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  • August 29, 2012
  • 10:53 PM
  • 357 views

What are we really recycling?

by Cath in Basal Science (BS) Clarified

Having grown up with reduce, reuse, recycle campaigns (Tweety’s Global Patrol circa 1990), recycling is part of my daily routine. In fact, I’ve even spent time at a Japanese university lab [...]... Read more »

Reck BK, & Graedel TE. (2012) Challenges in metal recycling. Science (New York, N.Y.), 337(6095), 690-5. PMID: 22879508  

  • August 29, 2012
  • 05:30 PM
  • 593 views

how to weave machinery into biology

by Greg Fish in weird things

As we’re starting to test artificially grown organs, scientists are wondering how to make sure that their methods result in viable tissues. One of the first steps was to take organ growth into three dimensions, letting the cells grow on a scaffold and self-organize into the right muscles, valves, and other soft tissue. Usually these scaffolds are derived from existing organs purified of all their old cells and many are designed to break down into [...]... Read more »

Bozhi Tian,, Jia Liu,, Tal Dvir,, Lihua Jin,, Jonathan H. Tsui,, Quan Qing,, Zhigang Suo,, Robert Langer,, Daniel S. Kohane,, & Charles M. Lieber. (2012) Macroporous nanowire nanoelectronic scaffolds for synthetic tissues. Nature Materials. DOI: 10.1038/nmat3404  

  • August 29, 2012
  • 09:08 AM
  • 1,042 views

Video Tip of the Week: GenoCAD for Synthetic Biology

by Mary in OpenHelix

The field of synthetic biology has been simmering for quite a while. It occasionally takes a big leap, such as when Venter’s team published about their work on M. genitalium, and it took a big leap recently with the paper about modeling a lot of the cellular processes in a simple cell that I talked [...]... Read more »

  • August 28, 2012
  • 02:20 PM
  • 1,136 views

How does an ant colony coordinate its behaviour?

by sedeer in Inspiring Science

A recent study looking at how colonies of ants regulate their foraging behaviour has caused a bit of a buzz online. A …Continue reading »... Read more »

  • August 27, 2012
  • 02:24 PM
  • 811 views

Developing New Astro Surgery Tools for NASA Deep Space Missions

by Perikis Livas in Tracing Knowledge

A team of biomedical engineering researchers from Carnegie Mellon University and the University of Louisville are developing surgical tools that could be used for future expeditionary spaceflights to the moon, an asteroid or Mars.

“In deep space, surgical procedures will be severely complicated by absence of gravity, where it becomes difficult to prevent cabin contamination from blood and body fluids,” said James Antaki, a professor of biomedical engineering at CMU.... Read more »

Carnegie Mellon University. (2012) Press Release: Carnegie Mellon University Biomedical Engineers Lead Collaborative Team Developing New Astro Surgery Tools for NASA Deep Space Missions. Press Release: Carnegie Mellon University. info:/

  • August 26, 2012
  • 02:44 PM
  • 628 views

The Logistics of Scientific Growth in the 21st Century

by caseybergman in I wish you'd made me angry earlier

Over the last few months, I’ve noticed an growing number of reports about declining opportunities and increasing pressure for early stage academic researchers (Ph.D. students, post-docs and junior faculty). For example, the Washington Post published an article in early July about trends in the U.S. scientific job market entitled “U.S. pushes for more scientists, but [...]... Read more »

  • August 22, 2012
  • 06:45 PM
  • 802 views

Sensor detects glucose in saliva and tears for diabetes testing

by Perikis Livas in Tracing Knowledge

Researchers have created a new type of biosensor that can detect minute concentrations of glucose in saliva, tears and urine and might be manufactured at low cost because it does not require many processing steps to produce.... Read more »

Emil Venere. (2012) Sensor detects glucose in saliva and tears for diabetes testing. Purdue University News. info:/

  • August 22, 2012
  • 10:43 AM
  • 559 views

Video Tip of the Week: G-nome Surfer for table-top genome browsing

by Mary in OpenHelix

The other day a tweet came over my “genome” search column that intrigued me: RT @oshaer: Our paper on a tabletop interface for collaborative exploration of genomic data is finally available online: http://t.co/VQMD67wi Tabletop interface? Wha? Ok–I had to check this out. And, in fact, this group has software that will let you explore eukaryotic [...]... Read more »

