Category Archives: Transhuman News

Great, wonderful, wacky things can come in small genomic packages.

That's one lesson to be learned from the carnivorous bladderwort, a plant whose tiny genome turns out to be a jewel box full of evolutionary treasures.

Called Utricularia gibba by scientists, the bladderwort is a marvel of nature. It lives in an aquatic environment. It has no recognizable roots. It boasts floating, thread-like branches, along with miniature traps that use vacuum pressure to capture prey.

A new study in the scientific journal Molecular Biology and Evolution breaks down the plant's genetic makeup, and finds a fascinating story.

According to the research, the bladderwort houses more genes than several well-known plant species, such as grape, coffee or papaya -- despite having a much smaller genome.

This incredibly compact architecture results from a history of "rampant" DNA deletion in which the plant added and then eliminated genetic material at a very fast pace, says University at Buffalo Professor of Biological Sciences Victor Albert, who led the study.

"The story is that we can see that throughout its history, the bladderwort has habitually gained and shed oodles of DNA," he says.

"With a shrunken genome," he adds, "we might expect to see what I would call a minimal DNA complement: a plant that has relatively few genes -- only the ones needed to make a simple plant. But that's not what we see."

A unique and elaborate genetic architecture

In contrast to the minimalist plant theory, Albert and his colleagues found that U. gibba has more genes than some plants with larger genomes, including grape, as already noted, and Arabidopsis, a commonly studied flower.

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Carnivorous plant packs big wonders into tiny genome

Geneticist Eric S. Lander, one of the principal leaders of the Human Genome Project that mapped the entire human genome in 2003, offered a rare glimpse into the genetic library of life being created by a global community of scientists. This veritable catalogue has already begun to help decode the genetic basis of certain cancers, heart disease and schizophrenia.

A packed audience of students, scientists and medical practitioners heard Prof Lander speak on The Human Genome and Beyond: A 35 year Journey of Genomic Medicine at the fifth edition of the Cell Press-TNQ Distinguished Lectureship Series at the All India Institute of Medical Sciences here on Monday.

Over the last decade, genetic research has been revolutionised and the costs of genome sequencing have dropped drastically. While mapping a single human genome (as part of the Human Genome Project 1990-2003) costs $3 billion, today it costs less than $ 3,000.

This breakthrough opens up enormous opportunities to understand diseases, he said. Today, for instance, over 108 genes can be associated with schizophrenia, and particular genetic mutations can be linked to heart attacks early in life.

And yet, we have only scratched the surface, Prof Lander said. Discoveries require studying huge samples for every major disease. And for that our healthcare systems have to turn into learning systems.

The Global Alliance for Genomics and Health comprising 246 organisations in 28 countries -- including India -- is one such endeavour to create a critical mass of data.

It is imperative, however that the data remains shareable, said Prof Lander, who is the Founding Director of the Broad Institute (linking MIT, Harvard University and hospitals).

But genetic data must belong to patients, who have the right to share it with their privacy protected.

India, with the extraordinary size of its population is, from the genetic point of view, the single most interesting population in the world.

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From the first human genome, to a great library of life

A study that examined 17 million mutations in the genomes of 650 cancer patients concludes that large differences in mutation rates across the human genome are caused by the DNA repair machinery.

'DNA spellchecker' is preferentially directed towards more important parts of chromosomes that contain key genes.

The study illustrates how data from medical sequencing projects can answer basic questions about how cells work.

The work, performed by two scientists from the EMBL-CRG Systems Biology Unit in Barcelona, will be published online in Nature on 23rd February. Copying the large book that it is our genome without mistakes every time a cell divides is a difficult job. Luckily, our cells are well-equipped to proof-read and repair DNA mistakes. Now, two scientists at the Centre for Genomic Regulation in Barcelona have published a study showing that mistakes in different parts of our genome are not equally well corrected. This means that some of our genes are more likely to mutate and so contribute to disease than others.

The scientists analysed 17 million 'single nucleotide variants' -- mutations in just one nucleotide (letter) of the DNA sequence -- by examining 650 human tumours from different tissues. These were 'somatic' mutations, meaning they are not inherited from parents or passed down to children, but accumulate in our bodies as we age. Such somatic mutations are the main cause of cancer. Many result from mutagens, such as tobacco smoke or ultraviolet radiation, and others come from naturally occurring mistakes in copying DNA as our tissues renew.

Ben Lehner and his team had previously described that somatic mutations are much more likely in some parts of the human genome, thus damaging genes that may cause cancer. In a new paper published on 23rd February in Nature, they show that this is because genetic mistakes are better repaired in some parts of the genome than in others. This variation was generated by a particular DNA repair mechanism called "mismatch repair" -- a sort of a spellchecker that helps fix the errors in the genome after copying. Lehner and Supek show that the efficiency of this 'DNA spellchecker' varies depending on the region of the genome, with some parts of chromosomes getting more attention than others.

