Scientists say rare plant has biggest genome yet

When it comes to genomes, size matters -- and British scientists say a rare and striking plant native to Japan is in a perilous position.
 

Researchers at Britain's Kew Botanical Gardens say the plant, Paris japonica, has the largest genome yet recorded, putting it at high risk of extinction.

"Some people may wonder what the consequences are of such a large genome and whether it really matters if one organism has more DNA than another," said Ilia Leitch, a researcher at Kew's Jodrell Laboratory. "The answer to this is a resounding 'yes'"

"Having a large genome increases the risk of extinction. The larger it is, the more at risk you are."

The vast range of genome size -- the amount of DNA -- in plants and animals has long fascinated and puzzled scientists.

With 152.23 picograms (pg) of DNA, the Paris japonica has around 15 percent more than the previous record holder, the marbled lungfish or Protopterus aethiopicus, with 132.83 pg.

It is also more than 50 times bigger than the human genome, which is 3.0 picograms. A picogram is one trillionth of a gram.

Leitch said the importance of size lies in the fact that the more DNA there is in a genome, the longer it takes for a cell to copy all of its DNA and divide.

"The knock-on effect of this is that it can take longer for an organism with a larger genome to complete its life cycle than one with a small genome," she said.

This explains why many plants living in deserts which must grow quickly after rains have small genomes enabling them to grow rapidly, while species with large genomes grow much more slowly and are not found in such harsh habitats.

Leitch said that in plants, research has shown that those with large genomes are at greater risk of extinction, are less adapted to living in polluted soils and are less able to tolerate extreme environmental conditions, factors which she said were "all highly relevant in today's changing world."

The smallest genome so far reported is in a parasite of humans and other mammals called Encephalitozoon intestinalis, which has just 0.0023 picograms of DNA.

The record holder among plants for 34 years was a species called Fritillaria assyriaca, until earlier this year when a group of Dutch scientists found that a natural hybrid of trillium and hagae, related to the herb paris, had a genome four percent larger than the fritillary at 132.50 pg.

According to Kew's scientists, this had been widely thought to be around maximum size a genome could reach until the recent discovery of the 152.23 pg Paris japonica genome.

The latest finding was reported in the Botanical Journal of the Linnean Society.

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TIFR Coming to Hyderabad | PM to lay foundation stone on october 19th

The family tree of the Tata Institute of Fundamental Research, which so far includes Mumbai, Pune and Bangalore, will soon have a fourth major branch: TIFR Hyderabad. The foundation stone will be laid by PM Manmohan Singh on October 19, as reported recently in the Times of India. TIFR Director Mustansir Barma and NCBS Director Prof. K. VijayRaghavan welcome and encourage all interested parties at NCBS to join them in Hyderabad for the event. See below for more details.
For those at NCBS who cannot make it, the PM's visit will be covered in a webcast, and food and refreshments will help to mark the occasion.

A message from Prof. Mustansir Barma, TIFR Director

Dear NCBS Colleagues:

I am very happy to inform you that the Prime Minister Dr. Manmohan Singh has consented to lay the foundation stone of the new campus of TIFR in Hyderabad at 2.30 p.m. on October 19, 2010. This will be followed by a few scientific talks. Those of you who would like to attend the function in Hyderabad, are requested to contact your Dean or Centre Director by noon on Monday, October 11, 2010. Further, in order to have the largest reach possible for the TIFR community, this historic event will be broadcast live to TIFR Mumbai, as well as to TIFR centres.

A message to All at NCBS from Prof. K. VijayRaghavan

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Scientists find clue to cell damage after stroke

Scientists have found that an enzyme is responsible for the death of nerve cells after a stroke and say an experimental drug that dramatically reduced brain damage in mice may also offer hope for humans.
Previous attempts to design drugs that can protect the brain from damage after a stroke have had limited success.

Dutch and German researchers said Tuesday that their work showed a potential new approach to treating stroke, which is the most common cardiovascular problem after heart disease and kills an estimated 5.7 million people worldwide each year.