Shaer O., Strait M., Valdes C., Wang H., Feng T., Lintz M., Ferreirae M., Grote C., Tempel K., & Liu S. (2012) The design, development, and deployment of a tabletop interface for collaborative exploration of genomic data. International Journal of Human-Computer Studies, 70(10), 764. DOI: 10.1016/j.ijhcs.2012.05.003  

  • August 19, 2012
  • 12:29 PM
  • 1,055 views

How to Build a Neuron: Step 1

by TheCellularScale in The Cellular Scale

There are many reasons to try to build a neuron, but fully building a model neuron is an extensive process with many steps.  Today we will discuss the very first step in the neuron-building process: determining the activity and  shape of the neuron. Biocytin filled cortical neurons (source)To determine the shape of neuron, you have to stain it somehow.  There are several ways to do this, but we will focus on the biocytin filling method. To determine the activity of a neuron, you have to use electrophysiology to record its electrical activity. The biocytin filling method makes use of the same patch clamp electrode to record the electrical activity of the neuron and to fill it with the biocytin molecule that can be later dyed.  So this method is perfect for building a neuron because with it you can correlate the shape of the neuron directly with its activity patterns.  Neural activity correlated with neural morphology (source)A recent Nature Protocols paper by Marx et al. (2012) provides step by step details for how to fill and dye a neuron using the biocytin method.  The basic biocytin staining protocol is as follows:1. make brain slices2. fill the neuron with biocytin while recording its electrical activity3. fix the brain slice in paraformaldehyde4. quench the endogenous peroxidase5. connect the biocytin to avidin (using the vectastain ABC kit)6. colorize the avidin (using DAB and nickel)7. mount the slices on gelatin subbed slides8. dehydrate the slices SLOWLY through very small steps of ethanol concentration9. clear with xylene and coverslipMarx et al. provide some excellent specifics in the paper that make the whole process understandable and more importantly, doable. They even have a troubleshooting section which explains what might have gone wrong under several conditions.Marx et al., 2012 Figure 2 One of their best tips in the paper is to dehydrate the slices very slowly.  They show that when you dehydrate the tissue quickly, you get a cork-screw artifact (A) that is not physiologically meaningful, but when you dehydrate slowly, you get a more accurate morphology.  So there you have it, Step 1 of neuron building.  Step 2 will be coming soon. © TheCellularScaleMarx M, Günter RH, Hucko W, Radnikow G, & Feldmeyer D (2012). Improved biocytin labeling and neuronal 3D reconstruction. Nature protocols, 7 (2), 394-407 PMID: 22301777... Read more »

Marx M, Günter RH, Hucko W, Radnikow G, & Feldmeyer D. (2012) Improved biocytin labeling and neuronal 3D reconstruction. Nature protocols, 7(2), 394-407. PMID: 22301777  

  • August 17, 2012
  • 06:20 AM
  • 735 views

What is the collective noun for a group of Systems Biologists?

by Duncan Hull in O'Really?

What happened was, I was looking for a Creatively Commons licensed picture of Pedro Mendes to upload to commons.wikimedia.org. That’s not the footballing Pedro Mendes who played for Rangers, Spurs, Pompey and Porto but the systems biologist Pedro Mendes who plays for Virginia Tech and Manchester. Thankfully, another systems biologist, Michael Hucka kindly pointed to his impressive collection of pictures, taken at various events over the years which include some shots of Pedro. Looking at these pictures made me idly wonder: What is the collective noun for a group of systems biologists?
Systems biology is the study networks of various kinds [2,3] so it’s ripe for a collective noun, and there were several suggested on twitter. Since twitter has recently developed a nasty habit of disappearing tweets, here is a collection gathered and preserved for posterity from the twitterome...... Read more »

Lander Arthur D. (2010) The edges of understanding. BMC Biology, 8(1). DOI: 10.1186/1741-7007-8-40  

Kitano Hiroaki. (2002) Systems Biology: A Brief Overview. Science, 295(5560), 1664. DOI: 10.1126/science.1069492  

Ideker Trey, Galitski Timothy, & Hood Leroy. (2001) Systems Biology: A new approach to decoding life . Annual Review of Genomics and Human Genetics, 2(1), 372. DOI: 10.1146/annurev.genom.2.1.343  

