047: Evolutionary origin of mammalian gene regulation unravelled 150 million years

Life Science Space (June 6, 2008)--Scientists at the Babraham Institute, the Sanger Institute, the University of Cambridge and the University of Melbourne and the University of Texas at San Antonio (all part of the SAVOIR consortium) have found that a complex, highly conserved and extremely important mechanism of controlling genes is over 150 million years old. The findings, reported today online in Nature Genetics, have provided new insights into the evolution of genomic or parental imprinting and epigenetic regulation in mammals.

A failure of these sophisticated processes is associated with many human genetic diseases, psychiatric and autoimmune disorders and ageing.

Epigenetic mechanisms are at the heart of developmental biology, orchestrating the formation of many different tissues and organs from a fertilised egg. Almost all cells in an individual have exactly the same genetic material, yet behave very differently depending on which organs they comprise. Epigenetic regulation enables the fine-tuning of our genes and their expression in different places at different times, leading to the amazing complexity we see in humans despite the relatively small number of unique genes.

We all get two copies of every gene, one from our mother and one from our father. In many cases both copies are used or ‘expressed’, however it is becoming clear that for some genes either the mother’s or the father’s version is used preferentially, a phenomenon known as genomic imprinting. Specific chemical modifications to the DNA, such as methylation, appear to give the chromosomes a ‘memory’ as to their parental origin. These ‘epigenetic’ imprints, from the Greek meaning ‘on top of’, modify the structure of the DNA but not its sequence. In addition to parental modifications, it is thought that epigenetic changes may also arise in response to environmental factors, enabling an organism's genes to adapt and respond differently, even though the gene sequence does not change.

Image Credit: Clinical Tools Inc.

The control of gene expression by imprinting mechanisms has been observed in plants and therians - placental mammals (eutherians) and marsupials (metatherians) - where the majority of imprinted genes are associated with controlling embryonic growth and development, including the development of the placenta. Other imprinted genes are involved in post-natal development, processes like suckling and metabolism.

Imprinting is thought to have evolved because of genetic conflict that influences the allocation of resources from parents to offspring. The origin of this seems to stem from there being different developmental priorities for each parent - the father desires one large, strong offspring from each possible mother whereas the mother prefers to distribute resources equally among all her young (or potential young).

The insulin-like growth factor signalling pathway, which has a major influence on fetal size, is exemplary of this parental-offspring conflict. It contains two components encoded by the oppositely imprinted genes, Igf2 (a growth promoting factor expressed from the father's version of the gene) and Igf2r (a growth inhibitory factor expressed from the maternal copy). In eutherians, these two genes lie on separate chromosomes and are imprinted by different epigenetic mechanisms. In marsupials, IGF2 and IGF2R are known to be imprinted but the IGF2R imprinting mechanism is different than in eutherians (much simpler) and the IGF2 imprinting mechanism is unknown.

Image credit: Nature Genetics

To unravel the origins of genomic imprinting and mechanisms underpinning parental specific gene expression, the SAVOIR consortium has planned to obtain and analyse the sequence of all major clusters of imprinted genes from mammals where imprinting has been observed including human, mouse and wallaby, with those apparently lacking imprinting mechanisms, such as platypus and chicken.

Mammals are divided into three groups; Monotremata, Marsupialia and Eutheria, the latter two forming the therian class. Recent evidence suggests that therians diverged from the egg-laying monotremes like the platypus approximately 180 million years ago, and then split into the eutherian and marsupials infra-classes around 150 million years ago.

The apparent absence of genomic imprinting in monotremes and presence in eutherians and marsupials suggests that imprinting has evolved at the boundary of monotremes and therians’ divergence. Interestingly, imprinting evolution paralleled the apparition of the placenta and implantation. Indeed, eutherian have a developed placenta that transfers a lot of nutrients to the fetus over a long gestation period while marsupials have a rudimentary placenta and give birth to very immature youngs that spend a long time in a pouch where they suckle milk. Both eutherian and marsupials having a placenta implies that the therian ancestor was a placental mammal. In contrast the monotremes’ gestation shows only gas exchange through the shell before the egg being laid. Hence, it is possible that imprinting and placentation co-evolved in the therian ancestor.

The paradigm of genomic imprinting, the IGF2-H19 imprinted gene cluster, has been studied extensively in eutherians. The IGF2 gene codes for a fetal growth enhancer protein. The H19 gene codes for a RNA whose role is still elusive. The eutherian IGF2 and H19 genes are reciprocally imprinted: IGF2 is exclusively expressed from the father's chromosome and H19 exclusively from the mother's. A paternally methylated element located just upstream of the H19 gene controls this reciprocal imprinting. The present study shows that the H19 non-coding RNA gene exists nearby the marsupial IGF2 gene, that their imprinting is recipocal and that the same paternally-methylated element controls this imprinting. Hence, the therian IGF2-H19 imprinted locus is unique by being a ‘cluster’ of imprinted genes also in marsupials (the few other genes found imprinted in marsupials are all singleton genes) and by having the same imprinting mechanism in both marsupials and eutherians, making it the most ancient imprinted locus in mammals.

The next stage is to look for the IGF2-H19 locus in another branch of mammals’ evolution – the monotremes (egg laying mammals which lactate) – where so far genomic imprinting has not been seen. The recent platypus genome project didn’t succeed in obtaining the sequence of the monotreme IGF2-H19 locus demonstrating the importance of both large scale and more focused genomics projects like ours. Hence the SAVOIR consortium will concentrate its efforts in obtaining the sequence of the monotreme IGF2 locus to provide further insights into the imprinting evolution and the mysteries of gene regulation in these curious creatures which carry mammalian, bird-like and reptilian characteristics.

