www.synbio.org.uk site news

Positions at Microsoft Research, Cambridge UK

Tue, 01 Feb 2011 00:52:59 +0100

The Biological Computation Group at Microsoft Research is seeking to hire outstanding scientists to conduct research into uncovering fundamental principles of biological information processing, including research in one or more of the following areas: fundamentals of biological computation, immunology, developmental biology, synthetic biology, DNA computing and neuroscience. The overall aim of the group is to transform our understanding of how biological systems compute. The group is studying biological systems across multiple scales and scientific domains, ranging from DNA computing and synthetic biology, through to developmental biology and immunology, tackling fundamental scientific questions in each domain. Further information about the group is available at http://research.microsoft.com/biology , including links to software tools, which are freely available for use by the scientific community.

Microsoft Research is seeking candidates with a strong research background in one of these areas, or a background in computer science, engineering, maths or physics and have applied their work in biological modelling. Candidates with an experimental background should be able to demonstrate strong computational or mathematical expertise. Postdoctoral positions are available for between two and three years, while permanent research positions are also available for more senior candidates. (online details at: https://research.microsoft.com/apps/tools/jobs/fulltime.aspx and in the Jobs section on this site)

Positions at Microsoft Research, Cambridge UK

Tue, 01 Feb 2011 00:48:47 +0100

http://research.microsoft.com/biology/jobs.aspx

The group is studying biological systems across multiple scales and scientific domains, ranging from DNA computing and synthetic biology, through to developmental biology and immunology, tackling fundamental scientific questions in each domain. Current projects include designing molecular circuits made of DNA, and programming single cells that cooperate to perform complex functions over time and space. We also aim to understand the computation performed by cells during organ development, and how the adaptive immune system detects viruses and cancers in the human body, focusing on mechanism and function. We are tackling these questions through the development of computational models and domain-specific computational tools, in close collaboration with leading scientific research groups. The tools we develop are being integrated into a common software environment, which supports simulation and analysis across multiple scales and domains. Further information about the group is available at http://research.microsoft.com/biology , including links to our software tools, which are freely available for use by the scientific community.

We are seeking to hire outstanding scientists to undertake research in one or more of the following areas: fundamentals of biological computation, immunology, developmental biology, synthetic biology, DNA computing and neuroscience. Candidates should have a strong research background in one of these areas, or a background in computer science, engineering, maths or physics and have applied their work in biological modelling. Candidates with an experimental background should be able to demonstrate strong computational or mathematical expertise.

Candidates will be expected to develop collaborations with leading research groups, particularly experimentalists, and to publish their research in leading peer-reviewed scientific journals. However, the primary expectation is more ambitious: to make important contributions that enable fundamental progress in biological science.

The Biological Computation Group is part of Microsoft’s Computational Science Laboratory, which is well-resourced and also includes a Computational Ecology group together with expertise in software development. This is an exciting opportunity to join a young, dynamic team with excellent opportunities for growth in the future, including plans for state-of-the art wet lab facilities.

Postdoctoral positions are available for between two and three years, while permanent research positions are also available for more senior candidates. To apply, please complete the online application athttps://research.microsoft.com/apps/tools/jobs/fulltime.aspx , preferably before February 28th. Any pre-application enquiries should be sent to Andrew Phillips ([email protected]" style="color: blue; text-decoration: underline; ">[email protected]) with subject “Hiring”. Applications will be considered on receipt, and suitable candidates will be interviewed on an ongoing basis.

iGEM2011 recruitment

Mon, 03 Jan 2011 17:25:34 +0100

Last call for applications

Are you a second year student at Cambridge? Would you like to participate in the international Genetically Engineered Machines competition in Synthetic Biology over the summer of 2011?

The University of Cambridge supports a student team in the annual iGEM competition in Synthetic Biology. We are assembling a team to apply for Wellcome Trust iGEM summer studentships over the summer of 2011.

iGEM is an international competition where student teams are given a kit of biological parts at the beginning of the summer from the MIT Registry of Standard Biological Parts. In Cambridge. we start with a two-week crash course in Synthetic Biology, with an interdisciplinary group of students and faculty. The iGEM students then face the challenge of designing a new biological system and constructing this over the summer, using standard parts and DNA synthesis to establish the system in living cells. The project culminates with an international meeting at MIT in November.

iGEM has grown as a summer competition, with 5 teams in 2004, 13 teams in 2005 - the first year that the competition grew internationally, 32 teams in 2006, 54 teams in 2007, 84 teams in 2008, 112 teams in 2009 and 130 teams in 2010. Projects have ranged from banana and wintergreen smelling bacteria, to an arsenic biosensor, to Bactoblood, and buoyant bacteria. Cambridge teams were finalists last year, with better engineered bioluminesence, and won the Grand Prize in 2009 with a scheme for sensitive biosensors that produced an array of colour biopigments (More information can be found on this site: http://www.synbio.org.uk/igem.html)

These are student driven projects, and the iGEM competition provides a opportunity to engage in original research as a team - with control over scientific direction and budget. It is fun and challenging.

The Wellcome Trust is offering a number of student stipends to support the participation of a limited number of UK teams in the international Genetically Engineered Machine competition (iGEM). The stipend will provide promising undergraduates with hands-on experience of synthetic biology during their 2011 summer vacation, with the aim of encouraging young scientists to consider a career in interdisciplinary research. The Cambridge iGEM teams have always been highly interdisciplinary, and we actively recruit students who may have little experience with biological systems, but who have complementary skills in engineering, computing or physical sciences.

Bursaries are available for a maximum of ten students per team and for up to ten weeks during the summer vacation. Each bursary provides a stipend of £180 per week. There may be only one application per team for a maximum of ten stipends. Application forms must be completed by a team adviser or sponsor. Each student must be at a university within the UK or the Republic of Ireland (RoI) and should be an undergraduate registered for a basic science, engineering, mathematical, physical science, social and ethical science, dentistry, medical or veterinary degree. Each student should be in the middle year/s of a first degree of study (i.e. not in their first or last year) or a medical student between the end of the second year and the end of the penultimate year. More information about the Wellcome Trust scheme can be found at: www.wellcome.ac.uk/igem.

If you are interested in applying for a Wellcome iGEM2011 studentship at the University of Cambridge, forward your details including, (i) a short description of why you would like to participate and how you might contribute, (ii) a CV, to Jim Haseloff at [email protected] by January 7th, 2011. This is the last call!

Manfrotto pocket series tripods

Sat, 11 Dec 2010 19:15:09 +0100

Manfrotto's MP3 digital-SLR pocket-sized tripod on display at Photokina 2010

Until such things as the Gorillapod appeared, one of the most annoying aspects of steady photography was lugging a tripod around. Now Manfrotto has unveiled a new pocket-sized tripod solution for both compact and digital SLR cameras that neatly folds away beneath the body of the camera so that both tripod and camera can fit in the pouch or bag.

The MP1 and MP3 pocket series tripods from Manfrotto screw onto the mount underneath just about any compact or digital SLR. When the moment calls for a steady shot, the three feet can be unfolded and the camera placed on any handy flat surface (such as a wall or table) for support. When not in use the tripod feet can be folded back underneath the camera body without any ungainly size increases. As such, it should be possible to stow away both camera and attached tripod into most pouches or bags until needed.

The pocket series tripods come in two sizes – one for compact and one for digital SLR -– with each available in either black or silver. They're not quite as versatile as the Gorillapod but they're more compact and also benefit from some protective buffers between tripod and camera to help keep your camera's base scratch-free.

Make: Online : Modular stackable Arduino enclosure

Sat, 11 Dec 2010 19:06:00 +0100

Modular stackable Arduino enclosure

Spotted in the MAKE Flickr Pool, this 3D printed set of chassis components from user nathanmatsuda:

So far I've made end panels for the duemilanove and the ethernet shield. Next up- a new top piece that'll have an opening for the prototyping shield. Also planning a top piece for the touch shield (but I don't have one of those yet).

The parts are available in his Shapeways shop.

Article from: http://blog.makezine.com/archive/2010/07/modular_stackable_arduino_enclosure.html

Wunderlist for iPhone Is an Elegant, Syncing To-Do Manager

Sat, 11 Dec 2010 18:59:17 +0100

From: http://lifehacker.com/5708801/wunderlist-for-iphone-is-an-elegant-syncing-to+do-manager?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+lifehacker%2Ffull+%28Lifehacker%29

We loved the Wunderlist desktop app for Mac and Windows and the iPhone app makes a perfect companion. With the same simple features, attractive interface, and syncing support, you can now easily manage your Wunderlist from your pocket.

There are a lot of desktop apps that find their way on the iPhone and feel liked dumbed-down versions of the software, but Wunderlist for iPhone pretty much packs every feature of the desktop app(including themes) into its mobile counterpart. If you're already set up on the desktop, you can just enter your account information into Wunderlist for iPhone and all your tasks will sync right up. If you're new to Wunderlist, you'll take to it quickly. It's not rich with features, but the minimalist approach to managing your tasks makes keeping on top of everything very simple. There are plenty of views to find the tasks you need to concentrate on now, tomorrow, or farther off in the future, and you can star important tasks so you're sure not to miss them.

Wunderlist is available right now, for free, in the iTunes App Store.

Wunderlist | iTunes App Store

Send an email to Adam Dachis, the author of this post, at [email protected]?subject=http://lifehacker.com/5708801/wunderlist-for-iphone-is-an-elegant-syncing-to+do-manager">[email protected].

Access the desktop version of Google Docs on your iPad

Sat, 11 Dec 2010 18:56:42 +0100

Access the desktop version of Google Docs on your iPad

by Samuel Gibbs at http://downloadsquad.switched.com/2010/12/10/access-the-desktop-version-of-google-docs-on-your-ipad/?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+weblogsinc%2Fdownloadsquad+%28Download+Squad%29

A couple of weeks ago, Google enabled Docs editing on iOS and Android devices through a lightweight, mobile-optimized version. Yesterday the iPad, with its larger screen real estate, got access to the full-blown desktop version of Docs -- there for when the mobile version simply won't cut it. You'll have access to all the formatting features available on the desktop when you need it, as well as formulae in spreadsheets. But Google recommends using it in one-off scenarios rather than as a full-time solution, with the mobile-optimized version staying as the default for now.

If you've ever needed more power than the mobile-optimized Docs will allow, now you have the option, just hit Desktop version, or go to spreadsheet view.

TAGS: APPLE, APPS, DOCS, GOOGLE, GOOGLE DOCS, GOOGLEDOCS, IOS, IPAD, PRODUCTIVITY

source: Google Docs Blog

Dynamics in the mixed microbial concourse.

Sat, 11 Dec 2010 18:41:59 +0100

Dynamics in the mixed microbial concourse.: "Publication Date: 2010 Dec 1 PMID: 21123647
Authors: Wintermute, E. H. - Silver, P. A.
Journal: Genes Dev

Isolated, clonal populations of cells are rarely found in nature. The emergent properties of microbial consortia present a challenge for the systems approach to biology, as chances for competition, communication, or collaboration multiply with the number of interacting agents. This review focuses on recent work on intercourse within biofilms, among quorum-sensing populations, and between cross-feeding metabolic cooperators. New tools from synthetic biology allow microbial interactions to be designed and tightly controlled, creating valuable model systems. We address both natural and synthetic partnerships, with an emphasis on how system behaviors derive from the properties of their components. Essential features of microbial biology arose in the context of a very mixed culture and cannot be understood without unscrambling it.

(Via Genes and Development.)

MicroRNAs prevent precocious gene expression and enable pattern formation during plant ...

Sat, 11 Dec 2010 18:41:15 +0100

MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis.: "Publication Date: 2010 Dec 1 PMID: 21123653
Authors: Nodine, M. D. - Bartel, D. P.
Journal: Genes Dev

Arabidopsis embryos lacking DICER-LIKE1 (DCL1), which is required for microRNA (miRNA) biogenesis, arrest early in development. To assess the functions of embryonic miRNAs, we determined the developmental and molecular consequences of DCL1 loss. We found that DCL1 is required for cell differentiation events as early as the eight-cell stage and soon thereafter for proper division of the hypophysis and subprotoderm cells. By the early globular ( approximately 32-cell) stage, dcl1-null mutant embryos overexpress approximately 50 miRNA targets. In dcl1 eight-cell embryos, the two most up-regulated targets are those of miR156 and encode SPL10 and SPL11 transcription factors. SPL10 and SPL11 are derepressed >150-fold in dcl1 embryos and are redundantly required for the dcl1 early patterning defects. Moreover, as early as the eight-cell stage, miR156-mediated repression of zygotic SPL transcripts prevents premature accumulation of transcripts from genes normally induced during the embryonic maturation phase. Thus, the first perceptible molecular function of plant embryonic miRNAs is the opposite of that in vertebrates; in vertebrates, miRNAs sharpen the first developmental transition, whereas in plants, they forestall developmental transitions by repressing mRNAs that act later. We propose that, by preventing precocious expression of differentiation-promoting transcription factors, miRNAs enable proper embryonic patterning.

(Via Genes and Development.)

Particular Significance of SRD2-Dependent snRNA Accumulation in Polarized Pattern Generation ...

Sat, 11 Dec 2010 18:35:34 +0100

Particular Significance of SRD2-Dependent snRNA Accumulation in Polarized Pattern Generation during Lateral Root Development of Arabidopsis.: "Publication Date: 2010 Dec PMID: 20965997
Authors: Ohtani, M. - Demura, T. - Sugiyama, M.
Journal: Plant Cell Physiol

Lateral root primordia are initiated by anticlinal division of cells in the pericycle and are constructed through an ordered set of cell divisions. At the completion of the development of the primordium, cell division ceases, after which the lateral root meristem is activated. In Arabidopsis, this course of lateral root morphogenesis was found to be significantly susceptible to srd2-1, a temperature-sensitive mutation of the SRD2 gene encoding an activator of small nuclear RNA (snRNA) transcription. The srd2-1 mutation altered the organization of cells of the root primordium and, importantly, maintained primordial cell division for a long period, resulting in the formation of abnormal hemispherical laterals. Expression patterns of various reporter genes suggested that both the apical-basal and radial axes were not well established in the lateral root primordia of the srd2-1 mutant. In the early stages of development of the primordium, the srd2-1 mutation reduced the amount of the auxin efflux facilitator PIN-FORMED (PIN) and, probably by this means, interfered with the generation of an auxin gradient. Spliceosomal snRNAs accumulated at high levels throughout young root primordia and then decreased in association with the arrest of cell division, and finally increased again when the apical meristem became activated. The accumulation of snRNAs was severely suppressed by the srd2-1 mutation, and this was detectable before any morphological defect became evident. These findings suggest that high-level accumulation of snRNA involving the SRD2 function is particularly important for expression of PINs in polarized pattern generation during the development of lateral root primordia.

(Via Plant and Cell Physiology.)

Rapid blue-light-mediated induction of protein interactions in living cells.

Sat, 11 Dec 2010 18:33:40 +0100

Rapid blue-light-mediated induction of protein interactions in living cells.: "Publication Date: 2010 Dec PMID: 21037589
Authors: Kennedy, M. J. - Hughes, R. M. - Peteya, L. A. - Schwartz, J. W. - Ehlers, M. D. - Tucker, C. L.
Journal: Nat Methods

Dimerizers allowing inducible control of protein-protein interactions are powerful tools for manipulating biological processes. Here we describe genetically encoded light-inducible protein-interaction modules based on Arabidopsis thaliana cryptochrome 2 and CIB1 that require no exogenous ligands and dimerize on blue-light exposure with subsecond time resolution and subcellular spatial resolution. We demonstrate the utility of this system by inducing protein translocation, transcription and Cre recombinase-mediated DNA recombination using light.

(Via Nature Methods.)

Making classic frequency counters into Nixie clocks

Sat, 11 Dec 2010 18:21:45 +0100

Making classic frequency counters into Nixie clocks: "One of our favorite longstanding projects-- which we dropped a hint about some time ago --is converting old HP Nixie-tube counters into happily glowing Nixie clocks. Here's how we do it.

We've converted a few different types, but our favorite clocks come from HP 5321B and 5221B electronic counters. These frequency counters were produced from about 1968-1970, in that brief window of time where the control electronics had transitioned from discrete-transistor logic to integrated circuits, but Nixie tubes were still the preferred display technology. (By 1971, HP's catalog was full of counters with high-tech light-emitting diode displays.)

You can often pick up counters like these at eBay or at various places that sell surplus electronics, and as they are rather obsolete, they're usually quite inexpensive. The condition that old electronics like these arrive in can vary greatly. We've acquired some that were barely repairable and mostly corroded, and others like this one that still have the calibration seal intact.

While shopping, you should be aware of is that counters that look like these may actually be populated with 4, 5, or 6 tubes. The good news is that they can be expanded even at this late date, by adding three chips and a tube (per digit) to the main circuit board. We'll get to that in a minute, but the point is that it's straightforward to combine parts from multiple units of the same model.

Under the top cover, you can see the main circuit board, which contains the display logic and the tubes themselves, socketed.

The main board is anchored in place with a couple of slot-tabs, and you essentially need to bend the board over a couple of tabs in order to slide it out. The nixie tubes hang upside down from the board, and have numbers that might seem upside down if you didn't know this.

The board itself is something of a masterwork. The traces are thick and gold plated. It's soldered on the back side only, apparently by a dip-solder process. The chips are all now-generic types, but under HP part numbers ('1820-0093...') and the protruding letters 'hp' are molded right into the cases of each package. (You can see this photo in monstrous resolution here, if you're so inclined.)

There are three rows of chips on the board. The ones furthest from the tubes are cascading decade counter chips, the middle row are buffer chips, and those closest to the tubes are the Nixie driver chips.

For a little background, consider how this board works as part of the overall counter instrument. The input clock signal to the board goes to one decade counter chip (the rightmost). When that chip overflows, i.e., counts up from 9 to 0, it also outputs a 'carry' signal to the next chip, which then counts at 1/10 the rate, and so on. By doing this, the decade counter chips, together, form a record of how many total input signals have been received since the instrument started counting. After the instrument counts the input signal for a set period of time (the 'gate' time), the values from those chips are loaded into the buffer chips, and the decade counters are reset to zero. The buffer chips output their stored values continuously to the Nixie driver chips, so that it can display the last count.

You'll notice that the back row appears to only have five decade counter chips on it. It actually has six, where the sixth is the large metal can. This is the decade counter chip for the rightmost decimal place on the counter, which has to count ten times as fast as its neighbor. For this counter chip alone, HP used a higher performance version (in the metal can) that can count faster than the others.

And, here's the block diagram from the manual showing how those pieces work together. The busses between the decade counter, buffer, and Nixie driver chips are 4-bit wide, binary coded decimal.

(They don't make 'em like they used to, referring to the manuals of course.)

Now, to begin modifications. The basic fact that we need to overcome is that this is a decade counter-- each digit rolls over from 9 to 0, while we want a digital clock to roll over from 59 to 0, 59 to 0, and 12 to 1.

Operating the clock, we count at 1 second intervals, triggered on internally-generated 1 s gate signal, counted down from the internal timebase. We could in 'open' gate mode, where we do not reset the count every time that there is a new gate. (In other words, we're using this clock like a pulse counter rather than like a frequency counter.)

To that end, we cut traces on the circuit board, and route signals to our own circuit board, strapped into the chassis with cable ties and insulated by foam rubber. The board has four 7402 'Quad Input NOR Gate' chips onboard, along with a 74107 'Dual J-K Flip Flop' and a couple of transistors.

For the two rightmost digits, the seconds on our clock, we look at the binary-coded decimal output of the counter chips, and detect when the displayed characters are '60.' That's actually simpler than it sounds, since we only need to detect the '6,' and that is represented by the first low on two specific pins of the decade counter BCD output.

Once we've detected the '6,' we reset that chip to zero and send the carry signal to the next chip over, the first digit of the minutes on our clock. The reset input for the chip takes a positive going pulse of 3 microseconds, driven through an npn transistor. We generate that pulse with a simple one-shot, built with two NOR gates-- a classic example of what is known as MML, 'Mickey Mouse Logic.'

For detecting 60 minutes, we do the exact same thing, carrying an output to increment the hours every 60 minutes.

It is somewhat more complex to display the hours. The 'native' counting order of the decade counters is 0,1,2,3,4,5,6,7,8,9,10,11,12,13 (...). However, we don't want to display zero; we want to wrap around and display the count as 1,2,3,4,5,6,7,8,9,10,11,12,1,2 (...).

We actually did this by rewiring the ten outputs of the Nixie decoder driver, between that chip and the tube (for the 1-hour place), so that the tube is lit up as '1' when its input is BCD0, and so forth. We then need to detect BCD9 (again, two specific lows detected with a NOR gate), to generate the carry signal to the ten-hours. After the chip outputs BCD9 (displaying '0') it increments to BCD0, where it displays '1'-- resetting itself.

