All about processes

Apo and Calcium-Bound Crystal Structures of Cytoskeletal Protein Alpha-14 Giardin (Annexin E1) from the Intestinal Protozoan Parasite Giardia lamblia.

Journal of Molecular Biology

- 21 hours and 36 minutes ago

Publication Date: 2008 Nov 20 PMID: 19046974br/Authors: Pathuri, P. - Nguyen, E. T. - Ozorowski, G. - Svard, S. G. - Luecke, H.br/Journal: J Mol Biolbr/br/Alpha-14 giardin (annexin E1), a member of the alpha giardin family of annexins, has been shown to localize to the flagella of the intestinal protozoan parasite Giardia lamblia. Alpha giardins show a common ancestry with the annexins, a family of proteins most of which bind to phospholipids and cellular membranes in a Ca(2+)-dependent manner and are implicated in numerous membrane-related processes including cytoskeletal rearrangements and membrane organization. It has been proposed that alpha-14 giardin may play a significant role during the cytoskeletal rearrangement during differentiation of Giardia. To gain a better understanding of alpha-14 giardin's mode of action and its biological role, we have determined the three-dimensional structure of alpha-14 giardin and its phospholipid-binding properties. Here, we report the apo crystal structure of alpha-14 giardin determined in two different crystal forms as well as the Ca(2+)-bound crystal structure of alpha-14 giardin, refined to 1.9, 1.6 and 1.65 A, respectively. Although the overall fold of alpha-14 giardin is similar to that of alpha-11 giardin, multiwavelength anomalous dispersion phasing was required to solve the alpha-14 giardin structure, indicating significant structural differences between these two members of the alpha giardin family. Unlike most annexin structures, which typically possess N-terminal domains, alpha-14 giardin is composed of only a core domain, followed by a C-terminal extension that may serve as a ligand for binding to cytoskeletal protein partners in Giardia. In the Ca(2+)-bound structure we detected five bound calcium ions, one of which is a novel, highly coordinated calcium-binding site not previously observed in annexin structures. This novel high-affinity calcium-binding site is composed of seven protein donor groups, a feature rarely observed in crystal structures. In addition, phospholipid-binding assays suggest that alpha-14 giardin exhibits calcium-dependent binding to phospholipids that coordinate cytoskeletal disassembly/assembly during differentiation of the parasite.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19046974title=Entrez+PubmedCiteULike/a

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E-Tip: 'Raw materials in mining'

Malwarebytes Anti-Malware 1.31

Position dependent mismatch discrimination on DNA microarrays - experiments and model.

BMC Bioinformatics

- 1 days and 1 hours ago

Publication Date: 2008 Dec 1 PMID: 19046422br/Authors: Naiser, T. - Kayser, J. - Mai, T. - Michel, W. - Ott, A.br/Journal: BMC Bioinformaticsbr/br/ABSTRACT: BACKGROUND: The propensity of oligonucleotide strands to form stable duplexes with complementary sequences is fundamental to a variety of biological and biotechnological processes as various as microRNA signalling, microarray hybridization and PCR. Yet our understanding of oligonucleotide hybridization, in particular in presence of surfaces, is rather limited. Here we use oligonucleotide microarrays made in-house by optically controlled DNA synthesis to produce probe sets comprising all possible single base mismatches and base bulges for each of 20 sequence motifs under study. RESULTS: We observe that mismatch discrimination is mostly determined by the defect position (relative to the duplex ends) as well as by the sequence context. We investigate the thermodynamics of the oligonucleotide duplexes on the basis of double-ended molecular zipper. Theoretical predictions of defect positional influence as well as long range sequence influence agree well with the experimental results. CONCLUSIONS: Molecular zipping at thermodynamic equilibrium explains the binding affinity of mismatched DNA duplexes on microarrays well. The position dependent nearest neighbor model (PDNN) can be inferred from it. Quantitative understanding of microarray experiments from first principles is in reach.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19046422title=Entrez+PubmedCiteULike/a