Finally, the conservation for 150 million years of the H19 non-coding RNA and of different features it harbours (as for example a microRNA hairpin) raises important questions about the function of this gene. MicroRNAs, also known as short interfering RNAs, are short (22-25 base) sequences that are copied from DNA (but do not code for protein) and control gene activity by binding to specific related sequences. This interferes with a gene’s ability to produce the proteins (translation) that co-ordinate cellular activities or can lead to destruction of other RNA molecules. Previous work has indicated that H19 may have a role either in tumour suppression or in oncogenesis, and our findings should give fresh impetus to discover what this intriguing RNA really regulates in normal development and in disease, and why it is so highly conserved

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Source: http://www.babraham.ac.uk/news2008/jun-29.html

Learn more about genomic imprinting @: http://www.nature.com/nrg/journal/v4/n5/box/nrg1062_BX3.htmlttp://www.babraham.ac.uk/news2008/jun-29.html

045: Sequencing the Cacao Genome to Safeguard Chocolate

Life Science Space (June 30, 2008)--During the past 15 years, the global cocoa industry has confronted a trio of devastating fungal diseases that cost growers an estimated $700 million in losses annually. Now scientists at the Agricultural Research Service (ARS) Subtropical Horticultural Research Station (SHRS) in Miami, Fla., are developing productive cacao (Theobroma cacao) trees resistant to these diseases: witches' broom, frosty pod and black pod.

The research has been based upon traditional varietal selection and breeding, enhanced by the use of molecular (DNA-derived) markers associated with disease resistance.

Field trials involving foreign cooperators are under way in South America, West Africa, Central America and Papua New Guinea to evaluate potential disease-resistant cocoa trees. Several of these tree selections were based upon disease-tolerance genes discovered in Miami.

Since 1999, ARS researchers at the SHRS, led by plant geneticist Ray Schnell, have worked in partnership with Mars Inc., the world’s largest manufacturer of chocolate-related products, to apply modern molecular genetic techniques to cocoa production.

This research, in collaboration with institutes in the Americas and Africa, has produced genetic linkage maps for cacao populations, segregating for resistance to the three fungal diseases. Today a new partnership was announced between ARS, Mars Inc., and IBM with the goal of sequencing the entire cacao genome. Once completed, the research results will be released into the public domain.

The partnership to sequence the cacao genome is financially backed and coordinated by Mars Inc. of McLean, Va. Scientific support is provided by SHRS in Miami, in collaboration with scientists at IBM’s Thomas J. Watson Research Center in Yorktown Heights, N.Y. The IBM team will use its Blue Gene supercomputer to analyze the cocoa genome. This is the first time that all three research groups are collaborating.

In addition to the three major partners, Washington State University will assist Schnell in developing detailed genetic maps and assembling the sequence fragments into the complete genome sequence.

ARS is a scientific research agency of the U.S. Department of Agriculture.
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Original article provided by USDA/Agricultural Research Service.
http://www.ars.usda.gov/is/pr/2008/080626.htm

040: Discovery proves 'selfish gene' exists

Life Science Space (June 21, 2008)--A new discovery by a scientist from The University of Western Ontario provides conclusive evidence to support decades-old evolutionary beliefs about the existence of a so-called selfish gene.

Since renowned British biologist Richard Dawkins ("The God Delusion") introduced the concept of the ‘selfish gene’ in 1976, scientists the world over have hailed the theory as a natural extension to the work of Charles Darwin. In studying genomes, the word ‘selfish’ does not refer to self-centred behaviour but rather to the blind tendency of genes wanting to continue their existence into the next generation. Ironically, this ‘selfish’ tendency can appear anything but selfish when the gene does move ahead for selfless and even self-sacrificing reasons.

For instance, in the honey bee colony, a complex social breeding system described as a ‘super-organism,’ female worker bees are sterile. The adult queen bee, selected and developed by worker bees, is left to mate with male drones. Because the ‘selfish’ gene controlling worker sterility has never been isolated by scientists, the understanding of how reproductive altruism can evolve has been entirely theoretical – until now.

Working with Peter Oxley of the University of Sydney in Australia, Western biology professor Graham Thompson has, for the first time, isolated a region on the honey bee genome that houses this ‘selfish’ gene in female workers bees. “We don’t know exactly which gene it is, but we’re getting close.” “This basically provides a validation for a huge body of socio-biology,” says Thompson, who adds the completion of Honey Bee Genome Project in 2006 was crucial to this discovery.

The research will be published in the July issue of Genetics.

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Image Credit: Peggy Greb

Source: Western news:
http://communications.uwo.ca/com/western_news/stories/discovery_proves_%27selfish_gene%27_exists_20080620442385/


For more information: Honey Bee Genome Project--http://www.nature.com/nature/focus/honeybee/#links

036: Lancelet genome shows how genes quadrupled during vertebrate evolution

Life Science Space (June 18, 2008)--The newly sequenced genome of a dainty, quill-like sea creature called a lancelet provides the best evidence yet that vertebrates evolved over the past 550 million years through a four-fold duplication of the genes of more primitive ancestors.

