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Genome scale view of great white shark uncovers unexpected and distinctive features

Nov. 19, 2013 — The great white shark, a major apex predator made famous by the movie "Jaws," is one of the world's most iconic species capturing an extraordinary amount of public fascination. An intriguing question is what makes a white shark so distinctive? One way to address this is to explore the genetic makeup of this remarkable animal.

A new study by scientists from Nova Southeastern University's (NSU) Save Our Seas Shark Research Centre and Cornell University published in final form today in the journal BMC Genomics now undertakes the first large-scale exploration of the great white shark's genetic repertoire, and comes up with unexpected findings.

The researchers compared the transcriptome (i.e., the set of RNA sequences expressed by the organism's genes) from the white shark heart to the transcriptomes from the best studied fish research model (the zebrafish) and humans to look for similarities and significant differences that might explain the distinctiveness of the white shark. So they had a common comparative base, the researchers compared gene products that had known functions in all three species.

Contrary to expectations, the researchers found that the proportion of white shark gene products associated with metabolism had fewer differences from humans than zebrafish (a bony fish) -- an unexpected result given that bony fishes are evolutionarily much more closely related to sharks.

Indeed, more broadly speaking, the researchers were also surprised to find that other aspects of the white shark heart transcriptome, including molecular functions as well as the cellular locations of these functions, also showed greater similarity to human than zebrafish. Like many first looks at complex scientific questions, the unexpected results of this study raises more questions than provides answers.

"It's intriguing why there are these fewer differences in the proportion of gene products between white sharks and humans, than white sharks and zebrafish, when the complete opposite was expected based on evolutionary affinities," said study co-author Mahmood Shivji, director of NSU's Save Our Seas Shark Research Center and Guy Harvey Research Institute. "One possibility for the apparent greater similarity between white sharks and humans in the proportion of gene products associated with metabolism might be due partly to the fact that the white shark has a higher metabolism because it is not a true cold-blooded fish like bony fishes; however this explanation remains a hypothesis to be further tested."

One of the notable biological properties of white sharks is that it is one of few fishes that is regionally warm-bodied, i.e., parts of its body (its viscera, locomotor muscles and cranium) are kept at a higher temperature than the surrounding water world -- a property known as regional endothermy. This warm-body property is in turn associated with elevated metabolic rates compared to true cold-blooded bony fishes.

"Additional comparative data from other white shark tissues and/or from other endothermic shark species such as makos would be required to see if this general similarity in gene products holds," said Michael Stanhope of Cornell, who co-led the study with Shivji. "Nevertheless, this preliminary finding opens the possibility that some aspects of white shark metabolism, as well as other aspects of its overall biochemistry, might be more similar to that of a mammal than to that of a bony fish."

Another curious feature of the genetic repertoire of the white shark heart was that the transcriptome revealed a much lower abundance of a certain type of DNA sequence that occurs in repeated triplet form, than found in other vertebrates. Interestingly, in human genes that contain such repeated triplet sequences, an aberrant increase in their number has been linked to a variety of neurological disorders. It's not known whether sharks are immune to neurological genetic diseases, but the fact that these DNA patterns occur in such low abundance in white shark genes may indicate a reduced chance of similar such disorders in this primitive vertebrate.

"Our results, along with other distinctive shark genome features reported by the very few studies in this area by others, are suggesting that we may be in for some surprises as we further explore sharks at their most fundamental level -- their genes," said Shivji. "We've just scratched the surface in terms of investigating what makes these evolutionary marvels, and in many cases threatened species, tick."

Latest Technology

Samsung Galaxy Gear scores 800,000 sales, gets first custom ROM

Smartwatches may still be in their infancy, but that hasn’t stopped Samsung’s Galaxy Gear smartwatch from selling an impressive 800,000 units in just two months.