Turning the tables on mutation rates

The work presented by Lehner and Supek sheds new light on a process that was unexplored -- what makes some parts of the human genome more vulnerable to damage? "We found that regions with genes switched on had lower mutation rates. This is not because less mistakes are happening in these regions but because the mechanism to repair them is more efficient," explains Ben Lehner, group leader, ICREA and AXA professor of risk prediction in age-related diseases at the EMBL-CRG Systems Biology unit in Barcelona. The 'mismatch repair' cellular machinery is extremely accurate when copying important regions containing genes that are key for cell functioning, but becomes more relaxed when copying less important parts. In other words, there appears to be a limited capacity for DNA repair in our cells, which is directed where it matters most.

The CRG researchers also found that the rate of mutation differs for around 10% of the human genome in cells originating from different tissues. In particular, liver, colorectal and lymphocyte malignancies present more mutations in some parts of our chromosomes, while breast, ovarian and lung cancers accumulate more mutations in other places. They found that genes that are important and switched on (expressed) in a particular tissue also exhibit less mutations in tumours of that tissue; the effect extends into the surrounding DNA. But what gives the important genes a higher resilience to damage?

"The difference is not in the number of new mutations but in the mechanism that keeps these mutations under control," comments Fran Supek, CRG postdoctoral researcher and first author of the paper. "By studying cancer cells, we now know more about maintaining DNA integrity, which is really important for healthy cells as well," he adds. Once the 'genomic spellchecker' has been disabled in a cell, the scientists observed that genetic information started decaying not only very rapidly, but also equally in all parts of the genome -- neither the important nor the less important parts can were repaired well anymore. DNA mismatch repair is known to be switched off in some tumours from the colon, stomach and uterus, producing 'hypermutator' cancer in those organs.

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'DNA spellchecker' means that genes aren't all equally likely to mutate

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Newswise (PHILADELPHIA) According to the public databases, there are currently approximately 1,900 locations in the human genome that produce microRNAs (miRNAs), the small and powerful non-coding molecules that regulate numerous cellular processes by reducing the abundance of their targets. New research published in the Proceedings of the National Academy of Sciences (PNAS) this week adds another roughly 3,400 such locations to that list. Many of the miRNA molecules that are produced from these newly discovered locations are tissue-specific and also human-specific. The finding has big implications for research into how miRNAs drive disease.

By analyzing human deep-sequencing data, we discovered many new locations in the human genome that produce miRNAs. Our findings effectively triple the number of miRNA-generating loci that are now known says Isidore Rigoutsos, Ph.D., Director of the Computational Medicine Center at Thomas Jefferson University, who led the study. This new collection will help researchers gain insights into the multiple roles that miRNAs play in various tissues and diseases.

For nearly three years, the team collected and sequenced RNA from dozens of healthy and diseased individuals. The samples came from pancreas, breast, platelets, blood, prostate, and brain. To their collection they also added publicly available data eventually reaching more than 1,300 analyzed samples representing 13 human tissue types. Their analyses uncovered 3,356 new locations in the human genome that generate over 3,700 previously undescribed miRNAs.

For a handful of the 13 tissues they studied, the team also had access to information describing miRNA association with Argonaute, an essential protein member of the regulatory complex that enables miRNA to interact with their targets. They found that 45 percent of the newly discovered miRNAs were in fact associated with Argonaute, a further indication that these molecules are involved in gene regulation. We anticipate that many more of the newly discovered miRNAs will be found loaded on Argonaute as additional such data become available for the other tissues, says Eric Londin, Ph.D., an Assistant Professor and co-first author together with Phillipe Loher, M.S., a computational biologist and software engineer, both members of Jeffersons Computational Medicine Center.

One of the key design choices that the team made was to not limit their search to conserved genomic sequences, i.e. to only those sequences that are shared across multiple organisms. Instead the researchers scanned the genome much more broadly. Advances in sequencing technology of the last several years made it easier to generate more data, from more tissues, and do so faster, says Dr. Rigoutsos who is also a researcher at the Sidney Kimmel Cancer Center at Jefferson. Investigating the alluring possibility that miRNAs with important roles might exist only in humans was within reach. And this is what we set out to do.

Of the new molecules, 56.7 are specific to humans and most of them (94.4 percent) are found only in primates. Because of this organism-specificity these RNA molecules are involved in regulatory events that are absent from model organisms such as mouse and the fruit fly.

Tissue-specificity is another important characteristic of these new miRNAs. It means that these molecules are behind molecular events that are present in a single tissue, or in only a few tissues. Some of these molecules could potentially prove useful as novel tissue-specific disease biomarkers.

The tissue- and primate-specificity of the new molecules are expected to have important implications for the communitys attempts to understand the causes of diseases. A first step in that direction requires the identification and validation of the targets for each of these 3,707 new miRNAs. To assist in these efforts, the team generated computational predictions of each miRNAs putative targets that are available from the Computational Medicine Centers website.

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Study Nearly Triples the Locations in the Human Genome That Harbor MicroRNAs