The marine invertebrate known as the lancelet, or amphioxus, has tentacle-like strands called oral cirri that strain phytoplankton out of the water. (Image Credit: The Biohistory Research Hall, Japan)

The late geneticist Susumu Ohno argued in 1970 that gene duplication was the most important force in the evolution of higher organisms, and Ohno's theory was the basis for original estimates that the human genome must contain up to 100,000 distinct genes. Instead, the Human Genome Project found that humans today have only 20,000 to 25,000 genes, which means that, if our ancestors' primitive genome doubled and redoubled, most of the duplicate copies of genes must have been lost. An analysis of the lancelet, or amphioxus, genome, being published in the June 19 issue of Nature, shows this to be the case.

"Amphioxus and humans had a common ancestor 550 million years ago, which allows us to use amphioxus as a surrogate for that ancestor in terms of understanding how vertebrate genomes evolved," said Daniel S. Rokhsar, a faculty member in the University of California, Berkeley's Center for Integrative Genomics and program head for computational genomics at the Department of Energy Joint Genome Institute (JGI) in Walnut Creek, Calif.

Rokhsar and JGI post-doctoral fellow Nicholas H. Putnam performed the sequencing, assembly and genome-wide analyses of the amphioxus genome and are lead authors of the Nature paper. "If you compare the 23 chromosomes of humans with the 19 chromosomes of amphioxus, you find that both genomes can be expressed in terms of 17 ancestral pieces. So, we can say with some confidence that 550 million years ago, the common ancestor of amphioxus and humans had 17 chromosomal elements."

JGI post-doctoral fellow Nicholas H. Putnam, along with Rokhsar and a large international group of collaborators from the United States, Japan, the United Kingdom, and Spain, reconstructed what happened next. Each of those 17 ancestral segments was duplicated twice in the evolution of vertebrates, after which most of the routine "housekeeping" genes lost the extra copies. Those left, totaling a couple thousand genes, found new functions that, Putnam said, make us different from all other creatures.

"These few thousand genes have been retooled to make humans more elaborate than their simpler ancestors. They are involved in setting up the body plan of an animal and differentiating different parts of the animal," he said. "The hypothesis, pretty strongly supported by this data, is that the multiplication of this particular kind of gene and differentiation into different functions was important in the formation of vertebrates as we know them."

"The most exciting thing that the amphioxus genome does is provide excellent evidence for the idea that Ono proposed in 1970, that the human genome had undergone two rounds of whole-genome duplication with subsequent losses," said coauthor Linda Z. Holland, an expert on the biology and genetics of amphioxus at the Scripps Institution of Oceanography at UC San Diego who led the community effort to sequence and annotate the genome. "We have been kicking that idea around with very little proof for a long time. This genome sequence really clinches that."

Interestingly, the sea squirt Ciona intestinalis, a tunicate, was previously thought to belong to the the earliest chordate lineage because of the sea squirt's very simple body plan. Comparison of the lancelet, sea squirt and human genomes, however, show instead that the lancelet lineage diverged before the tunicates and vertebrates.

"Sea squirts and their relatives have taken the basic chordate genome and simplified it in various ways, while amphioxus retains those features in its genome," said Rokhsar.

The researchers are trying to reconstruct what happened at the end of the Cambrian period 550 million years ago, when a creature similar to the lancelet evolved and diverged into three types of chordates: cephalocordates like the lancelet; urochordates like the sea squirt; and vertebrates like us. Cephalocordates and urochordates are invertebrates that have a flexible notochord rather than a bony spine protecting their spinal cord.

A cephalochordate, Lancelet, also a filter feeder has been regarded as the closest invertebrate relative to the vertebrates, possessing a vertebrate-like body plan, with nothocord, hollow dorsal nerve cord, segmented muscle blocks, perforated pharyngeal region and post anal tai (Image credit: Scienceblog.com)

The Florida lancelet, Branchiostoma floridae, looks a lot like a fish, but has a stiff cartilaginous notochord that it vibrates to swim and burrow in the sand, where it nestles during the day with its head sticking out to filter phytoplankton from the water. The lancelets typically emerge from the sand at night and swim with lateral movements.

"If you think about what the original ancestor of all bilaterally symmetric animals looked like, you can make a pretty good argument that it was a sort of worm-like creature - a finger length-long, floppy kind of worm like amphioxus," Rokhsar said.

With the aim of understanding the evolution of chordates, the JGI sequenced the amphioxus genome using lancelets that Holland collected from the 15-foot-deep waters of Tampa Bay, Fla. A thorough analysis led by Putnam, Rokhsar, Holland and colleagues Peter Holland of Oxford University in the U.K. and Noriyuki Satoh of Kyoto University shows that the creature's 19 chromosomes map onto the human genome in 17 segments, each of which is represented four times in the human genome.

"The human genome is a mosaic of these 17 ancestral pieces constructed by two rounds of duplication, followed by gene loss and chromosome rearrangments and fusions. That took some computational gymnastics to sort out, but the evidence is still there," said Rokhsar.

Putnam's analysis of the genome shows that many of the duplicated genes were subsequently lost, "mainly the housekeeping genes that code for structural proteins, enzymes, metabolic pathways - things you don't really need more than one copy of," Linda Holland said.

However, Rokhsar added, "a class of a couple thousand genes did not return to a single copy. Those extra copies of genes acquired some function that prevented them from being lost. The vast majority are regulatory genes highly enriched for transcription factors and genes involved in developmental signaling."