For rolling over from 12:59 to 1:00, we want to detect a reading of '13' on the display. This requires actually looking for an 'internal' reading of BCD1,BCD2. This is easily detected with a fourth NOR gate, reading the low signals that indicate both '1' and '2.' The output of this gate resets the two hour digit counters back to zero-- which is displayed as 01. Zero-blanking, to just display '1:00' canbe accomplished by simply disconnecting the trace that would otherwise light up the 0 on the ten-hours digit.

One might alternately wish to build this into a 24-hour clock. That would be equally straightforward, by detecting BCD '2,3' as the reset condition.

Here's the circuit board alone; nothing special about it, with one possible non-technical exception. As we said, making these clocks has been a longstanding project for us. And, this right here is the very first circuit board to bear the Evil Mad Scientist badge; it dates back to 2003.

There's one other feature on the circuit board that we haven't discussed yet, which is that it can recognize and indicate AM and PM times. Remembering which state we're in requires a single bit of memory, for which we use that flip-flop chip. We detect the switch from AM to PM times (and vice versa) when the clock reads '12', meaning that we read the BCD '1,1' on the two leading digits, using one NOR gate.

The state is stored by the flip flop, and indicated using the 'Gate' neon indicator, that you can see in the upper right corner of the front panel-- the neon light is on for PM times. You can't drive the neon bulb directly from the flip-flop chip, so we actually hijack the circuitry that originally drove that indicator. The 'Gate' indicator signal comes from the timebase board, not the main counting/display board that we've talked about so far, so the output from our flip-flop goes to that board, where we cut a trace and use our AM/PM signal instead.

Speaking of neon bulbs, there are two additional neon bulbs that we have added to the clock, which are the small 'decimal point' lights that you can see in the photo above, separating hours, minutes, and seconds.

The separators are plain miniature neon bulbs, and each has a series resistor hidden in the heat shrink tubing. They are wired in parallel, across line voltage (live to ground) so that they're always on when the clock is switched on.

This is the timebase board. There are similar frequency counters that use the line frequency as their reference, but this board is based around a 1 MHz quartz crystal. The seven cans at the back of the board are high frequency decade counter chips like the one found on the main board. They count down the timebase, giving 100 kHz, 10 kHz, 1 kHz, 100 Hz, 10 Hz, 1 Hz, and 0.1 Hz output signals that can be used for gating and frequency counting.

Here's what the underside of one of those boards looks like, as installed in the counter with our modifications. The circuit board color is slightly different in this particular unit, but it's the same otherwise.

The striped wire going to the middle left of the board is carrying our AM/PM signal to the logic that drives the front-panel neon bulb. The other wires are where we tap off the timing signals for our own purposes. The most important of these signals are the 1 Hz and 1 kHz signals. The 1 Hz signal is re-routed as the input to the counter-- the signal that we actually count to give the time -- and the 1 kHz signal is an auxiliary clock that we use as part of the time setting process.

We repurposed the rear-panel 'Storage' switch as another part of the system for setting the time.When 'storage' is off, the 1 Hz timing signal goes into the input. When 'storage' is on, the 1 Hz signal is disconnected, but the pressing the front-panel 'Reset' button advances the clock at 1 kHz, using the other signal that we picked off of the timebase board.

So, to set the time precisely, you can flip up the 'storage' switch, press 'Reset' until the time is within a minute of the actual time, and then flip down the 'storage' switch (to start running in real time again) when the clock displays the right time.

These counters are relatively old, and for the most part work surprisingly well considering their age. One place that failures can commonly crop up is on the power supply board. The one on the right had a resistor burn out at some point, which we replaced, and we also decided to replace its large electrolytic capacitors with ones 15-20 years younger.

And that's about the size of it.

These certainly aren't the only old frequency counters that can be made into clocks, but the particular blend of technology here-- easy to use TTL chips and Nixie tubes --is a friendly one for hacking, with potentially neat results. If you'd like to get into it, just grab a few of these old guys and poke and prod and see how they work. Get the manuals if you can, and keep in mind that there's plenty of line voltage, or even high voltage for the Nixie tubes, coursing through the veins of these boxes."

(Via Evil Mad Scientist Laboratories.)

MicroVision’s second-generation SHOWWX+ laser pico projector

Sat, 11 Dec 2010 18:18:04 +0100

MicroVision Inc. has just released the second generation of its SHOWWX laser pico projector that we caught at CES earlier this year. The new SHOWWX+ is powered by the same PicoP display engine and is the same pocket-friendly size as its predecessor, but packs a 50 percent brighter display to project images of up to 250cm (100 in) from mobile devices to provide a (relatively) big screen experience wherever you may be... Continue Reading MicroVision’s second-generation SHOWWX+ laser pico projector"

(Via gizmag: Mobile Technology.)

Xi3 modular computer to make global debut at CES 2011

Sat, 11 Dec 2010 18:13:12 +0100

There seems to be a different computer solution for every desktop and network problem - from home systems to home built machines to those that serve the business community. The Xi3 Corporation claims that its scalable, modular system offers a somewhat different approach to the rest of the field. Each palm-sized cube features interchangeable and adjustable boards for maximum adaptability, Dual Core processing power and low power consumption... Continue Reading Xi3 modular computer to make global debut at CES 2011

(Via gizmag: Personal Computing.)

Zoom Q3HD Handy Video Recorder released

Sat, 11 Dec 2010 18:12:34 +0100

We first looked at Zoom's Q3HD Handy Video Recorder when it was announced in October. The point-and-shoot unit combines HD audio recording with 1080p video at 30 frames per second, a 2.4-inch LCD screen for immediate playback and ... you can now get your hands on one... Continue Reading Zoom Q3HD Handy Video Recorder released

(Via gizmag: Cameras and Imaging.)

Multi-touch Desk with Curved Surface

Sat, 11 Dec 2010 18:11:43 +0100

Multi-touch Desk with Curved Surface: "

This ‘BendDesk’ is a proof of concept prototype which promises to change the way we interact with our workspace. The entire desktop includes the curved vertical surface as well as the horizontal and is a large seamless multi-touch surface. BendDesk’s touch sensitive surface recognizes ten touch points and processes your finger inputs using a system of IR LEDs, 3 cameras, and 2 projectors.

The German developers behind the project have kept the lower area free as a normal desk. Though it’s just a lab prototype now, from graphic work to a game arcade, who knows, it could catch on.

(Via Hack N Mod - Amazingly Cool Hacks, Mods, and DIY Projects.)

Glif tripod mount and stand for the iPhone 4

Sat, 11 Dec 2010 18:10:11 +0100

Glif tripod mount and stand for the iPhone 4: "

The Glif offers a simple and easy mount for your iPhone, to be used to connect to a tripod or as a propping mount for various functions. It is small and portable enough to fit snugly in your pocket or handbag, and comes with a 1/4'-20 thread that fits most standard tripods or camera mounts... Continue Reading Glif tripod mount and stand for the iPhone 4

(Via gizmag: Mobile Technology.)

The 4x4x4 LED Cube Using an Arduino

Sat, 11 Dec 2010 18:05:43 +0100

The 4x4x4 LED Cube Using an Arduino: "

Learn how to make a stunning LED cube using an Arduino. Although the image above looks a bit plain, you can control the colors and patterns of the 64 LEDs. Also, if you’re looking for a unique soldering challenge, this is a great projec to start with. The steps for the construction are detailed along with the Arduino source code.

Need more than 4x4x4? Check out the links below that walk you through a tutorial and a stunning 8x8x8 LED Cube project. The HacknMod store carries hundreds of LEDs from 5mm to 20mm in plenty of colors to fill all your DIY LED Projects.

(Via Hack N Mod - Amazingly Cool Hacks, Mods, and DIY Projects.)

Researchers develop genuine 3D camera

Sat, 11 Dec 2010 18:04:44 +0100

Cameras that can shoot 3D images are nothing new, but they don't really capture three dimensional moments at all - they actually record images in stereoscopic format, using two 2D images to create the illusion of depth. These photos and videos certainly offer a departure from their conventional two dimensional counterparts, but if you shift your view point, the picture remains the same. Researchers from Ecole Polytechnique Fédérale de Lausanne (EPFL) hope to change all that with the development of a strange-looking camera that snaps 360 degrees of simultaneous images and then reconstructs the images in 3D... Continue Reading Researchers develop genuine 3D camera

(Via gizmag: Cameras and Imaging.)

Rob's laser microscope build

Sat, 11 Dec 2010 18:02:49 +0100

Rob's laser microscope build: "

Rob Cruickshank built this sweet laser microscope based (at least partly, I presume) on my recent project. There are more pics in Rob's Flickr set, including one of the custom screw-fitting he made to hold down the momentary switch on his laser pointer. Rob also reports that water squeezed from an aquarium filter is an excellent source of microfauna-rich samples. [Thanks, Rob!]

More:

Read the Full Story » | More on MAKE » | Comments » | Read more articles in Biology | Digg this!"

(Via MAKE Magazine.)

Transparent Specimens

Sat, 11 Dec 2010 18:02:16 +0100

Transparent Specimens: "

Have you ever looked at a specimen in a jar and thought, ‘this just isn’t colorful or clear enough’. If so, then this new exhibit from Japanese artist Iori Tomita is for you.

From Cool Hunting.com:

His collection entitled ‘New World Transparent Specimens.’ takes a colorful approach to highlighting the complex compositions of marine life creatures. Tomita was first introduced to the creation of transparent specimens for the scientific purpose of examining minuscule bone structure as an undergraduate student majoring in fisheries. The specimens’ flesh is made translucent by a method that dissolves the creatures’ natural proteins. The artistry of nature and man-made design converge when vibrant dyes are introduced to the delicate skeletal system. Selectively injecting red dye into the hard bones and blue into the softer bones, Tomita underscores the other worldliness of aquatic life.

(Via Ripley's Believe It or Not!.)

New in the Maker Shed: Netduino Plus

Sat, 11 Dec 2010 17:58:50 +0100

New in the Maker Shed: Netduino Plus: "

Software, meet hardware. The Netduino Plus from the Maker Shed is an open source electronics platform using the .NET Micro Framework. The board features a 32-bit microcontroller and a rich development environment, making it a perfect solution for engineers and hobbyists alike. The Netduino Plus includes all hardware features of regular Netduino along with MicroSD storage (up to 2GB) and integrated Ethernet networking.

Note: We have a very limited supply of these amazing boards. Get them while you can!

(Via MAKE Magazine.)

Mini-Vise

Sat, 11 Dec 2010 17:57:51 +0100

I have been using this little vise since my interest in electronics was sparked by Make and Hackaday.com. Before I was just using the standard two-arm alligator-clip and magnifying glass holder from Xacto.

The Panavise is much more stable, adjustable and appropriate for breadboard soldering. It has the little grooves on the arms that your board can slip right into and a nice heavy base which means it doesn't need to be attached to a table if you like to move where you work around a bit. I've built several kits and designs of my own using this little vise. I am comfortable knowing *before* I start any project that this is one problem I am not going to have to solve.

-- David Van der Voort

Mini-Vise
$25

Available from Amazon

Manufactured by Panavise

(Via Cool Tools.)

Make It Last Build Series: The robot plants are in bloom!

Sat, 11 Dec 2010 17:55:15 +0100

We asked MAKE illustrator Damien Scogin to create some drawings so that folks could better understand the functioning of the basic robot plant design we're using in the Micochip/Energizer Make It Last Build Series, Project #2: The Robot Plant. As we've said, you don't have to make yours this way, this is just one idea, the one we're using in our build. We've already gotten some cool designs submitted to the MAKE Flickr pool. We're giving special prize bundles to the first five people who upload their robo-plant designs to the pool (tag them 'robotplant'). We still have a couple of packages to give away. See issue #2 of the Robot Plant Project Newsletter for more details on this little 'Plant Design Challenge' and see the Make It Last landing page for full details of the build series and the contest. Prizes for the winning robo-plants include a $200 gift card and copies of Make: Electronics.

If you're not signed up for the project mailing list, you can sign up here. It'll sign you up for this project/contest and similar future mailings. The next newsletter and blog post, covering construction of the flower and touch-sensing, will go out tomorrow.

Make It Last Build Series

(Via MAKE Magazine.)

Bench Cookies

Sat, 11 Dec 2010 17:50:56 +0100

Bench Cookies: "

I discovered Bench Cookies at the Rockler woodworking store more than a year ago. Billed as 'work grippers,' they have smooth plastic sides and textured rubber surfaces on top and bottom. You just place them under objects you're sanding, sawing or painting to hold the object in place. There's no clamping or screwing involved. They're amazing. Wood chips and dust have no effect - they do exactly what they're supposed to. So instead of rummaging for scraps of wood or an old book or two to prop up a project, I reach for bench cookies.

I took them to the print shop where I do intaglio printing. Inking and wiping a large copper or zinc plate on a glass table used to be a nightmare - bench cookies make it a breeze. They hold the plate in place and I can pick it up and turn it as I work, and since it's off the table I can wipe the edges, too. I don't think Rockler had any idea how useful they'd be in an art studio.

Their great function and inexpensive price make them a perfect present for anyone that does any kind of project. Turns out Rockler's even made some nice black ones now for uses outside the workshop, like holding up your turntable, keeping it stable and providing vibration reduction.

-- Jeff Woodbury

Bench Cookies
$12

Available from Amazon

Manufactured by Rockler

(Via Cool Tools.)

Nebulophone – A Miniature Arduino Powered Synth

Sat, 11 Dec 2010 17:49:32 +0100

Nebulophone – A Miniature Arduino Powered Synth: "

By Andrew Liszewski

You can compare this Nebulophone to the Stylophone that was re-released a few years ago, but that’s not really doing it justice. They can both be used to produce some retrorrific electronic music, but the Nebulophone is built on an Arduino so it’s compact and, well I’m just going to come out and say it, adorable.

It does require some electronics know-how since you have to build it yourself, like soldering and stripping wires and what-not. But because it came from your hands the final product will be all the more satisfying to play. As you can see it even has a tiny keyboard, but improves on the Stylophone with additional settings and dials for changing the waveform (ramp, triangle, square, pulse or noise), adjusting the decay, switching between major and chromatic keyboard mapping, arpeggio modes and three speed settings of portamento. Yeah, all that stuff. The only things you have to provide are a 9-volt battery, a speaker and talent. $54.99 from ThinkGeek.

[ Nebulophone Mini Arduino Synthesizer Kit ]

Matrox updates dual- and triple-head video breakout boxes

Sat, 11 Dec 2010 16:53:41 +0100

Matrox updates dual- and triple-head video breakout boxes: "Matrox's existing DualHead2Go and TripleHead2Go DP Edition graphics expansion modules (GXMs) now include a Mini DisplayPort to DisplayPort cable, making it easier for Mac users of Apple's latest notebooks and desktops and other computer owners with DisplayPort technology to hook up to three additional monitors or projectors to their machines. The DVI version of the boxes will also get a boost in an upcoming firmware upgrade, allowing dual 1600x900 resolution....
(Via MacNN | The Macintosh News Network.)

How to Travel Around the World for $418

Sat, 11 Dec 2010 16:51:34 +0100

From http://gizmodo.com/5710654/how-to-fly-35000-miles-visit-4-continents-9-countries-and-15-cities-for-418

Steve Kamb decided he wanted to travel the world for as little money as possible. This map is his travel plan: 35,000 miles, visiting four continents, nine countries and 15 cities for just $418. Here's how he got it:

"I have to tell you sir, this is easily the most ridiculous itinerary I've ever put together," said the American Airlines operator the other night as I finalized plans for a worldwide adventure that would make Marco Polo blush. "Well, that makes two of us!" I replied.

And just like that, I had committed myself to almost nine months of international travel.

Yes, that picture above is my actual itinerary.

Beginning this January, I'll start an epic journey that will take me across four continents, through at least nine countries, and into more than fifteen cities. I'll fly on fifteen flights covering a total distance of 35,000 miles. To put that in perspective, that's almost 1.5 times the circumference of the globe. While visiting these locations, I should be able to cross off over a dozen goals from my Epic Quest of Awesome.

Oh, and all of these flights are costing me a grand total of $418.36.

My itinerary

Although I plan to get to Sydney much sooner should a flight open up (and in turn extend some of my SE Asia stops), here is my rough itinerary for 2011:

• The Rock Boat – Jan 6 – 10
• Los Angeles—Jan 14 – Feb 13
• Sydney, Australia – Feb 15-20
• Auckland, New Zealand – Feb 20 – Mar 20
• Brisbane, Australia – Mar 20 – Apr 9
• Alice Springs, Australia – Apr 9 – 12
• Perth, Australia – Apr 12 – 14
• Singapore, Malaysia – Apr 14 – 16
• Bangkok, Thailand – Apr 16 – May 9
• Hong Kong – May 9 – 12
• Shanghai, China—May 12 – 22
• Tokyo, Japan – May 22 – May 27
• San Francisco – May 26 – Jun 3 (yes I go back in time on the flight home)
• Portland – Jun 3 – 7 (World Domination Summit!)
• Boston/Atlanta – Jun 8 – Jul 30
• Chicago – Jul 30 – Aug 4
• Dublin, Ireland—Aug 5 – Sep 2
• Madrid, Spain – Sep 2 – Oct 10
• Buenos Aires, Argentina? – Oct 15 – Nov 30 (not booked yet, but I still have enough miles to make it happen).

Unreal, right? If I were to pay for this adventure with cash and book individual flights, it would cost almost $6,000 (using the cheapest option for each leg on Expedia.com). The best part is, the dates of this adventure aren't set in stone – as long as I don't change WHERE I'm going, I can change the date and time of each stop without penalty.

Here's how I got this incredibly flexible itinerary for only $418.

The beauty of travel hacking

After buying travel guru Chris Guillebeau's Frequent Flyer Master e-book last fall, I became addicted to travel hacking, acquiring TONS of frequent flyer miles for various airlines through an assortment of lucrative credit card deals. I have excellent credit, generally get the first year fee waived, use the card for EVERYTHING, pay off each card in full, and receive a certain number of miles for spending enough money to receive the bonus.

In the past eleven months alone, I've earned without flying:

• 130,000 American Airline miles
• 105,000 British Airways Miles
• 40,000 Starwood Preferred Guest points
• 25,000 American Express points

I use these points to book insane trips around the world…like this one! To answer your first question, I didn't buy ANYTHING outside of what I would normally purchase to get these bonuses – I've lived extremely frugally over the past year. For example, to earn 100,000 British Airways points, I had to spend $2,000 in six months – after prepaying my car insurance for the year, and putting all of my other payments (gas, food, cable, gym, etc.) on the card for a few months I hit the bonus with ease.

For me to complete this particular trip, I had to use a combination of American Airline miles and Starwood Preferred Guest points. I had already used 32,000 AA points for my trip to Peru last month, so I simply transferred 40,000 Starwood Preferred Guest points into my AA account (complete with a 10,000 point transfer bonus), which gave me the 140,000 points needed to book my trip.

If you're interested in learning more about frequent flyer credit card programs and last-minute deals, head over to Frugal Travel Guy and check out the different cards listed in the right hand column. Rick runs THE best frequent flyer website out there, so start checking it daily if you're looking to take some fun trips for dirt cheap – his site is one of the sites I make sure to visit every morning.

Keeping an eye on special offers

The best deal right now is American Airlines Citi cards: first year fee waived, spend $4,000 within 6 months for 75,000 points.

This used to be only $1500 as early as a month ago, but it recently changed. Sign up for one (or two..or three) of those cards, hit the spending limit (by putting EVERYTHING YOU BUY on the card and paying it off in full), and you've just earned 75,000 points without ever stepping foot on an airplane. If you're a frugal spender, try doing things like pre-paying your car insurance, buying gift cards, or do a little research and to find out about some of the other methods for hitting spending limits. My friend Tyler got mighty creative…

You just have to keep an eye out for special deals (which is where Frugal Travel Guycomes in handy). Worried about your credit score? If you carry no credit card debt, pay off your cards in full, and then negotiate for fee-free cards after your first year your score will not be affected negatively. If you decide to cancel the cards after a year, depending on your credit history it can take a hit of a few points before rebounding. Do the research; it's not as terrifying as you'd imagine!

How to Use a OneWorld Award

As of three weeks ago, my plan was to book a one-way flight to Sydney and figure the rest out after that. However, after reading posts from Sean Ogle and Cody McKibben about Thailand, I knew I had to swing through Southeast Asia to check it out. I calculated that using points to go from Los Angeles to Sydney to New Zealand to Thailand back to Los Angeles would cost me around 110,000 points.

After looking at these beaches in Thailand, I knew I had to go:

So it was settled—I was going to Thailand.

I then discovered OneWorld Awards and my plans for 2011 exploded.

OneWorld Awards are flights that are based on how many TOTAL miles you fly instead of dealing with individual flights. They also allow you to fly on most of American Airlines' worldwide partners, and you can make a total of SIXTEEN STOPS.