To help boost sales the Galaxy Gear has also had its first custom ROM appear. Based off of Nova launcher, it features Bluetooth tethering, live wallpaper support, and video recording up to 60 seconds – all without needing to be paired to a smartphone.

Despite being largely dismissed in most reviews (including ours) as simply having too few features to warrant its $300 price tag, the Galaxy Gear has nevertheless been able to become the best selling wearable smart device to date. This is largely due to Samsung’s aggressive marketing campaign as well as collaboration with various fashion shows. A few promotions that let you have the Gear for much less if bundled with a new Galaxy Note 3 have helped, too.

The developer community has also taken the Galaxy Gear under its wing, with the new null custom ROM greatly enhancing the look and functionality of the Galaxy Gear. Otherwise limited, for the most part, to features provided while paired with a smartphone, the Galaxy Gear becomes much more of a standalone device thanks to the custom ROM. It gets native apps support as well as its own fully featured web browser.

To find out more, check out the xda-developers thread. As always, exercise caution when flashing custom ROMs.

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Latest Technology

Unboxing the Elite New Porsche Design P’9982 from BlackBerry

I’m pleased to introduce the elite, new, all-touch Porsche Design P’9982 Smartphone from BlackBerry. Today, in a press release, we announced the new smartphone. I’ve had my hands on it for a little while and filmed an exclusive unboxing video to share with you eager readers. Watch the video below and continue reading for highlights. […]
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Are You Using IPv6 Yet? Should You Even Care?

ipv6-or-ipv4

IPv6 is extremely important for the long-term health of the Internet. But is your Internet service provider providing IPv6 connectivity yet? Does your home network support it? Should you even care if you’re using IPv6 yet?

Switching from IPv4 to IPv6 will give the Internet a much larger pool of IP addresses. It should also allow every device to have its own public IP address, rather than be hidden behind a NAT router.

IPv6 is Important Long-Term

IPv6 is very important for the long-term health of the Internet. There are only about 3.7 billion public IPv4 addresses. This may sound like a lot, but it isn’t even one IP address for each person on the planet. Considering people have more and more Internet-connected devices — everything from light bulbs to thermostats are starting to become network-connected — the lack of IP addresses is already proving to be a serious problem.

This may not affect those of us in well-off developed countries just yet, but developing countries are already running out of IPv4 addresses.

So, if you work at an Internet service provider, manage Internet-connected servers, or develop software or hardware — yes, you should care about IPv6! You should be deploying it and ensuring your software and hardware works properly with it. It’s important to prepare for the future before the current IPv4 situation becomes completely unworkable.

But, if you’re just typical user or even a typical geek with a home Internet connection and a home network, should you really care about your home network just yet? Probably not.

server-racks

What You Need to Use IPv6

To use IPv6, you’ll need three things:

  • An IPv6-Compatible Operating System: Your operating system’s software must be capable of using IPv6. All modern desktop operating systems should be compatible — Windows Vista and newer versions of Windows, as well as modern versions of Mac OS X and Linux. Windows XP doesn’t have IPv6 support installed by default, but you shouldn’t be using Windows XP anymore, anyway.
  • A Router With IPv6 Support: Many — maybe even most — consumer routers in the wild don’t support IPv6. Check your router’s specifications details to see if it supports IPv6 if you’re curious. If you’re going to buy a new router, you’ll probably want to get one with IPv6 support to future-proof yourself. If you don’t have an IPv6-enabled router yet, you don’t need to buy a new one just to get it.
  • An ISP With IPv6 Enabled:  Your Internet service provider must also have IPv6 set up on their end. Even if you have modern software and hardware on your end, your ISP has to provide an IPv6 connection for you to use it. IPv6 is rolling out steadily, but slowly — there’s a good chance your ISP hasn’t enabled it for you yet.

linksys-router

How to Tell If You’re Using IPv6

The easiest way to tell if you have IPv6 connectivity is to visit a website like testmyipv6.com. This website allows you to connect to it in different ways — click the links near the top to see if you can connect to the website via different types of connections. If you can’t connect via IPv6, it’s either because your operating system is too old (unlikely), your router doesn’t support IPv6 (very possible), or because your ISP hasn’t enabled it for you yet (very likely).

test-ipv6

Now What?