  • August 16, 2012
  • 03:30 PM
  • 434 views

Studying the Effects of Confinement on Cell Division

by Hector Munoz in Microfluidic Future

On Microfluidic Future I like reviewing advancements in therapeutic or diagnostic devices because I’m really drawn to those areas of research. Every once in a while, however, I take interest in research for the sake for knowledge, like the Root Chip. I recently came across an article from Dino Di Carlo of UCLA that describes a microfluidic device used to study cancer cells. The article, “Increased Asymmetric and Multi-Daughter Cell Division in Mechanically Confined Microenvironments” appeared in PLoS ONE, which is an open access journal (very cool!).... Read more »

Henry Tat Kwong Tse, Westbrook McConnell Weaver, & Dino Di Carlo. (2012) Increased Asymmetric and Multi-Daughter Cell Division in Mechanically Confined Microenvironments. PLoS ONE, 7(6). info:/

  • August 15, 2012
  • 09:15 PM
  • 1,357 views

LMAYQ: Can Odor be recorded?

by TheCellularScale in The Cellular Scale

Let Me Answer Your Questions: part 2, in which I answer your very important questions via google search terms. Part 1 and all subsequent LMAYQ posts will be archived in the LMAYQ index.by LikariousSo let's get to it, what fascinating questions are you asking google? 1. "Can odor be recorded?"  This likely brought someone to my post "You can't trust your receptors:smell" in which I discuss the EOG (electrolfactogram) where you can record the electrical activity of a smell receptor while certain smells are presented.  But it does not answer the question of whether a smell itself can be recorded.So I looked into it a little bit and surprisingly, the answer is yes! Nakamoto and others have created an "odor recorder" Nakamoto 2005 figure 1Unlike visual recording, which only need red, green, and blue to make essentially all the colors, odor recording requires a few more components. For example, the authors created an apple smell using 8 components. I would love to say that this odor recorder is going to appear in every living room and plug into the TV so that restaurant and perfume marketing can be truly effective, I just don't see the demand being strong enough to make it worth mass producing. Though, I think it would be pretty amazing.  I also had doubts as to whether the odor recorder could accurately transmit the scent of a really nice perfume which is not static, but develops over time. But The 2005 Nakamoto paper shows that they can actually record the changes of an odor over time! While there is always the fact that a perfume reacts differently with every one's skin, the odor recorder actually seems like a promising device and might find a market in die hard perfume fans. or..."odor recorder prevents murder"The quest to permanently record the scent of a woman drives a man to murder in the mediocre movie "Perfume: the Story of a Murderer."  If only he was in possession of an odor recorder.© TheCellularScaleNakamoto T (2005). Study of odor recorder for dynamical change of odor. Chemical senses, 30 Suppl 1 PMID: 15738143... Read more »

  • August 15, 2012
  • 05:05 AM
  • 838 views

Geoengineering: taking control of our planet’s climate?

by Perikis Livas in Tracing Knowledge

Concerns about the likely consequences of continuing climate change have greatly increased interest in geoengineering – whether the Earth’s climate could be deliberately modified to counteract global warming due to anthropogenic greenhouse gas emissions. In November 2010, the Royal Society hosted a Discussion Meeting: ‘Geoengineering: taking control of our planet’s climate’ that critically assessed many of the schemes currently being considered. The meeting also took stock of the relationship of geoengineering to conventional greenhouse gas mitigation as well as how geoengineering is perceived by the public. Papers in this issue directly reflect the outcome of that Discussion Meeting.... Read more »

Andy Ridgwell, Chris Freeman, & Richard Lampitt. (2012) Geoengineering: taking control of our planet's climate?. Phil. Trans. R. Soc. A 13 , 370 (1974), 4163-4165. DOI: 10.1098  

  • August 10, 2012
  • 12:34 PM
  • 760 views

Promoting incompetence

by sedeer in Inspiring Science

From Dilbert’s PHB to The Office, the incompetent manager is such a popular trope that it’s in danger of becoming …Continue reading »... Read more »

Alessandro Pluchino, Andrea Rapisarda, & Cesare Garofalo. (2009) The Peter Principle Revisited: A Computational Study. Physica A 389 (2010) 467-472. arXiv: 0907.0455v3