Holland, a research biologist at Scripps in the Marine Biology Research Division, is the lead author of a companion paper appearing this week in the July issue of the journal Genome Research that looks at these genes in detail to see how vertebrates have employed old genes for new functions.

"We are finding that today's complicated vertebrate has not invented a lot of new genes to become complicated," she said. "Amphioxus shows us that vertebrates have taken old genes and recombined them, changed their regulation and perhaps changed the gene function."

Such duplication has given humans and other vertebrates a much larger "toolkit" for making various structures that are absent in amphioxus, including cells for pigment and collagen type II-based cartilage, for example.
Putnam noted another interesting finding reinforced by the amphioxus genome: Most creatures have a lot more genetic variation than humans. While two humans typically differ at only one nucleic acid per thousand in the genome, two lancelets differ at one of every 16 nucleic acids.

"Marine invertebrates actually vary about 6 percent, which means that, on average, one of every 16 bases is different, which is pretty remarkable - it's the difference between humans and certain types of apes," Putnam said. "Humans really are a special case, because of the recent out-of-Africa bottleneck and because of the size of our population. There is a lot less variation than in these little wormy guys that live by the millions in shallow water."

The amphioxus genome was sequenced by the Department of Energy (DOE) Joint Genome Institute under the auspices of the DOE's Office of Science, Biological and Environmental Research Program, Lawrence Berkeley National Laboratory, Lawrence Livermore National Laboratory and Los Alamos National Laboratory. UC Berkeley's Center for Integrative Genomics is funded by the Gordon and Betty Moore Foundation.

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Source:
UC Berkeley News: http://www.berkeley.edu/news/media/releases/2008/06/18_lancelet.shtml

035: MIT researchers unravel bacteria communication pathways

Science Space (June 18, 2008)--MIT researchers have figured out how bacteria ensure that they respond correctly to hundreds of incoming signals from their environment.

The researchers also successfully rewired the cellular communications pathways that control those responses, raising the possibility of engineering bacteria that can serve as biosensors to detect chemical pollutants. The work is reported in the June 13 issue of Cell.

Led by MIT biology professor Michael Laub, the team studied genomes of nearly 200 bacteria, which can have hundreds of different pathways that respond to different types of external stimuli. Nutrients, antibiotics, temperature or light can evoke a variety of responses, including transcription of particular genes.

Bacteria, both useful & harmful, are everywhere, this morning they reside on your toothbrush (Image credit: myorapure.com)

In most cases, the pathways involve two proteins. The first protein, an enzyme known as a histidine kinase, receives the external signal and then activates the second protein, known as a response regulator.

It's critical that each histidine kinase activate only the appropriate response regulator. Different histidine kinases are often very structurally similar, as are the response regulator proteins, so scientists have wondered how cells prevent signals from getting crossed.

"If an organism has tons of this class of signaling pathway, why do we not get a lot of crosstalk?" said Laub. "How does the kinase pick out the right target?"

Based on earlier studies, the MIT researchers theorized that the specificity of the interaction is determined by a subset of amino acids on the histidine kinase and a corresponding subset of amino acids on the response regulator.

To confirm their theory, they looked for patterns of amino acid co-evolution in pairs of histidine kinases and their target response regulators.

Co-evolution occurs when a mutation in one of the two proteins is followed by a secondary mutation in the corresponding amino acid on the other protein, allowing the protein pair to maintain their interaction.

After searching a vast database of nearly 1,300 protein pairs, they identified a small set of co-evolved amino acids. They then confirmed that these amino acids govern signaling specificity by successfully rewiring five of the pathways by mutating the target amino acids.

Such manipulation could allow scientists to engineer bacteria that exhibit novel behavior such as glowing when they detect the presence of a pollutant such as toluene, said Laub.

Lead author of the paper is Jeffrey Skerker, a former MIT postdoctoral associate now at the Broad Institute. Other MIT authors are Barrett Perchuk, technical associate in the Department of Biology, and graduate students Emma Lubin and Orr Ashenberg.

The research was funded by the U.S. Department of Energy and the National Institutes of Health.

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Source:
MIT news
http://web.mit.edu/newsoffice/2008/cell-rewire-0612.html

030: Coffee Beans may be newest stress-buster

Life Science Space (June 16, 2008) -- Just inhaling the aroma activated anxiety-relieving genes, rat research shows

Just sniffing that first hot cup of coffee in the morning may help ease some stresses you might be feeling, a South Korean trial indicates.

When rats inhaled the aroma of roasted coffee beans, a number of genes were activated, including some that produce proteins with healthful antioxidant activity, the researchers reported.

"The meaning of it is not totally clear yet," said Dr. Peter R. Martin, director of the Institute of Coffee Studies at Vanderbilt University. "What it does show is that coffee smells do change the brain to some degree, and it behooves us to understand why that is happening."

The findings, from a team led by Han-Seok Seo at Seoul National University in South Korea, were expected to be published in the June 25 issue of the Journal of Agricultural and Food Chemistry.

The experiment was done with laboratory rats, some of whom were stressed by being deprived of sleep. The researchers did detailed genetic studies that showed the activity of 11 genes was increased and the activity of two genes was decreased in the rats that smelled the coffee, compared to those who did not. In effect, the aroma of the coffee beans helped ease the stress of the sleep-deprived rodents.

The experiment provides "for the first time, clues to the potential antioxidant or stress-relaxation activities of the coffee bean aroma," the researchers wrote.

