amolecularmatter:

David S. Goodsell is an Associate Professor of Molecular Biology at The Scripps Research Institute in La Jolla, California. Both a researcher and an artist, Goodsell creates beautiful pictures of intracellular machinery alongside his scientific experimentation to help everyone visualise molecular and cell biology in a different - and stunningly beautiful - way.

When asked about his work, Goodsell responded, “Biological systems are a source of constant amazement for me. I use a combination of hand-drawn and computer graphics illustrations to reveal the invisible world of molecules inside cells. Computer graphics is a perfect way to display the atomic details of biological molecules. Using experimental coordinates determined by x-ray crystallography or other methods, we can see the position of every atom, and examine how they work together to catalyze a reaction or carry genetic information.”

His paintings are usually created through ink drawing and watercolour, taking inspiration from computer models and graphics of cells. The images shown here are six illustrations commissioned as a project for Biosite.

Top left: This illustration shows a portion of basement membrane, a structure that forms the support between tissues in the body. It is composed of a network of collagen (yellow green), laminin (blue-green cross-shaped molecules), and proteoglycans (deep green, with three arms).

Top right: A small portion of cytoplasm is shown, including three types of filaments that make up the cytoskeleton: a microtubule (the largest), an intermediate filament (the knobby one) and two actin filaments (the smallest ones). The large blue molecules are ribosomes, busy in their task of synthesising proteins. The large protein at bottom center is a proteosome.

Middle left: Blood serum is shown in the picture, with many Y-shaped antibodies, large circular low density lipoproteins, and lots of small albumin molecules. The large fibrous structure at lower left is von Willebrand factor and the long molecules in red are fibrinogen, both of which are involved in blood clotting. The blue object is poliovirus.

Middle right: Part of a muscle sarcomere is shown here, with actin filaments in blue and myosin filaments in red. The long yellow proteins are the huge protein titin.

Bottom left: This view shows DNA being replicated in the nucleus. DNA polymerase is shown at the center in purple, with a DNA strand entering from the bottom and exiting as two strands towards the top. The new strands are shown in white. Chromatin fibers are shown at either site of the replication fork.

Bottom right: A portion of a red blood cell is shown in this illustration, with the cell membrane at the top, and lots of hemoglobin (red) at the bottom.

All images courtesy of David. S. Goodsell, whose homepage can be found here.

Boston Molasses Disaster - Wikipedia, the free encyclopedia

At about 12:30 in the afternoon near Keany Square,[3] at 529 Commercial Street, a molasses tank 50 ft (15 m) tall, 90 ft (27 m) in diameter and containing as much as 2,300,000 US gal (8,700 m3) collapsed. Witnesses stated that as it collapsed, there was a loud rumbling sound, like a machine gun as the rivetsshot out of the tank, and that the ground shook as if a train were passing by.[4]

The collapse unleashed a wave of molasses 25 feet (7.6 m) high at its peak,[5] moving at 35 miles per hour (56 km/h).[1] The molasses wave was of sufficient force to damage the girders of the adjacent Boston Elevated Railway's Atlantic Avenue structure and tip a railroad car momentarily off the tracks. Author Stephen Puleo describes how nearby buildings were swept off their foundations and crushed. Several blocks were flooded to a depth of 2 to 3 feet (60 to 90 cm).

via Caleb

1 month ago - 1

sagansense:

Musical artist Imogen Heap has developed “gestural music gloves” which are poised to not only disrupt how we interact with our hard/software due to the availability and versatility of so many emerging technologies, but will change our experience with live music forever. What’s more, the ‘Music Gloves’ will be open-sourced, so they’ll be constantly in transition, with far-seeking applications into the future across multiple fields, if not all.

The brief rundown (from her website):

Using a unique gestural vocabulary, motion data-capture systems, and user interfaces to parameter functions developed by Imogen Heap and her team, artists and other users will be able to use their motion to guide computer-based digital creations. The Musical Gloves are both an instrument and a controller in effect, designed to connect the user fluidly with gear performers usually use, such as Ableton - think minority report for musicians brought to you by the DIY/maker revolution.

