MINNEAPOLIS (AP) ? Kevin Durant and the Oklahoma City Thunder have been blowing the doors off the rest of the Western Conference in these first two months, playing with the swagger born of their run to the NBA Finals last season.
J.J. Barea and the Minnesota Timberwolves tried to send a message on Thursday night that a second straight trip isn't going to come easy.
Playing with the tenacity that made him so important to the Mavericks' run to the title two years ago, Barea scored 14 of his 18 points in the fourth quarter to help the Timberwolves snap Oklahoma City's 12-game winning streak with a 99-93 victory over the Thunder.
Kevin Love had 28 points, 11 rebounds and seven assists and Nikola Pekovic had 24 points and 10 rebounds for Minnesota. But it was Barea who was the key, scoring 12 straight at one point for the Wolves to hold off the team with the best record in the league.
"It's important," coach Rick Adelman said of beating the best in the West. "But I would like to see us get to a point where this is not a big deal. It's a big game against the best team, but this is something we can do."
Kevin Durant had 33 points, seven rebounds and six assists and Russell Westbrook had 30 points, 11 rebounds and nine assists for the Thunder, who had not lost a game since Nov. 23 at Boston.
"It's not the end of the world. A lot of people said the world is going to end today, tomorrow, but it's not the end of the world," Durant quipped. "We lost to a good team (Thursday). They came out and played extremely hard and they beat us. We're 21-5 and we've just got to go back and work."
That it was Barea, and not the Olympian Love or the sensation Ricky Rubio who was chiefly responsible was the biggest surprise of all.
Barea didn't join the Timberwolves until training camp had already started last season, then languished through the first injury plagued year of his career. Finally healthy, he's getting back to the super pest that helped the Dallas Mavericks to the title two years ago.
With the Thunder charging early in the fourth quarter, the smallest guy on the court played the biggest.
After Durant's two free throws cut Minnesota's lead to 80-77, Barea hit two 3s and scored on a putback under the rim amid the tall trees, an 8-0 run by himself that gave the Wolves a little breathing room. His long 3 with 5:26 to play made it 92-81, and the Wolves held on.
"I love it," Barea said. "We just needed a little bit more tonight, a little energy and I'm glad I was able to provide that for us tonight."
Barea was also a nuisance on defense, drawing an offensive foul on Durant with 2:24 to play. The normally super-cool Durant uncharacteristically lost his composure, picking up a technical foul for arguing the call as well.
"Seems like him and Kevin Love don't miss against us," Durant said of Barea, who tormented them in the Western Conference finals in 2011 and had a triple-double in a double-overtime loss to the Thunder last season. "Seems like every team has that guy and I think those are the guys against us. Next time we've just got to do a better job."
Serge Ibaka had 14 points and nine rebounds, but Westbrook missed 19 shots and turned the ball over eight times in an off night.
Alexey Shved had 12 points, 12 assists and seven rebounds for the Wolves, who are trying to claw their way back to respectability after years at the bottom of the Western Conference.
With a nucleus of Love, Rubio and Pekovic, there is optimism here for the first time in a long time.
The Thunder stormed into Target Center riding the longest winning streak since the team moved to Oklahoma City, bullying opponents by an average of 14.2 points per game as they warm up for a run at a second straight finals appearance.
Rubio was playing his third game since being activated from a torn ACL in his left knee that had kept him out since March 9. He had a scintillating debut last Saturday, throwing no-look passes between his legs and looking as if he'd never left. But it's been slower going in the ensuing two games. He was a non-factor in a loss in Orlando on Monday and had trouble getting going again against the Thunder.
His handle wasn't nearly as sticky as usual and he was thwarted every time he tried to penetrate, then could be seen wincing in pain after an awkward landing on a shot in the second quarter. Adelman immediately pulled him, but Rubio returned in the second half.
"We battled, we fought. I'm proud of our guys," Thunder coach Scott Brooks said. "We had a great streak, a great month going. But we lost to a very good team. We knew sooner or later they were going to get hot. They got hot tonight."
NOTES: Kevin Martin did not play for the Thunder because of a right thigh contusion. ... The Timberwolves waived G/F Josh Howard on Thursday after an MRI revealed a torn ACL in his right knee. ... The Thunder lost for the first time in six tries on the second night of a back to back.
Dec. 21, 2012 ? Researchers at The University of Texas at Austin have designed a simulation that for the first time emulates key properties of electronic topological insulators.
