Monday, September 8, 2008

The DNA Network

The DNA Network

Genome Quilts! []

Posted: 08 Sep 2008 07:58 PM CDT

Stop everything you’re doing. Via BoingBoingGenome quilts!

Personal Genetics Education Project: Lesson 1 [Think Gene]

Posted: 08 Sep 2008 06:21 PM CDT

Dana Waring and colleagues at the Personal Genetics Education Project have put together an excellent set of resources for teachers and professors. The first few lesson plans are freely available for download at

For example, the first lesson plan is geared toward a general discussion of ethical questions regarding genetic testing and possible consequences. Discussion centers on the story of a young girl who, after watching her grandfather’s decline due to Huntington’s, decided to get herself tested and the fallout that ensued upon learning she tested positive.

There has been much media hype lately about genetic tests and genome wide SNP tests from companies such as 23andme and Navigenics, yet, many do not have a working understanding genetic testing and its implications. Waring does a good job discussing the possible negative outcomes of having a genetic test, and she demonstrates why it’s so important to consult with a physician or genetic counselor before getting a high penetrance genetic test such as the one for Huntington’s. Students are forced to think about the issues at hand and how genetic testing will play a large role in not only their medical futures, but also their day to day lives.

I’m looking forward to reviewing more of Dana and her team’s material, and I hope professors and teachers who read Think Gene will consider taking advantage of this educational resource and integrate it into their curriculum. This generation of students will be the first to have to make decisions about genetic tests, and I feel it’s our duty to properly educate them so they are prepared.

Back after a delay [The Daily Transcript]

Posted: 08 Sep 2008 05:58 PM CDT

Sorry folks, my new apartment is not yet hooked up to the web and on top of that I was down in NYC last week. As a result no new posts. And no facts ... but as soon as I have some time I'll continue that series. If you have some facts or stats about the current state of the US please post it (them) and alert me. These last few years have culminated into a horrible empirical result, a GOP lead government leads to failure. However the focus of this election has not been on that simple fact but instead seems to be about CRAP.

PS Over the weekend I picked up Naomi Klein's The Shock Doctrine, it is by far the best book I've read in the past few years. And if you've never read it be sure to get a copy of her other great book, No Logo.

PPS There's a Documentary out on Klein's book directed by Alfonso Cuarón. Here's a brief clip:

Read the comments on this post...

Do 68 molecules hold the key to understanding disease? [Think Gene]

Posted: 08 Sep 2008 03:25 PM CDT

Josh: Dr. Marth brings up some very good points. Many signaling molecules in cells are not just composted of proteins, but may be molecules that are a combination of protein and sugar (glycoprotein) or protein and fatty acid. Fatty acids alone may be signaling molecules, such as fatty acid derived prostanoids via cyclooxygenase (COX) that play a role in pain signaling. Since these molecules are created by enzymes, studying the genome or proteome alone is not sufficient to understand diseases caused or influenced by defects in them.

Why is it that the origins of many serious diseases remain a mystery? In considering that question, a scientist at the University of California, San Diego School of Medicine has come up with a unified molecular view of the indivisible unit of life, the cell, which may provide an answer.

Reviewing findings from multiple disciplines, Jamey Marth, Ph.D., UC San Diego Professor of Cellular and Molecular Medicine and Investigator with the Howard Hughes Medical Institute, realized that only 68 molecular building blocks are used to construct these four fundamental components of cells: the nucleic acids (DNA and RNA), proteins, glycans and lipids. His work, which illustrates the primary composition of all cells, is published in the September issue of Nature Cell Biology.

Like the periodic table of elements, first published in 1869 by Russian chemist Dmitri Mendeleev, is to chemistry, Marth’s visual metaphor offers a new framework for biologists.

This new illustration defines the basic molecular building blocks of life and currently includes 32 glycans (sugar linkages found throughout the cell) and eight kinds of lipids (which compose cell membranes) along with the more well-known 20 amino acids that are used to make proteins and the eight nucleosides that compose the nucleic acids, DNA and RNA.

“These 68 building blocks provide the structural basis for the molecular choreography that constitutes the entire life of a cell,” said Marth. “And two of the four cellular components are produced by these molecular building blocks in processes that cannot be encoded by the genes. These cellular components – the glycans and lipids – may now hold the keys to uncovering the origins of many grievous diseases that continue to evade understanding.”