And they added, "These results indirectly explain why so many people use coffee for staying up all night, although the volatile compounds of coffee beans are not fully consistent with those of the coffee extracts. In other words, the stress caused by sleep loss via caffeine may be alleviated through smelling the coffee aroma."

"They used the latest in technology to see how brain expression of RNA changed," Martin said. RNA is the molecule that carries out the instructions encoded in genes. "This is just the beginning of a very interesting line of investigation," he added.

The aromatic compounds responsible for coffee's odor may be antioxidants, "but they are not the same as the major antioxidants that are in the drink," said Joe A. Vinson, a chemistry professor at the University of Scranton in Pennsylvania.

Chemically, the antioxidants in liquid coffee are polyphenols, Vinson said. Those in the aroma are heterocycle compounds containing sulfur or nitrogen atoms.

"There are two ways to get things into your system, and the quickest way is to smell them," Vinson said. "Caffeine gets into the brain via the blood stream. Here, aromatic molecules get into the brain through the olfactory system. The levels in the air are parts per million, so obviously these are minor components in the air. But they are doing something."

Previous studies have shown that coffee consumption can reduce depression and suicide risk, as well as relieve stress, effects generally attributed to the caffeine in coffee, the researchers noted. But while some 900 compounds that float away from the bean have been identified, this is the first study to assay their possible effects, they added.

It's too early to recommend that people feeling stress sniff coffee to ease their way, Martin said. But, he added, "people who don't even drink coffee are fascinated by the odor of it. Ever since my little boy was two years old, he has loved the odor of coffee. I have always thought that coffee has some mystic quality, and there is some deep historical basis for it."

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Source:
http://health.usnews.com/articles/health/healthday/2008/06/13/coffee-beans-may-be-newest-stress-buster.html

See also @

Coffee Beans May Be Newest Stress-Buster--http://www.healthfinder.gov/news/newsstory.asp?docid=616459
Coffee's Aroma Kick-starts Genes In The Brain--http://www.sciencedaily.com/releases/2008/06/080616092116.htm
Coffee Perks--http://www.forbes.com/health/2005/10/11/coffee-health-benefits-cx_sy_1012feat_ls.html

026: Scientists discover gene linked to adult-onset obesity

gene is the basic unit of heredity

(Image Credit: library.thinkquest.org)

Life Science Space (June 10, 2008)--Researchers at the University of Minnesota have discovered a gene that may provide a clue as to why obesity rates increase with age. The research was published today in the Proceedings of the National Academy of Sciences.

Researchers in the lab of Kevin Wickman, Ph.D., associate professor of pharmacology at the University of Minnesota Medical School, removed a single gene from mice as part of an ongoing study to understand how the brain controls heart function. While some cardiac deficiencies were detected in these mice, the researchers unexpectedly found that these mice exhibited a predisposition to adult-onset obesity. "This was not an outcome we expected, but now we have an animal model that may provide new insight into human obesity," said Wickman, co-author of the article.

By examining closely where this gene, termed Girk4, is expressed in the body, the researchers found particularly high levels in the hypothalamus, a brain region involved in regulating food intake and energy expenditure. Wickman speculated that disruption of normal function in the hypothalamus may underlie the obesity seen in the mutant mice, but he acknowledges that more research is needed to understand where and how this gene works, and consequently, why mice missing this gene develop obesity.

The age-dependence of the obesity seen in this mouse model mimics human obesity patterns, researchers said. Indeed, the likelihood of people developing obesity more than doubles between the ages of 20 and 60.

"This is a novel finding that may provide important new insight to the underlying cellular mechanisms that influence obesity," said Catherine Kotz, Ph.D., co-author of the article, scientist at the Minneapolis VA Medical Center and adjunct professor in the Department of Food Science and Nutrition at the University of Minnesota.

This research was funded by the University of Minnesota Graduate School, a pilot award from the Minnesota Obesity Consortium, and a grant from the National Institutes of Health. The research was conducted in collaboration with the Department of Veterans Affairs.

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Article provided by eurekalert: http://www.eurekalert.org/pub_releases/2008-06/uom-uom061008.php

See also:
Predisposition to late-onset obesity in GIRK4 knockout mice

http://www.pnas.org/cgi/content/abstract/0803261105v1

Gene Linked To Adult-onset Obesity Discovered
www.sciencedaily.com/releases/2008/06/080610105943.htm

Girk4 Gene May Hold the Key to Why Obesity Increases with Age
www.seniorjournal.com/NEWS/Health/2008/20080610-2-Girk4.htm

025: Woolly mammoth family tree grows a new branch

Life Science Space (June 9, 2008)--Two bands of woolly brothers roamed the Siberian snows.

Wandering the snowy plains of Siberia up to 40,000 years ago lived not one, but two groups of long-haired and curly-tusked woolly mammoth, side by side.

An international team led by Thomas Gilbert at the University of Copenhagen in Denmark has sequenced five new complete genomes of mitochondrial DNA (mtDNA) of woolly mammoths (Mammuthus primigenius ). The tally of complete mtDNA genomes for this hairy beast now totals 18. The work is published in the Proceedings of the National Academy of Sciences (1).

Cold counterparts? Siberia's mammoths seem to have been split into two distinct groups (Image Credit: Britannica.com)

Gilbert and his team subjected five hair samples to a new technique that allows entire mtDNA genomes to be sequenced from a single piece of hair 2. His haul, when added to 13 previously-sequenced samples provided enough distinct samples to show that the woolly mammoth existed as two groups, or clades, originating from a common ancestor.

