scientists named Thomas D. Brock and Hudson Freeze discovered the enzyme Taq Polymerase in an achaea which they named Thermus Aquaticus. It was able to withstand high temperatures without denaturing as it is found thermal habitats around the world and more information regarding thermus aquaticus can be found here (http://www.absoluteastronomy.com/topics/Thermus_aquaticus). There are three steps involved in PCR which is exponential amplification, leveling off stage and plateau. The product is doubled for every cycle during the exponential amplification stage and only minimum amount of DNA (gene of interest) is required. During the leveling off stage, the reaction slows down and DNA polymerase (taq polymerase) will decrease in activity. Lastly, the reaction finally stops at the plateau stage due to lack of reagents. This technique has a number of uses which include DNA fingerprinting, gene cloning and recovery of ancient DNA (http://en.wikipedia.org/wiki/Polymerase_chain_reaction#PCR_in_diagnosis_of_diseases) has more information regarding the uses of PCR.

The Brilliant Invention of DNA Microarray

Due to the advances of DNA technology, many techniques have been invented to help us to solve problems at genetic levels at a more accurate and faster manner. One of the brilliant inventions is the DNA microarray. With this method, researchers are able to test thousands of genes simultaneously to determine which ones are expressed in a particular tissue under different environmental conditions, in various disease states or at different developmental stages. For example, we can use DNA microarray to detect genes that are responsible for breast cancer. We can compare the gene expression in a healthy breast tissue and a breast cancer tissue. First, we isolate the mRNA in the healthy breast tissue and breast cancer tissue. Then, by using reverse transcriptase, red fluorescently labeled cDNA is synthesized from the mRNA from the healthy breast issue while green dye fluorescently labeled cDNA is synthesized from the breast cancer tissue. Then we put the cDNA mixture into the microarray which consists of all the human genes and allow hybridization. In the microarray, red dyes represent genes that are expressed in the healthy tissue (or more than green dyes), green dyes represent genes that are expressed in the cancer tissue (or more than red dye) while yellow are the ones that have equal amounts of red and green dyes. However, we are interested in the green dyes as these are the genes that might be responsible for causing cancer. By knowing these genes, we can develop drugs to treat those breast cancer patients. This is a breakthrough as genes that are responsible for many diseases such as AIDS can be detected by using this method and therefore can help millions of people by studying these genes.

Menopause Timing Genes Found

May 26th 2009

Scientists have found up to 20 genetic variations that bring forward the menopause for a woman, a European conference was told. The variations were found in four different places on two chromosomes, 19 and 20.The findings came from an analysis of the genes of more than 10,000 women in Britain, the USA, the Netherlands, Iceland and Italy. Researcher Lisette Stolk, from Erasmus MC, Rotterdam, Netherlands, said: "We know that ten years before menopause women are much less fertile, and five years before many are infertile.

"In Western countries, where women tend to have children later in life and closer to menopause, age at menopause can be an important factor in whether or not a particular woman is able to become a mother." A second study published last night warns that women approaching the menopause may suffer loss of learning ability.In the journal Neurology, researchers say the problem surfaces during the period just before the menopause begins - but it is only temporary. The researchers say the problem might be treated by using hormone supplements. Researcher Dr Gail Greendale said: "The good news is that the effect of perimenopause on learning seems to be temporary. Our study found that the amount of learning improved back to premenopausal levels during the postmenopausal stage."

by: 42101327
http://www.staffnurse.com/nursing-news-articles/menopause-timing-genes-found-3556.html

Study reveals startling new role for the plant hormone auxin

A team of scientists from the University of California, Davis discovered something new about the hormone auxin in plants. They found that auxin acts as a morphogen which directs the pattern of cell development based on concentration.

Plants reproduction system is located within its flower, where pollens produce sperm cells while egg cells are in the ovule. During the development stage, the ovule will undergoes both meiosis and mitosis several times. This resulting in a structure of embryo sac together with the production of 8 nuclei and three of them are positioned near the opening of the ovule. Figure below shows the position of 8 nuclei in the embryo sac.

Caption: A gradient (red) in the concentration of the plant hormone auxin, determines that only one of the eight undifferentiated nuclei in a plant's embryo sac will become an egg. (In this image, a large vacuole dominates the central section of the embryo sac.)