According to their award chart, for only 120,000 points (10,000 more points than I would have used the other way) I could fly up to a total of 25,000 miles and make 16 stops anywhere along the way. However, for only an additional 20,000 points, I could fly up to 35,000 total miles instead…

Which got the gears turning in my head.

Because I had 140,000 AA points at my disposal, I decided to tack on a visit to both Dublin and Spain for next fall! Obviously it was a big decision to add a Europe portion to my trip, but it only cost me an additional 20,000 points, round-trip. Considering a round-trip flight to anywhere in the states is 25,000 points…I'd say it's a pretty good deal!

The funky rules of travel hacking

Now, there were some funky rules that I had to work around for my itinerary:

• I can't stopover in the same city twice, which is why I'm flying out of LA, then back in through San Francisco. It's also why I'm flying out of Chicago and back in through Boston when going to Europe.
• I can only have one open gap on the trip, which counts as one of my 16 ‘stops' but doesn't factor into the mileage calculation – my open segment is a gap between San Francisco and Chicago. I'm responsible for getting myself from San Fran to Chicago next summer.
• I can't change what airlines I fly and where I stop, but I can change the dates and times of ANY of the flights free of charge (as long as there is availability).
• I have to complete the whole trip within 12 months.

I have to give a HUGE shout out to the incredible community over at Flyer Talk.comfor helping me put together this trip and answering my questions. That is the place to be if you have any sort of interest in frequent flyer programs, travel hacking, and such. It can be quite intimidating due to the sheer amount of information on there, but once you get your feet wet it's easy to navigate and you can pretty much find an answer to ANYTHING.

How to build your award travel flight

If you're interested in seeing how many miles your dream flight would be, check outGreat Circle Mapper. Simply plug in your airport codes and it will tell you how long your flight is! Here is my crazy itinerary. I'm not kidding when I say that I spent probably more than 24 total hours in the past three weeks having a blast on this thing creating itineraries, checking mileage, and figuring out where the heck I could go without going over the limit.

Here's another invaluable tool: OneWorld "Who Flies Where?". This is where you can find out which OneWorld alliance airlines fly where, so you can put together a legitimate itinerary.

A few other tips:

• Try to book your trip either WAY in advance (flights open up generally 330 days in advance), or last minute like I did. If you NEED to go on specific days, book it as far in advance as possible, as each plane only has so many "award seats" available. When booking last minute, you might need to be flexible with your dates as often the most popular legs have already been filled.
• If you sign up for a Qantas FF number (you don't need miles or to fly them), you can search their database to see which flights have available award seats. You can also do the same for British Airways for flights that don't show up on Qantas (and vice versa). Between those two I was able to line up all of my flights before calling American Airlines to book them.
• When booking, it's a crap shoot how helpful your phone operator will be. I had to call back three times to get an agent that could help me re-calculate a segment of the trip that AA's computer had screwed up. It's not the agents' fault, some just happen to be more knowledgeable with this type of flight than others. If the one you have doesn't help, simply hang up and call back!
• Flights change. New award seats open up last minute, and these types of itineraries are free to change as long as you don't change the airline or destination. I plan on getting to Australia much sooner than February 13th when a flight opens up while I'm in Los Angeles.

Now, if you have your points in other airlines like Delta or United, they are part of their one worldwide alliances who ALSO offer flights like these…visit their websites, look up their alliances, and start planning.

How I am able to afford 6 months of adventure travel

Next week, I will be moving out of my apartment in Atlanta, and I have no plans to actually RENT a place in the United States until at least 2012. I will also be selling my car, and I don't expect to own a car until 2012 either. Once I'm not paying rent, car insurance, car payments, or fuel…my financial ties will be minimal (just some student loans and health insurance). When I don't have my money promised elsewhere, I can use the rest of my money to live VERY CHEAPLY overseas (hostels, couch surfing, etc.).

I am certainly not rich, but I'm incredibly fortunate to be 100% in control of my time and location because I am my own boss. I can operate Nerd Fitness from anywhere with an Internet connection, so I'll be working the entire time while traveling, connecting with readers, writing about my adventures, creating more awesome workout videos, and inspiring others to also do stuff that scares the crap out of them.

The Rebel Fitness Guide is still selling well, t-shirts are flying off the digital shelves, and I'm hard at work on my second e-book as well.

Because I'm traveling so cheaply, I'll be able to use the majority of my money to cross off some of the more expensive things on my Epic Quest list. These are the things I hope to accomplish in 2011:

• Skydive in New Zealand
• Scuba-dive the Great Barrier Reef
• Something Lord of the Rings-related in New Zealand
• Visit Ayers Rock in Australia
• Exercise on the Skybridge of Petronas Tower in Kuala Lumpur, Malaysia
• Visit Angkor Wat in Cambodia
• Visit the Great Wall of China
• Find the Ninja Warrior Course in Japan
• Kiss the Blarney Stone in Ireland
• Party on the island of Ibiza in Spain
• Wear a Tuxedo and gamble in Monte Carlo
• Climb the Eiffel Tower in Paris

Why this trip scares me

Eight months ago, I was sitting at a desk job dreaming about going to Australia "some day." Last night, I booked a trip that will not only take me halfway around the world, but it will keep me on the road for pretty much nine months. This scares the crap out of me.

Here's why:

• I speak English and Spanish, but I certainly don't speak any of the languages used in Southeast Asia, China, or Japan. I envision lots of things getting lost in translation. Looks like it's time to start reading everything Benny The Irish Polyglot's ever written.
• I'll be traveling alone. So much for strength in numbers!
• I'm a picky eater. Who KNOWS what kinds of situations I'm putting myself into!
• I have a feeling I will get mighty homesick, as I've never been out of the country for more than three weeks…which was my trip to Peru a month ago.
• I'm worried that something bad will happen that I can't get out of. Not that I plan on doing anything illegal (I don't use drugs and didn't even start drinking until 3 months after my 21st birthday), but I REALLY don't want to end up in a Cambodian jail strung up by my toes.

Now, fortunately the same reasons that I scare me also excite me. I don't speak the languages in Asia, so I'll have to start learning them. I also have to become resourceful, rely on my instincts, learn to navigate foreign environments, operate outside my comfort zone, expand my horizons when it comes to food, learn to deal with homesickness, and talk my way out of various situations. I have this vision in my head of me becoming a real life Jason Bourne (hopefully without the assassination stuff), and this is a fantastic way to find out what I'm made of.

I understand that not everybody can just pack up and leave for nine months, so I know this is the opportunity of a lifetime. I figure I might as well do this now when I'm 26, no wife, kids, or mortgage, because who knows what will happen a year from now. I plan on packing Nerd Fitness full of awesome stories, both good and bad, about the whole adventure. I'm looking forward to working on the road, exercising in unique locations, meeting amazing people, and going on some pretty epic adventures.

If you happen to live in one of these cities, or know a good friend that lives in one of these countries, [email protected]?subject=Gizmodo%20travel%20story">shoot me an email and maybe we can meet up!

Steve Kamb is the nerd-in-chief of NerdFitness.com, a site dedicated to helping nerds, desk-jockeys, and averages Joes level up their lives. You can sign up for the Nerd Fitness Newsletter here and follow him on Twitter.

The 50 Hottest Companies in Bioenergy for 2010-11 | Renewable Energy News Article

Sat, 11 Dec 2010 16:02:02 +0100

"The 50 Hottest Companies in Bioenergy for 2010-11

By Jim Lane, Biofuels Digest (http://www.renewableenergyworld.com/rea/news/article/2010/12/the-50-hottest-companies-in-bioenergy-for-2010-11?cmpid=rss)

Each year the Biofuels Digest ranks to 50 hottest companies working in the biofuel space; here are this year's results.

Do you like this article? Email Bookmark Print Feed Share Share 4 Florida, USA -- In Florida, renewable fuels and chemicals developer Amyris took the #1 spot in the 2010-11 '50 Hottest Companies in Bioenergy' rankings, published today in Biofuels Digest, the online daily bioenergy news service.

Solazyme (#2), POET (#3), LS9 (#4), Gevo (#5), DuPont Danisco Cellulosic Ethanol (#6), Novozymes (#7), Coskata (#8), Codexis (#9) and Sapphire Energy (#10) round out the top 10.

The rankings, which recognize innovation and achievement in bioenergy development, are based 50 percent on votes from a 75-member panel of international selectors, and 50 percent on votes from subscribers of Biofuels Digest and Renewable Chemicals Digest.

Ranked #11 through #20 are Virent, Mascoma, Ceres, Cobalt Technologies, Honeywell’s UOP, Enerkem, BP Biofuels, Genencor, Petrobars and Abengoa Bioenergy.

Notes on the votes

Among the Hot 50, 37 were US-based companies and 13 were from other countries. 15 are active in cellulosic ethanol development (down from 19 last year), five are developing algae-based energy solutions (down from seven last year), and 16 are producing ‘drop-in’ renewable biofuels such as biobutanol, renewable diesel, green gasoline and renewable jet fuel (up from 15 last year). 13 are developing capabilities to produce renewable chemicals.

Strategic investors such as Waste Management, Chevron, and Monsanto appeared in the rankings for the first time, while Shell advanced this year and BP Biofuels reached the top 20. DuPont was an investor in two tiop-50 companies, DDCE and Butamax.

Overall, more than 1,000 companies were eligible in the rankings and 301 companies received votes. Amyris Biotechnologies ranked #1 in the international Selector poll, while Solazyme ranked #1 in the subscriber poll.

New companies in the list this year include:

Cargill (#36), Butamax (#38), Cosan (#40), Waste Management (#42), Dynamic Fuels (#44), KiOR (#47), Chevron (#48), and Monsanto (#49).

Major positive movers this year were: LS9 (up four places to #4), Gevo (up 8, to #5), Codexis (up 26, to #9), Virent (up 10, to #11), Cobalt Technologies (up 16, to #14), Enerkem (up 9, to #16), Genencor (up 8, to #18), Joule Unlimited (up 10, to #22), Rentech (up 13, to #25), Neste (up 11, to #29), Lanzatech (up 10, to #31), Origin Oil (up 9, to #33), Cargill (unranked, to #36), SG Biofuels (up 12, to #37), and Terrabon (up 8, to #39).

‘The industry has spoken, and it appears that a successful IPO has put Amyris over the top after ranking #3 last year,’ said Jim Lane, editor and publisher of Biofuels Digest. ‘Biobutanol companies were up sharply this year, and there was a strong trend towards microbial fermentation using e.coli, yeast and algae as a platform – accounting for four of the top 5 this year. But the message from the Hot 50 this year is diversity – the range of feedstocks, fuels and processing technologies is really striking. ’

The 50 Hottest Companies in Bioenergy for 2009-10 are:

Last year’s rank (2009-10)

1. Amyris (3)

2. Solazyme (1)

3. POET (2)

4. LS9 (8)

5. Gevo (13)

6. DuPont Danisco (7)

7. Novozymes (11)

8. Coskata (6)

9. Codexis (35)

10. Sapphire Energy (5)

11. Virent (21)

12. Mascoma (10)

13. Ceres (28)

14. Cobalt Technologies (30)

15. Honeywell’s UOP (12)

16. Enerkem (25)

17. BP Biofuels (4)

18. Genencor (26)

19. Petrobras (18)

20. Abengoa Energy (15)

21. Qteros (22)

22. Joule Unlimited (32)

23. Shell (27)

24. Bluefire Renewables (19)

25. Rentech (38)

26. Algenol (24)

27. ZeaChem (20)

28. PetroAlgae (16)

29. Neste (29)

30. Synthetic Genomics (17)

31. LanzaTech (41)

32. Iogen (23)

33. OriginOil (42)

34. RangeFuels (14)

35. ExxonMobil (29)

36. Cargill (NR)

37. SG Biofuels (49)

38. Butamax (38)

39. Terrabon (47)

40. Cosan (NR)

41. Verenium (9)

42. Waste Management (42)

43. IneosBio (36)

44. Dynamic Fuels (NR)

45. Fulcrum Bioenergy (48)

46. KL Energy (34)

47. KiOR (NR)

48. Chevron (NR)

49. Monsanto (NR)

50. Inbicon (NR)

The award winners will officially be recognized at a reception at the Digest’s Advanced Biofuels Leadership Conference, in Washington DC, April 19-21, 2011.

Microbial Cell Factories: Engineering the cell surface display of cohesins for assembly of ...

Sat, 11 Dec 2010 15:59:12 +0100

Background The assembly and spatial organization of enzymes in naturally occurring multi-protein complexes is of paramount importance for the efficient degradation of complex polymers and biosynthesis of valuable products. The degradation of cellulose into fermentable sugars by Clostridium thermocellum is achieved by means of a multi-protein 'cellulosome' complex. Assembled via dockerin-cohesin interactions, the cellulosome is associated with the cell surface during cellulose hydrolysis, forming ternary cellulose-enzyme-microbe complexes for enhanced activity and synergy. The assembly of recombinant cell surface displayed cellulosome-inspired complexes in surrogate microbes is highly desirable. The model organism Lactococcus lactis is of particular interest as it has been metabolically engineered to produce a variety of commodity chemicals including lactic acid and bioactive compounds, and can efficiently secrete an array of recombinant proteins and enzymes of varying sizes.

Results Fragments of the scaffoldin protein CipA were functionally displayed on the cell surface of Lactococcus lactis. Scaffolds were engineered to contain a single cohesin module, two cohesin modules, one cohesin and a cellulose-binding module, or only a cellulose-binding module. Cell toxicity from over-expression of the proteins was circumvented by use of the nisA inducible promoter, and incorporation of the C-terminal anchor motif of the streptococcal M6 protein resulted in the successful surface-display of the scaffolds. The facilitated detection of successfully secreted scaffolds was achieved by fusion with the export-specific reporter staphylococcal nuclease (NucA). Scaffolds retained their ability to associate in vivo with an engineered hybrid reporter enzyme, E. coli β-glucuronidase fused to the type 1 dockerin motif of the cellulosomal enzyme CelS. Surface-anchored complexes exhibited dual enzyme activities (nuclease and β-glucuronidase), and were displayed with efficiencies approaching 104 complexes/cell.

Conclusions We report the successful display of cellulosome-inspired recombinant complexes on the surface of Lactococcus lactis. Significant differences in display efficiency among constructs were observed and attributed to their structural characteristics including protein conformation and solubility, scaffold size, and the inclusion and exclusion of non-cohesin modules. The surface-display of functional scaffold proteins described here represents a key step in the development of recombinant microorganisms capable of carrying out a variety of metabolic processes including the direct conversion of cellulosic substrates into fuels and chemicals.

35,000 plant specimens gathered over the past 200 years remain unclassified

Sat, 11 Dec 2010 15:46:33 +0100

35,000 plant specimens gathered over the past 200 years remain unclassified: "35,000 plant specimens gathered over the past 200 years remain unclassified Botanists estimate there are 70,000 species of flowering plant still waiting to be identified. They also suspect that about half of those were already found up to 200 years ago, and nobody has gotten around to identifying them yet.

This is what happens when there are way, way more plants than any human could ever hope to classify, particularly in an age before computers. For centuries, botanists have sought out any and all potential new plants, collecting and cataloging them in a special storage facility known as a herbarium. There are now about 3,000 herbaria all over the world, and each one contains several thousand specimens.

In order to build up collections of such size, botanists have sometimes had to focus on collecting and leave cataloging for another day. The only question is when that other day comes. According to a new study by Oxford's Dr. Robert Scotland, only 16% of plants are described in their first five years after collection, and a quarter of all plant species take over fifty years to be described. The record seems to be one particular plant species that was finally cataloged a whopping 210 years after its initial discovery.

Based on their figures, Scotland and his colleagues estimate over 35,000 new species should be discovered in existing herbarium collections between now and 2045. Botanists currently expect to find another 70,000 new species of flowering plants, so half their work should already be done for them. Indeed, Scotland says this reveals that rooting through the existing archives will be just as important as heading back out into the field:

'There are certainly places in the world which are under-collected where there's many things to be found. Botanists visit a particular rainforest, for example, and come back with a haul of species. '[But] out of that 70,000 species still to be found, more than half of those have already been collected in the world herbaria and are waiting for someone with

the relevant expertise and time to say 'that's a new one'.' This is also good news for anyone looking to discover their very own species. No longer will you need to plan an expensive expedition to the rainforest to find a new species - you just need to find your nearest herbarium and ask very nicely whether you can have a rummage through their archives. With any luck, you'll be rolling in new plants in no time at all.

[BBC News] from http://io9.com/5707997/35000-plant-specimens-gathered-over-the-past-200-years-remain-unclassified

Miniature Food Sculptures

Sat, 11 Dec 2010 15:42:04 +0100

Delicious looking food miniatures crafted out of polymer clay by Kim Burke.

According to the artist, the inspiration for each meal comes from scouring cooking books and pastry shops for ideas. [Kim's etsy store, via]

Delicious looking food miniatures crafted out of polymer clay by Kim Burke.

According to the artist, the inspiration for each meal comes from scouringcooking books and pastry shops for ideas. [Kim's etsy store, via]

From: http://www.toxel.com/inspiration/2010/12/07/miniature-food-sculptures/

Latex Hippo Mask - Archie McPhee & Co.

Sat, 11 Dec 2010 15:40:25 +0100

Latex Hippo Mask

Hippos are one of the world's most dangerous animals, but they are also darn cute. This Latex Hippo Mask is perfect for those times you want to wade anonymously. Fits most adult heads.

Brain Freeze Ice Cube Tray - Archie McPhee & Co.

Sat, 11 Dec 2010 15:39:17 +0100

Brain Freeze Ice Cube Tray

We humans are well known for our highly-evolved sense of humor - as evidenced by Brain Freeze, the 6" x 6" ice tray that makes 4 frosty brains. So let’s celebrate our comedic triumph by raising a glass. Because a brain (not to mention a cocktail) is a terrible thing to waste. Brain Freeze is molded from super-strong, dishwasher-safe pure silicone.

moss tables by ayodhya

Sat, 11 Dec 2010 15:15:07 +0100

'secret garden'
image © designboom

the secret garden collection by home furniture thai company ayodhya uses real dried
moss inserted under a glass table top. the indoor/outdoor collection has
been shown at the IFFS - international furniture fair in singapore 2010.

dried moss under the table top
image © designboom

'secret garden' table
image © designboom

Liverworts and Fungi

Wed, 08 Dec 2010 13:15:10 +0100

A new breakthrough by scientists at the University of Sheffield, involving scientists from Kew, has shed light on how the Earth’s first plants began to colonise the land over 470 million years ago by forming a partnership with soil fungi.

The research, which was published on 2 November 2010 in Nature Communications, has provided essential missing evidence showing that an ancient plant group worked together with soil-dwelling fungi to ‘green’ the Earth in the early Palaeozoic era, nearly half a billion years ago.

The research, which also involved experts from Kew, Imperial College London and the University of Sydney, has provided new insights into our understanding of the evolving dynamic behaviour of the Earth’s land plants and fungi.

By studying these ancient plants we open a window on the past to investigate how the earliest land plants evolved. Our results support the idea that the ‘greening’ of the Earth was promoted by a symbiosis between plants and fungi.

Professor David Beerling, from the Department of Animal and Plant Sciences at the University of Sheffield

Scientists have long-suspected that soil fungi formed mutually beneficial relationships with early land plants to play an essential role in assisting their initial colonisation of terrestrial environments. However, until now there has been a lack of evidence demonstrating if and how the earliest ancient land plants, from the early Palaeozoic era (over 470 million years ago), might have cooperated with fungi for mutual benefit.

Making this new discovery

The team studied a thalloid liverwort plant, which is a member of the most ancient group of land plants that still exists and still shares many of the original features of its ancestors. They used controlled-environment growth rooms to simulate a CO2-rich atmosphere, similar to that of the Palaeozoic era when these plants originated. This environment significantly amplified the benefits of the fungi for the plant’s growth and so favoured the early formation of the association between the plant and its fungal partner.

The team found that when the thalloid liverwort was colonised by the fungi, it significantly enhanced photosynthetic carbon uptake, growth and asexual reproduction, factors that had a beneficial impact on plant fitness. The plants grow and reproduce better when colonised by symbiotic fungi because the fungi provide essential soil nutrients. In return, the fungi also benefit by receiving carbon from the plants. The research found that each plant was supporting fungi that had an area of 1-2 times that of a tennis court.

A window into the past

Professor David Beerling, from the Department of Animal and Plant Sciences at the University of Sheffield, said: “By studying these ancient plants we open a window on the past to investigate how the earliest land plants evolved. Our results support the idea that the ‘greening’ of the Earth was promoted by a symbiosis between plants and fungi. It shows that plants didn’t get a toe-hold on land without teaming up with fungi – this has long been suspected, but until now not investigated. It will require us to think again about the crucial role of cooperation between organisms that drove fundamental changes in the ecology of our planet.”