If you can connect to the test website above via IPv6, congratulations! Everything is working as it should. Your ISP is doing a good job of rolling out IPv6 rather than dragging its feet.

There’s a good chance you won’t have IPv6 working properly, however. So what should you do about this — should you head to Amazon and buy a new IPv6-enabled router or switch to an ISP that offers IPv6? Should you use a “tunnel broker,” as the test site recommends, to tunnel into IPv6 via your IPv4 connection?

Well, probably not. Typical users shouldn’t have to worry about this yet. Connecting to the Internet via IPv6 shouldn’t be perceptibly faster, for example. It’s important for operating system vendors, hardware companies, and Internet service providers to prepare for the future and get IPv6 working, but you don’t need to worry about this on your home network.


IPv6 is all about future-proofing. You shouldn’t be racing to implement this at home yet or worrying about it too much — but, when you need to buy a new router, try to buy one that supports IPv6.

Image Credit: Adobe of Chaos on Flickr, hisperati on Flickr, Vox Efx on Flickr


    






Latest Technology, Nokia
Latest Technology

Viber and HERE Transit hit select Nokia Asha phones

Nokia’s touch-based Ashas are getting a couple of important apps – Here Transit Beta is now available to the Asha 50x range, while Viber has hit the Asha 3xx. Both of these apps were available for certain old-school S40 Nokias, but now owners of the touch-based Ashas can use them too.

Viber works just about like you would expect – it needs a mobile data connection or Wi-Fi, it supports push messages, it will sync your contacts and it even does voice calls, so it’s not just text.

The Viber app is available for the Asha 308, 310 and 311, grab it from the Ovi Store. Older versions of the app can be found for X3-02, C3-00, Asha 302, Asha 300, Asha 303.

Nokia’s HERE Transit for Asha supports the same 800 cities the Windows Phone 8 version supports. It has the same features too – you can check schedules for nearby stops, plan and visually inspect a door-to-door route (with walking directions included), even plan routes for future dates. That, plus the option to save routes for offline use, makes this app a great tool for planning a trip abroad.

This version of HERE Transit is in beta and is available for the Asha 500, 501 and 502. You can download it here (free registration required).

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Latest Technology

Nokia Lumia 2520 hitting Verizon on November 21

Nokia took the wraps of its Lumia 2520 at this year’s Nokia World in Abu Dhabi. The gorgeous looking slate is just about to go sale across the globe and Verizon has announced that it will be joining the fun starting from November 21.

The 10.1-inch Nokia Lumia 2520 will cost you $499.99 and the slate will also be up for grabs for $399.99 with a two-year contract. The Black color model will be available across all the Verizon stores, while if you order online you will be able to choose between the Black and the Red versions.

AT&T has also announced that it will be stocking the Lumia 2520, but it will be getting it a day later – November 22. AT&T does offer to subsidize the price to $200 if you opt to get the slate with one of the Nokia Lumia flagships, though.

If you are considering taking the plunge you might want to check out our hands-on with the slate to know more about it.

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Latest Technology, Nokia
PC & Laptop

Most promising 3D printing applications

From replacement kidneys to guns, cars, prosthetics and works of art, 3D printing is predicted to transform our lives in the coming decades as dramatically as the Internet did before it. "I have no doubt it is going to change the world," researcher Jam...
Latest Technology, Nokia
Latest Technology
Latest Technology

Initiating the First Global Campaign for Printing Solutions

London to Amsterdam, people have been spotting a sign of innovation, literally. Samsung Printing Solutions’ new slogan, “Samsung. Printing Innovation”, has been making appearances in various cities around Europe. Innovation is definitely not a foreign …