Inside the cell, an ocean of buffeting waves

Inside the cell, an ocean of buffeting waves: The cytoplasm is actually an elastic gel, it turns out, so it puts up some resistance to simple diffusion. But energetic processes elsewhere in the cell—in the cytoskeleton, especially—create random but powerful waves in the cytoplasm, pushing on proteins and organelles alike. Like flotsam and jetsam buffeted by the wakes of passing ships, suspended particles scatter much more quickly and widely than they would in a calm sea.

Scientists create artificial brain out of spongy goo | Science/AAAS | News

Scientists create artificial brain out of spongy goo | Science/AAAS | News: The rings are engineered to mimic the structure and function of the six layers of human cortical brain tissue. Scientists coaxed neurons (right) to grow around stiff, porous matrices made of silk proteins immersed in collagen gel. Then, they colored the layers with food dye and pieced them together like a jigsaw puzzle. By tweaking the size and orientation of matrix pores, researchers attempted to emulate variations of cellular structure and function in a real cortex. Unlike flat neuron cultures grown in petri dishes, the structure provides cells with something to cling to as they branch out and make connections, forming complex, 3D networks that more closely mimic real neural circuits, the authors say.

How bird flocks are like liquid helium | Science/AAAS | News

How bird flocks are like liquid helium | Science/AAAS | News: Using tracking software on the recorded video, the team could pinpoint when and where individuals decide to turn, information that enabled them to follow how the decision sweeps through the flock. The tracking data showed that the message to turn started from a handful of birds and swept through the flock at a constant speed between 20 and 40 meters per second. That means that for a group of 400 birds, it takes just a little more than a half-second for the whole flock to turn...

The team proposes that instead of copying the direction in which a neighbor flies, a bird copies how sharply a neighbor turns...

Interestingly, Cavagna adds, the new model is mathematically identical to the equations that describe superfluid helium.

Meet the electric life forms that live on pure energy - life - 16 July 2014 - New Scientist

Meet the electric life forms that live on pure energy - life - 16 July 2014 - New Scientist: Unlike any other living thing on Earth, electric bacteria use energy in its purest form – naked electricity in the shape of electrons harvested from rocks and metals...

First they measure the natural voltage across the sediment, before applying a slightly different one. A slightly higher voltage offers an excess of electrons; a slightly lower voltage means the electrode will readily accept electrons from anything willing to pass them off. Bugs in the sediments can either "eat" electrons from the higher voltage, or "breathe" electrons on to the lower-voltage electrode, generating a current. That current is picked up by the researchers as a signal of the type of life they have captured...

"This is huge. What it means is that there's a whole part of the microbial world that we don't know about..."

Muscle-powered bio-bots walk on command | News Bureau | University of Illinois

Muscle-powered bio-bots walk on command | News Bureau | University of Illinois: The new bio-bots are powered by a strip of skeletal muscle cells that can be triggered by an electric pulse...

“Skeletal muscles cells are very attractive because you can pace them using external signals,” Bashir said. “For example, you would use skeletal muscle when designing a device that you wanted to start functioning when it senses a chemical or when it received a certain signal. To us, it’s part of a design toolbox. We want to have different options that could be used by engineers to design these things.”

The design is inspired by the muscle-tendon-bone complex found in nature. There is a backbone of 3-D printed hydrogel, strong enough to give the bio-bot structure but flexible enough to bend like a joint. Two posts serve to anchor a strip of muscle to the backbone, like tendons attach muscle to bone, but the posts also act as feet for the bio-bot.

Human brain's ultimate barrier to open for first time - health - 18 June 2014 - New Scientist

Human brain's ultimate barrier to open for first time - health - 18 June 2014 - New Scientist: Next is a treatment called high-intensity focused ultrasound. The volunteers will wear a cap that contains an array of transducers that direct ultrasound waves into their brain. Just as the sun's rays can be focused by a magnifying glass, ultrasound waves can be concentrated inside the body to get the microbubbles to vibrate.

The vibrating bubbles will expand and contract about 200,000 times a second, which will force apart the endothelial cells that form the BBB. The idea is that this will allow the chemotherapy drug in the bloodstream to sneak through the gaps in the barrier and into any nearby tumour cells...

Quantum biology: Algae evolved to switch quantum coherence on and off

Quantum biology: Algae evolved to switch quantum coherence on and off: "Most cryptophytes have a light-harvesting system where quantum coherence is present. But we have found a class of cryptophytes where it is switched off because of a genetic mutation that alters the shape of a light-harvesting protein.
"This is a very exciting find. It means we will be able to uncover the role of quantum coherence in photosynthesis by comparing organisms with the two different types of proteins."

New Double Helix Visualization Revises What We Know About DNA

New Double Helix Visualization Revises What We Know About DNA: Results reaffirmed the structure first suggested by Watson and Crick in 1953. But surprisingly, the single-molecule images showed major variations in the depths and grooves in the double helix structure.