Their simulation, which was described this week in Nature Materials, is part of a rapidly moving scientific race to understand and exploit the potential of topological insulators, which are a state of matter that was only discovered in the past decade. These insulators may enable dramatic advances in quantum computing and spintronics.
"The discovery of these materials, which are insulators in their volume while capable of conducting current on their surface, was a bit of a surprise to the condensed matter community," said Gennady Shvets, professor of physics in the College of Natural Sciences. "Before that, we classified solid materials into three categories, based on their ability to conduct electric current: insulators, conductors, and semiconductors. Topological insulators fall somewhere in between."
Shvets co-authored the article with his physics department colleagues Alexander Khanikaev, S. Hossein Mousavi, Wang-Kong Tse, Mehdi Kargarian, and Professor Allan MacDonald.
He said that what's particularly exciting about topological insulators is that they can conduct electrons -- or in the case of photonic ones, photons -- in a way that protects them from scattering or reflecting when they encounter obstacles.
"Usually when photons run into an obstacle, they reflect," said Shvets. "We are basically designing interfaces in such a way that they lock photons into one spin state. So in one direction they're in one spin state, and when they're going in another direction they're locked into another spin state. In that configuration they cannot reflect without changing their spin, which is forbidden by the design of the photonic crystal. They flow around defects and can be routed along arbitrarily shaped paths defined by the interface."
If this property could be achieved with electrons it would be particularly relevant to quantum computers, which are likely to require their electrons to maintain coherence for a much longer time than digital computers.
Over the past decade scientists have had modest success making or finding electronic topological insulators. But these substances are limited both in what they can do and in what they can reveal about the potential of this new state of matter.
"Those systems are very difficult to study systematically, because when you have a real material it is what it is. You're limited to studying its properties," said Shvets. "Nature doesn't give you the knobs to increase or decrease various aspects of it, so it's very difficult to benchmark the existing theories against what's observed."
Shvets and his physics department colleagues expect that their simulated photonic insulator will be a much more powerful and flexible tool for studying the general properties of topological insulators.
"With these purely artificial photonic crystals, we can study these systems in a more systematic way," he said.
In order for their insights from the photonic system to be applicable to electronic systems, Shvets and his colleagues had to make their simulated photons behave sufficiently like electrons. To do that, they designed simulated "metamaterials." These are artificial electromagnetic materials that can be tuned to influence photons in ways that are otherwise impossible. Other metamaterials are being used to develop invisibility cloaks.
Shvets and his colleagues designed what they've called SPINDOMs (spin-degenerate optically-active metamaterials). When arranged periodically, the resulting meta-crystals are the first demonstration that it's possible to control the spin of photons in a way that emulates what can be done with electrons.
This is significant on a few fronts. Even as a computer simulation it allows researchers to explore the properties of topological insulators. When these photonic topological insulators are physically built, as Shvets and his colleagues hope will be done soon, they'll allow more exploration. And there's great promise that such insulators may eventually be used to reduce interference in wireless communications systems.
"Right now if you put multiple emitting or receiving antennas in close proximity to each other, whether on a semiconductor chip or on top of a cellular base station, the radiation from each antenna is affected by the others," he said. "To deal with this you have to design around it. What would be better is if all cross talk between emitting/receiving sources could just be eliminated. That's what we believe could be done by photonic topological insulators, which can directionally guide electromagnetic waves."
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The above story is reprinted from materials provided by University of Texas at Austin, via EurekAlert!, a service of AAAS.
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Journal Reference:
Alexander B. Khanikaev, S. Hossein Mousavi, Wang-Kong Tse, Mehdi Kargarian, Allan H. MacDonald, Gennady Shvets. Photonic topological insulators. Nature Materials, 2012; DOI: 10.1038/nmat3520
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After putting out an open call for original content last May, Amazon Studios is ready to begin production on six comedy pilots. Culled from a writer base consisting of industry vets (some award winning, some from the minds of Big Bang Theory stars, some backed by the adorably creepy Kristen Schaal) and unknowns, these scripted entries will be hosted for free on the company's Instant Video platform once completed. And since there's no better focus group than an existing customer base, Amazon intends take user feedback into account when selecting which of these pilots goes into full production. Series that do make it past that final greenlight will end up on the mega e-retailer's Instant Video and Lovefilm portals as exclusive content for Prime subscribers. Head past the break to check out the full list of eligible shows.