  • August 9, 2012
  • 04:47 PM
  • 613 views

Building the tallest sandcastle

by Cath in Basal Science (BS) Clarified

The Canadian National Exhibition (CNE) opens in Toronto next Friday (can’t wait!) and they hold an international sand sculpting competition every year. I’m always impressed by the size and detail [...]... Read more »

Pakpour M, Habibi M, Møller P, & Bonn D. (2012) How to construct the perfect sandcastle. Scientific reports, 549. PMID: 22870378  

  • August 9, 2012
  • 11:00 AM
  • 578 views

RULETOOL v2: L-systems and turtle graphics

by Alejandro Mosquera in amsqr

An L-system or Lindenmayer system is a parallel rewriting system, namely a variant of a formal grammar.I have implemented a simple L-system class with HTML5 Canvas or WebGL output. Feel free to explore the predefined models or create your own.... Read more »

Przemyslaw Prusinkiewicz, Aristid Lindenmayer. (1990) The Algorithmic Beauty of Plants. Springer-Verlag. pp. 101–107. DOI: 10.1016/S0168-9452(96)04526-8  

  • August 9, 2012
  • 02:14 AM
  • 819 views

“The beetle shows us how”

by Perikis Livas in Tracing Knowledge

Insects are experts when it comes to adhesion on dry surfaces. However, in nature, plants may be covered by water for quite a long period of time, especially after rain. The bionic expert Professor Stanislav Gorb of Kiel University, Germany, and the material scientist Professor Naoe Hosoda of the National Institute for Material Science in Japan, discovered the remarkable ability of the terrestrial leaf beetle to walk underwater. Picking up the beetle’s locomotion mechanism, they designed an artificial material, which sticks to surfaces underwater. Their scientific results are published today (8th August) in the online journal “Proceedings of the Royal Society B”.... Read more »

Kiel University Press, Text: Claudia Eulitz, & Translation: Ann-Christin Wimber. (2012) “The beetle shows us how”. Proceedings of the Royal Society B . info:/

  • August 7, 2012
  • 10:13 AM
  • 443 views

The Adventures of Ned the Neuron!

by Bradley Voytek in Oscillatory Thoughts

I've been itching to announce this for months, but I've been biting my tongue. Now I can finally let the neuron out of the bag.Ladies and gentlemen I'm proud to introduce to you a joint project between my wife Jessica Voytek and our friend Erica Warp: The Adventures of Ned the Neuron! To get the important pitch out of the way first, please go contribute some money to their Kickstarter campaign to help them get started if you want to help. Also, please consider following their company on Facebook. I promise they're not spammy.For several months now Jessica and Erica have been working on their company, Kizoom, to develop the first of what I hope to be many science education eBooks for kids. The fact that this is being built using open or semi-open tools and platforms is also pretty amazing.Note that I'm in no way connected to this company, though the obvious disclosure is that my wife and I are financially entwined and, as unbiased as I try to be, I of course cannot be completely so. I mean, I'm writing this post, aren't I? But... as a new father I'm coming to appreciate more and more the joys of well-written, scientifically accurate educational materials.So who are Erica and Jessica and why should you trust what they write?Erica earned her PhD in neuroscience from Berkeley working on spinal cord development. She published three super cool papers during that time, one each in Nature, PNAS, and Current Biology. I promise you she knows her brains.Jessica is the primary author on our brainSCANr paper which we published in The Journal of Neuroscience Methods earlier this year. She earned her Masters degree in Information Management and Systems at Berkeley, which she completed while very pregnant with our son. Not only does she know her brains, she's also technically and artistically very savvy.The two of them have been working hard on this baby of theirs (that's them celebrating after submitting their NIH grant). They have managed to put together a book that is fun and interactive for kids (their target audience) while being educational and totally neuroscientifically accurate.No neuro nonsense. Just good science and good fun.So many of us neuroscientists complain about the poor public understanding of our field that it's time for us to stop being critics and start trying to make the changes we want to see. And that's what I love about Kizoom and The Adventures of Ned the Neuron: two very smart neuroscientists and techies are putting themselves forward and trying to make science more approachable to the most scientifically vulnerable group.Kids.Erica wrote the story and drew the early artwork while Jessica has been working on getting the whole thing coded up, animated, etc. Basically the techy nerd work.What's impressed me the most is that, throughout all of this had work, they've also been doing a lot of science outreach and communication for kids. Jessica worked for the Girl Scouts for years, including developing a cookie booth finder to help people locate the nearest Girl Scout troop selling cookies in their area!In May Jessica and Erica volunteered at a Girl Scout event to teach young women about neuroscience and the brain with the help of Ned the Neuron!We also recently learned that, out of the thousands of abstracts and poster submissions to the Society for Neuroscience Conference this October, their poster "User experience design for children's neuroscience education" has been selected as one of nine in the new "Dynamic Posters" session.What's that? Well, according to the email they received,A dynamic poster is an electronic version of the current paper-based format, displayed on an LCD screen rather than a poster board. However, it’s more than just an e-poster, which is typically an electronic - but still static - PDF version of a paper poster. Embedding multimedia content is encouraged such as videos, slides, animated charts or graphs, scrolling text, or a 3D rotation of a model. A dynamic poster presentation is designed for face-to-face interaction: like a regular poster presentation, the dynamic presentation will be driven by the primary author while attendees visit the poster. Some text elements of the poster will always be viewable for browsing by people walking by or waiting for their turn to speak with the presenter. Other parts of the poster will be operated by the presenter, who can click on and play a video or enlarge a graph to better illustrate a method or result.I definitely applaud the Society for Neuroscience for finally taking this kind of tech-based approach.I wish I could convey to you in words the emotional love the both of them have for this project. I'm really proud to have seen it grow from nothing into a nearly completed project. Please check it out and consider helping if you can.Thanks everyone.Voytek JB, & Voytek B (2012). Automated cognome construction and semi-automated hypothesis generation. Journal of neuroscience methods, 208 (1), 92-100 PMID: 22584238Warp E, Agarwal G, Wyart C, Friedmann D, Oldfield CS, Conner A, Del Bene F, Arrenberg AB, Baier H, & Isacoff EY (2012). Emergence of patterned activity in the developing zebrafish spinal cord. Current biology : CB, 22 (2), 93-102 PMID: 22197243... Read more »