Credit: Monica Alandete-Saez/UC Davis

The studies discovered that the only nuclei that receive most hormone auxin will continue to develop into egg cell and later to be fertilized with sperm cell. Based on their observation, the hormone auxin is concentrated nearer to the opening of the embryo sac. Thus, the nucleus that is nearer to the opening of ovule will become egg cell. The researchers had carried out a trial to test this hypothesis where they purposely shifted the position of one nucleus nearer to end of embryo sac of plant Arabidopsis. And the result was; instead of one, two egg cells were produced.

Furthermore, they found out that this hormone auxin is produced within the embryo sac itself. This discovery may help in enhancing the fertility of crop plants where greater number of eggs could be developed into mature plants.

This article was published on June 4, 2009.
Article links: http://www.genengnews.com/news/bnitem.aspx?name=55667708
By Zaira Hidayah Mohd Arshad 42102119

'Warrior Gene' Linked To Gang Membership, Weapon Use

A new study has been carried out recently by The Florida State University that confirms an MAOA gene sometimes called the "warrior gene" link to gangs and weapons. However, this only applies to males where females seems to have resistance towards the violent effect of the gene.

'The MAOA gene affects levels of neurotransmitters such as dopamine and serotonin that are related to mood and behavior, and those variants that are related to violence are hereditary. Some previous studies have found the "warrior gene" to be more prevalent in cultures that are typified by warfare and aggression.' This MAOA gene is detected on the X - chromosome. Therefore it has more effect on males since male has one X - chromosome and a Y- chromosome while female has two X- chromosomes. For females, if there is the risk allele in one of the chromosome, there is another allele that can compensate for it. This is probably why the effect of MAOA has only been detected in males.

Link to the original article:
http://www.sciencedaily.com/releases/2009/06/090605123237.htm

by:42122809

Enzyme Necessary for DNA Synthesis Can Also Erase DNA

New mechanism that causes some changes in DNA content has been found by a group of Uppsala University scientists and it is due to something has happened in bacteria that live as a parasite inside the cells of other organisms.

Change in the amount of DNA in the chromosomes of bacteria can be either by gene amplification and gene deletion by which the amount is increasing and decreasing respectively.

Currently a genetic analysis on salmonella mutant done by a PhD student, Sanna Koskiniemi has shown that in order for spontaneous deletions are to take placed in the bacteria a special type DNA-synthesizing enzyme must be present. The decreased or increased rates of deletion up to 30 times are proven by genetically inactivating or overproducing these enzymes.
Professor Dan Andersson suggests that bacteria that live either as parasites inside cells or in symbiosis with other organisms are of special interest with regard to this new mechanism. As DNA has disappeared during evolution, thus, these bacteria often have small chromosomes. With these new findings we can better understand and predict how DNA is eliminated from chromosomes.

Link to the original article:
http://www.sciencedaily.com/releases/2009/06/090608182541.htm

By: 42111577

Cats' Central Nervous System Can Repair Itself And Restore Function

A team of researchers from the University of Wisconsin-Madison reports that the restoration in cats of myelin can lead to functional recovery from a severe neurological disorder. Myelin is a fatty substances that coats the nerve fibers known as axon and help in the conduction of nerve signals. This myelin can loss through disease causing impairment of sensation, movement, cognition and other functions, depending on which nerves are affected.

This finding is essential as myelin can be reestablished as the therapy for treating a range of severe neurological diseases associated with the loss or damage of myelin, without affecting the nerve themselves. A test also had been done to some cats to see their growth and development by giving the irradiated diet. Some of the cats show severe neurological dysfunction, including movement disorders, vision loss and paralysis. As the diet been taken off, the cats recovered slowly and all of the lost functions were restored.

article from...
http://www.sciencedaily.com/releases/2009/03/090330200722.htm

by: Nawwarah (42115799)

Blood clotting: Key Discovery

Scientists from Harvard University have discovered a molecular mechanism that is key to regulating the way blood clots.