Martin Bidartondo from the Jodrell Laboratory at Kew, said: “Fungi are present in every type of habitat throughout the world and are essential for many plants to grow. It is exciting that we are now beginning to discover the fungi associated with 'lower' plants, and that many more still remain to be investigated."

Scientific Research & Data

Mutualistic mycorrhiza-like symbiosis in the most ancient group of land plants, by Claire P. Humphreys , Peter J. Franks , Mark Rees, Martin I. Bidartondo, Jonathan R. Leake & David J. Beerling, published in Nature Communications
Find out more about the work of Kew's Mycology Team

Presidential Commission reports on Synthetic Biology

Mon, 22 Nov 2010 06:55:21 +0100

The Presidential Commission for the Study of Bioethical Issues advises the US President on bioethical issues that may emerge from advances in biomedicine and related areas of science and technology. They are compiling a report on the potential impact of Synthetic Biology. A collection of resources, including transcripts of consultations, can be found at: http://www.bioethics.gov/transcripts/synthetic-biology/

Hard Candy Cases offers Candy stylus and pen for iPad

Tue, 16 Nov 2010 06:21:31 +0100

Hard Candy Cases offers Candy stylus and pen for iPad: "Hard Candy Cases has introduced the Candy Stylus for Apple iPad, iPhone, and iPod touch. Not only is it a stylus, the accessory also doubles as a pen.

(Via Macworld.)

Apple releases XCode 4 Preview 5 to developers

Tue, 16 Nov 2010 06:19:36 +0100

Apple releases XCode 4 Preview 5 to developers: "Apple today posted Build 4A225 of its forthcoming XCode 4, now shaping up as a significant upgrade for developers. This fifth preview version brings a number of new features, including independent and assistant editor panes with their own histories, independent and 'tearable' tabs, new configurable alerts and more. The new preview build also enhances tab behavior, general preferences and editor views, among other changes....

(Via MacNN | The Macintosh News Network.)

thetrainline.com update app allows travellers to buy tickets via iPhone

Tue, 16 Nov 2010 06:17:10 +0100

thetrainline.com update app allows travellers to buy tickets via iPhone: "thetrainline has announced the thetrainline.com iPhone application now allows travelers to buy train tickets via their smartphone for the very first time.

(Via Macworld UK.)

Geneious 5.3.0 - Sequence analysis software for all molecular biologists. (Free)

Tue, 16 Nov 2010 06:15:21 +0100

Geneious 5.3.0

Geneiousis research software for biologists, not computer scientists.

Geneious combines all the major DNA and protein sequence analysis tools into one revolutionary software solution! Its ease of use makes bioinformatics accessible to any biologist. It even runs on all major operating systems and is very affordable.

Features include: Sequence alignment, Contig assembly, primers, restriction analysis, BLAST, phylogenetics, automatic publication updates and more.

WHAT'S NEW

Version 5.3.0:

Next-Gen Sequencing:
- Can split unprocessed 454 paired reads apart based on the presence of a linker in the middle of a sequence using \'Set Paired Reads\' from the Sequence menu
- Can split multiplexing data (e.g. 454 MID sequences) using \'Separate Reads by Barcode\' from the Sequence menu
- Can split Polonator paired reads in half from using \'Set Paired Reads\' from the Sequence menu
- The Geneious reference sequence assembler fine tuning option can be applied to existing contigs without needing to reassemble them
BLAST:
- Custom BLAST databases created from sequences in Geneious will now store annotations and return fully annotated hits
- If Maximum Hits is set to 1 in Sequence Search, all results are downloaded to a single folder instead of creating many sub-folders
- Custom BLAST can now use multiple CPU cores (advanced option added)
- Blast hits now have a column in the document table listing the percentage of the query sequence covered by the hit
- Can view query centric alignments vertically compressed (like the \'Vertically Compress Contig\' setting in previous versions)
Full support for importing GFF 3 format annotations and better options for choosing which sequence(s) to annotate
Trees can now be printed across multiple pages
ACE format exporter for assemblies
GC graph now has \'frame plot\' option to show GC content in each codon position
Can resize chromatogram traces by dragging them up/down in the Sequence and Alignment Views
Individual chromatogram traces (A,C,G and T) can be hidden in the Sequence and Alignment Views
When viewing vertically compressed contigs/alignments, it shows sequence names even when zoomed out if there is only 1 sequence in the row within the visible region
In an alignment view if you set a reference sequence then the statistics list the percentage of the reference sequence covered by other sequences in the alignment
Tree view allows setting of a maximum length for tip labels, truncating longer labels
Binning parameters can be set for individual folders or documents by turning on \'Enable per folder/document binning\' in the binning preferences
Primer trimming now has a \'Minimum Match Length\' option, allowing better trimming of partial primers binding sites
Go to next/previous disagreement button now skips over the middle of contiguous disagreements
Sequence Searches now show up in Operations Table
Whole Genome Shotgun sequences from NCBI can be imported and downloaded
When assembler saves unused reads it puts unused paired reads in a separate list from unused unpaired reads
SNP/Variation finder: Added option to not find variations in regions covered by particular annotation types

New features:

Reduced memory usage when importing big sequences, contigs, and alignments

Bugs fixed:

Editing the consensus sequence in a contig/alignment doesn\'t modify the reference sequence now
Fixed assembly sometimes introducing excessive gaps around regions that don\'t closely align
Fixed Maq importer setting incorrect paired read expected distance on some contigs
Numerous small bug fixes in Operations Table
Fixed incorrect concatention of mixed quality and non-quality alignments
Ace importer brings in sections of reads which fall outside the consensus
Trim By primers matches primers partially off the end of a sequence
Fixed base numbering on blasts that find hits on the reverse complement
Fixed unresponsiveness when loading long sequences with many restriction sites into viewers
Fixed bug introduced into multi-user chat in Geneious 5.1

REQUIREMENTS

Mac OS X 10.4 or later
64-bit version requires at least 4GB RAM
Java 1.5 or later

PRICE

Free

DEVELOPER

Biomatters Ltd.

Genomic comparison of ocean microbes reveals East-West divide in populations

Tue, 16 Nov 2010 06:09:37 +0100

Genomic comparison of ocean microbes reveals East-West divide in populations: Much as an anthropologist can study populations of people to learn about their physical attributes, their environs and social structures, some marine microbiologists read the genome of microbes to glean information about the microbes themselves, their environments and lifestyles.

Using a relatively new methodology called comparative population genomics, these scientists compare the entire genomes of different populations of the same microbe to see which genes are 'housekeeping' or core genes essential to all populations and which are population-specific. Scientists are able to read a genome and translate the genes into proteins that serve particular functions. Population-specific genes sometimes tell a very clear story about the environment, for instance temperature and the availability of light and particular elements, and over time, they can point to the microbes' evolutionary adaptation to changes in the ecosystem. Occasionally, as was the case with recent research at MIT, the population-specific genes reveal this information with crystal clarity, even providing unmistakable clues about lifestyle.

Professor Sallie (Penny) W. Chisholm of MIT's Department of Civil and Environmental Engineering (CEE) and former doctoral student Maureen Coleman compared the genetic makeup of two populations of the same oceanic photosynthetic bacterium, Prochlorococcus, one living in the Atlantic Ocean and one in the Pacific.

They found that although a continent separates the populations, they differ significantly in only one respect: those in the Atlantic have many more genes specifically related to the scavenging of phosphorus, an essential element for these microbes. And just as the variations in the beaks of Darwin's finches were evolutionary adaptations related to food availability, so too are the variations in the Prochlorococcus genes related to phosphorous gathering. Both are examples of a powerful evolutionary force at work.

'We expected to see some difference in the genes related to phosphorous, because the Atlantic Ocean has an order of magnitude lower concentration of phosphorus than the Pacific, so Atlantic populations of Prochlorococcus carry many more genes involved in extracting phosphorus from the seawater. They need more creative ways of gathering it. But we didn't expect it to be the only difference,' said Chisholm. 'This indicates that phosphorus availability is the dominant selective force in defining these populations.'

The researchers also noted that the microbes in the Atlantic Ocean had increased numbers of phosphorous-related genes that helped them neutralize arsenic, an element they sometimes take up by mistake when they're scavenging for phosphorous. This finding 'buttresses the assertion' that this is the result of a strong selective process, Chisholm said.

'We're really diagnosing the ecosystem using a specific species of microbe as a reporter,' said Chisholm. 'We're letting the cells tell us what they have to deal with in their environment.'

She and Coleman also compared the genomes of two populations of a neighboring bacterium, Pelagibacter, and found that genes related to phosphorus gathering in that bacterium appear in far greater numbers in the Atlantic Ocean population, but with a twist. These microbes have a somewhat different repertoire of phosphorus-related genes, suggesting subtle differences between these two microbial groups with respect to how they scavenge phosphorus. This could reflect an adaptive behavior known as 'niche partitioning,' which allows cells sharing a microenvironment to apportion resources according to a cell's 'lifestyle' rather than all competing for the same element or same form of that element.

To obtain these findings, which will appear in the online Early Edition of the Proceedings of the National Academy of Sciences the week of Oct. 11, the two scientists used the complete genomes of 13 strains of lab-cultured Prochlorococcus and Pelagibacter as reference genes, and compared these with the genes of well-documented wild microbe populations gathered at long-term oceanographic study stations near Bermuda (BATS) and Hawaii (HOTS). The work was funded by the Gordon and Betty Moore Foundation, the National Science Foundation and the U.S. Department of Energy.

The next step in this research is to make similar studies at different depths and locations to study the effects of temperature and chemical gradients on the genomes of microbial populations.

'How fast marine microbes adapt to environmental change is a big unknown,' said Coleman, who is now a postdoctoral associate at Caltech. 'One way to address this is to sample the population genomes over time, with parallel environmental monitoring. We might then be able to catch evolution in action. Long term study sites like HOT and BATS are crucial for this effort.'

Source : Massachusetts Institute of Technology

Algal Fuels: Just around the Corner or 10 Years Away?

Tue, 16 Nov 2010 06:05:13 +0100

Algal Fuels: Just around the Corner or 10 Years Away?: " In California, a new report from the Energy Biosciences Institute (EBI) in Berkeley projects that development of cost-competitive algae biofuel production will require much more longterm research, development and demonstration."

(Via Bioenergy News - RenewableEnergyAccess.com.)

Lux Research: Innovation Will Grow Biofuels Market

Tue, 16 Nov 2010 06:03:10 +0100

Lux Research: Innovation Will Grow Biofuels Market: " The biofuels market has struggled to get off the ground for a number of years with many startups languishing in the valley of death if not succumbing to it completely. But a study published by consulting firm Lux Research this week shows that despite the fact that biofuel capacity represents only 3% of the petroleum fuels it seeks to replace, all is not lost for the industry."

(Via Bioenergy News - RenewableEnergyAccess.com.)

Gold Nanoparticles Could Turn Trees into Streetlights

Tue, 16 Nov 2010 05:59:16 +0100

Scientists in Taiwan discovered that placing gold nanoparticles in plants made them glow, which could turn them into an effective form of nighttime illumination:

By implanting the gold nanoparticles into the leaves of the Bacopa caroliniana plants, the scientists were able to induce the chlorophyll in the leaves to produce a red emission. Under a high wavelength of ultraviolet light, the gold nanoparticles were able to produce a blue-violet fluorescence to trigger a red emission in the surrounding chlorophyll.[...]

‘In the future, bio-LED could be used to make roadside trees luminescent at night. This will save energy and absorb CO2 as the bio-LED luminescence will cause the chloroplast to conduct photosynthesis,’ Dr. Yen-Hsun Su said in an interview with Chemistry World.

Link via Popular Science | Photo (unrelated) by Flickr user Irargerich used under Creative Commons license

(Via Neatorama.)

Potechi no Te Popcorn no Te Set - USD 29

Tue, 16 Nov 2010 05:49:27 +0100

Potechi no Te Popcorn no Te Set - USD 29: "Calling all lazy eaters and lovers of crazy gadgets! Takara Tomy's hilarious grabber toys are finally available as one great set! The Potechi no Te and the Popcorn no Te are 'hands' meant to help you in the difficult task of eating potato chips and popcorn respectively. Never has it been so easy! Just use the button to control the sophisticated fingers and then pick up your desired snack. No more greasy fingers!

This great set features one caramel colored Popcorn no Te and one green Potechi no Te so you can switch between the grabbers as your apetite takes you!

The Potechi no Te Popcorn no Te Set features:

Potechi no Te (potato chip grabber) x1 and Popcorn no Te (popcorn grabber) x1 Colors: green (Potechi no Te) and caramel (Popcorn) Size: 40 x 180 x 40mm (1.6 x 7.1 x 1.6') each

(Via Japan Trend Shop - English.)

Awesome Vintage Tech Ads | UNEASYsilence

Tue, 16 Nov 2010 05:46:00 +0100

Awesome Vintage Tech Ads

From (http://uneasysilence.com/archive/2010/10/15478/) and they just posted 116 More Vintage Ads!

You can laugh now, but some years ago you were getting a very nice deal by buying a $3398 10MB hard drive.

A sexy modem? Come on!

Two are always better than one. At least according to this 1978 ad from Technico Inc. TMS9900.

Remember Elvira, Mistress of the Dark? Besides appearing on TV in features like Elvira’s Movie Macabre Halloween Special, Elvira also invited Computerworld readers to “cut through paper-based CASE [computer-aided software engineering] methods with LBMS” software.

This ad won’t make any sense if you’re not a follower of the TV series Lost. However, if you are, you’ll find it amusing…

It’s small and light at ‘only’ 11+ lbs.

“With WordStar, you have a true screen image of what your printout will look like before you print it! With WordStar, you’ll erase, insert, delete and move entire blocks of copy.” Gee, it’s like magic!

Would you say this ad was a little sexist?

Every Kid Should Have an Apple after School.

In the future, everyone will use floppy disks.

Original Apple Computer Up For Sale

Tue, 16 Nov 2010 05:35:41 +0100

Original Apple Computer Up For Sale:

The first ever Apple computer that company founder Steve Jobs sold from his parents' garage is up for sale. It originally cost $666.66, but is expected to fetch $242,000. There were about 200 examples of the original 'Apple-1' that were launched in 1976 and only a few survive today.

This computer will be the first ever to be sold by a major auction house when it goes under the hammer at Christie's of London. It comes with the original packaging, instruction manuals and a signed letter by Steve Jobs. (Via The Presurfer.)

USB Battleship: A Visual Weight for Chaotic USB Cables

Tue, 16 Nov 2010 03:42:33 +0100

USB Battleship: A Visual Weight for Chaotic USB Cables: "

The USB Battleship is a new 5-port USB hub by design duo giffin'termeer. Not just a pretty hub, the device was designed to visually anchor the cable chaos surrounding most of our workspaces, with a toy-like, miniature ship. The piece was introduced during ICFF, and is now available for purchase from Kikkerland.

According to giffin'termeer, the symbol of the boat is especially significant to computer-based deskspaces. Below, they explain the parallel:

Boats are interesting because for the most part, the bottom half is simple and sleek. The top half, however, is usually covered with radar equipments, guns, lifeboats, and other necessary structures—in other words, chaos, and like the physical area around our workspaces, chaos. The thought was that maybe a boat shape could be an 'organizing image' to visually manage the tangle that emanates from my notebook.

(Via Core77.)

Cambridge presentation 2010

Tue, 16 Nov 2010 03:14:13 +0100

See the video of the Cambridge team's presentation at the iGEM2010 Jamboree. The video is hosted at the iGEM HQ site at http://2010.igem.org/files/video/Cambridge.mp4.
The Cambridge team consisted of Bill Collins, Hannah Copley, Peter Emmrich, Will Handley, Anja Hohmann, Emily Knott, Paul Masset, Ben Reeve and Theo Sanderson. They were finalists in the competition, and received a Gold Medal and shared prizes for Best Wiki, and iGEMers award. Click here to play

iGEM2010 Jamboree

Thu, 11 Nov 2010 11:49:30 +0100

Photo of the Awards ceremony at iGEM2010 jamboree, with thanks to iGEM HQ and Justin Knight. (http://www.flickr.com/photos/igemhq/5162172432/) The Cambridge team was one of the 6 finalists, gold medalist, and shared the best wiki prize and the iGEMers award.

Improved BioBrick components for bioluminescence

Thu, 11 Nov 2010 11:22:38 +0100

The Cambridge iGEM2010 team built a set of BioBricks to allow bioluminescence in a wide range of colours which have applications both as reporters for biosensors and as natural light sources. They adopted a number of strategies to extend the use of firefly luciferase: (i) codon optimisation for increased light output, (ii) use of a luciferin regenerating enzyme and (iii) mutagenesis to create a number of different colours. The team also created a BioBrick version of the Vibrio fischeri Lux operon which results in light emission in E. coli without the need for addition of any external substrate. This produces a high light output (as demonstrated by Ben Reeve and Theo Sanderson above!)

iGEM2010 Jamboree results

Tue, 09 Nov 2010 12:29:02 +0100

Grand Prize, Winner of the BioBrick Trophy: Slovenia
1st Runner Up: Peking
2nd Runner Up: BCCS-Bristol

Finalists:

BCCS-Bristol
Cambridge
Imperial College London
Peking
Slovenia
TUDelft

Track Award Winners:

Best Food or Energy Project: BCCS-Bristol
Best Environment Project: Peking
Best Health or Medicine Project: Washington & Freiburg Bioware (Tie)
Best Information Processing Project: ETHZ Basel & Tokyo Tech (Tie)
Best Manufacturing Project: MIT
Best New Application Area: Slovenia
Best Foundation Advance: Paris Liliane Bettencourt
Best Software Tool: USTC Software

Special Prizes Winners:

Best BioBrick Part, Natural: Minnesota (BBa_K311004)
Best New BioBrick Part or Device, Engineered:Slovenia (BBa_K323135)
Best Human Practices Advance: Imperial College London
Safety Commendation: SDU Denmark & VT-ENSIMAG Biosecurity (Tie)
Best Experimental Measurement: Duke
Best Model: Edinburgh
Best Wiki: Cambridge & Imperial College London (Tie)
Best Poster: KIT-Kyoto
Best Presentation: TUDelft

see http://2010.igem.org/Main_Page

Cambridge team at the iGEM2010 Jamboree

Sun, 07 Nov 2010 12:12:13 +0100

The iGEM2010 Jamboree is here again, running Nov 6th-8th. The Cambridge team presented the E.glowli story, showing a set of BioBricks to allow generation of bioluminescence in a wide range of colours which have applications both as reporters for biosensors and as natural light sources.

A number of strategies were used to extend the use of firefly luciferase: (i) codon optimisation for increased light output, (ii) use of a luciferin regenerating enzyme, and (iii) mutagenesis to create a number of different colours.

Light producing systems from Vibrio fischeri were also explored. The team created the first BioBrick to emit light in normal E. coli strains without the addition of any external substrate.

The team made extensive use of Gibson Assembly to manufacture these parts, and have submitted an RFC to the BioBricks Foundation to help promote use of this technique.

In addition, new software tools were built. (i) Gibthon Construct Designer allows the user to enter a series of BioBrick or GenBank IDs in a specific order and computes the appropriate primers for Gibson Assembly. (ii) BioBrick → GenBank allows parts from the registry to be downloaded in .gb format, making them compatible with a wide range of biological software. (iii) The Ligation Calculator is a small calculator to help you work out the proportions to use for ligation in BioBrick assembly without having to worry about units.

Finally, the E.glometer is a cheap, easily built, piece of electronics for measuring bioluminescence. It allows scientists without access to expensive plate readers to measure bacterial light output and has potential applications in quantitative biosensors.

Commentary for Daisy Ginsberg's work

Sat, 09 Oct 2010 22:57:40 +0100

Fresh as a daisy: Alexandra Daisy Ginsberg

Paola Antonelli¹

Paola Antonelli is senior curator in the MoMA's Department of Architecture and Design. In 2008, she organized the exhibition Design and the Elastic Mind, a showcase of the latest developments at the interface between design and science.

When I was looking for new work to feature in my upcoming show Talk to Me, an exhibition on the communication between people and objects that is slated to open at The Museum of Modern Art (MoMA) in New York next summer, I immediately thought of Alexandra Daisy Ginsberg, a remarkable recent graduate of the Design Interactions program at the Royal College of Art (RCA) in London. The clarity, aesthetic and intellectual elegance conveyed in Ginsberg's art marries an undeniable design talent with a deep passion for science.

University of Cambridge team wins iGEM synthetic biology competition

Sat, 09 Oct 2010 22:46:18 +0100

Aleszu Bajak, Biotechniques.com

Seven undergraduates from the University of Cambridge have taken gold at the 2009 International Genetically Engineered Machine (iGEM) competition. The student team designed two biosensor parts to create a tunable biosensor that uses color as its output. iGEM is a global synthetic biology competition that challenges undergraduates worldwide to build simple biological systems from a supplied kit of standard, interchangeable parts.The team of undergraduates won the competition by engineering two biological parts that overcome limitations of current biosensor designs

Seven undergraduates from the University of Cambridge have taken gold at the 2009 International Genetically Engineered Machine (iGEM) competition.