Currently, the vast majority of medical research looks to the human genome and proteome for answers, but those answers remain elusive, and perhaps for good reason.

“We have now found instances where the pathogenesis of widespread and chronic diseases can be attributed to a change in the glycome, for example, in the absence of definable changes in the genome or proteome,” Marth said, adding that, as biomedical researchers, “we need to begin to cultivate the integration of disciplines in a holistic and rigorous way in order to perceive and most effectively manipulate the biological mechanisms of health and disease.”

“What is important is that no one has composed it and laid it out so clearly before,” said Ajit Varki, M.D., Distinguished Professor of Medicine and Cellular and Molecular Medicine and founder and co-director of the Glycobiology Research and Training Center at UC San Diego School of Medicine, and chief editor of the major textbook in the field, The Essentials of Glycobiology. “Glycobiology, for example, is a relatively new field of study in which researchers at UC San Diego have much expertise, and Dr. Marth’s work further illustrates the importance of these glycan molecules.”

Marth believes that biology should become more integrative both in academic and research settings. “I’m one who believes that we don’t need to sacrifice breadth of knowledge in order to acquire depth of understanding.”

Source: University of California - San Diego

A unified vision of the building blocks of life. Jamey D. Marth. Nature Cell Biology. September 2008 - Vol 10 No 9. doi:10.1038/ncb0908-1015

LHC's first beam on Wednesday... [Bayblab]

Posted: 08 Sep 2008 12:24 PM CDT

If you're reading the bayblab you're probably as excited as us about the LHC getting switched on this week (and maybe you have that tune in your head). Well the good news is that you'll be able to watch it live in a webcast. And in the odd chance that the doomsday sayers were right, you'll have front seats to the apocalypse. For folks in Ottawa the show should be on at 3:00 AM on Wed. For others check here.

Privacy vs. Technology: Selling Your Surfing Habits to Advertisers [adaptivecomplexity's column]

Posted: 08 Sep 2008 11:31 AM CDT

Is it eavesdropping when your ISP sells your web surfing habits to advertisers? Lawyers and legislators are debating whether such practices violate the 1986 Electronic Communications Privacy Act, designed to keep phone companies for listening in on their customer's phone calls.


"If you care about food, you would be well-served by reading Tomorrow's Table" [Tomorrow's Table]

Posted: 08 Sep 2008 11:11 AM CDT

Karl Mogel, geneticist, blogger, radio show host and journalist, has just posted a review of Tomorrow's Table.

Here is teaser from the review:

"The chapter on politics... begins with a grisly scene..." Read on

What's worse: cell phones or cigarettes? [adaptivecomplexity's column]

Posted: 08 Sep 2008 10:23 AM CDT

We know what's worse for your health (in case you were wondering: we know cigarettes cause cancer, and there is no reliable link between cell phones and cancer), but what about your sanity:

Novelist Jonathan Franzen on cell phones:


Dark Energy [Sciencebase Science Blog]

Posted: 08 Sep 2008 10:14 AM CDT

Type 1a Supernova Credit: NASA/Swift/S. Immler)

Forget the Large Hadron Collider (LHC), with its alleged ability to create earth-sucking microscopic black holes, its forthcoming efforts to simulate conditions a trillionth of a second after the Big Bang 100 metres beneath the Swiss countryside. There is a far bigger puzzle facing science that the LHC cannot answer: What is the mysterious energy that seems to be accelerating ancient supernovae at the farthest reaches of the universe?

In the late 1990s, the universe changed. The sums suddenly did not add up. Observations of the remnants of stars that exploded billions of years ago, Type Ia supernovae, showed that not only are they getting further away as the universe expands but they are moving faster and faster. It is as if some mysterious
force that
pervades the cosmos
is working
against gravity and
accelerating the expansion of
the universe
some mysterious hidden force that pervades the cosmos is working against gravity and accelerating the expansion of the universe. This force has become known as dark energy and although it apparently fills the universe, scientists have absolutely no idea what it is or where it comes from, several big research teams around the globe are working with astronomical technology that could help them find an answer.