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Discourse Analysis: Investigating Processes of Social Construction

ConMan 0.2.3 (Default branch)

Osmius: 9.01 beta available for download

Experiment provides "body swapping" experience

Boing Boing

- 1 days and 6 hours ago

In a strange neuroscience experiment, researchers determined that and individual wearing virtual reality goggles showing video streaming from another person's body can have the sensation that the other body is his or her own. The results of the experiments, conducted at the Karolinska Institutet in Stockholm, Sweden, were published in the journal Public Library of Science ONE. From the abstract: The concept of an individual swapping his or her body with that of another person has captured the imagination of writers and artists for decades. Although this topic has not been the subject of investigation in science, it exemplifies the fundamental question of why we have an ongoing experience of being located inside our bodies. Here we report a perceptual illusion of body-swapping that addresses directly this issue. Manipulation of the visual perspective, in combination with the receipt of correlated multisensory information from the body was sufficient to trigger the illusion that another person's body or an artificial body was one's own. This effect was so strong that people could experience being in another person's body when facing their own body and shaking hands with it. Our results are of fundamental importance because they identify the perceptual processes that produce the feeling of ownership of one's body. "If I Were You: Perceptual Illusion of Body Swapping" (PLoS ONE), "How To Use Neuroscience to Become Your Avatar" (Wired)...br style="clear: both;"/ a href="http://www.pheedo.com/click.phdo?s=45747936f83f596fa512cec569d00d44p=1"img alt="" style="border: 0;" border="0" src="http://www.pheedo.com/img.phdo?s=45747936f83f596fa512cec569d00d44p=1"//a img src="http://www.pheedo.com/feeds/tracker.php?i=45747936f83f596fa512cec569d00d44" style="display: none;" border="0" height="1" width="1" alt=""/

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Process Manager for Windows 1.0.112 Beta 1 beta

Blue Fang Adopts Hansoft Tools For Project Management

Gamasutra News

- 1 days and 11 hours ago

pimg src="http://www.gamasutra.com/db_area/images/news2001/21291/bluefanganimals.jpg" align="left" hspace="5"/Game development tool vendor Hansoft announced that developer Blue Fang Games (Zoo Tycoon series) has integrated Hansoft's project management and QA tools into its existing development processes. Hansoft's software has been licensed by a number of development studios, such as Ubisoft Paris, Black Lantern, Artificial Mind and Movement, and Ninja Theory, for project management, bug tracking, workload coordination, and document management. The tool is designed on principles of collaborative scheduling, task tracking, instant communication, Agile, .../p pmap name="google_ad_map_nM4zPNZJI-tBTV9SORD8acakuY8_"area shape="rect" href="http://imageads.googleadservices.com/pagead/imgclick/nM4zPNZJI-tBTV9SORD8acakuY8_?pos=0" coords="1,2,367,28"/area shape="rect" href="http://services.google.com/feedback/abg" coords="384,10,453,23"//mapimg usemap="#google_ad_map_nM4zPNZJI-tBTV9SORD8acakuY8_" border="0" src="http://imageads.googleadservices.com/pagead/ads?format=468x30_aff_imgclient=ca-pub-3896033488060561channel=feedburner-rssoutput=pngcuid=nM4zPNZJI-tBTV9SORD8acakuY8_url=http%3A%2F%2Fwww.gamasutra.com%2Fphp-bin%2Fnews_index.php%3Fstory%3D21291"//pdiv class="feedflare" a href="http://feeds.feedburner.com/~f/GamasutraNews?a=GsQgO"img src="http://feeds.feedburner.com/~f/GamasutraNews?i=GsQgO" border="0"/img/a a href="http://feeds.feedburner.com/~f/GamasutraNews?a=rp5QO"img src="http://feeds.feedburner.com/~f/GamasutraNews?i=rp5QO" border="0"/img/a a href="http://feeds.feedburner.com/~f/GamasutraNews?a=MXfkO"img src="http://feeds.feedburner.com/~f/GamasutraNews?i=MXfkO" border="0"/img/a /divimg src="http://feeds.feedburner.com/~r/GamasutraNews/~4/473661760" height="1" width="1"/