Manchester - Do you understand and recognise digital art? After seeing an amazing piece of digital art on Facebook, I contacted the artist, British digital artist and photographer Adrian McGarry, to find out more about his life, work, talents, and pieces of artwork. Adrian McGarry who was born, raised and still lives in the area of Manchester, a city in the North West of England, says he has two identities. He is a full-time professional graphic designer, web designer, and marketing consultant at Mediaworx Creative Services and a photographer and digital artist. How long have you been working in the field of design?
Adrian McGarry
Adrian McGarry, photographer and digital artist
image:135845:2::0
Well, my career within the creative and publishing industries has spanned almost 40 years. I've always been interested in art, photography, computer design so it's no great surprise that my life has been spent creating graphical output in one form or another! During that time I have been extremely fortunate to work alongside and learn from extremely talented individuals; from my early mentors to gifted collaborators on design and photography projects.
How did you start out?
It started with my love to create images but my early work was mostly creating graphic design for brochures, catalogues, in-store retail promotions.
Did you train / qualify or are you self taught?
I'm mostly self-taught through a lifetime of experience!
Adrian McGarry
Manchester's industrial heritage overlooked by contemporary architecture.
image:135849:4::0
How long have you had your own design business?
I have run my own business for the last 12 years and I have worked with a varied customer base that includes blue-chip corporates, national retailers, property developers, recruitment agencies, travel companies and private clients. At one stage I employed full-time staff and drafted in freelancers but I now prefer to work on my own from my home in the leafy suburbs of South Manchester.
How did you shift over from straightforward design to digital art and photography?
I have always enjoyed all forms of photography from film and dark-room processing to today's digital revolution. So, I began introducing my photography into the workflow about 7 years ago when I realised that the early growth of online retailers would give me an opportunity to add 'table-top' photography to my list of services. Quickly that grew into providing shots for product backgrounds and in-store promotions etc. and eventually I was photographing for full publications such as property development brochures.
Adrian McGarry
Autumn Path
image:135846:3::0
Where has your work been used or published?
My photography, artwork and design has appeared in many publications, high street stores, local galleries and on the web. I have worked both directly and indirectly (through agencies) for Next, Cotton Traders, Marks & Spencers, B&Q, Littlewoods, Evans, Virgin Wine and Manchester Art Gallery.
Have you received any awards?
A recipient of the Royal Photographic Society's LRPS distinction; my photography and art continues to evolve and win approval.
Has your work taken you to any interesting places?
Over the years I have been fortunate to visit many European cities on business and as recently as last year had photo assignments in Bilbao and Madrid.
Adrian McGarry
Venetian Ambiance. The canals of Venice
image:135850:3::0
Has the way you approach your work changed over the years?
Recently I have begun to alter my approach to the assignments that I take on. The artist within is gaining an ever-increasing voice and is convincing me that I have untapped resources that will not be explored within my commercial workload. However, at the moment, a lot of my photographic time is spent creating commercial images for my clients making it difficult to devote time and energy to create nature, landscape and travel images which I love to do. In addition, I have a desire to further express myself within my photography that goes beyond a camera's capabilities. So, I have started to balance the time I spend on commercial work with time spent on my personal projects.
When did you move into digital art and why?
I have been creating digital art for over twenty years. I wanted and needed an outlet to further express myself beyond the capture of a photographic image. Whilst my earlier creations were never destined to be shared with the world, I did gain an appreciation of what this then emerging technology had to offer and how I could adapt it to my particular style and taste.
What is Digital Art? How do you create digitised paintings?
I create images that are a fusion of conventional photography and painting. I refer to these images as 'Pixel Painted.' Using a graphics tablet and pen, I recreate each pixel in an image by hand, utilising digital paint media to express myself in the overall appearance as it takes on a painted look. My images are a transformation of one or more of my photographs and sometimes are a fusion of multiple elements from my shots. The ambiance of an image will change and I can allow my imagination to play a much greater role in the final result. I don't apply 'one-stop' painting filters or apps on the images, I prefer recreating the image from scratch and building textures from within rather than letting computer algorithms decide the outcome. Over the years I have painted in traditional oils, acrylic and watercolour and this experience helps me when creating digital art.
What technology do you use?