In tests on mice, the scientists found that an experimental drug, known as VAS2870 and being developed by the German biotech firm Vasopharm, dramatically reduced brain damage and preserved brain functions, even when given hours after the stroke.
"The indications are very strong that the same mechanism may apply for human stroke," said Harald Schmidt from Maastricht University in the Netherlands, who led the study with Christoph Kleinschnitz from Wurzburg University in Germany.

Ischaemic stroke is the most common kind of stroke, caused by a clot or other blockage disrupting the flow of blood to the brain.
The only currently available treatment is a clot-busting drug called a t-PA, or tissue plasminogen activator, but it must be given within three hours of a stroke and only around five to 10 percent of stroke victims get it.
Scientists facing a paucity of effective stroke drugs have been investigating whether tissue damage after stroke may be linked to a mechanism called oxidative stress, in which reactive oxygen species (ROS) accumulate within a cell.

Previous experimental drugs designed to "soak up" loose ROS after stroke have failed in late-stage clinical trials. A compound from AstraZeneca called NXY-059 proved to be an expensive flop for the Anglo-Swedish drugmaker in 2006.
But in this study, published in the Public Library of Science (PLoS) Biology journal, Schmidt and Kleinschnitz focused on finding and then trying to block the source of ROS.

The enzyme they identified is called NOX4, and by blocking NOX4 with the experimental drug in mice with stroke, they dramatically reduced brain damage.

They also found that eliminating the gene linked to NOX4 in mice did not result in any abnormalities, suggesting that "no obvious side-effects are to be expected from a future NOX4 inhibitor drug," they wrote in the study.

"This approach focuses on keeping the neurons alive -- it preserves the neurons and brain function," Schmidt said in a telephone interview. "We show here that if you identify the real source (of oxidative stress), there is a huge potential benefit if you are then able to inhibit it."
Schmidt said the findings may also have implications for other diseases which are assumed to be linked to oxidative stress, such as heart attacks and some cancers, and for other forms of nerve cell degeneration such as in Parkinson's or Alzheimer's disease.

"We now have a concept that we can follow in all these conditions -- identify the source, try to inhibit it, and see if that makes a difference," he said.

 

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Searching in the Microbial World for Efficient Ways to Produce Biofuel

With the help of genetic materials from a cow's rumen, U.S. Department of Agriculture (USDA) scientists are developing new ways to break down plant fibers for conversion into biofuel.

To convert corn stover and switchgrass into biofuel, the plant fibers must first be broken down into sugars. But cell wall polymers are cross-linked in various ways that make them very resistant to breaking down, according to Dominic Wong, a chemist at the USDA Agricultural Research Service (ARS) Western Regional Research Center, in Albany, Calif.

Previous studies have shown that a special group of enzymes known as feruloyl esterases (FAEs) are capable of breaking apart key links between the polymers, and that the enzymes are produced by certain types of microbes that degrade plant materials. Wong collected the microbial population from a cow's rumen, and screened their genetic compositions to find genes that produce FAE enzymes.

Working with scientific partners at Cargill, Wong has isolated, sequenced and cloned 12 genes capable of being introduced into Escherichia coli for production of the enzymes, which can then be used to break loose the polymeric network in the plant cell wall. Wong and the Cargill team have filed a provisional patent application on the FAE genes and enzymes.
In addition to increasing the efficiency of biomass conversion to biofuel, the enzymes could also be used to enhance the digestibility and the nutritional qualities of animal feeds, aid in the development of nutritional supplements, and prove useful in the development of other value-added products.
 