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Ride the D-Bus, Control your Linux desktop from the shell

CoLocalizer Pro 2.5 - Scientific calculator of colocalization coefficients. (Updater)

MacUpdate - Mac OS X

- 1 days and 14 hours ago

CoLocalizer Pro 2.5

CoLocalizer Pro is a professional scientific program for quantitative colocalization analysis of multicolor confocal fluorescence microscopy images. It enables deeper insight into the nature of biological processes by calculating colocalization coefficients and manages obtained data without limitations of the proprietary confocal microscope systems. CoLocalizer Pro is a more advanced tool than colocalization modules of the newest confocal microscopes:

Designed from the ground up with the user/researcher in mind.
More advanced than colocalization modules of the newest confocal microscopes.
Guides through the necessary steps to ensure that images are prepared appropriately for the reliable calculation of colocalization coefficients.
Compatible with image files in a variety of formats, including TIFF, JPEG, PICT, and BMP.
Compatible with Apple iLife software suite.
Offers unparalleled power and flexibility in exporting obtained data for further use.
The ability of CoLocalizer Pro to export PDF, HTML, and Excel files enables presenting the results of calculations to others and easily sharing ideas across computer platforms.
A native Mac OS X application, localized in English and Japanese
Breakthrough price: ten times more affordable than competitors.

WHAT'S NEWVersion 2.5:

Added more viewing options: rotate left, rotate right, flip horizontal, flip vertical.
Improved Check for Updates functionality.
Purchased licenses are now personalized.
Updated the Help and User Guides.
Fixed a case when some 300 dpi images were not properly merged.
Updated application and toolbar icons.
Made minor UI adjustments.
Updated License Agreement.

REQUIREMENTSMac OS X 10.2.8 or later, QuickTime 6.0 or later.
DEVELOPERCoLocalization Research Software
DOWNLOADS3913
DOWNLOAD NOW (16.3 MB)
More information

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Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis

Lets Take A Lesson From The Chip Industry: Turn The Big 3 Auto Makers Into Car Foundries . . .

Silicon Valley Watcher--reporting on the business and culture of disruption

- 1 days and 16 hours ago

The reason we have such a huge choice of low cost computers and all sorts of gizmos and gadgets, smart phones, and electronic toys is because of the amazing advances in chip designs. Hundreds of small chip design firms are producing incredibly advanced semiconductors that power a slew of innovative devices.

But the reason we have so much innovation in the chip industry is because of a manufacturing revolution that began more than twenty years ago. In 1987, Taiwan Semiconductor Manufacturing Company (TSMC) was founded as a new type of chip company--it was a semiconductor foundry--it made chips for other companies.

This completely transformed the chip industry and ushered in an innovation explosion. Chip designers didn't have to build their own chip factories, they could buy production time from chip foundries. Previously, chip startups had to raise hundreds of millions of dollars, primarily to pay for chip production--yet their value was in the designs.

Chip foundries led to a dramatic cut in the cost of establishing a chip company. Investment now went into chip design, not building a manufacturing line and learning how to run it.

This simple manufacturing revolution is responsible for all the innovation in electronics. And that's a model that could be effectively applied in the automotive world, and unleash a wave of innovation.

Manufacturing expertise . . .

I support a bailout of the automakers for one key reason: manufacturing expertise. If they shut down then we lose many decades of manufacturing knowledge and processes--it would be hugely expensive to recreate.

That manufacturing expertise can be used to build a Hummer, or it can be used to build hybrids, electric cars, and anything with wheels and an engine.

There is a tremendous amount of innovation in transportation that could be unlocked if you didn't have to have build your own factory to make the vehicles.

General Motors and the other car makers know how to re-tool lines to make all sorts of vehicles. They know what designs, and components work, and what doesn't; they have relationships with parts manufacturers, they have software design systems, test systems, air tunnels, algorithms...