Until type Ia supernovae appeared on the cosmological scene, scientists thought that the expansion of the universe following the Big Bang was slowing down. Type Ia supernovae are very distant objects, which means their light has taken billions of years to reach us. But, their brightness could be measured to a high degree of accuracy that they provide astronomers with a standard beacon with which the vast emptiness of space could be illuminated, figuratively speaking.

The supernovae data, obtained by the High-Z SN Search team and the Supernova Cosmology Project, rooted in Lawrence Berkeley National Laboratory, suggested that not only is the universe expanding, but that this expansion is accelerating. to make On the basis of the Type Ia supernovae, the rate of acceleration of expansion suggests that dark energy comprises around 73% the total energy of the universe, with dark matter representing 24% of the energy and all the planets, stars, galaxies, black holes, etc containing a mere 4%.



Professor Karl Gebhardt and Senior Research Scientists Dr Gary Hill and Dr Phillip McQueen and their colleagues running the Hobby Eberly Telescope Dark Energy Experiment (HETDEX) based at the McDonald Observatory in Texas are among the pioneers hoping to reveal the source and nature of dark energy. Those ancient supernovae are at a “look-back time” of 9 billion years, just two-thirds the universe’s age. HETDEX will look back much further to 10 -12 billion years.

HETDEX will not be looking for dark energy itself but its effects on how matter is distributed. “In the very early Universe, matter was spread out in peaks and troughs, like ripples on a pond, galaxies that later formed inherited that pattern,” Gebhardt explains. A detailed 3D map of the galaxies should reveal the pattern. “HETDEX uses the characteristic pattern of ripples as a fixed ruler that expands with the universe,” explains Senior Research Scientist Gary Hill. Measuring the distribution of galaxies uses this ruler to map out the positions of the galaxies, but this needs a lot of telescope time and a powerful new instrument. “Essentially we are just making a very big map [across some 15 billion cubic light years] of where the galaxies are and then analyzing that map to reveal the characteristic patterns,” Hill adds.

“We’ve designed an upgrade that allows the HET to observe 30 times more sky at a time than it is currently able to do,” he says. HETDEX will produce much clearer images and work much better than previous instruments, says McQueen. Such a large field of view needs technology that can analyze the light from those distant galaxies very precisely. There will be 145 such detectors, known as spectrographs, which will simultaneously gather the light from tens of thousands of fibers. “When light from a galaxy falls on one of the fibers its position and distance are measured very accurately,” adds Hill.

The team has dubbed the suite of spectrographs VIRUS. “It is a very powerful and efficient instrument for this work,” adds Hill, “but is simplified by making many copies of the simple spectrograph. This replication greatly reduces costs and risk as well.”

McQueen adds that after designing VIRUS, the team has built a prototype of one of the 145 unit spectrographs. VIRUS-P is now operational on the Observatory’s Harlan J. Smith 2.7 m telescope, he told us, “We’re delighted with its performance, and it’s given us real confidence in this part of our experiment.”

VIRUS will make observations of 10,000 galaxies every nightVIRUS will make observations of 10,000 galaxies every night. So, after just 100 nights VIRUS will have mapped a million galaxies. “We need a powerful telescope to undertake the DEX survey as quickly as possible,” adds McQueen. Such a map will constrain the expansion of the universe very precisely. “Since dark energy only manifests itself in the expansion of the universe, HETDEX will measure the effect of dark energy to within one percent,” Gebhardt says. The map will allow the team to determine whether the presence of dark energy across the universe has had a constant effect or whether dark energy itself evolves over time.

“If dark energy’s contribution to the expansion of the universe has changed over time, we expect HETDEX to see the change [in its observations],” adds Gebhardt, “Such a result will have profound implications for the nature of dark energy, since it will be something significantly different than what Einstein proposed.”


Scientific scrutiny of the original results has been so intense that most cosmologists are convinced dark energy exists. “There was a big change in our understanding around 2003-2004 as a triangle of evidence emergedThere was a big change in our understanding around 2003-2004 as a triangle of evidence emerged,” says Bob Nichol of the University of Portsmouth, England, who is working on several projects investigating dark energy.


First, the microwave background, the so-called afterglow of creation, showed that the geometry of the universe has a mathematically “flat” structure. Secondly, the data from the Type Ia supernovae measurements show that the expansion is accelerating. Thirdly, results from the Anglo-Australian 2dF redshift survey and then the Sloan Digital Sky Survey (SDSS) showed that on the large scale, the universe is lumpy with huge clusters of galaxies spread across the universe.