The Cambridge team focused on building a biosensor from their materials, since it recognized two limitations in current designs that they could address: the sensitivity of their promoters and the way they report their output. A biosensor is any integrated device capable of detecting a biological reaction or analyte and converting it into a signal that can be processed. A common example of a biosensor is the glucose monitoring device used by diabetes patients. Team Cambridge developed a signal transduction system that picks out a particular input, amplifies that signal internally to the cell using an input-sensitive promoter, and then produces a pigment output that is easy to see by eye or with a spectrometer.

The team developed a way to tune a biosensor’s sensitivity, allowing it to report meaningful concentrations of the inducer. The group also engineered pigment-producing operons into E. coli to enhance the output. These two parts would improve current biosensor designs by providing user-friendly output within a variable range suitable to the application.

If a biosensor only has an input-sensitive promoter, its output generally varies linearly with input. The Cambridge team placed different sensitivity tuners downstream of varying promoters, resulting in sigmoidal output with distinctive thresholds.

“The team characterized a set of amplifiers of varying sensitivities and gains,” said Robert Carlson, an iGEM judge and Principal of a Seattle-based engineering and consulting firm, and “added a whole range of new colors to the palette available for future projects.”

Color output of the Cambridge team's biosensor part.

The color generators for output were created by mining bacterial genomes for pigment-producing operons, selecting the strongest candidates, and transforming them into E. coli. The resulting bacterial strains could produce red, orange, brown, violet, and green pigments. The team employed three different pigment systems: carotenoids for red and orange, melanin for brown, and violacein for violet and green. The team believes that this technology could be used at the bench, where the presence of a pollutant in a well, for example, would trigger a pigment change in bacteria. Beyond bacterial biosensors, the team imagined future applications including a multicolored biosensor for detecting changes in human GI tract microflora.

iGEM has become the premier international undergraduate synthetic biology competition. Thirteen teams competed in 2005, 54 teams in 2007, and 112 teams this year. The competition began in 2003 when two MIT-based groups worked towards improving biological oscillators during their Independent Activity Periods. At the beginning of the summer, each team receives a kit of biological building blocks from MIT’s Registry of Standard Biological Parts. Under the supervision of several advisors, each team of students build biological systems that operate in living cells from the biological parts that they received from the registry and that they design themselves.

This year, the National Science Foundation (NSF), Invitrogen, and the Federal Bureau of Investigation (FBI) were among those sponsoring over 1700 participants. Laboratory space, equipment, and expertise came from each team’s institution and faculty members. The summer-long competition is organized by MIT and concludes with a weekend jamboree where the entries are judged and winners announced. This year's event was held between Oct. 31 and Nov. 2 on the MIT campus.

The research conducted by these undergraduates offers potential benefits for the future of biotechnology. Runners-up included a team from Valencia, Spain that demonstrated a circuit in yeast that converts external electrical systems into light. “We can’t expect them to generate Nobel-quality projects,” Carlson told BioTechniques, but results like these will “certainly be reused in both academia and industry.”

'Building block' biology

Sat, 09 Oct 2010 22:44:27 +0100

'Building block' biology

25 March 2010. By Mun-Keat Looi (http://www.wellcome.ac.uk/News/2010/Features/WTX059005.htm)

The new field of synthetic biology aims to make biology controllable, predictable and designable. Mun-Keat Looi asks if you can really engineer a biological organism and hears how a unique competition for undergraduates is helping the field gather momentum.

What if you could engineer an organism to do whatever you want: produce life-saving drugs cheaply, generate energy, or detect and clear waste from a polluted lake? And what if building that organism was like constructing a model using toy bricks or piecing together an electronic circuit? Welcome to the world of synthetic biology.

"The theory is that we now know enough about biological systems to be able to start putting them together," says Dr Gos Micklem, Director of the Cambridge Computational Biology Institute. "At that point it becomes relevant to apply engineering principles."

The essence of synthetic biology is to make biology controllable, predictable and designable. A 2009 report from the Royal Academy of Engineering defined it as an attempt to "design and engineer biologically based parts, novel devices and systems as well as redesign existing, natural biological systems".

By producing standard biological parts, scientists can assemble synthetic DNA circuits that produce specific functions within cells, like putting together transistors or capacitors in electronics. Through this, researchers hope to build organisms with an efficiency that promises benefits in a variety of fields.

Take drug development and production, for example. One of the biggest achievements in synthetic biology to date is the engineering of yeast cells to produce a precursor of the antimalarial drug artemisinin, which is expensive to produce when derived naturally from the plant sweet wormwood.

This landmark, by researchers at University of California, Berkeley, showed the power of synthetic biology. Because yeast is used widely in industry (for brewing, among other things), the method could be widened to an industrial scale, bringing down the cost of the drug. Moreover, because the artemisinin-producing yeast is engineered from controllable parts, it could make it easier to create new variants of the drug that can overcome resistance mechanisms in the malaria parasite.

"The standard parts approach broadens the horizons for us to use biology in different ways," says Professor Richard Kitney, co-Director of the new Engineering and Physical Sciences Research Council Centre for Synthetic Biology and Innovation at Imperial College London. "And it is not application-specific. It can be applied to a whole range of fields, from biofuels to pharmaceuticals."

iGEM

When you have, as Kitney puts it, a "paradigm shift in how you approach genetic engineering", how do you explore the possibilities it offers, not to mention build a critical mass of scientists who can expand the nascent field? That's where iGEM comes in.

Started in 2003, the International Genetically Engineered Machine competition sets university teams from all over the world a simple challenge: if you could make anything, what would you make?

"It's the opportunity to make things, design things of your own choice and test them out - a very fundamental human activity," says Randy Rettberg of the Massachusetts Institute of Technology (MIT) and Director of iGEM.

Diagram of Cambridge 2009 iGEM project. Dipstick wells contain genetically engineered E. coli. When the sensor detects the substance it sends a signal to the tuner - this ensures that pigment is produced only when the concentration is above a certain threshold (which can be ‘tuned’ to different levels). Each well contains different bacteria tuned to react to different concentrations - higher concentrations activate more wells along the dipstick and warning colours can be used to indicate unsafe levels.

Each team is given a set of parts from MIT's 'BioBricks' Registry of Standard Biological Parts, an open-access archive being developed by synthetic biologists worldwide.

After a crash course in basic biology, the teams use the ten or so weeks over the summer to come up with an idea, design it, model it, build it and test it in the lab, before presenting the final results at a showpiece event at MIT in November.

It's a daunting task, but one that teams consistently rise to. Successful ideas range from bacteria that detect arsenic in water to a 'clutch' mechanism allowing you to control the movement of bacteria.

In 2009, the competition involved 120 universities worldwide. The Imperial College London team placed fourth overall with their idea of creating a bacterial pill for ingestion that would manufacture specific therapeutic proteins and then encapsulate itself to form a 'micro-pill'. "The overall aim was to design a modular system that could be adapted to produce a variety of drugs," says Kitney.

But the competition was won by the University of Cambridge team, who provided a simple, elegant engineering solution to an everyday problem. The aim was create a simple visual signal to represent something detected by a biosensor, such as the arsenic detector developed by a University of Edinburgh team in a previous iGEM competition.

They plundered simple, known metabolic pathways from different organisms, using different combinations in E. coli to produce a variety of coloured pigments: orange and red from carotenoids, brown from melanin, violet from violacein and green by knocking out a gene in the violacein pathway. The team created a number of different colour readouts, as well as sensitive tuners that allow the system to respond precisely to input from different sensors.

Imagine you have a dipstick with a range of wells along it, each containing different E. coli tuned to respond to different signal strengths (the concentration of heavy metals in the environment, for instance), and each producing a different coloured pigment in response to that. Testing a water sample will produce a kind of 'live barchart' on the dipstick in rainbow colours, with the well containing the most sensitive bacteria at the base of the bar chart, and progressively less sensitive bacteria further up.

"Our hope is to take our parts along with the biosensors that people like the Edinburgh team have produced and put them together for use in the field," says Micklem.

Student activism

European teams at the 2009 iGEM jamboree event, including University of Cambridge and Imperial College London. Credit: Gos Micklem

To achieve such feats in just ten weeks is remarkable - and even more so because the participants in iGEM are not experienced scientists or even PhD students, but undergraduates. Yet that lack of experience can also have its benefits in terms of fresh ideas and raw enthusiasm.

"The students at iGEM haven't been told that things aren't possible," says Kitney, "They start doing things that one would have imagined were impossible."

Professor Paul Freemont, Kitney's co-Director at the EPSRC Centre, agrees. "The young people who are coming into the field don't have any baggage. They simply don't think that engineering biology is impossible, that it will never be predicable or robust enough."

And iGEM provides almost as much opportunity for the professional scientists as their students. The competition involves just about every academic institution currently involved in synthetic biology in the world, encouraging a sense of community and collaboration, with teams earning extra points for helping other teams, particularly new ones, get set up.

The highlight is the annual jamboree at MIT bringing together everyone involved in one location, infused with the infectious enthusiasm of 10 000 undergraduates.

"The atmosphere is electric," says Micklem. "The students get to meet everyone in the world who is working this area, right from world-leading labs to those who are just starting out. And most undergraduates don't work on a big team project or get flown out to a big international meeting. It's tremendously exciting for everyone."

Social engineering

The iGEM competition also feeds into itself, and the MIT Registry. Any new parts created in each year's competition must be sent to the Registry and made available to the following year's teams. Those that work well are soon picked out because they are reused, retested and revalidated by new teams, filtering what is robust and reliable from what isn't.

However, not everyone agrees that the BioBricks approach is the most efficient way forward for synthetic biology. As Micklem tells me, large labs with substantial funding can now order their DNA made-to-measure from external companies. This avoids a lot of tedious and slow lab work, and with the price of DNA synthesis falling all the time, this is becoming more cost-effective than working with biobricks.

iGEM: your ticket to adventures in synthetic biology. Credit: jurvetson on Flickr

Yet the simplicity of the BioBricks approach allows undergraduates - and indeed non-biologists - to take part, and this is enabling what might be thought of as a form of social engineering. By bringing together large numbers of student life scientists, mathematicians, physicists, engineers and computer scientists, iGEM is seeding a new generation of researchers with enthusiasm for and commitment to the field - a generation who may end up in faculty positions, setting up labs and sitting on grant funding bodies (indeed, Rettberg tells me several iGEM graduates are already on tenure-track faculty positions).

"Biology is at a stage - and not for the first time - where it needs to draw on people and ideas from other disciplines," says Professor Steve Oliver, Director of the Cambridge Systems Biology Centre. "Things like iGEM can really enthuse young scientists. Catch them young and they can make a huge amount of progress."

It's also a great way for universities with no synthetic biology experience to get started. Dr Anne Smith, a computational biologist who this year leads a team from St Andrews University into iGEM for the first time, is excited by the possibilities.

"Synthetic biology is the next step for where engineering is going," she says. "Biology has a lot of power that it has developed through evolution to do things. Through synthetic biology, we might be able to piggyback on all of that and get it to do things for us."

And synthetic biology could also make a significant contribution to biology itself.

Says Freemont, "We learn about fundamentals of biological systems by trying to build new systems - how difficult they are to regulate, control, work with, and how biology overcame all these problems. As Richard Feynman once said, 'What I cannot create, I do not understand'."

Nevertheless, he says, the application-driven approach is one of synthetic biology's biggest advantages. "Here is a field with real direction and purpose, not just understanding the fundamentals of things. And when you've got that it can be really powerful."

As a field in its most nascent stages, it's hard to say what impact synthetic biology will have, or if it really will be the revolution in biology, engineering, science and technology that some think it could be.

"We're just ten years into synthetic biology," says Rettberg. "The internet took 30 years to become significant. And the most significant things we only recognise as such after they've happened."

Top image: The iGEM 'BioBrick' trophy. Credit: Gos Micklem

Unusual vegetables and fruit

Sat, 09 Oct 2010 22:26:31 +0100

1. Purple Haze Carrots

Orange carrots are an excellent source of vitamin A and contain phytochemicals that have antioxidants, anti-bacterial, anti-inflammatory, and other health enhancing qualities. Purple carrots, also contain all of these elements, but have have anthocyanins – potent antioxidants. These anthocyanins play an important role in the reduction of risk to diabetes and cornorary heart disease.

2. Okinawan Sweet Potato

The Okinawan sweet potatoe is named for its origins in Okinawa Japan. The residents of Okinawa are known for having one of the longest life expectancies in the world. Some researchers are attributing thier long life expectancy to their diet – in particular their purple colored sweet potatoe. This potatoe’s nutritional qualities are known to directly control blood sugar levels, lower risks of diabetes, and contain more antioxidants than blueberries.

3. Buddha’s Hand

Buddha’s hand is one of the weirdest looking fruits on our list. Reminding me of Davey Jones from the Pirate’s of the Carribean movie, the Buddha’s hand is in the citron family and is one of hte oldest members. It is entirely rind based and has an extremely low number of calories and has health benefits similar to that of a lemon.

4. Cape Broccoli (Purple Cauliflower)

Purple cauliflower is very semilar to it’s more normally seen green colored variation. The purple tint is caused by the presense of the antioxidant group, anthocyanin. The cauliflower is low in fat, high in fiber, folate, water and vitamin C. Consumption of cauliflower has been linked to lower risks of prostate cancer.

5. Square Watermelon

While nutritionally no different than a normal round watermelon, the square-shaped watermelon is just cool to look at. It is forced into this shape during growth and the main reasoning behind it is that its easier to stack and store.

6. Pitahaya

Pitahaya is the fruit of several cactus species, and are commonly referred to as “Dragon Fruit”. The fruit is native to Mexico, Central and South America and Asia. The Piahaya is rich in fiber and minerals, contains poly-unsaturated fatty acids, and antioxidants which help prevent cancer. The fruit also lowers cholesteral and blood pressure, and can alleviate chronic respiratory tract alliments.

7. Romanesco Cauliflower

Also known as coral broccoli, Romanesco broccoli, which has a very fractal appearance, is rich in vitamin c, fiber, potassium and caretonoids. Health benefits of this broccoli include improved eyesight, fights viral infections, colds and flus, and can improve cholesterol, blood sugar levels, and blood pressure levels.

8. Cherimoya

Native to South America, and more specifically Bolivia, Chile, Equador, and Peru, the Cherimoya looks like a cross between an apple and the insides of a coconut. The fruit has been shown to help control blood sugar levels and provides slowly released sustained energy. It also helps increase the elasticity, firmness and suppleness to the skin. The fruit is rich in vitamin c and b, fiber and potassium.

9. Durian

The durian is a very unique looking tree fruit that is around the same size as a watermelon but has a spikey outer shell with yellowish innards. The fruit is known for having a pungeant and sometimes offensive smell and taste. The smell can sometimes be so bad, that it has been banished from some hotels and public transportation in Asia. The fruit contains a high amount of sugar, vitamin c, and potassium and is a good source of carbohydrates, proteins and fat. The fruit also contains rich levels of estrogen which may increase fertility

10. Lychee

The lychee is a tropical and subtropical fruit native to China. The outside of the fruit looks similar to a strawberry while the inside looks like an egg or golfball that is a sweet fleshy substance. Lychee contain an average of 72mg of vitamin c – 9 of them would average out to an adults daily recommended amount.

11. Carambola – Star Fruit

Carambola, also called Star Fruit because of their shape, is native to the Philippines, Indonesia, India and Sri Lanka. The Carambola is rich in antioxidants and vitamin c, but are low in sugar, sodium and acids, and can be compared to the health benefits of strawberries. There are some risk to eating the star fruit though. People with kidney failure have been shown to suffer from hiccups, vomiting, nasuea, and mental confusion. Even fatal outcomes have been documented in some instances.

12. Rambutan

Rambutans, which look like hairy or spiny strawberries, and is comparable to the Lychee. The rambutan fruit is high in vitamin c, carbohydrates, protein, fat, phosphorus, iron, and calcium.

From: http://www.cuisinevegan.com/vegan-fun/fruits-vegetables-youve-never-heard-of/

Reversal of an epigenetic switch governing cell chaining in Bacillus subtilis by protein ...

Sat, 09 Oct 2010 21:44:50 +0100

Reversal of an epigenetic switch governing cell chaining in Bacillus subtilis by protein instability.: "Publication Date: 2010 Oct PMID: 20923420
Authors: Chai, Y. - Kolter, R. - Losick, R.
Journal: Mol Microbiol

Bacillus subtilis forms long chains of cells during growth and biofilm formation. Cell separation is mediated by autolysins, whose genes are under the negative control of a heteromeric complex composed of the proteins SinR and SlrR. Formation of the SinR-SlrR complex is governed by a self-reinforcing, double-negative feedback loop in which SinR represses the gene for SlrR and SlrR, by forming the SinR-SlrR complex, titrates SinR and prevents it from repressing slrR. The loop is a bistable switch and exists in a SlrR(LOW) state in which autolysin genes are on, and a SlrR(HIGH) state in which autolysin genes are repressed by SinR-SlrR. Cells in the SlrR(LOW) state are driven into the SlrR(HIGH) state by SinI, an antirepressor that binds to and inhibits SinR. However, the mechanism by which cells in the SlrR(HIGH) state revert back to the SlrR(LOW) state is unknown. We report that SlrR is proteolytically unstable and present evidence that self-cleavage via a LexA-like autopeptidase and ClpC contribute to its degradation. Cells producing a self-cleavage-resistant mutant of SlrR exhibited more persistent chaining during growth and yielded biofilms with enhanced structural complexity. We propose that degradation of SlrR allows cells to switch from the SlrR(HIGH) to the SlrR(LOW) state.

(Via Molecular Microbiology.)

In an early branching metazoan, bacterial colonization of the embryo is controlled by maternal ...

Sat, 09 Oct 2010 21:40:43 +0100

In an early branching metazoan, bacterial colonization of the embryo is controlled by maternal antimicrobial peptides.: "Publication Date: 2010 Oct 4 PMID: 20921390
Authors: Fraune, S. - Augustin, R. - Anton-Erxleben, F. - Wittlieb, J. - Gelhaus, C. - Klimovich, V. B. - Samoilovich, M. P. - Bosch, T. C.
Journal: Proc Natl Acad Sci U S A

Early embryos of many organisms develop outside the mother and are immediately confronted with myriads of potential colonizers. How these naive developmental stages control and shape the bacterial colonization is largely unknown. Here we show that early embryonic stages of the basal metazoan Hydra are able to control bacterial colonization by using maternal antimicrobial peptides. Antimicrobial peptides of the periculin family selecting for a specific bacterial colonization during embryogenesis are produced in the oocyte and in early embryos. If overexpressed in hydra ectodermal epithelial cells, periculin1a drastically reduces the bacterial load, indicating potent antimicrobial activity. Unexpectedly, transgenic polyps also revealed that periculin, in addition to bactericidal activity, changes the structure of the bacterial community. These findings delineate a role for antimicrobial peptides both in selecting particular bacterial partners during development and as important components of a 'be prepared' strategy providing transgenerational protection.

(Via PNAS.)

Mini-documentary about the desks of creative people

Sat, 09 Oct 2010 21:29:38 +0100

Mini-documentary about the desks of creative people: "

In this first episode 'The Desk,' we talked to experts Alice Twemlow, Eric Abrahamson, Massimo Vignelli, David Miller, Kurt Andersen, Søren Kjær, Alfred Stadler, Jennifer Lai, and Ben Bajorek and creates an historical and relevant film about the relationship between the worker and the desk and how this reflects on personality and habits.

[Via Kottke]

(Via MAKE Magazine.)

PaperPro Makes “Quite Possibly the Best Staplers Ever” | Gadget Lab | Wired.com

Sat, 09 Oct 2010 21:25:38 +0100

PaperPro Makes “Quite Possibly the Best Staplers Ever”

From: http://www.wired.com/gadgetlab/2010/10/paperpro-makes-quite-possibly-the-best-staplers-ever/

PaperPro’s staplers use a patented staple-gun-like spring-and-lever mechanism to turn 8lbs of finger pressure into 30lbs of staple-driving force. They’re quickly attracting a devoted following.

OfficeSupplyGeek does pretty thorough product reviews, so when he says “I have found the only stapler I’ll ever use,” I believe him. Paper capacity, ease-of-use, ergonomics, style — the entire range from the teeny Nano (which is the size of a staple remover, but can staple through 12 sheets) to their professional/high-capacity 100-sheet staplers exceeded all expectations.

He even made a video showing the PaperPro throwing a fastener through cardboard with just one finger’s pressure:

I also like the concept of the Long Reach Stapler (pictured at right), which lets you staple across a long sheet of paper rather than along the edge. It looks like a cheap and easy way to make (or repair) your own ‘zines.