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As the only ever female solo artist to be awarded a Grammy for best-engineered album (Ellipse, 2009), this solution sees the creativity of Imogen Heap applied to music technology in a complete symbiosis between invention, composition and performative innovation.

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The gloves are in a pre-commercial status, Imogen being the Alpha tester. The team is currently looking for other artists wanting to become beta-testers and get a custom set of gloves made for their anatomy and creative ambitions. Please feel free to contact us if you want to join the project’s evolution and be part of making this available to more talents and purposes.

Read the full story on these “magical music gloves as Imogen refers to them, and watch Heap perform, showcasing the Music Gloves during a 2012 Wired Talk (spoiler alert: it’s amazing).

I have music in my hands, and the playground of the stage around me.” — Imogen Heap

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Image above from TEDGlobal 2012, where Imogen Heap performed with the gloves on stage for the first time.

Visit The Gloves Project for more on this game-changing tech, along with Imogen Heap’s new website dedicated to the Music Gloves.

(Source: vimeo.com)

How the Recession Reshaped the Economy, in 255 Charts

Incredible visualization by the NYTimes of the economic changes in the US over the last 5 years. Great job using interactive visualization to make lots of disparate data intelligible and explorable on one page. 

via Caroline McCarthy

2 months ago

See New York's future defenses against storms and rising sea levels

via andybons

2 months ago

Visual account of protein investment in cellular functions

New paper out today from the Milo Lab at Weizmann (that I contributed to very minorly). Author summary - we made pretty pictures of proteomes of 10 organisms ranging from cyanobacteria to humans. The figure above is of the proteome of a Synechocystis cyanobacterium. The pictures are both pretty and useful, we think. You can easily see which proteins and which biological systems are abundant in different growth conditions in your favorite organism at http://proteomaps.net/

2 months ago

BrewPi released! All source code online, a wiki, a forum, a bug tracker.. Let's go! - BrewPi.com

Very cool open source beer fermenting system. Via Elad Noor.

2 months ago

Q: Why Do Animal Cells Stay So Small? A: Gravity

Biologists have generally attributed the limit to the difficulty that large-volume cells face in obtaining nutrients. But researchers at Princeton are now offering another answer, one that has nothing to do with food and everything to do with force: gravity. Clifford Brangwynne, an assistant professor of chemical and biological engineering and the scientist who led the research, has put bioengineering techniques to use to suggest that it’s gravitational force that imposes the size limit on cells. The rare cells that are larger than 10 microns in diameter, his work has found, seem to be the exceptions that prove the rule: They have evolved as they have in part to support their contents against gravity.

3 months ago

Some Thoughts on Protein Stability

For the fourth time in recent memory, I find myself in a class where I’m told that proteins are not very stable. I find this jarring every time I hear it because, in the same breath, the honored professor says most protein folding reactions have Gibbs energies ranging between -5 and -8 kCal/mol (~ 20-35 kJ/mol for European protein scientists, see BNID 107069). A metabolic reaction with ∆G < -7 kcal/mol (-30 kJ/mol) is usually considered irreversible, so how is that protein biologists consider that same ∆G “not very stable?” It took me a bit to wrap my head around why protein and metabolism folks don’t see eye to eye on J. Willard Gibbs, so I thought I’d share the insight. Special thanks to Andy Martin for directing me towards the light.

I’ll take a second to reflect on the numbers. The standard change in Gibbs due to a reaction is just a measure of the reaction’s equilibrium; i.e. if I let it run till the end of time in a closed vessel, how many reaction substrates and products will I have in there. The equilibrium ratio between the product and substrate concentrations is called the equilibrium constant Keq = [P] / [S]. ∆G = - RT ln(Keq) is just a log-scaled version of the equilibrium constant (R is the gas constant, T is the absolute temperature). At a given temperature, ∆G determines the equilibrium constant and vice-versa. 