The two clades lived in the same place at the same time — although the mammoths from one clade stuck to one small area, and died off much sooner than their relations in the other clade.

Like mother, like childThe DNA in mitochondria is passed only through the mother’s line, and doesn’t give information about changes in gene function, as nuclear DNA can. But it is useful because it doesn’t change from parent to offspring, making it easy to show when different animal groups are present.

Gilbert and his co-workers found that the mtDNA sequences were obviously different between the two clades. They then looked at the geographical locations of the different beasts, and used carbon dating methods to deduce when the animals lived. “You can see that you get both groups in the same place at the same time,” says Gilbert. But the two groups had quite different tendencies to roam. One group “is quite geographically limited”, says Gilbert. It stayed in the middle of the high Arctic, whereas the other group wandered much farther afield, he says.

Carbon dating shows that mammoths in the group with the limited range became extinct around 40,000 years ago, whereas the wider-ranging mammoths were still wandering the same areas until around 10,000 years ago.

Gilbert points out that carbon dating can have wide error margins, so we will never know with certainty that both groups were there at the same time. “We can’t get any closer [without] going back in time and seeing.”
Hairy dataThe work shows the usefulness of the technique to get genetic information from hair — previously thought to be a very poor source of DNA — says Adrian Lister, from the Natural History Museum in London, UK. But the question of groups and species will take a while to work out, he says. “It is too soon to say if the mitochondrial clades represent two groups, subspecies or, at the extreme, species,” says Lister. “The genetics has not yet been related to morphology."

Without nuclear DNA analysis, Gilbert can’t answer this question, but he is working on this now. “It’s really hard to call,” he says, but he thinks that the mtDNA work hints at something more than just groups of different mammoths. “My hope is that there are two different subspecies,” he says.

Reference:
(1) Gilbert, M. T. P. et al. Proc. Nat. Acad. Sci. USA advance online publication doi: 10.1073/pnas.0802315105 (2008).

(2) Gilbert, M. T. et al. Science 317, 1927–1930 (2007).

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Nature News: http://www.nature.com/news/2008/080609/full/news.2008.881.html

012: DNA defect may fix with vitamin supplement

Life Science Space (June 3, 2008)--As the cost of sequencing a single human genome drops rapidly, with one company predicting a price of $100 per person in five years, soon the only reason not to look at your "personal genome" will be fear of what bad news lies in your genes.

University of California, Berkeley, scientists, however, have found a welcome reason to delve into your genetic heritage: to find the slight genetic flaws that can be fixed with remedies as simple as vitamin or mineral supplements."I'm looking for the good news in the human genome," said Jasper Rine, UC Berkeley professor of molecular and cell biology.

"Headlines for the last 20 years have really been about the triumph of biomedical research in finding disease genes, which is biologically interesting, genetically important and frightening to people who get this information," Rine said. "I became obsessed with trying to decide if there is some other class of information that will make people want to look at their genome sequence."

What Rine and colleagues found and report this week in the online early edition of the journal Proceedings of the National Academy of Sciences (PNAS) is that there are many genetic differences that make people's enzymes less efficient than normal, and that simple supplementation with vitamins can often restore some of these deficient enzymes to full working order.

First author Nicholas Marini, a UC Berkeley research scientist, noted that physicians prescribe vitamins to "cure" many rare and potentially fatal metabolic defects caused by mutations in critical enzymes. But those affected by these metabolic diseases are people with two bad copies, or alleles, of an essential enzyme. Many others may be walking around with only one bad gene, or two copies of slightly defective genes, throwing their enzyme levels off slightly and causing subtle effects that also could be eliminated with vitamin supplements."Our studies have convinced us that there is a lot of variation in the population in these enzymes, and a lot of it affects function, and a lot of it is responsive to vitamins," Marini said. "I wouldn't be surprised if everybody is going to require a different optimal dose of vitamins based on their genetic makeup, based upon the kind of variance they are harboring in vitamin-dependent enzymes."

Though this initial study tested the function of human gene variants by transplanting them into yeast cells, where the function of the variants can be accurately assessed, Rine and Marini are confident the results will hold up in humans. Their research, partially supported by the Defense Advanced Research Projects Agency (DARPA) and the U.S. Army, may enable them to employ U.S. soldiers to test the theory that vitamin supplementation can tune up defective enzymes.

"Our soldiers, like top athletes, operate under extreme conditions that may well be limited by their physiology," Rine said. "We're now working with the defense department to identify variants of enzymes that are remediable, and ultimately hope to identify troops that have these variants and test whether performance can be enhanced by appropriate supplementation."

In the PNAS paper, Rine, Marini and their colleagues report on their initial analysis of variants of a human enzyme called methylenetetrahydrofolate reductase, or MTHFR. The enzyme, which requires the B vitamin folate to work properly, plays a key role in synthesizing molecules that go into the nucleotide building blocks of DNA. Some cancer drugs, such as methotrexate, target MTHFR to shut down DNA synthesis and prevent tumor growth.

Using DNA samples from 564 individuals of many races and ethnicities, colleagues at Applied Biosystems of Foster City, Calif., sequenced for each person the two alleles that code for the MTHFR enzyme. Consistent with earlier studies, they found three common variants of the enzyme, but also 11 uncommon variants, each of the latter accounting for less than one percent of the sample.