PaperPro’s staplers are relatively inexpensive (I priced the midrange Prodigy at $25 on Amazon, compared to $30 for a commercial-grade Swingline with comparable capacity)

Image via PaperPro; video by OfficeSupplyGeek

Amazing Casio Calculator Plots Equations Onto Photographs

Sat, 09 Oct 2010 21:23:39 +0100

Casio Prizm Calculator Plots Equations Onto Photographs

From: http://www.wired.com/gadgetlab/2010/10/casio-prizm-calculator-pulls-equations-from-photographs/

If you’ve ever looked at the curve of a hill, the cables of a suspension bridge or the arc of a coastline and wondered, “I wonder what function would fit that line?” — congratulations, you’re a nerd. And Casio has a surprising new calculator that will answer your question.

Casio’s new Prizm calculator is to the graphing calculators of my school-days as the iPad is to the slates we scratched on with sticks of chalk. It has a color, 216×384 pixel display, 16MB of memory, a USB-port, and will do all of your math homework for you.

I hated graphing equations in school. I did a math A (advanced)-level, which is the equivalent of, I don’t know, a Nobel prize or something in the U.S. One of our tasks was to look at equations and do a quick eyeball sketch. No plotting, just guesstimates. I was hopeless, failing on anything more complex than x=y+1. Worse, I had a primitive graphing calc in my bag that I wasn’t allowed to use.

Any graphing calculator will let you input an equation and show you the result. Casio’s Prizm does this in reverse. The color screen will display a picture, and will draw a line over the top of any shape you like. It will then give you an equation for this line.

If that wasn’t amazing enough, that USB port lets you hook the calc up to a compatible Casio projector to show off the results on the big screen.

Now the beautiful math plots and photographs of math artist Nikki Graziano are within reach of any high school calculus student — at least in principle.

With tech like this, I’m surprised anyone actually goes to school anymore. After all, you don’t actually need to do any work there, it’s all done for you. If you have any doubt as to the disappearing math abilities of the developed world, think about this: why are there so many tip-calculators in the App Store? Can you really not work out 15-percent in your head?

$130, available now.

Casio Unveils Next-Generation Graphing Calculator – PrizmTM [Casio]

(Via Wired News.)

App Magnets – upgrade your fridge with some app-etising icons

Sat, 09 Oct 2010 21:01:06 +0100

App Magnets – upgrade your fridge with some app-etising icons: "

App Magnets are little fridge magnets in the form of smartphone icons which you can use to leave notes, photos or directions to the pizza place for the household to digest. A perfect gift for the phone obsessed geek in your family. $12.99 [...](Via The Red Ferret Journal - gadgets, cool sites, freeware and tech trivia.)

New Pogo Stylus And Stand Clip For iPhone 4

Sat, 09 Oct 2010 20:59:33 +0100

New Pogo Stylus And Stand Clip For iPhone 4: "

Ten One Design have launched a new Pogo Stylus and clip stand designed specifically for the new iPhone 4. The clip when not clips onto your iPhone 4 and the stylus fits neatly on to its side when not in use. You can now Sketch, type and navigate with greater precision.

The stylus its self is similar to others fo the iPad created by Ten One and offers a soft, durable tip, precision-formed to the perfect size for the keyboard keys. It glides easily over the surface of the display.

The new stand and stylus is available to purchase from Ten One Design for $14.99 and is available in four colours

Via SlashGear

(Via Geeky-Gadgets.)

Hackintosh In A Cardboard Box

Sat, 09 Oct 2010 20:57:43 +0100

Hackintosh In A Cardboard Box: The guys over at 1 Block Off The Grid needed a high end computer that would easily run Adobe After Effects, rather than buying a Mac Pro for about $3,000 they decided to build their own Hackintosh. What makes this Hackintosh unique is the case, instead of paying for a case they decided to use the Amazon cardboard box that the computer parts were shipped in. The end result was a saving of over $2,000, and the specifications include an Intel Core i5 2.66GHz processor, a 1TB hard drive, 8GB of 1,333MHz DDR3 RAM and an XFXRadeon HD 5770 1GB DDR5 graphics card.(Via Geeky-Gadgets.)

GM profit boost to non-GM crops

Sat, 09 Oct 2010 20:56:42 +0100

By Richard BlackEnvironment correspondent, BBC News

The corn borer can devastate plants, but GM varieties produce a defensive bacterial toxin

Insect pest control by genetically-modified crops can raise yields and profits from non-GM varieties grown nearby, a study from the US indicates.

Researchers looked at maize grown in five US states, where plants are affected by the European corn borer.

They found fewer borers - and higher profits - in GM fields, and in neighbouring non-GM fields.

Writing in the journal Science, they say this is the first time that a wider impact on profits has been shown.

Maize (known as corn in the US) can be genetically modified with a gene taken from a bacterium, Bacillus thuringiensis (Bt).

“Start Quote

With fewer corn borers around, it clearly makes economic sense to increase the proportion of non-Bt strains”

Bill HutchisonUniversity of Minnesota

The introduced gene makes a toxin that kills corn borers - in principle rendering the plants immune to its attack, and increasing yields.

Bt varieties now make up about two thirds of the US maize crop.

But regulations require farmers to plant conventional varieties as well, which is intended to stop the borers becoming resistant.

Previous research has shown that Bt plants can curb insect damage in neighbouring non-GM fields, because their presence reduces the overall number of pests.

"This area-wide suppression effect has been documented in China and here in the US," said study leader Bill Hutchison from the University of Minnesota in St Paul.

"But as far as I'm aware, this is the first time that the economic benefits have been documented," he told BBC News.

Conventional economics

By comparing actual insect damage against estimates of what damage would have occurred - derived from historical data and other measures of borer abundance - the researchers calculated that over the 14 years of their study, use of Bt varieties improved farmers' profits by about $3.2bn in Illinois, Minnesota and Wisconsin.

But most of this benefit - $2.4bn - was accrued in non-Bt fields.

Non-Bt seeds are cheaper - but they also gained in yield through their proximity to the GM fields.

A similar pattern pertains in Iowa and Nebraska, the team calculates.

Professor Matin Qaim, who studies the economics of GM agriculture at the University of Goettingen, said the ecological and economic benefits would depend on the characteristics of the particular pest.

"If your crop plant is the main host for the insect, then area-wide suppression is likely to happen," he said.

"Resistance might develop - however, that hasn't become a big problem under practical conditions."

Rotating benefits

A certain amount of maize grown in the US - and a larger proportion in other countries - is grown using organic techniques; and Bill Freese of the anti-GM group Center for Food Safety noted that other forms of pest control were available.

"Organic farmers use a lot of cultural techniques to combat insects, such as crop rotation, and that's very beneficial," he said.

Populations of European corn borer are declining across the US, largely because of Bt crops

"But in most of these mid-western farms there is hardly any crop rotation - the most you might get is corn-soy-corn - so these cultural methods are being forgotten, and I think that's a shame."

The Environmental Protection Agency (EPA) mandates that at least 20% of non-GM varieties must be planted alongside the Bt strains.

But recently, companies have released "stacked" varieties containing up to six introduced genes, each producing a toxin to a specific pest; and for these, the EPA is relaxing the requirement for non-GM refuges.

However, Professor Hutchison said his work might convince previously reluctant farmers that the conventional seeds should be sown even if regulations do not mandate it.

"Many growers are very smart, they see the suppression in their [non-GM] fields," he said.

"It depends how risk-averse they want to be; but in the modern climate, with fewer corn borers around, it clearly makes economic sense to increase the proportion of non-Bt strains."

[email protected]">[email protected]

(http://www.bbc.co.uk/news/science-environment-11496710)

Solar Cockroach – creepy gets eco crawlier

Sat, 09 Oct 2010 20:41:24 +0100

Solar Cockroach – creepy gets eco crawlier: "

This Solar Cockroach is everyone’s idea of a perfect eco pet, right? Small black, wriggly. Saving the planet. Wait… $15.00.

Cockroach design # Powered by sunlight # Works directly under sunlight # Size: 40*19*19mm # Weight: 5g

Tags: solar+cockroach, [...](Via The Red Ferret Journal - gadgets, cool sites, freeware and tech trivia.)

Solar Cockroach – creepy gets eco crawlier

Sat, 09 Oct 2010 20:41:24 +0100

Solar Cockroach – creepy gets eco crawlier: "

This Solar Cockroach is everyone’s idea of a perfect eco pet, right? Small black, wriggly. Saving the planet. Wait… $15.00.

Cockroach design # Powered by sunlight # Works directly under sunlight # Size: 40*19*19mm # Weight: 5g

Tags: solar+cockroach, [...](Via The Red Ferret Journal - gadgets, cool sites, freeware and tech trivia.)

BBC News - Which country has the best brains?

Sat, 09 Oct 2010 20:40:11 +0100

Over the past week, the Nobel prizes have been awarded in chemistry, medicine, peace, physics and literature.

The awards are an annual ritual celebrating human intellectual endeavour that began in 1901. They were set up by Alfred Nobel, a Swedish inventor and arms manufacturer, who requested in his will that his fortune be used to create a series of prizes for those who confer the "greatest benefit on mankind".

Nobel winners in their own words

The BBC has unearthed previously unseen interviews with Nobel scientists in its archives
These have now been digitised, see link below

Watch Nobel scientists in conversation

Over the intervening 109 years, more than 500 prizes have been awarded. But which nation can claim the most winners?

We have trawled throught the archives to produce a definitive list of the nations with the biggest brains.

A clear winner would be the United States which comes out top overall, as well as in five of the six categories. The UK is next, with 117 Nobel medals. However, France, which bumps along in fourth or fifth, is clearly ahead when it comes to literature.

But there are a total of 69 countries or territories whose citizens have picked up the prize, from St Lucia to this week's latest addition, Peru, birthplace of author Mario Vargas Llosa.

Document

DownloadNobel prizes by country _[37kb]

Notes:

The figures include all Nobel Prizes awarded up to and including 8 October 2010
Prizes are allocated to the country/countries stated on the winner's biography on the website of the Nobel Prize committee (www.nobelprize.org)
Where the website mentions multiple countries in relation to a prize winner (country of birth; country of citizenship; country of residence at time of award) each of those countries is credited as having won the prize
Where a prize has multiple winners, the country (or countries) of each winner are credited
Prizes which were declined by the winner are included
Prizes won by organisations are not allocated to countries
The Prize in Economic Sciences in Memory of Alfred Nobel is not a Nobel Prize per se, but it is awarded by the Royal Swedish Academy of Sciences according to the same principles as for the Nobel Prizes. We therefore include it

BBC News - Nobel prize winners warn against immigration cap

Sat, 09 Oct 2010 20:38:06 +0100

BBC News - Nobel prize winners warn against immigration cap: "Nobel prize winners warn against immigration cap

The scientists join other groups to have voiced concerns about the cap The UK's cap on immigration threatens the country's future as a centre of scientific excellence, a group of Nobel prize-winning scientists has warned.

In a letter to the Times, the eight UK academics said the visa curbs would deprive science and industry of talent.

They said it was a 'sad reflection' that scientists and engineers could not be afforded the same exception to the rules as Premier League footballers.

The Home Office said it had consulted widely on the immigration cap.

It introduced a limit for work visas for non-EU citizens in June.

Continue reading the main story Related stories

Rees: Lift non-EU scientists' cap No 10 rejects Cable migrant claim Student migration 'unsustainable' A key part of the Conservative election manifesto, the temporary cap of 24,100 will be replaced by permanent measures from April 2011.

In their letter, the academics wrote: 'The government has seen fit to introduce an exception to the rules for Premier League footballers.

'It is a sad reflection of our priorities as a nation if we cannot afford the same recognition for elite scientists and engineers.'

They added: 'International collaborations underlie 40% of the UK's scientific output, but would become far more difficult if we were to constrict our borders.

'The UK produces nearly 10% of the world's scientific output with only 1% of its population; we punch above our weight because we can engage with excellence wherever it occurs.

'The UK must not isolate itself from the increasingly globalised world of research - British science depends on it.'

The CBI, the Royal Society and university vice-chancellors have already voiced concerns about the immigration cap.

Thinnest material Sir Harry Kroto, who won the Nobel Prize in Chemistry told BBC Radio 4's Today programme that one of his own researchers had been refused permission to study at Cambridge University under the rules and will now stay at a US university.

Cannot play media.You do not have the correct version of the flash player. Download the correct version

'The UK loses out and in the future we can see the UK can only survive on its intellectual property, rather than as a country that provides things, with countries like India and China providing things more cheaply, so we need to look at that,' he said.

Continue reading the main story ‘ Start Quote

We will continue to attract and retain the brightest and the best people who can make a real difference to our economic growth’

Damian Green Immigration minister 'If one looks over the years, one quarter of the Nobel Prizes that came to the UK were won by immigrants from outside. It's probably very unwise to not look very carefully at the scientists, engineers and technologists who could come to this country and give this country the extra support it needs to compete in the future.'

Liberal Democrat Business Secretary Vince Cable has said the measure is doing 'huge damage' to British firms.

Downing Street said the limit would be implemented in a way that still allowed the brightest and best to come to Britain.

Minister for Immigration Damian Green said Britain could benefit from migration but not uncontrolled migration.

'Britain remains open for business and we will continue to attract and retain the brightest and the best people who can make a real difference to our economic growth, but unlimited migration places unacceptable pressure on public services.

'We have consulted with business and other interested parties on how the limit should work and have also asked the Migration Advisory Committee to consult on what the actual limit should be. These consultations are now closed and we will announce the findings in due course.'

Two of the scientists behind the letter are Russian migrants, Professor Andre Geim and Professor Konstantin Novoselov, of the University of Manchester, who won the Nobel prize for physics on Tuesday.

They invented graphene, the world's thinnest material which is 200 times stronger than steel.

The other signatories are Sir Paul Nurse, Sir Tim Hunt, Sir Martin Evans, Sir Harry Kroto, Sir John Walker and Sir John Sulston.

How-To: Sensor Tutorial -- IR remote receiver-decoder tutorial

Sat, 09 Oct 2010 20:35:52 +0100

How-To: Sensor Tutorial -- IR remote receiver-decoder tutorial: "

Nice tutorial from Ladyada, she writes -

Here is a new SENSOR TUTORIAL! IR detector Make remote controls and listeners Making an Intervalometer, Read IR commands from an Apple remote, use for your projects and more!.

What is an IR detection sensor?

IR detectors are little microchips with a photocell that are tuned to listen to infrared light. They are almost always used for remote control detection - every TV and DVD player has one of these in the front to listen for the IR signal from the clicker. Inside the remote control is a matching IR LED, which emits IR pulses to tell the TV to turn on, off or change channels. IR light is not visible to the human eye, which means it takes a little more work to test a setup.

There are a few difference between these and say a CdS Photocells:

IR detectors are specially filtered for Infrared light, they are not good at detecting visible light. On the other hand, photocells are good at detecting yellow/green visible light, not good at IR light

IR detectors have a demodulator inside that looks for modulated IR at 38 KHz. Just shining an IR LED wont be detected, it has to be PWM blinking at 38KHz. Photocells do not have any sort of demodulator and can detect any frequency (including DC) within the response speed of the photocell (which is about 1KHz)

IR detectors are digital out - either they detect 38KHz IR signal and output low (0V) or they do not detect any and output high (5V). Photocells act like resistors, the resistance changes depending on how much light they are exposed to

In this tutorial we will show how to

Test your IR sensor to make sure its working

Read raw IR codes into a microcontroller

Create a camera intervalometer

Listen for 'commands' from a remote control on your microcontroller

Read more!

(Via MAKE Magazine.)

Electronic Blinking Eyeballs

Sat, 09 Oct 2010 18:42:52 +0100

Electronic Blinking Eyeballs: "

By Andrew Liszewski

Working in a home office can get a little boring at times, so ThinkGeek has once again come to the rescue with this pair of electronic blinking eyes from Japan that will allow you to anthropomorphize any inanimate object in your home to become your new best friend. They attach to almost anything via suction cups or hooks and the mechanical shutter mechanism stays synced between the two eyes at all times thanks to an IR signal. At three inches in size they’re probably better suited for bringing larger items like filing cabinets or fridges to life, and each eye is powered by 3xAAA batteries. $34.99, sold in a pair of course. No discounts for cyclops fans.

[ Electronic Blinking Eyeballs ]

(Via OhGizmo!.)

Trends in Web Logo Design

Sat, 09 Oct 2010 18:39:17 +0100

11 Trends in Web Logo Design: The Good, the Bad and the Overused:

from http://mashable.com/2010/09/28/web-logo-design-trends/ (Jolie O'Dell)

This series is brought to you by the Intel AppUp℠ Developer Program, which provides developers with everything they need to create and then sell their applications to millions of Intel Atom™ processor-based devices. Learn more here.

Designing and critiquing logos for web-based companies and startups is a pursuit of endless fascination for many of us. Over the years, we’ve seen enough startups come and go (and rebrand and merge) to fill a volume with how and how not to develop and execute a logo for a web company.

We’ve also picked up some knowledge about trends in this field. Some of the trends are good; others, regrettable. Others still are simply overused, which is the saddest scenario of them all. We hate to see a good design trick or typeface grow hackneyed over the course of a few months, but it happens all the time, unfortunately.

In this article, we’ve identified 11 trends in web company logo design. Hopefully, you’ll see a few here that apply to the startups and web apps we write about every day. And of course, we’ve included some handy illustrations as a sort of field guide to the logos of the web.

Take a look, and let us know what you think of these trends — and what trends we should have included — in the comments.

1. Badges and Buttons

We’ve moved away from the once-ubiquitious BETA! button, but location-esque badges, app-like icons, and “play” buttons are still showing up all over the web. These logos tend to be quite “shiny,” thanks to a few carefully-blended white gradient layers. The square logos have rounded corners. Some appear to glow as if lit from within, which is a compelling and trendy effect in itself. All in all, the badge-and-button set look quite touchable.

Still, this trend’s days may be numbered, if only due to overuse and association-bordering-on-marriage with the Apple/iPhone brand. See also: Wet floor effect. Unless you’re designing for a pure-play iPhone app shop, sail these seas with caution.

2. Speech Bubbles and Megaphones

If social web apps are all about communication, then it stands to reason that many social web company logos are all about talking. We see fewer logos that revolve around listening (if you happen to see a giant ear logo in the wild, do let us know), but megaphones and speech bubbles abound.

3. Fun With Opacity!

Remember the first time you discovered Multiply and Overlay blend modes in Photoshop? If that moment changed your life forever, then you probably understand the beauty of a simple, elegant logo that delicately plays with opacity.

While this logo treatment won’t work for every web app, it’s a versatile and timeless way to present classic shapes in a new light. We’re seeing this basic effect used simply in MasterCard-reminiscent designs, and we’re seeing much more complex opacity effects used in logos for HTML5 and Microsoft Silverlight, for example.

Playing with blending modes, opacity and overlapping shapes can also be a fun way to experiment with analogous color schemes.

4. Kawaii Illustration

Calling all woodland creatures: You’re wanted on the Internet. In fact, the only time you’ve been in greater demand than you are now was when Disney was making those saccharine “princess” films.

Why are these wide-eyed, adorable critters making their way into logo design? Apps are for adults, right? Especially apps such as Seesmic, a powerful web app dashboard for power users and the enterprise, and GitHub, an industry standard for source code hosting.

We don’t know exactly how, when or why kawaii made a comeback into serious-business logo design, but with logos this cute, who are we to complain?

5. Scripts, Slabs and Other Cool Fonts

Say it with me: “I will not use Archer for a web company’s logo design.”

Archer and its ilk were used to great effect over the past couple years on a number of memorable web company logos. That being said, the Year of the Slab is definitely not over. In fact, it’s more of an epoch than a traditional Gregorian year at this point. Slab serif fonts — if they’re unique fonts — are still a viable alternative to been-there-done-that sans serifs in logos, and the web community still enjoys them.

That being said, a good, juicy script can be one of the liveliest, most unexpected logo choices yet, particularly if your logo is solely typographic. Rephoria uses my personal favorite, Candy Script, a swash-heavy number that’s almost too voluptuous for work but which still makes the cut for a single-word logo.

Just remember: When using more unusual fonts for logo design, restraint and legibility are key.

6. Verdant and Plant-Inspired

Plants and leaves aren’t just for green tech companies, folks. When you’re trying to project growth, one of the most obvious logo choices is flora. A shy set of leaves, a furling bud, a sprouting seed — what could better convey your company’s fresh problem solving and rapid expansion?

7. Quadrangles

It’s not a rectangle, it’s not a square, but whatever it is, it’s popping up everywhere. Quadrangles are, if the web is to be believed, the new dots. From rhombuses to parallelograms to indescribable yet angular blobs, these shapes strive for post-modern and consumer-friendly.