Adrian McGarry
Adrian McGarry, photographer and digital artist
image:135847:2::0
I work on a Mac, I'm a huge fan of Apple hardware and software and have always used the equipment since the late 1980's. I have a 27inch iMac in the office, a 15inch MacBook Pro laptop, a 13inch Macbook Air laptop and an Apple iPad - even my phone is an iPhone so you could call me a Mac-addict! The software I use is mostly Adobe PhotoShop and Corel Painter. I use the full and latest versions but for someone just starting out both software packages have 'lite' versions and are available on both Mac and Windows platforms.
Which camera do you use?
I use Canon camera equipment. I mostly use a Canon 7D camera and a range of Canon lenses: generally speaking an 18-200mm lens for travel, a 100-400mm for general hand-held wildlife shots and I hire a longer lens (500mm, 600mm etc.) if I anticipate that wildlife subjects will not allow me to get close.
How long would it take you to create a piece of digital art?
Digital art can be time-consuming. The recent Manchester image took about 30 hours spread over a couple of weeks. The Eagle took about 3-4 hours in one day. The process can be intense and I tend to work on one piece at a time. Normally I will complete a piece and then leave it for a few days, when I return to it I can be more objective (fresh eyes and perspective) and make final amendments and tweaks. But really my work-flow changes from image to image depending on the complexity of my composition. My Christmas Card image this year was a painting using up to 10 separate image elements combined to make a single scene. This one took about 10 hours in total.
Do you print your work yourself?
My prints are usually output by a professional lab onto high quality fine-art paper. I use a textured paper that is similar to a watercolour artist paper. I also print onto high quality canvas. I have plans to sell prints through various on-line galleries in the new year as well as from my own website. I'm currently looking for galleries in the North West UK to partner with and sell through.
How popular is digital art?
My more recent work is beginning to find a market and I have an emerging customer following. Digital art is becoming a recognised art-form and I believe that the future of creative photography lies in the potential of post processing. Many leading graphic artists are creating work solely on a computer. More and more galleries are exploring the genre and artists such as David Hockney are creating work solely on computers.
So do you consider yourself a graphic designer, artist or photographer?
For a while I have asked myself "Am I a photographer or an artist?" The answer is that I have reached is that I am both. When I'm behind the camera I am very much a photographer utilising the camera and lens to create a perfect record of my subject. When I work in software then I'm an artist and I can approach a piece of work exactly the same as working on canvas with paint. The magic of the traditional artist will never be replaced but the craft of a digital artist cannot be ignored and I believe will both will sit alongside in galleries of the future.
Where does your inspiration come from?
My inspiration is taken from traditional artists from old masters to modern contemporary artists.
Any future plans?
Next year, I hope to embark on a tour of North West UK camera clubs to introduce my work to a wider audience who may wish to add my techniques to their work-flow and hopefully workshops will follow. I have plans for an e-book and I have begun a dialogue with the Royal Photographic Society to recognise my work within their visual arts category.
Do people commission pieces?
I have had a few commissions, it's not something that I am actively looking for at the moment but never say never!
Where can people find you and your work?
I have 500px and Flickr accounts - these are photo sharing sites. My wildlife portfolio at the Royal Photographic Society. I'm happy to promote my Facebook account and encourage people adding me as a friend or subscribing to me, currently this is the best way to keep-up-to-date with me. I don't use a business page on Facebook as I prefer to interact with people and not just 'sell' to them. At the moment I am not selling art through any agencies but I will in the new year.
So if you want an early morning tea break or afternoon visual delight - do as I have done, start by 'friending' Adrian McGarry on Facebook.
Every person that owns a website wants to know how they can improve it. Whether it be getting more traffic, improving their SEO for organic rankings, or just making their website have a better look and feel. Many times when you ask a Phoenix web design company this the answer is very pricey and the things that they tell you are correct. However during times where you don?t have the extra money to invest in your website especially during the holiday season what can be done to improve your website that is in need of updates? This is something as a Phoenix web design team we have pondered and came up with a list of simple updates that can improve the look and feel of your website until you can afford to make the major updates your website is needing.
File Size ? Make sure that the file sizes for images, videos and other things that need to upload when somebody visits your site are small. This will help your websites load time which is not only important to the site visitor but also to your organic rankings that you should be trying to improve through search engine optimization.
Consistency ? If your website is not already make your website consistent. Keep the font styles and sizes consistent as well as the Menus. If you have a menu on the right side of your website keep it consistent throughout your website.