We biologists like to use incubators to regulate the temperature of our experiments. Mammals like to use homeostatic mechanisms to regulate the temperature of their bodies. Lots of organisms are found in characteristic temperature ranges, so much so that they are called mesophiles, thermophiles or psychrophiles according to their preferred temperature range. So, for the time being, let’s fix the temperature of our thought experiment to 25 C (298 K), since it’s a temperature that is relevant to a lot of life. In this case, a ten-fold increase in Keq (ten-fold more reaction products than substrates in equilibrium) results in a ∆G that is RT ln(10) = 1.4 kcal/mol = 5.7 kJ/mol smaller. That is, 1.4 kcal/mol more negative, more favoring the reaction products, more stable. In other words, every ~1.4 kcal/mol favors the reaction products over substrates by a factor of 10. If we let a protein with 5.6 kCal/mol stability fold forever, we’d find only 1 unfolded protein for every 10,000 folded ones. This, to me, sounds very very stable, so you can understand my confusion.

Turns out that my analogy to metabolism may have been the source of my confusion. In the context of metabolism, many reactions are reversible in the sense that they run in different directions in different cellular conditions. For example, most of the reactions in glycolysis are reversed when glucose is synthesized through gluconeogenesis. Many isomerization reactions like the one catalyzed by phosphoglycerate mutase (2-phosphoglycerate <=> 3-phosphoglycerate) have very small standard ∆Gs and are, therefore, easily reversed with small changes in the concentrations of reactants (try playing with reactant concentrations here). On the other hand, some metabolic reactions are irreversible (i.e. not easily reversed by changes in the concentrations of reactants) and the “reverse” reaction is actually catalyzed by a different enzyme using different co-factors. For example, the hexokinase reaction phosphorylating glucose to glucose 6-phosphate with ATP as the phosphate donor is a nearly irreversible reaction - it has a ∆G ~ -6 kcal/mol and would therefore require a roughly 10,000-fold change in the concentration ratio [glucose 6-phosphate] / [glucose] to proceed in the direction of ATP synthesis (presuming that the ATP and ADP concentrations are controlled homeostatically). So it’s not surprising that no ATP is synthesized from glucose 6-phosphate during gluconeogenesis - inorganic phosphate is produced instead. Indeed, phosphorylating glucose with inorganic phosphate is considered a different reaction than if ATP is used as the phosphate donor. And this makes tons of sense - the hexokinase reaction in glycolysis (glucose + ATP -> glucose 6-phophate + ADP) strongly favors the direction of phosphorylation while the phosphatase reaction in gluconeogensis favors the dephosphorylation (glucose-6p + water => Pi + glucose). 

When we think about protein folding, however, we take for granted that the folding reaction will proceed in the direction of, well, folding (some fascinating proteins like subtilisin notwithstanding). So when protein scientists say that -7 kcal/mol is not very stable, they must mean something different than what metabolism researchers mean when they say a reaction is “reversible.” Indeed, it would be strange if small changes in the concentration of a folded protein could change the net direction of a folding reaction - unfolded proteins are generally not active and have a tendency to aggregate. So therein lies the difference between metabolism and protein folding. In metabolism, some enzymatic reactions are regulated (e.g. hexokinase) while others mostly flow with the prevailing winds, catalyzing in the direction determined by metabolite concentrations. In contrast, protein production and degradation are regulated as a rule, not as an exception. Transcriptional and translational regulation of protein production is ubiquitous and regulated degradation through ubiquitination and other mechanisms is also … ubiquitous. So, while it would be odd for protein folding reactions to be “reversible” in the sense used in metabolism, protein folding and unfolding must be catalyzable on the energy scales available to cells in order for production and degradation to be regulated. It is, therefore, no surprise that the average stability of proteins is on the same order as the stability of ATP (∆G ~ -9 kcal/mol). After all, folding chaperones like GroES/GroEL and unfolding proteases like the proteasome couple the energy of ATP to the folding and unfolding of proteins.

Woodworkers Explanation of the Diffusion Equation

via Pops. Really interesting and fun application of the heat/diffusion equation to woodworking. Learned a lot.

5 months ago - 1