8. Retro Game References

Perhaps it’s because the newer crop of web designers are also children of the late eighties, but we’ve been seeing a lot of pseudo-retro, video game-inspired logo work lately. While these designs are definitely quirky, geeky and cool, beware using them for a general audience; not everyone feels the same nostalgia we do for an 8-bit, pixelated graphic of a mushroom.

9. Color-Coordinated Compound Words

Web startup names and logos are inextricably linked. We’re a couple years past the compound word phase (which was most virulent right before the tragic “missing vowel” phase that gave birth to web companies with names like “Packg” and “Clevrr”), but we haven’t left behind our love for merged-word logos in two snappy, coordinating colors.

This trick is one of the oldest in the book. It was notably used for Vignelli Associates’ 1967 rebranding of American Airlines, whose two-word name became a one-word logo in red and blue.

10. Logotypes

The big boys of the web, sites such as Google and Facebook, have inspired the logo design of a generation with their utter simplicity. In many cases, those initial logotypes were less legitimate logo design and more “put our startup’s name in a simple font and stick it up on the web, we’ll deal with branding later.”

The name-in-a-sans-serif look says your company has nothing to prove and that you focus on product over promotion. If it’s well-executed, it’s a powerful statement to make. However, if poorly executed, it looks hasty, sloppy, juvenile and amateurish.

Logotypes can also be a great excuse to play with exciting typefaces and trendy treatments, such as the embossed or letterpress look that’s getting so much play these days, thanks to CSS3.

11. Nodes, Spokes and Hubs

Between concepts such as linked data and the synaptic web, you had to see these designs coming. They remind us of molecular structure and K’nex, an updated take on the crop of mid-century modern Sputnik-inspired designs of the 1950s. These logos are usually intended to represent the interconnectedness of people and content on the web, or, in a more literal interpretation, computer hardware circuitry.

An excellent study of this concept is Bernard Barry’s designs for the 2010 f8 conference.

This Lung-On-A-Chip

Sat, 09 Oct 2010 18:31:00 +0100

This Lung-On-A-Chip Is The First Lab-Ready Mini-Organ to Be Used in Drug Research: Scientists create a vacuum in the green channels bordering the blue rubber strip, which forces it to stretch, contract, and simulate breathing. Kristin Johnson/Donald Ingber/Benjamin Matthews/Martin Montoya/Dongeun Huh/Akiko Mamoto/Hong Yuan Hsin

The ersatz lung, no bigger than a multivitamin, could represent a new pharmaceutical testing method. On it, researchers have created an artificial alveolus, one of the sacs in the lungs where oxygen crosses a membrane to enter the body's blood vessels. A polymer sheet that stands in for the membrane is in the blue strip. On one side of the sheet, blood-vessel cells mimic a capillary wall; on the other, lung-cancer cells mimic lung epithelial cells. Scientists have tested the chip's immune response, and it behaves just like real tissue would, a first step to having lifelike organ systems on which drugs can act. The chip's primary developer, biomedical engineer Dongeun (Dan) Huh of Harvard University, hopes that within two years, the chip will succeed in mimicking the process by which the lungs swap oxygen for carbon dioxide. Huh would like to create a suite of artificial organs to be used in cosmetics testing and pharmaceutical safety trials.

(Via Popular Science -.)

Pickle Adhesive Bandages

Sat, 09 Oct 2010 18:24:46 +0100

Pickle Adhesive Bandages

Band Aids are boring. Never underestimate the protective pickle power. These juiceless Pickle Bandages take the sting out of your cuts and scrapes.

Next time you hurt yourself, you can sport one of these cool looking bandages. But don’t hurt yourself on purpose. For those of us over the age of 5, boo-boos have become quite fashionable. Even if you do not have a cut, the designer bandage is the latest accessory and form of body art. If you do have a cut, at least you will have something stylish to cover it up.

Treat your minor cuts, scrapes and scratches with the incredible healing power of a designer bandage. And if a fancy bandage isn't enough to dry up your tears, how about a FREE PRIZE!

Price: $4.95

USB Mix Tape

Sat, 09 Oct 2010 18:20:02 +0100

USB Mix Tape

Before the days of digital music we made compilation cassettes to share our favorite tunes. Recreate the magic with the Mix Tape USB retro gift pack.

Remember the days before MP3 players? If you do, then you probably made compilations of all your favorite music, to share with your friends and loved ones, on good old fashioned blank cassette tapes. If you miss making mix tapes this product will inspire you again!

Store your own mix on the USB stick by plugging into your PC or Mac, then adding MP3 or any other files. Stores up to 1 hour of high quality digital music, the same amount as you get on a C60 cassette tape. Perfect for creating your own unique compilation. When you have 60 minutes you have to think carefully about what you are going to put on there! Write your own title, messages and play list all over the retro gift pack.

Price: $19.95 http://www.merlinsbox.com/

hal 9000 decal: turn your macbook into a murderous machine

Sat, 09 Oct 2010 18:09:18 +0100

hal 9000 decal: turn your macbook into a murderous machine: "

MacBooks already have a distinctive Apple logo, but some smart people are doing some really great decals that will make you pause and wonder if you should finally give them a go. The HAL 9000 decal is pretty amazing. It not just reminds me of 2001: Space Odyssey, but also of the Cylons from Battlestar Galactica.

This great decal will change the color of your Apple logo to a nice evil red. It’s available for $15 from Expendable Decals. What do you guys think? Cylons or HAL?

[via geek-gadgets]

Bookends 11.0.9

Sat, 09 Oct 2010 17:55:30 +0100

Bookends 11.0.9:

About Bookends
A full featured and cost-effective bibliography/reference and information management system for students and professionals. Access the power of Bookends directly from Mellel, Nisus Writer Pro, or MS Word (including Word 2011): Bookends allows you to scan your existing word processor files and automatically generate finished manuscripts with properly formatted bibliographies. You can also scan Apple Pages ‘08 or ‘09 and OpenOffice 3 files, or RTF files saved from any word processor.

Bookends allows you to share your references over the Internet with anyone, on any platform! And with Bookends you can directly search and import references from numerous sources:

- EndNote
- PubMed
- Web of Science
- JSTOR
- Google Scholar
- Amazon
- the Library of Congress
- and hundreds of other online sources.

(Via Downloads - Mac OS X - Productivity Tools.)

Test of the Mac Pro 12 Cores

Sat, 09 Oct 2010 17:53:33 +0100

Test of the Mac Pro 12 Cores:

ArsTechnica published a in depth test of the Mac Pro 12 cores clocked at 2.66 GHz, and compared it with the previous high end model from 2009 (8 cores at 2.66 GHz). As you can imagine, this computer has a huge raw power thanks to its 24 logical cores. But at the end, beside for some specific applications, it does not deliver much more than the 2009 models:

With other application such as Final Cut, the difference is hardly noticeable. We will not deny the potential of Mac Pro 2010 models, but users might have a better deal in purchasing a Mac Pro 2009 from the RefurbStore and add a Radeon HD5870. The other good deal for price/performance, is the Mac Pro 2010 single CPU 6 cores clocked at 3.33 GHz.

(Via HardMac.com.)

Pogo Stylus updated for iPhone 4 with Travel Clip

Sat, 09 Oct 2010 17:48:56 +0100

Pogo Stylus updated for iPhone 4 with Travel Clip: "Ten One Design, makers of the popular Pogo Stylus for iOS devices, are taking pre-orders for a new version designed for the iPhone 4. Available in Black, Hot Pink, Burnt Orange and Cactus, the styluses offer greater accuracy than a finger, while the black Travel Clip that keeps the stylus in place doubles as a stand in both landscape and portrait mode....
(Via MacNN | The Macintosh News Network.)

Monster illustrations from Ultraman sonosheet book

Sat, 09 Oct 2010 17:41:05 +0100

These Ultra Monster illustrations by Toshio Okazaki are from 'The Return of Ultraman' sonosheet book (Volume 1) published by Elm in 1971.

Gesura, MAT Sub [+]

Jirass, MAT Arrow 1, MAT Arrow 2 [+]

Gorbagos, Suflan, Kiyla [+]

Mognezun, Kemular [+]

Dorako, Ultraman, Gomora [+]

Alien Mephilas, Hydra, Jamila, Ultraman [+]

[More: Ultra Monster paintings by Toshio Okazaki]

(Via Pink Tentacle.)

Vintage Ads from Fictional Futures

Sat, 09 Oct 2010 17:34:03 +0100

Writer Mark Rayner holds contests in which he invited people to create vintage ads from the 1940s-1960s. Except that these ads would be from future environments depicted in science fiction. Rayner has now held a new contest with the same theme. You can view the winners at his site: http://markarayner.com/vintageads/ Extract below.....

Details on how to enter are below. See the finalists from the first contest here.

Finalists

Okay, I'll admit it, I wimped out. Getting the list down to five was impossible, and to be honest, six was brutal too, but I just can't afford to give away so many copies of Marvellous Hairy. (Available on Kindle for $1.99, Amazon for $10.99.) Thanks to everyone for their creativity and willingness to play!

Vote using the poll to the right -- you have until October 11th!


Title: Yes We Can Based on: The Wizard of Oz Submitted by: Webmonkees		Title: Suk Doctors Based on: Dune (The Suk Doctors) Submitted by: Morgan H.


Title: The Exciting New Soylent Bar Based on: Soylent Green Submitted by: Javier B.		Title: Enjoy Slurm Based on: Futurama Submitted by: Olav S.

Title: Gonzo Based on: Fear & Loathing In Las Vegas Submitted by: David H.		Title: Eloi - The Other White Meat Based on: The Time Machine Submitted by: Randy S.

The Contest Gallery


Sample: based on The Road Get the T-shirt!		Sample: based on The Postman


Title: Yes We Can Based on: The Wizard of Oz Submitted by: Webmonkees		Title: The Korova Milkbar Based on: A Clockwork Orange Submitted by: Mike W.


Title: Delos - The Safer Vacation Based on: Westworld/Futureworld Submitted by: Andy H.		Title: The Portal Gun Based on: Portal (video game) Submitted by: Vegard S. (Norway)


Title: Prophetic computing Based on: Nostradamus Submitted by: Brian W.		Title: Why Not? Based on: Devil Woman (song) Submitted by: Ingvild D. (Norway)


Title: Suk Doctors Based on: Dune (The Suk Doctors -wiki) Submitted by: Morgan H.		Title: The Exciting New Soylent Bar Based on: Soylent Green Submitted by: Javier B.

Title: Lady GaGalaxy Based on: ? Submitted by: Mike Hayward		Title: Eloi - The Other White Meat Based on: The Time Machine Submitted by: Randy S.


Title: Modern New Houses Based on: Lord of the Rings Submitted by: Jonas M. (Norway)		Title: Noob Tube Based on: Modern Warfare (video game) Submitted by: Martin L. (Norway)

Title: Sears Wishbook, 1975 Based on: Dr. Who Submitted by: Webmonkees		Title: Enjoy Slurm Based on: Futurama Submitted by: Olav S.

Title: Gonzo Based on: Fear & Loathing In Las Vegas Submitted by: David H.		Title: Broomstick Based on: Harry Potter Submitted by: Susan L.

Title: RealCrave: the small difference between mecha and glamour girl Based on: Artificial Intelligence (AI) Submitted by: Raleigh M.		Title: Pan-Galactic Gargle Blaster Based on: Hitchhiker's Guide to the Galaxy Submitted by: Darron M.

Title: Don't do it. Based on: Logan's Run Submitted by: Dave S. (Twitter)

Title: Satellite of Love Based on: mst3k Submitted by: Jeff H.		Title: Power-Loader Based on: Aliens Submitted by: Daniel M.

Link via Nerdcore

(Via Neatorama.)

15 Cool Stickers for your iPhone

Sat, 09 Oct 2010 17:28:46 +0100

Unique and clever vinyl stickers that will spice up the look of your iPhone.

Cassette Tape iPhone Sticker

Creative vinyl skin will make your iPhone look like a cassette tape. [link]

Game Boy iPhone Sticker

iPhone 4 decal inspired by Game Boy game system from Nintendo. [link]

R2-D2 iPhone Sticker

Cool sticker designed for the fans of R2-D2 droid from Star Wars. [link]

SMS iPhone Stickers

Booklet of stickers with ego-stroking text messages printed on them. [link]

Han Solo iPhone Sticker

Creative vinyl sticker inspired by Han Solo frozen in carbonate. [link]

Rainbow Apple Logo iPhone Sticker

Cool vinyl sticker inspired by the rainbow “bitten” Apple logo. [link]

Fake Call iPhone Stickers

iPhone 4 stickers make it look like famous people are calling you. [link]

End Call iPhone 4 Sticker

Creative sticker will help you solve iPhone 4’s antenna problems. [link]

Leica M9 iPhone Sticker

Vinyl decal will make your iPhone 4 look like a Leica camera. [link]

NES Controller iPhone Sticker

Decorate your iPhone with a sticker inspired by an NES controller. [link]

Homer Simpson iPhone Sticker

iPhone decal made of high quality, self-adhesive transparent vinyl. [link]

Japanese Cityscapes With Monster-Sized Wildlife

Sat, 09 Oct 2010 17:22:52 +0100

Japanese Cityscapes With Monster-Sized Wildlife: "

Artist Shuichi Nakano's 'Searching for Paradise' paintings depict Godzilla-sized animals towering over the urban sprawl of Japan.

Low cost spectroscope

Sat, 09 Oct 2010 16:54:47 +0100

Cell phones and spectroscopy in the classroom

CHAMPAIGN, Ill. — University of Illinois chemistry professor Alexander Scheeline wants to see high school students using their cell phones in class. Not for texting or surfing the Web, but as an analytical chemistry instrument.

Scheeline developed a method using a few basic, inexpensive supplies and a digital camera to build a spectrometer, an important basic chemistry instrument. Spectrophotometry is one of the most widely used means for identifying and quantifying materials in both physical and biological sciences.

“If we want to measure the amount of protein in meat, or water in grain, or iron in blood, it’s done by spectrophotometry,” Scheeline said.

Many schools have a very limited budget for instruments and supplies, making spectrometers cost-prohibitive for science classrooms. Even when a device is available, students fail to learn the analytical chemistry principles inherent in the instrument because most commercially available devices are enclosed boxes. Students simply insert samples and record the numbers the box outputs without learning the context or thinking critically about the process.

“Science is basically about using your senses to see things — it’s just that we’ve got so much technology that now it’s all hidden,” Scheeline said.

“The student gets the impression that a measurement is something that goes on inside a box and it’s completely inaccessible, not understandable — the purview of expert engineers,” he said. “That’s not what you want them to learn. In order to get across the idea, ‘I can do it, and I can see it, and I can understand it,’ they’ve go to build the instrument themselves. “

So Scheeline set out to build a basic spectrometer that was not only simple and inexpensive but also open so that students could see its workings and play with its components, encouraging critical-thinking and problem-solving skills. It wouldn’t have to be the most sensitive or accurate instrument — in fact, he hoped that obvious shortcomings of the device would reinforce students’ understanding of its workings.

“If you’re trying to teach someone an instrument’s limitations, it’s a lot easier to teach them when they’re blatant than when they’re subtle. Everything goes wrong out in the open,” he said.

In a spectrometer, white light shines through a sample solution. The solution absorbs certain wavelengths of light. A diffraction grating then spreads the light into its color spectrum like a prism. Analyzing that spectrum can tell chemists about the properties of the sample.

For a light source, Scheeline used a single light-emitting diode (LED) powered by a 3-volt battery, the kind used in key fobs to remotely unlock a car. Diffraction gratings and cuvettes, the small, clear repositories to hold sample solutions, are readily available from scientific supply companies for a few cents each. The entire setup cost less than $3. The limiting factor seemed to be in the light sensor, or photodetector, to capture the spectrum for analysis.

“All of a sudden this light bulb went off in my head: a photodetector that everybody already has! Almost everybody has a cell phone, and almost all phones have a camera,” Scheeline said. “I realized, if you can get the picture into the computer, it’s only software that keeps you from building a cheap spectrophotometer.”

To remove that obstacle, he wrote a software program to analyze spectra captured in JPEG photo files and made it freely accessible online, along with its source code and instructions to students and teachers for assembling and using the cell-phone spectrometer. It can be accessed through the Analytical Sciences Digital Library.

Scheeline has used his cell-phone spectrometers in several classroom settings. His first classroom trial was with students in Hanoi, Vietnam, as part of a 2009 exchange teaching program Scheeline and several other U. of I. chemistry professors participated in. Although the students had no prior instrumentation experience, they greeted the cell-phone spectrometers with enthusiasm.

In the United States, Scheeline used cell-phone spectrometers in an Atlanta high school science program in the summers of 2009 and 2010. By the end of the 45-minute class, Scheeline was delighted to find students grasping chemistry concepts that seemed to elude students in similar programs using only textbooks. For example, one student inquired about the camera’s sensitivity to light in the room and how that might affect its ability to read the spectrum.

“And I said, ‘You’ve discovered a problem inherent in all spectrometers: stray light.’ I have been struggling ever since I started teaching to get across to university students the concept of stray light and what a problem it is, and here was a high school kid who picked it right up because it was in front of her face!” Scheeline said.

Scheeline has also shared his low-cost instrument with those most likely to benefit: high school teachers. Teachers participating in the U. of I. EnLiST program, a two-week summer workshop for high school chemistry and physics teachers in Illinois, built and played with cell-phone spectrometers during the 2009 and 2010 sessions. Those teachers now bring their experience — and assembly instructions — to their classrooms.

Scheeline wrote a detailed account of the cell-phone spectrometer and its potential for chemistry education in an article published in the journal Applied Spectroscopy. He hopes that the free availability of the educational modules and software source code will inspire programmers to develop smart-phone applications so that the analyses can be performed in-phone, eliminating the need to transfer photo files to a computer and turning cell phones into invaluable classroom tools.

“The potential is here to make analytical chemistry a subject for the masses rather than something that is only done by specialists,” Scheeline said. “There’s no doubt that getting the cost of equipment down to the point where more people can afford them in the education system is a boon for everybody.”

Editor’s note: To contact Alexander Scheeline, call 217-333-2999; e-mail [email protected]">[email protected].

Welwitschia Mirabilis

Sat, 09 Oct 2010 01:05:37 +0100

Namibia's plant Welwitschia Mirabilis can truly claim to be one of a kind. From: http://www.darkroastedblend.com/2007/02/strangest-plant-on-earth.html

(images credit: Friedrich A. Llohmuller)

(images via)

Welwitschia plant consists of only two leaves and a sturdy stem with roots. That's all! Two leaves continue to grow until they resemble the shaggy mane of some sci-fi alien. The stem thickens, rather than gains in height , and can grow to be almost 2 meters high and 8 meters wide. Their estimated lifespan is 400 to 1500 years.

(image credit: Botanik-Fotos.de, photo by Karlheinz Knoch)

(image credit: Peter v. Sengbusch)

(image credit: Botanik-Fotos.de)

The sexes are separate, i.e. male plants and female plants.
Male & Female Cones:

Female plant at beginning of reproductive season. Craterlike apical part of trunk about 17 cm wide. (Drawn by M.Steyn):

Let's see the close-up of its growing stages. It all starts with two leaves:
(Photos by Karlheinz Knoch)

seeds:

(images credit: Botanik-Fotos.de, photo by Karlheinz Knoch)

Welwitschia is thought to be a relic from the Jurassic period when such plants (called "gymnosperms") dominated the world's flora. Its ancestor got trapped in an arid environment, and all its close relatives long since disappeared.

The plant is said to be very tasty either raw or baked in hot ashes, and this is how it got its other name, onyanga, which means onion of the desert.
Also some like to wear its unique shape as a jewelry:

Namibia's Desert is home to other strange growths

French photographer Christophe Courteau captures the esoteric beauty of the desert and its sparse inhabitants:

Desert Edelweis:

Sources and further reading: Platz Africa, Peter v. Sengbusch

Carnivorous Plants

Sat, 09 Oct 2010 00:42:03 +0100

(images via)

For all you geeks out there – and, yes, we know who you are – it's commonly thought that the first depiction of a salad making a meal out of a man comes from Dr. Carl Liche, writing in 1881. J.W. Buel echoed the idea in his Land and Sea in 1887 (see below). Unluckily for Liche and Buel they've been since exposed as 'imaginative' instead of 'accurate.' ("The Day of the Triffids" by John Wyndham also deserves a mention). Hate to disappoint but true man-eating plants are a total myth:

(image via, click to enlarge)

But that doesn't mean that the next time you sit down to feast on a supposedly defenseless potato there aren't other forms of plant life that are also having a tasty meal of, while not us humans, then most definitely other animals – and sometimes rather large animals.

(images credit: Barry Rice, 2)

Venus Entrapment

The poster-plant for botanical carnivores has got to be the legendary Venus Flytrap. A resident of swamps and bogs, the flytrap has evolved a dramatic solution to its lack-of-nutrient diet: it catches flies – and pretty much anything big enough to get caught.