Bad Links and Images ? Make sure your website doesn?t have any broken links or images on your website. Go through your website and fix all the links and images that may be broken. This looks bad to visitors to your website and may make them never comeback.
Contact Information ? Make all your contact information prominent. There is no bigger frustration when somebody needs to get a hold of you and can?t find your contact information anywhere on your website. This makes potential customer frustrated and not want to do business with you.
Browser Compatibility ? Make sure your website is compatible in all browsers. There is no way of now what browsers the traffic to your website will be using so you need to make sure your website is working perfectly across all browsers.
External Links ? Make sure all external links are opening in a new tab. You don?t want people leaving your website as they may not find it again. If an external link opens in a new tab then it keeps your potential customer on your website for later viewing.
These are some simple and cost effective ways to improve your website. HireAWiz is a professional Phoenix web design company that would be happy to review your website and show you ways we can improve it. Contact us today for a free evaluation and quote.
Contact: Jade Boyd jadeboyd@rice.edu 713-348-6778 Rice University
Genomes of limpet, leech and worm put spotlight on lophotrochozoans
HOUSTON -- (Dec. 19, 2012) -- A new report in the journal Nature unveils three of the first genomes from a vast, understudied swath of the animal kingdom that includes as many as one-quarter of Earth's marine species. By publishing the genomes of a leech, an ocean-dwelling worm and a kind of sea snail creature called a limpet, scientists from Rice University, the University of California-Berkeley and the Department of Energy's Joint Genome Institute (JGI) have more than doubled the number of genomes from a diverse group of animals called lophotrochozoans (pronounced: LOH-foh-troh-coh-zoh-uhns).
Lophotrochozoans are a diverse group of animals that includes mollusks such as snails, clams and octopuses -- and annelids -- such as leeches and earthworms. Like humans and all other animals, lophotrochozoans can trace their evolutionary history to the earliest multicellular creatures. But the lophotrochozoan branch of the evolutionary tree diverged more than 500 million years ago from the branch that produced humans.
"Most animals, including people, have body plans with bilateral symmetry, which means they have left and right sides that are mirror images of one other," said co-author Nicholas Putnam, assistant professor of ecology and evolutionary biology at Rice. "When you look at all bilaterian species, you can divide them into three big groups that biologists call clades.
"Lophotrochozoans are one of these clades, and when we looked at all of the genomes that had been sequenced, we found that only two were lophotrochozoans," he said. "That left a big hole in the genetic record, and our goal with this study was to fill in some of the gaps in that blank space."
Genome sequencing for the new study was performed at JGI in Walnut Creek, Calif. The three newly sequenced species are Capitella teleta, an ocean-dwelling worm; Helobdella robusta, a freshwater leech; and Lottia gigantean, a large marine mollusk.
Putnam's co-investigators included Daniel Rokhsar, of both Berkeley and JGI; David Weisblat and Eric Edsinger-Gonzales, both of Berkeley; Elaine Seaver of the University of Hawaii; and Oleg Simakov of the European Molecular Biology Laboratory at Heidelberg, Germany. Putnam's group, which included Rice graduate student Jie Lv and scientific programmer Paul Havlak, focused on genomic analysis.
"At Rice, we work on comparative genomics," Putnam said. "We look for recognizable similarities across genomes, and we are interested in similarities among the genes themselves and also among the patterns of genetic organization. These structural similarities can tell us a lot about the evolution of individual genes and functional gene groups, like chromosomes."
Almost all published genomes are from the animal kingdom's most-studied clades: deuterostomes, which includes humans and other vertebrates, and ecdysozoans, which includes insects. Only two lophotrochozoan genomes have been previously mapped, and both are for parasitic worms, which aren't representative of most species in the clade, Putnam said.
In examining the lophotrochozoan genomes, Putnam's group developed new computational tools to examine and compare the differences among the three new genomes and hundreds of known genomes, including those for humans and oft-studied model organisms like the fruit fly.
The tools streamlined the search for similarities among the genomes and also helped the researchers trace evolutionary changes that occurred in specific groups of genes.
"Using these tools, we focus on the part of the evolutionary tree where specific mutations took place," Putnam said. "For example, we can say, 'A mutation occurred here that moved a big chunk of this chromosome, and it must have happened after lophotrochozoans diverged from deuterostomes but before the split between mollusks and annelids.'"
So far, Putnam's group has traced 17 "ancestral linkage groups," large groups of genes that are similar in structure to chromosomes, to the last common ancestor of all the bilaterians.