They also know how to get through the red tape of qualifying vehicles for US roads. There is a massive amount of knowledge and expertise within the Big 3 that could be applied to producing the greenest of green vehicles.

My proposal is to use government monies to convert the Big 3 auto makers into car making foundries, in a similar fashion to chip-making foundries. That way, small startups with great ideas could quickly get their designs into production without requiring massive amounts of capital and learning how to build and operate a car factory.

Tesla Motors . . .

Take a look at Tesla Motors, one of the most innovative car companies of the past decade. The Tesla Roadster is an innovative all-electric sports car made with a carbon fiber body that has a range of 244 miles and does zero to sixty in less than 4 seconds. It received Time Magazine's 2nd best inventions of 2008.

But you have to very rich to buy one of these $109,000 cars primarily because building a manufacturing line is so expensive. It also means that Tesla had to raise massive amounts of capital to fund the manufacturing lines. This means the innovative Tesla technology will take years to trickle down to mainstream models--yet that's where it's lower carbon-footprint would have the most value.

Tesla ran into lots of delays because of manufacturing problems, and also problems with some of the components.

What if Tesla contracted with GM to make its cars? GM would know how to quickly tool up a production run, it probably would be able to help out with some of the drive-train problems Tesla had. GM would know what things work and how to avoid many problems that Tesla had to learn the hard way..

It is this kind of manufacturing expertise that could be leverage across a new industry. Small startups with great designs and technologies could quickly come to market without having to build their own production lines.

Car foundries could set off a huge wave of innovation at precisely the right time when we are searching for more responsible and sustainable forms of transport. And the US could grab a leadership position with such a plan.

Let's turn the Big 3 auto makers into foundries that can create a platform for a new type of innovative auto industry.

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The GABAergic anterior paired lateral neuron suppresses and is suppressed by olfactory learning.