(left via; right image credit: Karoshi)

What's amazing about this plant is its mechanism. Anything that happens to stumble between the two halves of its unique mechanism will find itself in caught in a quickly-snapping-shut botanical bear trap. What's even worse is that after being caught the Venus then fuses those leaves together, turning them into a kind of stomach to digest its prey. What's extra-fascinating is that the trap has two triggers, and that both of them have to be tripped for the leaves to snap shut, to avoid misfires.

(image via)

Alluring Perfume in a Deadly Pitcher

While the flytrap looks like something out of a monster movie it rarely grows to any really impressive size – unless you happen to be a housefly. But one carnivorous plant that really is impressive, and recently discovered, is what's called a passive hunter. Instead of using snapping traps its family instead has evolved fluid-filled pitfalls lined with very slippery sides, and baited with a very alluring perfume.

(right: Sarracenia hybrid - images credit: Helene Schmitz, National Geographic)

Pitcher plants come in a wide variety of shapes, types, and sizes – including a special one native to the Philippines. Most pitchers feast on bugs and sometimes small lizards: pretty much whatever's unfortunate enough to get seduced by the plant's alluring smells and is small enough to fit down its leafy throat. While its mechanism is similar to its smaller kin, nepenthes attenboroughii (named after journalist and TV presenter David Attenborough), has traps that are large enough to catch not only bugs, lizards, and – what's more than a bit scary – rats (more info).

(images via 1, 2)

(image credit: Caroling)

(images credit: Shatalkin)

A Cobra Lily

"A pale green butterfly senses nectar and alights on a rare California pitcher plant. Also called a cobra lily for its bulbous head, forked tongue, and long tubular pitcher, it grows in mountainous parts of the West Coast and is an oddity among its kind. Although it traps prey in a manner similar to other pitcher plants, its leaves contain no digestive enzymes. Instead, it relies on symbiotic bacteria to turn captured insects into usable nutrients." (see the whole gallery).

(left: Cobra Lily; right: Nepenthes lowii - images credit: Helene Schmitz, National Geographic)

(image credit: Noah Elhardt)

Pretty, Pretty Sundew

Another device carnivorous plants use is to make its prey stick around long enough to be digested. The sundew, for instance, has leaves covered with dozens of tiny stalks, and each stalk is covered with very, very, very sticky stuff. When a bug happens to walk across these leaves it gets – you guessed it – very, very, very stuck. What's more, though, is that the plant then contracts, bringing more and more of those stalks into contact with its prey, completely trapping and then digesting it:

(images credit: Helene Schmitz, National Geographic)

(images via 1, 2)

Here is a great video depicting the "War between Carnivorous Plants and Herbivorous insects" - YouTube link.

(image credit: Olga Sytina)

Enter the Kudzilla!

But then there's the other, the monster, the beast, the chlorophyll creature that could – if any plant could be – considered a bona fide killer. Innocently imported to the US in 1876 from its native Japan, it was sold as a botanical miracle: ink, paper, jelly, tea, you name it and you could make it from this wonderful plant. But what no one could expect that this so-called marvel would have darker roots.

(image credit: MissyPrince)

(image credit: Patrick Walker)

Kudzu is its name and right now it covers – in some cases quite literally – a huge part of the Southeastern United States. While bamboo is a racehorse at two foot a day, Kudzu is hardly a slacker at covering half that distance in the same amount of time. In the South there are homes, cars, houses and entire communities that have been hungrily, potentially, covered – and subsequently strangled – by this ferociously determined plant.

(images via 1, 2, 3, 4)

(image credit: Kyle Telechan)

Sure, kudzu may not be carnivorous, but it's green infestation, it's emerald conquest, it's verdant domination is definitely worth a mention – and maybe a serious shudder of fear. Or, as they sometime say in the South: "A cow won't eat kudzu, but kudzu will definitely eat a cow."

Bacterial cell wall engineering

Fri, 08 Oct 2010 23:21:23 +0100

A team of Yale University scientists has engineered the cell wall of the Staphylococcus aureus bacteria, tricking it into incorporating foreign small molecules and embedding them within the cell wall.

The finding, described online in the journal ACS Chemical Biology this week, represents the first time scientists have engineered the cell wall of a pathogenic "Gram-positive" bacteria—organisms responsible not only for Staph infections but also pneumonia, strep throat and many others. The discovery could pave the way for new methods of combating the bacteria responsible for many of the most infectious diseases.

The team engineered one end of their small molecules to contain a peptide sequence that would be recognized by the bacteria. In Staphylococcus aureus, an enzyme called sortase A is responsible for attaching proteins to the cell wall.

"We sort of tricked the bacteria into incorporating something into its cell wall that it didn't actually make," said David Spiegel, a Yale chemist who led the study. "It's as if the cell thought the molecules were its own proteins rather than recognizing them as something foreign."

The scientists focused specifically on the cell wall because it contains many of the components the cell uses to relate to its environment, Spiegel said. "By being able to manipulate the cell wall, we can in theory perturb the bacteria's ability to interact with human tissues and host cells."

The team used three different small molecules in their experiment — including biotin, fluorescein and azide — but the technique could be used with other molecules, Spiegel said, as well as with other types of bacteria. Another advantage to the new technique is that the scientists did not have to first genetically modify the bacteria in any way in order for them to incorporate the small molecules, meaning the method should work on naturally occurring bacteria in the human body.

Staph infections, such as the drug-resistant MRSA, have plagued hospitals in recent years. More Americans die each year from Staphylococcus aureus infections alone than from HIV/AIDS, Parkinson's disease or emphysema.

Being able to engineer the cell walls of not only Staphylococcus aureus but a whole family of bacteria could have widespread use in combating these illnesses, Spiegel said, adding that any number of small molecules could be used with their technique. "For example, if we tag these bacteria with small fluorescent tracer molecules, we could watch the progression of disease in the human body in real time." The molecules could also be used to help recruit antibodies that occur naturally in the bloodstream, boosting the body's own immune response to diseases that tend to go undetected, such as HIV/AIDS or cancer.

"This technique has the potential to help illuminate basic biological processes as well as lead to novel therapeutics from some of the most common and deadly diseases affecting us today," Spiegel said.

Source : Yale University

(Via Biology News Net - Microbiology.)

Bacon inspired Gifts

Fri, 08 Oct 2010 23:18:41 +0100

Bacon Gift Wrap

Everything is better when it's wrapped in bacon! Two 20" x 30" sheets of quality wrapping paper decorated with mouth watering strips of bacon.

Bacon Platter

Bacon Wallet

Bacon Bandages

Sushi Decorative Tape

Sausage Decorative Tape

Gravy Fountain Joke Gift Box

Bacon Tuxedo Joke Gift Box

Musical Tie of the Month Club Joke Gift Box

Bacon Soap

Bacon Air Freshener

Bacon Placemat

Bacon Squeezins Water Bottle

Bacon Tuxedo Puzzle

Sunrise in Meatopia Puzzle

Bacteria are able to extend psuedo-legs and walk upright

Fri, 08 Oct 2010 22:49:40 +0100

Some microorganisms undergo a genetic change when they land on a solid surface. New research shows that these microbes cope with solid surfaces by standing upright, projecting tiny legs, and walking. The result are microbes that turn into what researchers call biofilms. A biofilm is much harder to eradicate than a simple microbe. Rather than just swim along, when the potentially deadly Pseudomonas aeruginosareaches a solid surface, it uses appendages called pili to stand upright and walk. This new posture is ideal for exploring surfaces, and makes it easier for them to detach and spread, enlarging the biofilm. P. aeruginosa biofilm infections are the leading killer in people with cystic fibrosis, and are incredibly resistant to antibiotics. By understanding how they move and spread, we have a better chance of stopping them, and other biofilm related problems, too. Research published in Science (Via io9.).

Japanese flower has the largest known genome

Fri, 08 Oct 2010 22:48:25 +0100

A rare flower known as Paris japonica has a genome 50 times bigger than humans'. With 149 billion base pairs of DNA, it's the biggest genome in the world, and stretched out end-to-end it would be taller than Big Ben. The flower has 19 billion more base pairs than the previous record holder, the marbled lungfish, whose 130 billion base pairs weigh in at 132.83 picograms. By genomic standards, that's still utterly massive. But having such a big genome isn't actually much of an advantage - because it takes so long to replicate such a massive genome, such organisms grow very slowly and have trouble coping with the mildest environmental pressures. (from io9.com, and the Botanical Journal of the Linnean Society)

Gibson Assembly Song

Fri, 08 Oct 2010 09:03:21 +0100

See a video by the Cambridge iGEM2010 team - extolling the benefits of using Dan Gibson's DNA assembly protocol.

DIYbio articles in Nature

Fri, 08 Oct 2010 08:56:46 +0100

Heidi Ledford. Garage biotech: Life hackers. Amateur hobbyists are creating home-brew molecular-biology labs, but can they ferment a revolution? Nature 467, 650-652 (2010) | doi:10.1038/467650a (http://www.nature.com/news/2010/101006/full/467650a.html)

Editorial. Garage biology: Amateur scientists who experiment at home should be welcomed by the professionals. Nature. Volume 467: p.634 (07 October 2010) doi:10.1038/467634a (http://www.nature.com/nature/journal/v467/n7316/full/467634a.html)

Gibson Assembly Song

Fri, 08 Oct 2010 08:43:31 +0100

University of Cambridge iGEM2010 team's video description of Dan Gibson's DNA assembly protocol - and tribute to its use in Synthetic Biology.

ChouChou Electric Butterfly

Wed, 06 Oct 2010 22:52:34 +0100

ChouChou Electric Butterfly

Realistic butterfly in a jar

Keeping a butterfly in a jar is a childhood memory we all share. Unfortunately real butterflies only last a day and we cannot preserve the sensation of watching their beauty time after time. Until now. TheChouChou is an amazingly realistic butterfly toy that will, yes, fly and move inside a jar when you tap on the lid.

Simple but mesmerizing, this award-winning creature dazzled visitors to the Tokyo Toy Show 2010 and is likely to become a bestseller on its release in November.

The ChouChou features:

Electric "butterfly" in jar
Responds to vibrations by flying and flapping wings
Colors: yellow, blue, pink
Power: AA x3

In Living Color: Bacterial Pigments as an Untapped Resource in the Classroom and Beyond

Wed, 06 Oct 2010 22:46:04 +0100

Charkoudian LK, Fitzgerald JT, Khosla C, Champlin A (2010) In Living Color: Bacterial Pigments as an Untapped Resource in the Classroom and Beyond. PLoS Biol 8(10)

Recent advances in the study of natural products made by bacteria have laid the foundation for engineering these molecules and for developing cost-effective ways to manufacture them. In our lab, we study a number of natural products that are synthesized by harmless soil bacteria of the Streptomyces genus. Whereas our primary interest in these molecules is due to their antibiotic properties, many of these natural products have distinct colors [1]. (The reasons for why Streptomyces make antibiotics or pigments remain mysterious.) This article is intended to make the case to the scientific and educational communities thatStreptomyces-derived natural products are an untapped source of useful biopigments. By sharing some of our own experiences in harnessing these pigments to create paint and paintings, we also hope to inspire others to explore the potential ofStreptomyces-derived pigments in art, industry, and perhaps most importantly, the classroom.

The pedagogical value of bacterial pigments is highlighted by the wide range of concepts and methods in chemistry, biology, and art that can be introduced to students in this context (see Box 1). Teachers can incorporate bacterial pigments into their lessons while introducing fundamental scientific principles ranging from the physics of color to the chemistry behind paints that fade in sunlight. Painting with living bacteria (Box 2) or extracting pigments from bacterial cultures (Box 3) provides a visual and kinesthetic activity to support key aspects of scientific investigations and methods learned in the classroom. Because the methods to do so are safe, inexpensive, and easily implementable in the everyday world, it is possible to use biopigments as a vehicle to introduce school children to science via art and vice versa. While many of these concepts and techniques are appropriate for the advanced high school or undergraduate classroom, even elementary school children can use bacterial paints prepared by their teacher to create art, an activity that may teach children at a young age that bacteria are a source of valuable materials rather than merely agents of disease.

Comprehensive analysis of CLE polypeptide signaling gene expression and over-expression ...

Wed, 06 Oct 2010 22:32:47 +0100

Comprehensive analysis of CLE polypeptide signaling gene expression and over-expression activity in Arabidopsis.: "Publication Date: 2010 Sep 30 PMID: 20884811
Authors: Jun, J. - Fiume, E. - Roeder, A. - Meng, L. - Sharma, V. K. - Osmont, K. S. - Baker, C. - Ha, C. M. - Meyerowitz, E. M. - Feldman, L. J. - Fletcher, J.
Journal: Plant Physiol

Intercellular signaling is essential for the coordination of growth and development in higher plants. Although hundreds of putative receptors have been identified in Arabidopsis thaliana, only a few families of extracellular signaling molecules have been discovered and their biological roles are largely unknown. To expand our insight into the developmental processes potentially regulated by ligand-mediated signal transduction pathways, we undertook a systematic expression analysis of the members of the Arabidopsis CLAVATA3/ESR-RELATED (CLE) small signaling polypeptide family. Using reporter constructs we show that the CLE genes have distinct and specific patterns of promoter activity. We find that each Arabidopsis tissue expresses at least one CLE gene, indicating that CLE-mediated signaling pathways are likely to play roles in many biological processes during the plant life cycle. Some CLE genes that are closely related in sequence have dissimilar expression profiles, yet in many tissues multiple CLE genes have overlapping patterns of promoter-driven reporter activity. This observation, plus the general absence of detectable morphological phenotypes in cle null mutants, suggests a high degree of functional redundancy exists among CLE gene family members. Our work establishes a community resource of CLE-related biological materials and provides a platform for understanding and ultimately manipulating many different plant signaling systems.

(Via Plant Physiology.)

Multifactorial determinants of protein expression in prokaryotic open reading frames.

Wed, 06 Oct 2010 22:31:48 +0100

Multifactorial determinants of protein expression in prokaryotic open reading frames.: "Publication Date: 2010 Oct 8 PMID: 20727358
Authors: Allert, M. - Cox, J. C. - Hellinga, H. W.
Journal: J Mol Biol

A quantitative description of the relationship between protein expression levels and open reading frame (ORF) nucleotide sequences is important for understanding natural systems, designing synthetic systems, and optimizing heterologous expression. Codon identity, mRNA secondary structure, and nucleotide composition within ORFs markedly influence expression levels. Bioinformatic analysis of ORF sequences in 816 bacterial genomes revealed that these features show distinct regional trends. To investigate their effects on protein expression, we designed 285 synthetic genes and determined corresponding expression levels in vitro using Escherichia coli extracts. We developed a mathematical function, parameterized using this synthetic gene data set, which enables computation of protein expression levels from ORF nucleotide sequences. In addition to its practical application in the design of heterologous expression systems, this equation provides mechanistic insight into the factors that control translation efficiency. We found that expression is strongly dependent on the presence of high AU content and low secondary structure in the ORF 5' region. Choice of high-frequency codons contributes to a lesser extent. The 3' terminal AU content makes modest, but detectable contributions. We present a model for the effect of these factors on the three phases of ribosomal function: initiation, elongation, and termination.

(Via Journal of Molecular Biology.)

Cell Surface- and Rho GTPase-Based Auxin Signaling Controls Cellular Interdigitation in Arabidopsis.

Wed, 06 Oct 2010 22:27:55 +0100

Cell Surface- and Rho GTPase-Based Auxin Signaling Controls Cellular Interdigitation in Arabidopsis.: "Publication Date: 2010 Oct 1 PMID: 20887895
Authors: Xu, T. - Wen, M. - Nagawa, S. - Fu, Y. - Chen, J. G. - Wu, M. J. - Perrot-Rechenmann, C. - Friml, J. - Jones, A. M. - Yang, Z.
Journal: Cell

Auxin is a multifunctional hormone essential for plant development and pattern formation. A nuclear auxin-signaling system controlling auxin-induced gene expression is well established, but cytoplasmic auxin signaling, as in its coordination of cell polarization, is unexplored. We found a cytoplasmic auxin-signaling mechanism that modulates the interdigitated growth of Arabidopsis leaf epidermal pavement cells (PCs), which develop interdigitated lobes and indentations to form a puzzle-piece shape in a two-dimensional plane. PC interdigitation is compromised in leaves deficient in either auxin biosynthesis or its export mediated by PINFORMED 1 localized at the lobe tip. Auxin coordinately activates two Rho GTPases, ROP2 and ROP6, which promote the formation of complementary lobes and indentations, respectively. Activation of these ROPs by auxin occurs within 30 s and depends on AUXIN-BINDING PROTEIN 1. These findings reveal Rho GTPase-based auxin-signaling mechanisms, which modulate the spatial coordination of cell expansion across a field of cells.

(Via Cell.)

www.synbio.org.uk site news

Positions at Microsoft Research, Cambridge UK

Positions at Microsoft Research, Cambridge UK

http://research.microsoft.com/biology/jobs.aspx

iGEM2011 recruitment

Manfrotto pocket series tripods

Make: Online : Modular stackable Arduino enclosure

Modular stackable Arduino enclosure

Wunderlist for iPhone Is an Elegant, Syncing To-Do Manager

Access the desktop version of Google Docs on your iPad

Access the desktop version of Google Docs on your iPad

Dynamics in the mixed microbial concourse.

MicroRNAs prevent precocious gene expression and enable pattern formation during plant ...

Particular Significance of SRD2-Dependent snRNA Accumulation in Polarized Pattern Generation ...

Rapid blue-light-mediated induction of protein interactions in living cells.

Making classic frequency counters into Nixie clocks

MicroVision’s second-generation SHOWWX+ laser pico projector

Xi3 modular computer to make global debut at CES 2011

Zoom Q3HD Handy Video Recorder released

Multi-touch Desk with Curved Surface

Glif tripod mount and stand for the iPhone 4

The 4x4x4 LED Cube Using an Arduino

Researchers develop genuine 3D camera

Rob's laser microscope build

Transparent Specimens

New in the Maker Shed: Netduino Plus

Mini-Vise

Make It Last Build Series: The robot plants are in bloom!

Bench Cookies

Nebulophone – A Miniature Arduino Powered Synth

Matrox updates dual- and triple-head video breakout boxes

How to Travel Around the World for $418

From http://gizmodo.com/5710654/how-to-fly-35000-miles-visit-4-continents-9-countries-and-15-cities-for-418

My itinerary

The beauty of travel hacking

Keeping an eye on special offers

How to Use a OneWorld Award

The funky rules of travel hacking

How to build your award travel flight

How I am able to afford 6 months of adventure travel

Why this trip scares me

The 50 Hottest Companies in Bioenergy for 2010-11 | Renewable Energy News Article

Microbial Cell Factories: Engineering the cell surface display of cohesins for assembly of ...

35,000 plant specimens gathered over the past 200 years remain unclassified

Miniature Food Sculptures

Latex Hippo Mask - Archie McPhee & Co.

Latex Hippo Mask

Brain Freeze Ice Cube Tray - Archie McPhee & Co.

Brain Freeze Ice Cube Tray

moss tables by ayodhya

Liverworts and Fungi

Making this new discovery

A window into the past

Scientific Research & Data

Presidential Commission reports on Synthetic Biology

Hard Candy Cases offers Candy stylus and pen for iPad

Apple releases XCode 4 Preview 5 to developers

thetrainline.com update app allows travellers to buy tickets via iPhone

Geneious 5.3.0 - Sequence analysis software for all molecular biologists. (Free)

Genomic comparison of ocean microbes reveals East-West divide in populations

Algal Fuels: Just around the Corner or 10 Years Away?

Lux Research: Innovation Will Grow Biofuels Market

Gold Nanoparticles Could Turn Trees into Streetlights

Potechi no Te Popcorn no Te Set - USD 29

Awesome Vintage Tech Ads | UNEASYsilence

Awesome Vintage Tech Ads From (﻿http://uneasysilence.com/archive/2010/10/15478/) and they just posted 116 More Vintage Ads!

Original Apple Computer Up For Sale

USB Battleship: A Visual Weight for Chaotic USB Cables

Cambridge presentation 2010

iGEM2010 Jamboree

Improved BioBrick components for bioluminescence

iGEM2010 Jamboree results

Cambridge team at the iGEM2010 Jamboree

Commentary for Daisy Ginsberg's work

Fresh as a daisy: Alexandra Daisy Ginsberg

Paola Antonelli1

University of Cambridge team wins iGEM synthetic biology competition

'Building block' biology

iGEM

Student activism

Awesome Vintage Tech Ads

From (http://uneasysilence.com/archive/2010/10/15478/) and they just posted 116 More Vintage Ads!

Paola Antonelli¹

1. Purple Haze Carrots

PaperPro Makes “Quite Possibly the Best Staplers Ever”

Casio Prizm Calculator Plots Equations Onto Photographs