Warp E, Agarwal G, Wyart C, Friedmann D, Oldfield CS, Conner A, Del Bene F, Arrenberg AB, Baier H, & Isacoff EY. (2012) Emergence of patterned activity in the developing zebrafish spinal cord. Current biology : CB, 22(2), 93-102. PMID: 22197243  

Marriott G, Mao S, Sakata T, Ran J, Jackson DK, Petchprayoon C, Gomez TJ, Warp E, Tulyathan O, Aaron HL.... (2008) Optical lock-in detection imaging microscopy for contrast-enhanced imaging in living cells. Proceedings of the National Academy of Sciences of the United States of America, 105(46), 17789-94. PMID: 19004775  

Wyart C, Del Bene F, Warp E, Scott EK, Trauner D, Baier H, & Isacoff EY. (2009) Optogenetic dissection of a behavioural module in the vertebrate spinal cord. Nature, 461(7262), 407-10. PMID: 19759620  

  • August 3, 2012
  • 03:47 AM
  • 560 views

Where did all the BBC programme metadata go? The infax catalogue online

by Duncan Hull in O'Really?

Over at @BBCSport and @BBC2012 there are some Olympian feats of big data wrestling going on behind the scenes for London 2012 [1]. While we all enjoy the Olympics on a range of platforms and devices, a team of twenty engineers is busy making it all happen. It’s great that the BBC, unlike other large organisations, can talk openly about their technology and share hard-won knowledge widely.... Read more »

  • August 1, 2012
  • 01:48 AM
  • 756 views

Holistic Design Factors in Space Colonies

by Jason Carr in Wired Cosmos

Assuming that we never achieve FTL travel, generational colony ships may become a necessary method used to traverse great distances. Inherent in the term generational, individuals will live their entire lives on these massive spaceships as will their descendants. In other words, these space ships will be the only home many generations of inhabitants will [...]... Read more »

Apostolos Papanikolaou. (2010) Holistic ship design optimization . Computer-Aided Design, 42(11), 1028-1044. info:/10.1016/j.cad.2009.07.002

Cooper RA. (2008) Quality-of-life technology. A human-centered and holistic design. IEEE engineering in medicine and biology magazine : the quarterly magazine of the Engineering in Medicine , 27(2), 10-1. PMID: 18472458  

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