Engineers design ‘living materials’ | MIT News Office

Engineers design ‘living materials’ | MIT News Office: By programming cells to produce different types of curli fibers under certain conditions, the researchers were able to control the biofilms’ properties and create gold nanowires, conducting biofilms, and films studded with quantum dots...

“It’s a really simple system but what happens over time is you get curli that’s increasingly labeled by gold particles. It shows that indeed you can make cells that talk to each other and they can change the composition of the material over time,” Lu says. “Ultimately, we hope to emulate how natural systems, like bone, form. No one tells bone what to do, but it generates a material in response to environmental signals.”

Rats induced into hibernation-like state | Life | Science News

Rats induced into hibernation-like state | Life | Science News: But Tupone and colleagues bypassed the rats’ defenses against the cold with a compound that’s similar to adenosine, a molecule in the body that signals sleepiness. After about an hour in a room chilled to 15 Celsius, the rats grew lethargic. Their brain waves slowed, their heart rates dropped and their heart occasionally skipped beats.

The rats’ core temperature dropped from about 38� �to about 28� C, or 82� Fahrenheit, the authors report �in the Sept. 4 Journal of Neuroscience. Tupone and his colleagues measured even lower temperatures in further experiments — rats’ core body temperature reached 15� C or about 59� F. “That is a pretty amazing temperature. No one has done this before,” he says.

The rats weren’t in a coma, nor were they asleep or truly hibernating. Hibernating animals’ metabolisms plummet and their temperatures sink much lower; an Arctic ground squirrel, for instance, cools to about —3� C when it hibernates.

“It’s a new state,” Tupone says. “We don’t really know what it is.”

Stem cells mimic human brain : Nature News & Comment

Stem cells mimic human brain : Nature News & Comment: ...in the latest advance, scientists developed bigger and more complex neural-tissue clumps by first growing the stem cells on a synthetic gel that resembled natural connective tissues found in the brain and elsewhere in the body. Then, they plopped the nascent clumps into a spinning bath to infuse the tissue with nutrients and oxygen...

Under a microscope, researchers saw discrete brain regions that seemed to interact with one another. But the overall arrangement of the different proto-brain areas varied randomly across tissue samples — amounting to no recognizable physiological structure.

“The entire structure is not like one brain,” says Knoblich, adding that normal brain maturation in an intact embryo is probably guided by growth signals from other parts of the body. The tissue balls also lacked blood vessels, which could be one reason that their size was limited to 3–4 millimetres in diameter, even after growing for 10 months or more.

New prototype device recognizes electrical properties of infected cells as signatures of disease

New prototype device recognizes electrical properties of infected cells as signatures of disease: Several types of infection, including malaria, alter a cell's impedance...

To find out, first authors... built a microfluidic device capable of measuring the magnitude and phase of the electrical impedance of individual cells. The device is essentially a cell-counting device, similar in approach to other low-cost, portable devices being developed to diagnose illnesses such as HIV.
The challenge, however, involved optimizing the electronics to allow very accurate measurements of impedance for each cell as it passes by...
In tests of cells of four cell types—uninfected cells and infected cells at the ring, trophozoite and schizont stages—the device detected small differences in measures of magnitude and seemingly random differences in phase, but not quite enough to definitively differentiate among stages.
However, by mathematically combining the measures into an index called delta, the differences between uninfected cells and all three stages became clear.

How neurons ‘decide’ to create axons or dendrites | KurzweilAI

How neurons ‘decide’ to create axons or dendrites | KurzweilAI: They found that embryonic nerve cells manufacture a signaling enzyme called Atypical Protein Kinase C (aPKC) in two varieties: a full-length one and a shorter one...
When the researchers blocked the production of the short form, the nerve cell grew multiple axons and no dendrites. When they created an artificial abundance of the short form, dendrites formed at the expense of axons.

Watch Lab-Grown Heart Tissue Beat On Its Own [Video] | Popular Science

Watch Lab-Grown Heart Tissue Beat On Its Own [Video] | Popular Science: Using various enzymes and special cleansing detergents, the researchers stripped a mouse heart of all its cells to create a scaffold for induced pluripotent stem cells (iPS cells), adult human cells that are reprogrammed to act like embryonic cells. They treated the iPS cells taken from a skin biopsy to become multipotential cardiovascular progenitor (MCP) cells, the precursor cells that can become any of the three types of cells found in the heart...
After a period of a few weeks, the human cells had repopulated the mouse heart, and it began beating at a rate of 40 to 50 beats per minute.