"For us, the interesting thing is finding genes that exist today in different species, tracing those to a single gene in a common ancestor and then using the patterns we find to test hypotheses about evolutionary processes," Putnam said. "Sometimes the genes today might still have the same function, but other times they have evolved an entirely new function."
Putnam said the team has been able to trace the lineage of almost half of the genes in the three new genomes, and the work continues.
"These studies teach us important lessons about ourselves and other vertebrates," Putnam said. "Looking across the animal kingdom gives us more resolution and clarity about what in our genome is new and what has been preserved from our ancient ancestors."
###
Additional co-authors include Ferdinand Marletaz, Tomas Larsson and Detlev Arendt, all of the European Molecular Biology Laboratory; Sung-Jin Cho, Dian-Han Kuo and David Lindberg, all of UC-Berkeley; Uffe Hellsten, Jarrod Chapman, Harris Shapiro, Andrea Aerts, Robert Otillar, Astrid Terry, Jeffrey Boore and Igor Grigoriev, all of JGI; Robert Savage of Williams College at Williamstown, Mass.; Kazutoyo Osoegawa and Pieter de Jong, both of Children's Hospital Oakland Research Institute in Oakland, Calif.; and Jane Grimwood of both JGI and Hudson Alpha Institute for Biotechnology in Huntsville, Ala.
The research was supported by DOE, the Gordon and Betty Moore Foundation, R. Melmon, the National Science Foundation, the National Institutes of Health, the Boehringer Ingelheim Fonds and the National Human Genome Research Institute.
A high-resolution image is available for download at:
http://news.rice.edu/wp-content/uploads/2012/12/1221-METAZOAN-limpet1-lg.jpg
CAPTION: The genomes of the owl limpet (pictured), a freshwater leech and an ocean-dwelling worm are among the first sequenced genomes from a vast, understudied swath of the animal kingdom known as lophotrochozoans, which includes as many as one-quarter of Earth's marine species.
CAPTION: The genomes of the ocean-dwelling worm Capitella teleta (pictured), the owl limpet and a freshwater leech are among the first sequenced genomes from a vast, understudied swath of the animal kingdom known as lophotrochozoans, which includes as many as one-quarter of Earth's marine species.
CAPTION: The genomes of the freshwater leech Helobdella robusta (pictured), the owl limpet and an ocean-dwelling worm are among the first sequenced genomes from a vast, understudied swath of the animal kingdom known as lophotrochozoans, which includes as many as one-quarter of Earth's marine species.
CREDIT: Ajna S. Rivera/UC-Berkeley
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Contact: Jade Boyd jadeboyd@rice.edu 713-348-6778 Rice University
Genomes of limpet, leech and worm put spotlight on lophotrochozoans
HOUSTON -- (Dec. 19, 2012) -- A new report in the journal Nature unveils three of the first genomes from a vast, understudied swath of the animal kingdom that includes as many as one-quarter of Earth's marine species. By publishing the genomes of a leech, an ocean-dwelling worm and a kind of sea snail creature called a limpet, scientists from Rice University, the University of California-Berkeley and the Department of Energy's Joint Genome Institute (JGI) have more than doubled the number of genomes from a diverse group of animals called lophotrochozoans (pronounced: LOH-foh-troh-coh-zoh-uhns).
Lophotrochozoans are a diverse group of animals that includes mollusks such as snails, clams and octopuses -- and annelids -- such as leeches and earthworms. Like humans and all other animals, lophotrochozoans can trace their evolutionary history to the earliest multicellular creatures. But the lophotrochozoan branch of the evolutionary tree diverged more than 500 million years ago from the branch that produced humans.
"Most animals, including people, have body plans with bilateral symmetry, which means they have left and right sides that are mirror images of one other," said co-author Nicholas Putnam, assistant professor of ecology and evolutionary biology at Rice. "When you look at all bilaterian species, you can divide them into three big groups that biologists call clades.
"Lophotrochozoans are one of these clades, and when we looked at all of the genomes that had been sequenced, we found that only two were lophotrochozoans," he said. "That left a big hole in the genetic record, and our goal with this study was to fill in some of the gaps in that blank space."
Genome sequencing for the new study was performed at JGI in Walnut Creek, Calif. The three newly sequenced species are Capitella teleta, an ocean-dwelling worm; Helobdella robusta, a freshwater leech; and Lottia gigantean, a large marine mollusk.