How Comics Can Save Us From Scientific Ignorance

Wired Top Stories

- 1 days and 22 hours ago

!-- pageType= magazinewide slug= pl_print section= culture subsection= education headline= How Comics Can Save Us From Scientific Ignorance authorName= Barry Harbaugh -- pWhat's the solution to America's crisis in science education? More comic books. In December comes citea href="http://us.macmillan.com/thestuffoflife"The Stuff of Life/a: A Graphic Guide to Genetics and DNA/cite, a remarkably thorough explanation of the science of genetics, from Mendel to Venter, with a strand of social urgency spliced in. "If there was ever a time that we needed a push to make science a priority, it's now," says Howard Zimmerman, the book's editor and, not coincidentally, a former elementary-school science teacher. "Advances in treatments for disease cannot take place in a society that shuns science." Zimmerman works with the New York literary publishing house Hill and Wang, which discovered Elie Weisel and has been creating a new niche for itself as one of the premiere producers of major graphic "nonfiction novels" like the war on terror primer citeAfter 9/11/cite and the bio-comic citeRonald Reagan/cite./p pciteStuff of Life/cite is the first in a series dedicated to the hard sciences. The author is Mark Schultz, a DC Comics veteran and creator of the postapocalyptic classic citea href="http://www.darkhorse.com/Books/11-653/Xenozoic-Tales-Volume-1-TPB"Xenozoic Tales/a/cite. The 160-page work, illustrated by Kevin Cannon and Zander Cannon (improbably, no genetic relation), covers the regenerative processes of DNA, human migratory patterns, cloned apples, and stem cells. In a rapidly changing field, it's as up-to-date and accurate as possible./p pSchultz, like Zimmerman, was attracted by the possibilities of using comics as an educational medium. "It's not prose, and it's not documentary film," Schultz says. "It's kind of its own animal." And the graphic novel market is drawing in different readers than he's accustomed to at DC. "The manga phenomenon," he notes as one example, "is attracting new demographics, like younger women, who weren't picking up on traditional comics."/p pNot that this is the first time comics have been enlisted for educational purposes. The field goes back to the 1940s, when Will Eisner turned Army instruction manuals into a href="http://www.nytimes.com/2005/01/05/books/05eisner.html"graphic guides for soldiers/a. Also, there's Larry Gonick's citeCartoon Guides/cite of the '80s, with his citeCartoon Guide to Genetics/cite being the most obvious precursor here. citeStuff of Life/cite builds on Gonick, updating his science and employing a silly yet more effective narrativemdash;alien scientist Bloort 183 presents a PowerPoint on human genetics to his slow-learning leader./p pUp next? Possibly evolution. After all, Zimmerman says, "more than half of adult Americans think Earth is about 6,000 years old."/pbr style="clear: both;"/ a style='font-size: 10px; color: maroon;' href='http://www.pheedo.com/hostedMorselClick.php?hfmm=v3:c697aae688cafb8ebff3f3dfc81ef4b1:kWNqo0CWaxUCPlQ862WjV%2Balw1dDPHHbxsG5R6RLNumBA6dqmaUzJ0rIFAtYHrLeXcoxw9t1S6%2FvCQ%3D%3D'img border='0' title='Add to Facebook' alt='Add to Facebook' src='http://www.pheedo.com/images/mm/facebook.gif'//a a style='font-size: 10px; color: maroon;' href='http://www.pheedo.com/hostedMorselClick.php?hfmm=v3:86c1fbc9187e4f24cf9a5a5eafe0fdc5:5XGKbzvUKAI0Kx5FZes5y1sqRuGVnkfa%2F2GMTmuae6avdXHUZlvetqQSSbkB8N4HZsdWYM%2FFKPm0'img border='0' title='Add to Reddit' alt='Add to Reddit' src='http://www.pheedo.com/images/mm/reddit.png'//a a style='font-size: 10px; color: maroon;' href='http://www.pheedo.com/hostedMorselClick.php?hfmm=v3:ff53e8831b23a3ca1b664762b4ec2d64:qdsrAbd53IpU3uv9X3yTGy9dDBJt3P8FLT42bezjy2bBgstcBO4kp8FLCSXp9eAosvHFSzqJUCEA'img border='0' title='Add to digg' alt='Add to digg' src='http://www.pheedo.com/images/mm/digg.gif'//a a style='font-size: 10px; color: maroon;' href='http://www.pheedo.com/hostedMorselClick.php?hfmm=v3:2bda3dd732da236562d797c09f1f3069:OweWO7olqgIAwBtWs9rgqwXhRLUB2O%2FRVl5j0vSP1mK9xWueXeIrmcj9pOzR%2FjUccmEfqd%2F1fTx2'img border='0' title='Add to Google' alt='Add to Google' src='http://www.pheedo.com/images/mm/google.png'//a br style="clear: both;"/ a href="http://www.pheedo.com/click.phdo?s=ca0551678d4065f628e3993770cdbd2fp=1"img alt="" style="border: 0;" border="0" src="http://www.pheedo.com/img.phdo?s=ca0551678d4065f628e3993770cdbd2fp=1"//a img src="http://www.pheedo.com/feeds/tracker.php?i=ca0551678d4065f628e3993770cdbd2f" style="display: none;" border="0" height="1" width="1" alt=""/ pa href="http://feeds.wired.com/~a/wired/index?a=ZuR1VA"img src="http://feeds.wired.com/~a/wired/index?i=ZuR1VA" border="0"/img/a/pimg src="http://feeds.wired.com/~r/wired/index/~4/473261696" height="1" width="1"/

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scientists,adults,accustomed,documentary,veteran

Protein kinase R reveals an evolutionary model for defeating viral mimicry.