Electron microscope image of budding yeast, Saccharomyces cerevisiae.

UC Berkeley researchers insert variants of human enzymes into yeast to see if these enzymes can be tuned up with vitamins. (Image Credit: UC Berkeley)

They then synthesized the gene for each variant of the enzyme, and Marini, Rine and their UC Berkeley colleagues inserted these genes into separate yeast cells in order to judge the activity of each variant. Yeast use many of the same enzymes and cofactor vitamins and minerals as humans and are an excellent model for human metabolism, Rine said.

The researchers found that four different mutations affected the functioning of the human enzyme in yeast. One of these mutations is well known: Nearly 30 percent of the population has one copy, and nine percent has two copies.

The researchers were able to supplement the diet of the cultured yeast with folate, however, and restore full functionality to the most common variant, and to all but one of the less common variants.

Since this experiment, the researchers have found 30 other variants of the MTHFR enzyme and tested about 15 of them, "and more than half interfere with the function of the enzyme, producing a hundred-fold range of enzyme activity. The majority of these can be either partially or completely restored to normal activity by adding more folate. And that is a surprise," Rine said.

Most scientists think that harmful mutations are disfavored by evolution, but Rine pointed out that this applies only to mutations that affect reproductive fitness. Mutations that affect our health in later years are not efficiently removed by evolution and may remain in our genome forever.

The health effects of tuning up this enzyme in humans are unclear, he said, but folate is already known to protect against birth defects and seems to protect against heart disease and cancer. At least one defect in the MTHFR enzyme produces elevated levels in the blood of the metabolite homocysteine, which is linked to an increased risk of heart disease and stroke, conditions that typically affect people in their post-reproductive years. "In those people, supplementation of folate in the diet can reduce levels of that metabolite and reduce disease risk," Marini said.

Destroying cancer with its favorite food, folate (vitamin B). any types of cancer cells have a great appetite for folate because they need the nutrient to grow. In fact, cancer cells have evolved a mechanism to capture folate more effectively than normal cells. (Image Credit: Endocyte Inc.)

Marini and Rine estimate that the average person has five rare mutant enzymes, and perhaps other not-so-rare variants, that could be improved with vitamin or mineral supplements. "There are over 600 human enzymes that use vitamins or minerals as cofactors, and this study reports just what we found by studying one of them," Rine said. "What this means is that, even if the odds of an individual having a defect in one gene is low, with 600 genes, we are all likely to have some mutations that limit one or more of our enzymes."

The subtle effects of variation in enzyme activity may well account for conflicting results of some clinical trials, including the confusing data on the effect of vitamin supplements, he noted. In the future, the enzyme profile of research subjects will have to be taken into account in analyzing the outcome of clinical trials.

If one considers not just vitamin-dependent enzymes but all the 30,000 human proteins in the genome, "every individual would harbor approximately 250 deleterious substitutions considering only the low-frequency variants. These numbers suggest that the aggregate incidence of low-frequency variants could have a significant physiological impact," the researchers wrote in their paper.

All the more reason to poke around in one's genome, Rine said. "If you don't give people a reason to become interested in their genome and to become comfortable with their personal genomic information, then the benefits of much of the biomedical research, which is indexed to particular genetic states, won't be embraced in a time frame that most people can benefit from," Rine said. "So, my motivation is partly scientific, partly an education project and, in some ways, a partly political project."

Marini and Rine credit Bruce Ames, a UC Berkeley professor emeritus of molecular and cell biology now on the research staff at Children's Hospital Oakland Research Institute, with the research that motivated them to look at enzyme variation. Ames found in the 1970s that many bacteria that could not produce a specific amino acid could do so if given more vitamin B6, and in recent years he has continued exploring the link between micronutrients and health.

"Looked at in one way, Bruce found that you can cure a genetic disease in bacteria by treating it with vitamins," Rine said. Because the human genome contains about 6 billion DNA base pairs, each one subject to mutation, there could be between 3 and 6 million DNA sequence differences between any two people. Given those numbers, he reasoned that, as in bacteria, "there should be people who are genetically different in terms of the amount of vitamin needed for optimal performance of their enzymes."

This touches on what Rine considers one of the key biomedical questions today. "Now that we have the complete genome sequences of all the common model organisms, including humans, it's obvious that the defining challenge of biology in the 21st century is not what the genes are, but what the variation in the genes does," he said.

Rine, Marini and their colleagues are continuing to study variation in the human MTHFR gene as well as other folate utilizing enzymes, particularly with respect to how defects in these enzymes may lead to birth defects. Rine also is taking advantage of the 1,500 students in his Biology 1A lab course to investigate variants of a second vitamin B6-dependent enzyme, cystathionine beta-synthase.

He also is investigating how enzyme cofactors like vitamins and minerals fix defective enzymes. He suspects that supplements work by acting as chaperones to stabilize the proper folding of the enzyme, which is critical to its catalytic activity. "That is a new principle that may be applicable to drug design," Rine said.

Coauthors with Rine and Marini are UC Berkeley research assistant Jennifer Gin and Janet Ziegle, Kathryn Hunkapiller Keho, David Ginzinger and Dennis A. Gilbert of Applied Biosystems, which also funded part of the study. The work was supported by a University of California Discovery Grant, DARPA and the National Institutes of Health.