Putnam's co-investigators included Daniel Rokhsar, of both Berkeley and JGI; David Weisblat and Eric Edsinger-Gonzales, both of Berkeley; Elaine Seaver of the University of Hawaii; and Oleg Simakov of the European Molecular Biology Laboratory at Heidelberg, Germany. Putnam's group, which included Rice graduate student Jie Lv and scientific programmer Paul Havlak, focused on genomic analysis.
"At Rice, we work on comparative genomics," Putnam said. "We look for recognizable similarities across genomes, and we are interested in similarities among the genes themselves and also among the patterns of genetic organization. These structural similarities can tell us a lot about the evolution of individual genes and functional gene groups, like chromosomes."
Almost all published genomes are from the animal kingdom's most-studied clades: deuterostomes, which includes humans and other vertebrates, and ecdysozoans, which includes insects. Only two lophotrochozoan genomes have been previously mapped, and both are for parasitic worms, which aren't representative of most species in the clade, Putnam said.
In examining the lophotrochozoan genomes, Putnam's group developed new computational tools to examine and compare the differences among the three new genomes and hundreds of known genomes, including those for humans and oft-studied model organisms like the fruit fly.
The tools streamlined the search for similarities among the genomes and also helped the researchers trace evolutionary changes that occurred in specific groups of genes.
"Using these tools, we focus on the part of the evolutionary tree where specific mutations took place," Putnam said. "For example, we can say, 'A mutation occurred here that moved a big chunk of this chromosome, and it must have happened after lophotrochozoans diverged from deuterostomes but before the split between mollusks and annelids.'"
So far, Putnam's group has traced 17 "ancestral linkage groups," large groups of genes that are similar in structure to chromosomes, to the last common ancestor of all the bilaterians.
"For us, the interesting thing is finding genes that exist today in different species, tracing those to a single gene in a common ancestor and then using the patterns we find to test hypotheses about evolutionary processes," Putnam said. "Sometimes the genes today might still have the same function, but other times they have evolved an entirely new function."
Putnam said the team has been able to trace the lineage of almost half of the genes in the three new genomes, and the work continues.
"These studies teach us important lessons about ourselves and other vertebrates," Putnam said. "Looking across the animal kingdom gives us more resolution and clarity about what in our genome is new and what has been preserved from our ancient ancestors."
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Additional co-authors include Ferdinand Marletaz, Tomas Larsson and Detlev Arendt, all of the European Molecular Biology Laboratory; Sung-Jin Cho, Dian-Han Kuo and David Lindberg, all of UC-Berkeley; Uffe Hellsten, Jarrod Chapman, Harris Shapiro, Andrea Aerts, Robert Otillar, Astrid Terry, Jeffrey Boore and Igor Grigoriev, all of JGI; Robert Savage of Williams College at Williamstown, Mass.; Kazutoyo Osoegawa and Pieter de Jong, both of Children's Hospital Oakland Research Institute in Oakland, Calif.; and Jane Grimwood of both JGI and Hudson Alpha Institute for Biotechnology in Huntsville, Ala.
The research was supported by DOE, the Gordon and Betty Moore Foundation, R. Melmon, the National Science Foundation, the National Institutes of Health, the Boehringer Ingelheim Fonds and the National Human Genome Research Institute.
A high-resolution image is available for download at:
http://news.rice.edu/wp-content/uploads/2012/12/1221-METAZOAN-limpet1-lg.jpg
CAPTION: The genomes of the owl limpet (pictured), a freshwater leech and an ocean-dwelling worm are among the first sequenced genomes from a vast, understudied swath of the animal kingdom known as lophotrochozoans, which includes as many as one-quarter of Earth's marine species.
CAPTION: The genomes of the ocean-dwelling worm Capitella teleta (pictured), the owl limpet and a freshwater leech are among the first sequenced genomes from a vast, understudied swath of the animal kingdom known as lophotrochozoans, which includes as many as one-quarter of Earth's marine species.
CAPTION: The genomes of the freshwater leech Helobdella robusta (pictured), the owl limpet and an ocean-dwelling worm are among the first sequenced genomes from a vast, understudied swath of the animal kingdom known as lophotrochozoans, which includes as many as one-quarter of Earth's marine species.
CREDIT: Ajna S. Rivera/UC-Berkeley
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Public release date: 19-Dec-2012
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