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Interesting Questions from Genetics

hi friends ... just check out this question

The horse(Equus caballus) has a diploid complement of 64 chromosomes including 36 acrocentric autosomes;  the ass (Equus asinus ) has 62 chromosomes including 22 acrocentric autosomes.

a) predict the number of chromosomes to be found in the hybrid offspring (mule) produced by matinga male ass (jack) to a female horse(mare).

b) Why are mules usually sterile ?

and the answers are
first bit is easy ... second one is interesting

a) now as we know the sperm(jack) will carry haploid(n) set of chromosomes i.e; n = 31 here and the same way the egg (mare) will have n= 32 (haploid again) ; and hence the resulting hybrid mule wud have diplod set of chromosomes (formed by the union of gametes) with 31+ 32 = 63 chromosomes ...

b) as  seen in the question the haploid set of chromosome in horse has 18 acrocentric chromosomes , which are so dissimilar from the haploid set in jack having only 11 acrocentric chromosomes . so different that , meiosis in the mule germ line cannot proceed beyond first prophase where synapsis of homologues occur.. thereby mules are incapable of producing viable gametes ...they r sterile...

PROBLEM 2:
The absence of legs in cattle ("amputated") has been attributed to a completely recessive lethal gene. A normal bull is mated with a normal cow and they produce an amputated calf (usually death at birth). The same parents are mated again.

a) what is the chance that of the next calf being amputated?

b) what is the chance of these parents having two calves, both of which are amputated?

c) Bull carrying the amputated allele (heterozygous) are mated to noncarrier cows. The F1 is allowed to mate at random to produce the F2. What genotypic ratio is expected in the adult F2?

d)Suppose that each F1 female in part (c) rears one viable calf (i.e; each of the cows that throws an amputated calf is allowed to remate to a carrier sire until she produces a viable offspring). What genotypic ratio is expected in the adult F2?

(For convenience assign (AA Aa aa) as gene symbols.where "a" is the lethal gene)

the answers are -
a)25%
b)1/16
c)9AA:6Aa (or 3AA:2Aa)
d)7AA:5Aa

could anyone pls explain me the fourth bit ...

pls do add if u have any questions related to genetics in dis blog 

all d best everyone...:)

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Seaweed to tackle obesity :)

Seaweed could hold the key to tackling obesity after it was found it reduces fat digestion by more than 75 per cent, new research has shown.

Now the team at Newcastle University are adding seaweed fibre to bread to see if they can develop foods that could help you lose weight while you eat them.

A team of scientists led by Dr Iain Brownlee and Prof Jeff Pearson have found that dietary fibre in one of the world's largest commercially-used seaweed could reduce the amount of fat available for absorption by the body by around 75 per cent.

The Newcastle University team found that Alginate – a natural fibre found in sea kelp – stops the digestion of fat better than most anti-obesity treatments currently available over the counter.

Using an artificial gut, they tested the effectiveness of more than 60 different natural fibres by measuring the amount of fat that was digested and absorbed with each treatment.

Presenting their findings today at the American Chemical Society Spring meeting in San Francisco, Dr Brownlee said the next step was to recruit volunteers and study whether the effects they have modelled in the lab can be reproduced in real people, and whether such foods are truly acceptable in a normal diet.

"The aim of this study was to put these products to the test and our initial findings are that alginates significantly reduce fat digestion," explains Dr Brownlee.

"This suggests that if we can add the natural fibre to products commonly eaten daily - such as bread, biscuits and yoghurts – up to three quarters of the fat contained in that meal could simply pass through the body.

"We have already added the alginate to bread and initial taste tests have been extremely encouraging. Now the next step to to carry out clinical trials to find out how effective they are when eaten as part of a normal diet."

The research is part of a three year project being funded by the Biotechnology and Biological Sciences Research Council. It addresses the new regulations set out by the European Food Safety Authority that any health claims made on a food label should be substantiated by scientific evidence.

"There are countless claims about miracle cures for weight loss but only a few cases offer any sound scientific evidence to back up these claims," explains Dr Brownlee.

Alginates are already commonly used at a very low level in many foods as thickeners and stabilisers and when added to bread as part of a blind taste test, Dr Brownlee said the alginate bread actually scored higher for texture and richness than a standard white loaf.

"Obesity is an ever-growing problem and many people find it difficult to stick to diet and exercise plans in order to lose weight," explained Dr Brownlee.

"Alginates not only have great potential for weight management - adding them to food also has the added advantage of boosting overall fibre content."

What is a dietary fibre?