They detected an area on the von Willebrand factor (VWF) blood-clotting protein which contains a molecular sensor to regulate the size of the protein, important for it to work effectively.
VWF is essential to the body's circulation. It controls the balance between blood clotting and bleeding. Abnormalities affecting VWF can lead to health problems such as bleeding disorders and heart attacks.

The team said that this discovery will improve understanding on how body regulates the formation of blood clots, and could also add some information into how bleeding disorders, such as von Willebrand disease, disrupt this regulation system. They also said that this finding has the potential to lead the new avenues for treatment and diagnosis.

Links to original article:
http://news.bbc.co.uk/2/hi/health/8082692.stm

More on this topic:
http://generalmedicine.suite101.com/article.cfm/blood_clotting_disorders
http://www.uch.edu/conditions/blood/blood-clotting-disorders/index.aspx
http://www.theuniversityhospital.com/adultgenetics/blood.htm
http://news.bbc.co.uk/2/hi/health/7833978.stm

Risks Of Sharing Personal Genetic Information Online Need More Study, Bioethicists Say

The advancement of the world today lead us to know our own genetic risk as easy as just provide our salive. Bioethicists from the Stanford University School of Medicine, claimed that, sharing genetic information online will raises a host of ethical questions.


As genetic information is unique in that it's not only relevant for the individuals who receive the information, but also for their family members, their children and even their children's children," said Sandra Soo-Jin Lee, PhD, senior research scholar at the school's Center for Biomedical Ethics.

"if you receive information on your breast cancer risk and share it with others, you might also be sharing information about your daughter's risk for breast cancer — even though she never consented to have that information shared."

Right now, there are nearly 100 companies around the world that provide some form of direct-to-consumer genetic testing. Customers just need to mail their DNA sample for sequencing, and then get both raw data and an interpretation of their genetic profile. After that, customers can create a public profile and share their genetic data through a company-sponsored social networking site. Due to that, experts fear that consumers may share genetic data without realizing the potential implications for themselves and their families. For now, there aren't any laws that govern the exchange of genetic information online.

article from : http://www.sciencedaily.com/releases/2009/06/090605075051.htm
picture : http://www.turbosquid.com/FullPreview/Index.cfm/ID/277513

42115696

GM MONKEY WITH JELLYFISH GENE

Eight years back ANDi, the first genetically modified monkey carried green fluorescent protein (GFP) gene which being transferred from its parents. However, this is a faulty gene since ANDi cannot glow green as expected.

Now, scientist is inserting this green fluorescent protein (GFP) gene into marmoset which is another monkey species. This is a very important research since if this genetic modification is a success, scientist will use GM monkey to study human disease since GM primates provide better model than GM mice.

For this research, viral vectors method was used to introduce green fluorescent protein (GFP) gene from jelly fish into the host cell (marmoset).The modified virus that carried the gene of interest is injected into the monkey embryos. Then, these embryos being inserted into seven surrogate mothers which four gave birth, producing 1 male and 4 female marmosets that carried the green fluorescent protein (GFP) gene.

Later, when the male baby was sexually mature, he successfully fathered a single offspring which also glowed green, showing that it had inherited the GFP gene. One of the females also produced IVF embryos carrying the gene thus shows that this research is success.

References:
http://www.newscientist.com/article/dn17194
http://www.newscientist.com/article/dn319-monkey-business.html

By:
Siti Nur Hasanah Binti Mohd Yusuf
42102052

Biofuel Production Won't Erode Global Food Supply

A newly bioprocess to produce biofuels without stressing on the global food supply has been discovered by a group of scientists in California. This approach involves the use of genetically engineered microbes with the ability to convert switchgrass, corn cobs and other organic materials into methyl halides - the raw material for producing gasoline.

Methyl halides are produced naturally by plants and microbes, but the amount is too small for commercial use. With the help of a database of 89 genes from plants, fungi and bacteria that are known to produce methyl halides, genes that were most likely to produce methyl halides were isolated and spliced into Brewer's yeast, so that these yeast cells will produce methyl halides instead of alcohol. These genetically engineered microbes boosted methyl halide production from agricultural waste to levels with commercial potential.

Prepared by:
Maisarah (42101484)

Source:
http://www.sciencedaily.com/releases/2009/05/090511115003.htm