The SDSS carried out the biggest galaxy survey to date and confirmed gravity’s role in the expansion structures in the universe by looking at the ripples of the Big Bang across the cosmic ocean. “We are now seeing the corresponding cosmic ripples in the SDSS galaxy maps,” Daniel Eisenstein of the University of Arizona has said, “Seeing the same ripples in the early universe and the relatively nearby galaxies is smoking-gun evidence that the distribution of galaxies today grew via gravity.”

But why did an initially smooth universe become our lumpy cosmos of galaxies and galaxy clusters? An explanation of how this lumpiness arose might not only help explain the evolution of the early universe, but could shed new light on its continued evolution and its ultimate fate. SDSS project will provide new insights into the nature of dark energy’s materialistic counterpart, dark matter.

As with dark energy, dark matter is a mystery. Scientists believe it exists because without it the theories that explain our observations of how galaxies behave would not stack up. Dark matter is so important to these calculations, that a value for all the mass of the universe five times bigger than the sum of all the ordinary matter has to be added to the equations to make them work. While dark energy could explain the accelerating acceleration our expanding universe, the existence of dark matter could provide an explanation for how the lumpiness arose.

“In the early universe, the interaction between gravity and pressure caused a region of space with more ordinary matter than average to oscillate, sending out waves very much like the ripples in a pond when you throw in a pebble,” Nichol, who is part of the SDSS team, explains. “These ripples in matter grew for a million years until the universe cooled enough to freeze them in placeripples in matter grew for a million years until the universe cooled enough to freeze them in place. What we now see in the SDSS galaxy data is the imprint of these ripples billions of years later.”

Colleague Idit Zehavi now at Case Western University adds a different tone. Gravity’s signature could be likened to the resonance of a bell she suggests, “The last ring gets forever quieter and deeper in tone as the universe expands.” It is now so faint as to be detectable only by the most sensitive surveys. The SDSS has measured the tone of this last ring very accurately.”

“Comparing the measured value with that predicted by theory allows us to determine how fast the Universe is expanding,” explains Zehavi. This, as we have seen, depends on the amount of both dark matter and dark energy.

The triangle of evidence - microwave background, type Ia supernovae, and galactic large-scale structure - leads to only one possible conclusion: that there is not enough ordinary matter in the universe to make it behave in the way we observe and there is not enough normal energy to make it accelerate as it does. “The observations have forced us, unwillingly, into a corner,” says Nichol, “dark energy has to exist, but we do not yet know what it is.”

The next phase of SDSS research will be carried out by an international collaboration and sharpen the triangle still further along with the HETDEX results. “HETDEX adds greatly to the triangle of evidence for dark energy,” adds Hill, “because it measures large-scale structure at much greater look-back times between local measurements and the much older cosmic microwave background,” says Hill. As the results emerge, scientists might face the possibility that dark energy has changed over time or it may present evidence that requires modifications to the theory of gravity instead.


The Anglo-Australian team is also undertaking its own cosmic ripple experiment, Wiggle-Z. “This program is measuring the size of ripples in the Universe when the Universe was about 7 billion years old,” Brian Schmidt at Australian National University says. Schmidt was leader of the High-Z supernovae team that found the first accelerating evidence. SDSS and 2dF covered 1-2 billion years ago and HETDEX will measure ripples at 10 billion years. “Together they provide the best possible measure of what the Universe has been doing over the past several years,” Schmidt muses.


The Dark Energy Survey, another international collaboration, will make any photographer green with envy, but thankful they don’t have to carry it with them. The Fermilab team plans to build an extremely sensitive 500 Megapixel camera, with a 1 meter diameter and a 2.2 degree field of view that can grab those millions of pixels within seconds.

The camera itself will be mounted in a cage at the prime focus of the Blanco 4-meter telescope at Cerro Tololo Inter-American Observatory, a southern hemisphere telescope owned and operated by the National Optical Astronomy Observatory (NOAO). This instrument, while being available to the wider astronomical community, will provide the team with the necessary power to conduct a large scale sky survey.