Nature

- 2 days and 2 hours ago

Publication Date: 2008 Nov 30 PMID: 19043403br/Authors: Elde, N. C. - Child, S. J. - Geballe, A. P. - Malik, H. S.br/Journal: Naturebr/br/Distinguishing self from non-self is a fundamental biological challenge. Many pathogens exploit the challenge of self discrimination by employing mimicry to subvert key cellular processes including the cell cycle, apoptosis and cytoskeletal dynamics. Other mimics interfere with immunity. Poxviruses encode K3L, a mimic of eIF2alpha, which is the substrate of protein kinase R (PKR), an important component of innate immunity in vertebrates. The PKR-K3L interaction exemplifies the conundrum imposed by viral mimicry. To be effective, PKR must recognize a conserved substrate (eIF2alpha) while avoiding rapidly evolving substrate mimics such as K3L. Using the PKR-K3L system and a combination of phylogenetic and functional analyses, we uncover evolutionary strategies by which host proteins can overcome mimicry. We find that PKR has evolved under intense episodes of positive selection in primates. The ability of PKR to evade viral mimics is partly due to positive selection at sites most intimately involved in eIF2alpha recognition. We also find that adaptive changes on multiple surfaces of PKR produce combinations of substitutions that increase the odds of defeating mimicry. Thus, although it can seem that pathogens gain insurmountable advantages by mimicking cellular components, host factors such as PKR can compete in molecular 'arms races' with mimics because of evolutionary flexibility at protein interaction interfaces challenged by mimicry.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19043403title=Entrez+PubmedCiteULike/a

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San Francisco event: Leah Buechley

MAKE Magazine

- 2 days and 2 hours ago

Those near Berkeley should make time tomorrow for an excellent speech:

Leah Buechley, MIT Media Lab

New Craft - A Marriage of High and Low Tech

Wednesday December 3 6:00 - 7:30 pm

BCNM Commons* UC Berkeley

People knit scarves, build furniture, sew clothing, and solder radios together in their homes and garages. Diverse groups of people--girls and boys, grandparents and college students--lovingly engage in these hands-on low-tech hobbies. In contrast, companies produce high-tech things by high-tech processes, using teams of people and sophisticated machinery to build devices like cell phones, computers, pharmaceutical drugs, and cars. But this clear division between high-tech and low-tech is beginning to blur. A host of new tools is making many of the resources previously available only to companies accessible to individuals, empowering people to design, engineer, and build devices that integrate high and low technology.

This talk will discuss this "new craft", envisioning a future in which individuals integrate
traditional craft, engineering, and web-honed communication skills to build and share information about "high-low tech" devices like temperature sensing scarves, algorithmically generated furniture, and radically customized cell phones. The presentation will discuss burgeoning high-low tech communities, focusing on ways that professional designers and engineers can support and encourage this new creative movement. It will present examples of high-low tech artifacts--including embroidered circuits and paper computers--and examples of tools that empower others to construct high-low tech devices--including the LilyPad Arduino, a construction kit that enables novices to build fabric-based wearable computers.

Check out Leah's (many, excellent) projects here.

a href="http://blog.makezine.com/archive/2008/12/san_francisco_event_leah.html?CMP=OTC-0D6B48984890" /Read more/a | a href="http://blog.makezine.com/archive/2008/12/san_francisco_event_leah.html?CMP=OTC-0D6B48984890" / Permalink/a | a href="http://blog.makezine.com/archive/2008/12/san_francisco_event_leah.html?CMP=OTC-0D6B48984890#comments" /Comments/a | a href="http://blog.makezine.com/archive/events/?CMP=OTC-0D6B48984890" /Read more articles in Events/a | a href="http://digg.com/submit?url=blog.makezine.com%2Farchive%2F2008%2F12%2Fsan_francisco_event_leah.htmltitle=San%20Francisco%20event%3A%20Leah%20Buechleybodytext=%20Those%20near%20Berkeley%20should%20make%20time%20tomorrow%20for%20an%20excellent%20speech%3A%20Leah%20Buechley%2C%20MIT%20Media%20Lab%20New%20Craft%20-%20A%20Marriage%20of%20High%20and%20Low%20Tech%20Wednesday%20December%203%206%3A00%20-%207%3A30%20pm%20BCNM%20Commons%2A%20UC%20Berkeley%20People%20knit...topic=tech_news" /Digg this!/a

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