Flatworms lose their heads but not their memories: Study finds memories stored outside the brain

Flatworms lose their heads but not their memories: Study finds memories stored outside the brain:
Automated video tracking and subsequent computer analysis of the worms' movements (image above) showed that the group familiarized to the rough-floored dishes overcame aversion to the light significantly more quickly and spent more time feeding in the illuminated space than did the non-familiarized group...

Both groups of worms were then decapitated and housed in a smooth-floored environment while their heads regenerated. Two weeks later, the fully regenerated segments were again tested. Worms regenerated from the familiarized group were slightly but not significantly quicker to feed in the lighted part of the container. However, when both groups of worms were given a brief refresher session of feeding in the textured environment, then removed and retested four days later, the planaria generated from familiarized segments were significantly quicker to feed than those regenerated from unfamiliarized worms—showing that they retained recognition of the link between this type of surface and a safe feeding environment.

Robot face lets slime mould show its emotional side - tech - 08 August 2013 - New Scientist

Robot face lets slime mould show its emotional side - tech - 08 August 2013 - New Scientist: Gale placed slime mould on a forest of 64 micro electrodes, along with some oat flakes. As the mould moved across the electrodes towards the food, it produced electrical signals, which Gale converted into sound frequencies...

Using a popular psychological model, the team was then able to assign each sound chunk an emotion...

What We Can Learn From the Quantum Calculations of Birds and Bacteria - Wired Science

What We Can Learn From the Quantum Calculations of Birds and Bacteria - Wired Science: We can now show that a single electronic excitation acting as a probability amplitude wave can simultaneously sample the various molecular paths connecting the antenna cells to the reaction center. The excitation effectively “picks” the most efficient route from leaf surface to sugar conversion site from a quantum menu of possible paths. This requires that all possible states of the traveling particle be superposed in a single, coherent quantum state for tens of femtoseconds.

We have seen this remarkable phenomenon in the green sulphur bacteria, but humans have not yet figured out how it is that nature can stabilize a coherent electronic quantum state in such complex systems for such long periods of time...

Remarkably, it seems that these photosynthesizing bacteria can actually use decoherence to speed up the transfer of electronic information by accessing vibrational energies in the protein bath surrounding the biological-quantum wire without losing the integrity of the information...

It seems that quantum mechanical processes in the avian eye send signals to the brain that are sensitively dependent on the angle of change in magnetic field inclination, thereby allowing the bird to map routes. The hypothesis is that pairs of light-absorbing molecules in the bird retina produce quantum mechanically entangled electrons whose quantum mechanical state depends on the angular inclination of the field and which catalyze chemical reactions that send differently valued signals to the brain depending upon the degree of inclination.

A Mind-Blowing Dome Made by 6,500 Computer-Guided Silkworms | Wired Design | Wired.com

A Mind-Blowing Dome Made by 6,500 Computer-Guided Silkworms | Wired Design | Wired.com: An aluminum scaffold was constructed and a CNC robot was used to string a lattice of silk starter threads across it in patterns that would provide a base for the worms to operate. The aluminum and string frame was hung in an atrium at MIT and thousands of silkworms were released on it...
The project is a unique hybrid of structural and biological engineering. Using her custom-developed CAD tools, Oxman was able to control the material properties of the pavilion in much the same way an architect would specify a certain type of steel to use in a building. The density of the starter strings determined the opacity of a given panel. The structure’s integrity arose from their orientation. The output can’t be fully controlled, but the emergent behavior of the worms can lead to unexpected textures and features that would be impossible to plan.

Slime mould could make memristors for biocomputers

Slime mould could make memristors for biocomputers: The feeding fronds of the slime mould Physarum polycephalum turn out to have memory resistance – or memristance...

..."Slime mould can be used to perform all the logic functions that conventional computer hardware components can do," says Gale.

Her team is also exploring whether, in addition to number-crunching, slime mould's knack for finding the shortest path to nutrients can be used to design the most efficient circuit patterns for biocomputers.

Cells as living calculators - MIT News Office

Cells as living calculators - MIT News Office: MIT engineers have transformed bacterial cells into living calculators that can compute logarithms, divide, and take square roots, using three or fewer genetic parts.

Inspired by how analog electronic circuits function, the researchers created synthetic computation circuits by combining existing genetic “parts,” or engineered genes, in novel ways...


To create an analog adding or multiplying circuit that can calculate the total quantity of two or more compounds in a cell, the researchers combined two circuits, each of which responds to a different input. In one circuit, a sugar called arabinose turns on a transcription factor that activates the gene that codes for green fluorescent protein (GFP). In the second, a signaling molecule known as AHL also turns on a gene that produces GFP. By measuring the total amount of GFP, the total amount of both inputs can be calculated.

To subtract or divide, the researchers swapped one of the activator transcription factors with a repressor, which turns off production of GFP when the input molecule is present. The team also built an analog square root circuit that requires just two parts, while a recently reported digital synthetic circuit for performing square roots had more than 100.