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Article providied by UC Berkeley: http://www.berkeley.edu/news/media/releases/2008/06/02_genomes.shtml

008: sex chromosome secret revealed

If a sperm with an X chromosome unites with an egg cell, the result is a baby girl.

If a sperm carrying a Y chromosome unites with an egg cell, the result is a baby boy.

Life Science Space (May 29, 2008)--An enzyme that binds differently to male and female sex chromosomes helps males to make up for their X chromosome shortage.

Researchers from the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, and the EMBL-European Bioinformatics Institute (EMBL-EBI) in Hinxton, UK, have revealed new insights into how sex chromosomes are regulated. A chromatin modifying enzyme helps compensate for the fact that males have only one copy of the sex chromosome X, while females have two. The enzyme distinguishes between male and female sex chromosomes in fruit flies and binds to different locations on the male and female X chromosome, the scientists report in the current issue of the journal Cell. The evolutionarily conserved enzyme is also found in humans.

In species ranging from insects to humans, sex chromosomes, the famous X and Y, are responsible for determining gender. Females have two copies of the X chromosome while males have one X and one Y. This could mean that females produce twice as many proteins from the genes carried on the X chromosome as males. However, fruit flies compensate for the sex chromosome difference by doubling the activity of genes on the X chromosome in males – a vital process called dosage compensation. Biologists already know that a molecular machine called the MSL complex achieves dosage compensation in flies, but it remains unclear how exactly it accomplishes its function.

Now researchers from the lab of Asifa Akhtar at EMBL and the groups of Nick Luscombe and Paul Bertone at EMBL-EBI have uncovered how one component of the MSL complex, an enzyme called MOF, ensures that the activity of only male X chromosome genes get ratcheted up. MOF relaxes the structure of chromatin – tightly packaged DNA, to allow the transcription machinery to access genes on the DNA.

“We were very surprised to find MOF bound not only to the X chromosome in males, but also to all the other chromosomes in the nucleus. This suggests the enzyme as a universal regulator of transcription that has evolved to play a specific role in dosage compensation,” says Akhtar.

A closer look revealed that MOF binds differently to chromosomes from males and females. On autosomes, chromosomes that are not involved in determining sex, and the X chromosome in females, MOF binds mostly to the beginning of a gene where transcription starts. On the X chromosome in males, however, MOF binds also towards the end of the gene. Most likely MOF opens up the DNA towards the end of the genes and ensures that transcription is completed successfully.

“One can imagine the transcriptional machinery moving along the DNA like a train on a railway track. When the tracks are blocked the train could derail, resulting in incomplete transcription,” explains Juanma Vaquerizas of Luscombe’s lab, who contributed to the analysis of Akhtar’s data. “It appears that MOF clears the tracks throughout the male X chromosome, while on a female X obstructions are more likely to occur.”

More complete transcription results in more proteins produced from the single X chromosome in males than from either of the two X chromosomes in females, thereby balancing out their excess. MOF is the first enzyme in the MSL complex to behave differently according to whether the target gene is located on the sex chromosome versus other chromosomes in males.

“MOF is conserved across species and also has a human homolog. Since the mechanism of dosage compensation is radically different in mammals, it will be very interesting to discover what functional role this enzyme might play in that context,” says Bertone.

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Source: http://www.eurekalert.org/pub_releases/2008-05/embl-xce052908.php

001: First DNA Sequencing of a Woman

Life Science Space (May 27, 2008)--In 2001, the DNA sequence was published of a combination of persons. The DNA sequences of Jame Watson, discoverer of the DNA’s double helix structure, followed in 2007, and later the DNA of gene hunter Craig Venter. Recently the completion of the sequences of two Yoruba Africans was announced.

Now geneticists of Leiden University Medical Centre (LUMC) in The Netherlands have determined the first DNA sequence of a woman, Dr. Marjolein Kriek, a clinical geneticist at LUMC- and also the first European. This has been announced by the researchers during a special press conference at 'Bessensap', a yearly meeting of scientists and the press in the Netherlands. Following in-depth analysis, the sequence will be made public, except incidental privacy-sensitive findings. The results will contribute to insights into human genetic diversity

22 billion base pairs - eight times the size of the human genome.

The DNA sequencing was done with the Illumina 1G equipment. This has been installed in January 2007 in the Leiden Genome Technology Center, the genomics facility of LUMC and CMSB. In total, approx. 22 billion base pairs (the ‘letters’ of the DNA language) were read. That is almost eight times the size of the human genome.

Dr. Johan den Dunnen, project leader at the Leiden Genome Technology Center: "This high coverage is needed to prevent mistakes, connect the separate reads and reduces the chance of occasional uncovered gaps." Johan den Dunnen: "The sequencing itself took about six months. Partly since it was run as a ‘side operation’ filling the empty positions on the machine while running other projects. Would such a job be done in one go, it would take just ten weeks.”

The cost of the project was approximately €40.000, which does not include further in-depth bioinformatics analysis.

The researchers announced their news at the yearly ‘Bessensap’ meeting, bringing together the Dutch scientists and the press. The Netherlands Organization for Scientific Research NWO organizes this event jointly with the Association of Science Writers VWN and Science Center NEMO.

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Adapted from materials provided by Leiden University Medical Centre.
see more details @

1. First DNA Sequencing Of A Human Female-- http://www.eurekalert.org/pub_releases/2008-05/nofs-lss052708.php


2. First Female DNA Sequenced-- http://www.sciencedaily.com/releases/2008/05/080526155300.htm