Over five years, DES will use almost a third of the available telescope time to carry out its wide survey. The team hopes to achieve exceptional precision in measuring the properties of dark energy using counts of galaxy clusters, supernovae, large-scale galaxy clustering, and measurements of how light from distant objects is bent by the gravity of closer objects between it and the earth. By probing dark energy using four different methods, the Dark Energy Survey will also double check for errors, according to team member Joshua Frieman.


Subaru 51

According to Nichol, “The discovery of dark energy is very exciting because it has rocked the whole of science to its foundations.” Nichol is part of the WFMOS (wide field multi-object spectrograph) team hoping to build an array of spectrographs for the Subaru telescopes. These spectrographs will make observations of millions of galaxies across an enormous volume of space at a distances equivalent to almost two thirds the age of the universe. “Our results will sit between the very accurate HETDEX measurements and the next generation SDSS results coming in the next five years,” he explains, “All the techniques are complimentary to one another, and will ultimately help us understand dark energy.”


If earth-based studies have begun to reveal the secrets of dark energy, then three projects vying for attention could take the experiments off-planet to get a slightly closer look. The projects all hope to look at supernovae and the large-scale spread of matter. They will be less error prone than any single technique and so provide definitive results.

SNAP, SuperNova/Acceleration Probe, is led by Saul Perlmutter of Lawrence Berkeley National Laboratory in Berkeley, California, one of the original supernova explorers. SNAP will observe light from thousands of Type Ia supernovae in the visible and infra-red regions of the spectrum as well as look at how that light is distorted by massive objects in between the supernovae and the earth.

Adept, Advanced Dark Energy Physics Telescope, is led by Charles Bennett of Johns Hopkins University in Baltimore, Maryland. This mission will also look at near-infrared light from 100 million galaxiesThis mission will also look at near-infrared light from 100 million galaxies and a thousand Type Ia supernovae. It will look for those cosmic ripples and so map out the positions of millions of galaxies. This information will allow scientists to track how the universe has changed over billions of years and the role played by dark energy.

Destiny, Dark Energy Space Telescope, led by Tod Lauer of the National Optical Astronomy Observatory, based in Tucson, Arizona, will detect and observe more than 3000 supernovae over a two-year mission and then survey a vast region of space looking at the lumpiness of the universe.


So, what is dark energy? “A this point it is pure speculation,” answers Hill, “The observations are currently too poor, so we are focusing on making the most accurate measurements possible.” Many scientists are rather embarrassed but equally excited by the thought that we understand only a tiny fraction of the universe. Understanding dark matter and dark energy is one of the most exciting quests in science. “Right now, we have no idea where it will lead, adds Hill.

Supernovae (NASA collage)

“Despite some lingering doubts, it looks like we are stuck with the accelerating universe,” says Schmidt. “The observations from supernovae, large-scale structure, and the cosmic microwave background look watertight,” he says. He too concedes that science is left guessing. The simplest solution is that dark energy was formed along with the universe. The heretical solution would mean modifying Einstein’s theory of General Relativity, which has so far been a perfect predictor of nature. “Theories abound,” Schmidt adds, “whatever the solution, it is exciting, but a very, very hard problem to solve.”

This David Bradley special feature article originally appeared on Sciencebase last summer, having been published in print in StarDate magazine - 2007-07-01-21:12:X1

Dark Energy

Personalized Medicine Since 1986! [The Gene Sherpa: Personalized Medicine and You]

Posted: 08 Sep 2008 09:16 AM CDT

First I would like to apologize for the lack of postings on interesting topics lately. I am glad that others have picked up my slack. Notably Hsien and Bertalan's interesting posts this week. Or for...

[[ This is a content summary only. Visit my website for full links, other content, and more! ]]

Knome Delivers First Genomic Sequencing [The Genetic Genealogist]

Posted: 08 Sep 2008 07:44 AM CDT

Knome, a personal genomics company that launched within the past year, has just delivered the first genomic sequencing to customers according to a report in the MIT Technology Review.

After paying $350,000 for sequencing, customers receive their genetic sequence on an 8-gigabyte USB drive in an engraved silver box.  The USB is encrypted and contains special genome browsing software.

For the first time in history, it is unclear how many complete human genomes have been sequenced by scientists.  Prior to Knome, we knew exactly how many had been completed.  Now, and probably ever after, genomes will be sequenced and analyzed without all the typical fanfare and press releases.  Instead of just 2 or 3 genomes, there will soon be tens of genomes, then hundreds, and then thousands.