Dietary fibre would be scientifically classified as a group of carbohydrates of plant origin that escape digestion by the human gut.

"Actually, there's still quite a lot of confusion about fibre," says Dr Brownlee. "I think most people would describe it as roughage – the bit of your food that keeps you regular and is vital for a healthy gut.

"Both of these facts are true but the notion that all fibre is the same and that it simply goes through your system without having an effect is wrong."

Fibre is made up of a wide range of different molecules called polysaccharides and although it is not digested by the human gut, it both directly and indirectly affects a number of bodily processes.

Dr Brownlee adds: "These initial findings suggest alginates could offer a very real solution in the battle against obesity."

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Scientists 'Clone' Human Virus Responsible for Congenital Malformations and Other Life-Threatening Diseases

Human cytomegalovirus (HCMV) is a major infectious cause of congenital malformations worldwide. The virus is also known to cause life-threatening disease in transplant patients and people with HIV/AIDS. The development of new treatments has been hampered as scientists have been unable to stably replicate HCMV outside the human body. Dr Richard Stanton from Cardiff University's School of Medicine who led the joint research, said: "HCMV has by far the largest genome of all viruses affecting humans -- consequently it was technically difficult to clone in an intact form in the laboratory.

"Cloning a copy of the virus from a strain isolated by Cardiff Public Health Laboratories has enabled us to identify the genes causing the instability of the virus outside the body.

"Following the identification of these genes, we have successfully developed cells in which we can grow virus that corresponds to that which exists in the human body."

Cloning the virus for the first time will help virologists develop antivirals and vaccines against the virus that causes clinical disease.

Following the study, the clone has already been distributed to research laboratories worldwide, and is being tested by the World Health Organisation (WHO) as part of a study to develop an international diagnostic standard with which to compare clinical isolates.

"For the first time our work has enabled us to create an exact copy of the virus outside of the body offering a vital step forward in the development of new treatments."  The virus, named Merlin, was isolated from a clinical sample identified by the Diagnostic Unit, Public Health Wales.

Reconstruction of the complete human cytomegalovirus genome in a BAC reveals RL13 to be a potent inhibitor of replication -- is available in the on-line edition of TheJournal of Clinical Investigation.

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Genetically altered trees, plants could help counter global warming

Forests of genetically altered trees and other plants could sequester several billion tons of carbon from the atmosphere each year and so help ameliorate global warming, according to estimates published in the October issue of BioScience.

The study, by researchers at Lawrence Berkeley National Laboratory and Oak Ridge National Laboratory, outlines a variety of strategies for augmenting the processes that plants use to sequester carbon dioxide from the air and convert it into long-lived forms of carbon, first in vegetation and ultimately in soil.

Besides increasing the efficiency of plants' absorption of light, researchers might be able to genetically alter plants so they send more carbon into their roots—where some may be converted into soil carbon and remain out of circulation for centuries. Other possibilities include altering plants so that they can better withstand the stresses of growing on marginal land, and so that they yield improved bioenergy and food crops. Such innovations might, in combination, boost substantially the amount of carbon that vegetation naturally extracts from air, according to the authors' estimates.

The researchers stress that the use of genetically engineered plants for carbon sequestration is only one of many policy initiatives and technical tools that might boost the carbon sequestration already occurring in natural vegetation and crops.

The article, by Christer Jansson, Stan D. Wullschleger, Udaya C. Kalluri, and Gerald A. Tuskan, is the first in a Special Section in the October BioScience that includes several perspectives on the prospects for enhancing biological carbon sequestration. Other articles in the section analyze the substantial ecological and economic constraints that limit such efforts. One article discusses the prospects for sequestering carbon by culturing algae to produce biofuel feedstocks; one proposes a modification of the current regulatory climate for producing genetically engineered trees in the United States; and one discusses societal perceptions of the issues surrounding the use of genetically altered organisms to ameliorate warming attributed to the buildup of greenhouse gases.

