squidboot

Researchers make the leap to whole-cell simulations

squidboot — Thu, 31 Mar 2011 09:13:37 +0000

Researchers have built a computer model of the crowded interior of a bacterial cell that – in a test of its response to sugar in its environment – accurately simulates the behavior of living cells.

The new “in silico cells” are the result of a collaboration between experimental scientists at the Max Planck Institute of Biology in Germany and theoretical scientists at the University of Illinois using the newest GPU (graphics processing unit) computing technology.

Their study appears in the journal PLoS Computational Biology.

“This is the first time that we’re modeling entire cells with the complete contents of the cellular cytoplasm represented,” said Illinois postdoctoral researcher and lead author Elijah Roberts. “We’re looking at the influence of the whole cellular architecture instead of modeling just a portion of the cell, as people have done previously.”

University of Illinois chemistry professor Zaida Luthey-Schulten, who led the research, had done molecular dynamics simulations of individual molecules or groups of molecules involved in information processing, but never of a system as large and complex as the interior of an entire cell.

Then in 2006 she saw a paper by Wolfgang Baumeister and his colleagues at Max Planck that located every one of a bacterium’s ribosomes, its protein-building machines, inside the cell.

That image spurred Luthey-Schulten to think about modeling an entire cell, and she asked Baumeister and his colleague Julio Ortiz if they would repeat the study in Escherichia coli (E. coli), a bacterium that has been the subject of numerous molecular studies.

Once the new ribosome data were available, Roberts looked to other studies that described the size distribution of the rest of the molecules that take up space in the cell. By adding these to the ribosome data, he developed a three-dimensional model that showed the degree of “molecular crowding” in a typical E. coli cell.

Luthey-Schulten was amazed at how little “space” remained inside the cell, she said.

“I think, like everybody else, my perception of the cell up until Wolfgang and Julio’s 2006 article had always been that it’s a pretty big sack of water where a lot of chemical reactions occur,” she said.

“But in fact there are a lot of obstacles in the cell, and that is going to affect how individual molecules move around and it’s going to affect the reactions that occur.”

Other researchers have begun studying the effects of molecular crowding on cellular processes, but never at the scale of an entire cell.

Those studying live cells can – by conducting fluorescence experiments – discover variations in the copy number of a particular protein in a population of cells. But they are less able to observe the microscopic details that give rise to such differences between genetically identical cells. Well-designed computer simulations of whole cells can track every reaction within the cells while also accounting for the influence of molecular crowding and other variations between cells, Luthey-Schulten said.

For example, by running simulations on models of two E. coli strains, the researchers were able to see that “bacterial cell architecture does indeed affect the reactions that occur within the cells,” Luthey-Schulten said. When sugar was present in its environment, a longer, narrower E. coli strain was able to ramp up production of a sugar-transporter protein much more quickly than a bigger strain, the researchers found. That difference had a lot to do with the distribution of molecules in each cell type, Roberts said.

The computer simulation also showed how molecular crowding influences the behavior of a molecule that, when it binds to DNA, shuts down production of the sugar-transporter protein. Even when it wasn’t bound to DNA, this repressor remained close to the binding site because other molecules in the cell blocked its escape. These intracellular obstacles reduced its ability to diffuse away.

The new model is only a first step toward an accurate simulation of a whole working cell, the researchers said. The development of better models will rely on the work of those conducting research on actual cells. Their data provide the framework for improving computer models, Luthey-Schulten said, and offer a real-world test of the in silico cells’ ability to recreate the behavior of living cells

Model predicts ‘religiosity gene’ will dominate society

squidboot — Thu, 31 Mar 2011 07:28:18 +0000

link to physorg article

In the past 20 years, the Amish population in the US has doubled, increasing from 123,000 in 1991 to 249,000 in 2010. The huge growth stems almost entirely from the religious culture’s high fertility rate, which is about 6 children per woman, on average. At this rate, the Amish population will reach 7 million by 2100 and 44 million by 2150. On the other hand, the growth may not continue if future generations of Amish choose to defect from the religion and if secular influences reduce the birth rate. In a new study, Robert Rowthorn, emeritus professor of economics at Cambridge University, has looked at the broader picture underlying this particular example: how will the high fertility rates of religious people throughout the world affect the future of human genetic evolution, and therefore the biological makeup of society?