The article also reveals that, as I had predicted a few months ago, Knome is about to announce a lower cost for its services due to the plummeting cost of genetic sequencing.  No word on what the new cost will be.

Scientists - Get Networked [Bitesize Bio]

Posted: 08 Sep 2008 06:46 AM CDT

Social networking is the latest buzz on the internet. You’ve heard about it, but what does it mean to you as a scientist? Well for one thing, it means that networking has never been easier. Here are five of the best social networking sites for scientists that are designed to help you make and maintain your professional contacts.

1. SciLink is a souped-up networking site that actually knows who a lot of your contacts will be before you even sign up. Uniquely, SciLink mines literature databases to build a network of professional relationships that you can slot into (and of course expand further) when you sign up. You can also find jobs, discussion, news etc on the site.

2. MyNetResearch is a powerful website for finding collaborators for your project. You set up your own account/profile and build a network of contacts as with the other social networks but MyNetResearch is designed to help you find people who work in the areas you are interested in (or interested in expanding into) and arrange collaborations with them.

3. The Nature Network. As you might expect, this is the grand-daddy of science social networks. Not only can you set up a contact network, but you can also browse niche-specific forums and groups, start your own blog, and much more.

4. LinkedIn is a site professional networking site for all professions. Unlike the science-specific networking sites,your LinkIn contact list can contain contacts who are not scientists, which is useful if you actually know people in the real world too :) and it has a more professional atmosphere than Facebook so people of all ages are more likely to join up.

5. Labmeeting primarily allows you to archive, track and share your literature. From your account you can search for papers of interest and upload the PDFs to your account for later retreival. You can also set up streams to keep you informed of the latest publications in your fields of interest, which you can then add to your archive. However, you can also set up a group area to share papers and talk about your interests, and to schedule events, such as lab meetings.

What social networking sites do you use?

Would you blog at Reportergene? [Reportergene]

Posted: 08 Sep 2008 05:56 AM CDT

Community call!

I've coined the term "reportergenomic" to identify the discipline in which passionates in reporters/probes  will work close to people interested in mathematical modelling in order to get a system biology picture via a reporter assay based approach.

Models of blog by Robin Hamman

So, to sustain such new discipline, Reportergene claims to be the main repository of news and tools for reportergenomists. Of course, this is a long-term project and the first community members Reportergene needs are a couple of bloggers/reporters able to find new (relevant) improvements in recent literature/congresses. This is pivotal to reportergenomic maturity.

What's in it for you?
This is a real opportunity to promote yourself online. Are you interested? Do you know anybody that may be interested? Please let me know!

Debunking the ‘GE Crops are Bad’ Myth [Bitesize Bio]

Posted: 08 Sep 2008 05:19 AM CDT

As I noted in last Friday’s Around the Blogs post (and for a day put up the wrong link), Pamela Ronald has an article up for anyone interested in the pro’s and con’s of genetically engineered or genetically modified crops. In 10 Things About GE Crops to Scratch from your Worry List, there are brief but succinct explanations of why common arguments against GE crops are without merit.

The first two myths are the most critical to set straight. For instance, the notion that GE crops require more pesticides - the opposite is actually true - “In China, cotton farmers were able to eliminate 150 million pounds of insecticide in a single year by using GE varieties.” (Just for a significant example)

Or the notion that corporate control of GE seeds forces poor farmers to buy seed each year - “Although the US seed industry is dominated by large corporations, this was the case before GE came into play. In some less developed countries, such as Bangladesh, national breeding programs distribute seed (GE or conventional) freely to farmers who can then self their own seed. For example a flood-tolerant gene cloned in my lab and used to develop new varieties in collaboration with colleagues has been distributed to Bangladeshi farmers through national breeding programs. The farmers are now saving the seed to share with neighbors.”

The key message though that I would emphasize, and I’m sure experts in the field such as Pam Ronald would agree with, is that GE crops should be judged on a case-by-case basis. And indeed they are, going through appropriate technical and regulatory hurdles before widespread dissemination to farmers.

If you like this topic, check out Pam’s blog, Tomorrow’s Table on a regular basis. As an expert in Plant pathology and genetics, she’s poised to discuss the merits and drawbacks of various GE crops, and the directions that forthcoming GE crops are taking.

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