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For the First Time, Monkeys Recognize Themselves in the Mirror, Indicating Self-Awareness

Typically, monkeys don't know what to make of a mirror. They may ignore it or interpret their reflection as another, invading monkey, but they don't recognize the reflection as their own image. Chimpanzees and people pass this "mark" test -- they obviously recognize their own reflection and make funny faces, look at a temporary mark that the scientists have placed on their face or wonder how they got so old and grey

For 40 years, scientists have concluded from this type of behavior that a few species are self-aware -- they recognize the boundaries between themselves and the physical world.

Because chimps, our closest relatives, pass the test, while almost all other primate species fail it, scientists began to discuss a "cognitive divide" between the highest primates and the rest.

But a study published Sept. 29 in PLoS ONE by Luis Populin, a professor of anatomy at the University of Wisconsin-Madison, and colleagues shows that under specific conditions, a rhesus macaque monkey that normally would fail the mark test can still recognize itself in the mirror and perform actions that scientists would expect from animals that are self-aware.

The finding casts doubt on both the relevance of the mark test and on the existence of a definitive cognitive divide between higher and lower primates.

Populin, who studies the neural basis of perception and behavior, had placed head implants on two rhesus macaque monkeys, while preparing to study attention deficit disorder. Then Abigail Rajala, an experienced animal technician who is in the university's Neuroscience Training Program, mentioned that one of the monkeys could recognize himself in a small mirror. "I told her the scientific literature says they can't do this," says Populin, "so we decided to do a simple study."

Much to his delight, it turned out that the graduate student was right.

In the standard mark test, a harmless mark is put on the animal's face, where it can only be seen in a mirror. If the animal stares at the mirror and touches the mark, it is said to be self-aware: It knows that the mirror shows its own reflection, not that of another animal. (Animals that lack self-awareness may, for example, search for the "invading" animal behind the mirror.)

Rhesus macaques, a mainstay of medical and psychological research, have long failed the mark test.

But in Populin's lab, the monkeys that got the implants were clearly looking in the mirror while examining and grooming their foreheads, near the implant. Tellingly, they were also examining areas on their body, particularly the genitals, that they had never seen before. In some cases, the monkeys even turned themselves upside down during these examinations. In other cases, they grasped and adjusted the mirror to get a better view of themselves.

When the researchers covered the mirror glass with black plastic, these behaviors disappeared, and the monkeys ignored what had been a subject of fascination.

Furthermore, although a macaque will often interpret its reflection as representing an intruding monkey and adopt either an aggressive or submissive response, the implanted monkeys showed dramatically fewer of those "social" behaviors compared to the behaviors, such as exploring hidden body parts, that indicate self-awareness, Populin says.

"This report makes a unique contribution to our views about primate self-awareness because the 'mirror test' has been the traditional gold standard for determining if a person and/or animal met a criterion for having a sense of self," says Christopher Coe, a primatologist and professor of psychology at UW-Madison. "If a young child, brain-damaged adult or animal was able to recognize and appreciate that the image in the reflection was really them, then it was interpreted as proof of being aware."

Thus, Coe says, "If we follow that logic through with the belief that mirror recognition is proof of a sense of self, then we need to extend that attribute at least to rhesus monkeys."

Scientists who have used the mark test to explore self-awareness have found the quality in one species of bird, in one individual elephant, and in dolphins and orangutans. And so instead of asking how self-awareness evolved only among primates, they face the larger question of how it evolved multiple times in distantly related species.

The study may refine how the mark test is used, Populin says. "We clearly have data showing that these animals recognize themselves in the mirror, but fail the mark test."

The mounting data on self-awareness has undermined the concept of a cognitive divide in the primate lineage, Populin says. "There is another idea in primatology, and Charles Snowdon of UW-Madison has contributed to this, that instead of a divide, self-awareness has evolved along a continuum, so we will find it in different forms in different locations on the tree of evolution. I think the mark test may not be sensitive enough to detect self-awareness in the lower species; they may have it, but in a different form, and it may show up in different situations, using different tests."

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Mesenchymal Stem Cells - - Human MSCs & Differentiation Media Bone marrow Mesenchymal Stem Cells

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