works in progress (drawings for colouring/painting)

squidboot — Sun, 16 Jan 2011 10:58:26 +0000

this way for the gas, ladies and gentlemen – before colouring

squidboot — Wed, 14 Jul 2010 17:52:49 +0000

click to enlarge

for a book cover comp

Sir Thomas Urquhart at his desk in Cromarty Castle – before colouring

squidboot — Fri, 18 Jun 2010 19:58:03 +0000

click to enlarge

Royal Arms partially coloured

squidboot — Wed, 12 May 2010 14:12:24 +0000

click to enlarge

ithinktheythinkithinktheythink

squidboot — Thu, 21 Jan 2010 21:39:11 +0000

The Anti-Christ(mas)

squidboot — Fri, 11 Dec 2009 19:50:14 +0000

Have you not heard of that child who found where his presents were hidden, ran to the shops, and cried incessantly: “I am looking for Santa! I am looking for Santa!” As many of those who did not believe in Santa were standing together there, he excited considerable laughter. Have you lost him, then? said one. Did he get stuck up a chimney? said another. Or was his beard shaved off by mischievous elves? Have they staged a coup? Did Rudolf’s nose go critical ? Or has the north-pole melted? Thus they shouted and laughed. The child sprang into their midst and pierced them with his glances.

“Where has Santa gone?” he cried. “I shall tell you. We have killed him – you and I. We are his murderers. But how have we done this? How were we able to eat all the mince pies? Who gave us the pudding to soak up all the brandy? What did we do when we roofied Rudolf’s carrot? Who will deliver the presents? Who reads our letters? Our mum and dad? Isn’t Christmas a bit crap now? Socks, aftershave, heartburn and ennui, in all directions? Is there any magic left? Are we not tearing as through an infinite wrapping? Do we not feel the breeze from grandma’s snores? It doesn’t even snow anymore, and they start bloody advertising in October. Do we not hear anything yet of the noise of the gravediggers who are burying Santa? Do we not smell anything yet of Santa’s decomposition? Cola sponsored god analogues too decompose. Santa is dead. Santa remains dead. And we have killed him. How shall we, murderers of all murderers, console ourselves? That which was the fattest and jolliest of all that the world has yet possessed has bled to death under our knives. Who will wipe this blood off us? How much eggnog do we need to purify ourselves? What Seasonal Comedy Specials, what party games shall we need to invent? Is not the greatness of this deed too great for us? Must we not ourselves become fat and jolly, and beardy, simply to be worthy of it? There has never been a greater deed; and whosoever shall be born after us – for the sake of this deed he shall be part of a fatter, beardier and jollier history than all history hitherto.”

Here the child fell silent and again regarded his listeners; and they too were silent and stared at him in astonishment. At last he threw his new bike to the ground, and it broke. “I have come too early,” he said then; “my time has not come yet. The tremendous event is still on its way, still traveling – it has not yet reached the ears of men. Lightning and thunder require time, the light of the stars requires time, deeds require time even after they are done, before they can be seen and heard. This deed is still more distant from them than the distant stars – and yet they have done it themselves.”

It has been further related that on that same day the child entered divers grottos and there sang a requiem. Led out and quietened, he is said to have retorted each time: “what are these grottos now if they are not the tombs and sepulchres of Santa?”

Friedrich Wilhelm Nietzsche – The Anti-Christ(mas)

dirty rat

squidboot — Fri, 04 Dec 2009 17:55:43 +0000

pencil/ink
winter 2009

my parasite

squidboot — Tue, 01 Dec 2009 11:14:25 +0000

I will choke my parasite on its own sewage. I will harvest its corpse then cook it in its juices. I will pin out its innards and draw its guts in exquisite detail. I will make a puppet from its skin and abandon it to the whim of children. I will take possession of its sensorymotor system. I will polish its neurones to a mirror shine. I will prod it with hot qualia. I will go home and laugh about it with my friends. I will have sex with its sister and not call her back.