Researchers at University of Rochester Medical Center injected mice that had spinal cord injury with a derivative of food coloring Blue Number One. The Brilliant Blue G (BBG) dye, which helps control the activity of ATP by blocking its activation of P2X7 receptors, was shown to help repair the injured spinal cords when treated animals even started moving their previously paralyzed limbs. Interestingly, it was recently discovered that excessive release of ATP, a compound typically known as a biological power source, augments tissue injury by activating these high-affinity P2X7 receptors.
University of Rochester explains:

“While we achieved great results when oxidized ATP was injected directly into the spinal cord, this method would not be practical for use with spinal cord-injured patients,” said lead researcher Maiken Nedergaard, M.D., D.M.Sc., professor of Neurosurgery and director of the Center for Translational Neuromedicine at the University of Rochester Medical Center. “First, no one wants to put a needle into a spinal cord that has just been severely injured, so we knew we needed to find another way to quickly deliver an agent that would stop ATP from killing healthy motor neurons. Second, the compound we initially used, oxidized ATP, cannot be injected into the bloodstream because of its dangerous side effects.”
Neurons in the spinal cord are so susceptible to ATP because of a molecule known as “the death receptor.” Scientists know that the receptor – called P2X7 – plays a role in regulating the deaths of immune cells such as macrophages, but in 2004, Nedergaard’s team discovered that P2X7 also is carried in abundance by neurons in the spinal cord. P2X7 allows ATP to latch onto motor neurons and send them the flood of signals that cause their deaths, worsening the spinal cord injury and resulting paralysis.
So the team set its sights on finding a compound that not only would prevent ATP from attaching to P2X7, but could be delivered intravenously. In a fluke, Nedergaard discovered that BBG, a known P2X7R antagonist, is both structurally and functionally equivalent to the commonly used FD&C blue dye No. 1. Approved by the Food and Drug Administration as a food additive in 1982, more than 1 million pounds of this dye are consumed yearly in the U.S.; each day, the average American ingests 16 mgs. of FD&C blue dye No. 1.
“Because BBG is so similar to this commonly used blue food dye, we felt that if it had the same potency in stopping the secondary injury as oxidized ATP, but with none of its side effects, then it might be great potential treatment for cord injury,” Nedergaard said.
The team was not disappointed. An intravenous injection of BBG proved to significantly reduce secondary injury in spinal cord-injured rats, who improved to the point of being able to walk, though with a limp. Rats that had not received the BBG solution never regained the ability to walk. There was one side effect: Rats who were injected with BBG temporarily had a blue tinge to their skin.

More from National Geographic…
Abstract in PNAS: Systemic administration of an antagonist of the ATP-sensitive receptor P2X7 improves recovery after spinal cord injury
Press release: Common Food Dye May Hold Promise in Treating Spinal Cord Injury

When looking for a new substance to act as a pharmaceutical agent, researchers have to sift through a lot of chemical structures to find good candidates. To help filter through the huge number of possible candidates, researchers at the Max Planck Institute of Molecular Physiology in Dortmund, Germany have developed a new application that matches the chemical space of a given compound to the possibility that it will bind to a protein in question. The Scaffold Hunter application, in addition to matching known compounds, can also suggest unknown yet unobserved ones that may become possible matches to a protein.
More details from the Max Planck Society:

The scientists focus on the medically relevant section of the chemical space, in which molecules contain ring-shaped structures. To do this, they reduce the molecules to their characteristic scaffolds. Scaffold Hunter then orders these structures in a kind of family tree based on their similarities: the program assigns smaller ‘parent’ scaffolds to each scaffold by gradually removing rings from the original ‘child’ scaffold. This generates innumerable parent-child relationships – structurally related molecules of varying complexity. The advantage lies in the fact that chemically similar compounds are very likely to display similar biological activity.
"These structurally-based lineages form the branches of the tree," explains Stefan Wetzel: "With the help of Scaffold Hunter we move along the branches from complex to increasingly simple structures which may be similar in their effect." Thus, the researchers identify structurally simple scaffolds with promising characteristics as the starting point in the quest for new active agents: chemists can then vary the scaffolds with different appendages to synthesize the optimal active agent. Scaffold Hunter can also be used to predict bioactive molecules that do not arise in nature but are very likely to display similar activity to related natural molecules, as the program also creates and visualizes virtual scaffolds. The researchers immediately demonstrated how efficiently the program works by discovering new inhibitors of pyruvate kinase. The inhibition of this enzyme is seen as a promising approach to the treatment of cancer and malaria.
An even more detailed search can be carried out if the scientist can enter information about biological activity – if available – at the beginning of the navigation process. In this case, Scaffold Hunter only links the scaffolds that are known to display the same biological activity to the branches. As a result, these branches are very likely to bear fruit: active substances are probably also located in the branches between the substances whose biological activity is already known. "In this way, we tracked down new inhibitors for 2-lipoxygenase and the oestrogen receptor alpha," says Steffen Renner, a former researcher at the Max Planck Institute and now an employee of the Novartis pharmaceutical concern. 5-lipoxygenase is a target protein in the treatment of inflammation and bladder cancer, while the oestrogen receptor alpha is an important starting point in the treatment of breast cancer.

Press release: Navigating in the ocean of molecules
Image: The search for active agents in the tree of structures: Basic chemical scaffolds are linked initially on the basis of their structural similarity. Compounds that influence the enzyme pyruvate kinase are shown in blue, the virtual scaffolds in grey. Variants of the virtual scaffold shaded in red (top right) were tested for their biological potency and pointed to other active substances (bottom right)).
Abstract in Nature Chemical Biology:Bioactivity-guided mapping and navigation of chemical space

Stuart Kauffman, a theoretical biologist and author from the University of Calgary, has been hypothesizing about the possible underlying physical nature of the consciousness. Just like Roger Penrose, whom we immensely respect, Dr. Kauffman believes that quantum mechanics plays a central role, creating an unpredictable output but which is not random. So there are laws that play a part, but the result cannot be algorithmically predicted, allowing for what looks like an independent consciousness.
Article abstract from arXiv:

Since Descartes’ dualism, with his res extensa and res cogitans, six fundamental problems in the philosophy and natural history of mind are these: 1. how does mind act on matter? 2. If mind does not act on matter is mind a mere epiphenomenon? 3. What might be the source of free will? 4. What might be the source of a responsible free will? 5. Why might it have been selectively advantageous to evolve consciousness? 6. What is consciousness? I approach the first five of the above six problems based on two physical postulates. First the mind-brain system is a quantum coherent, but reversibly decohering and recohering system. This allows me to answer 1) above, mind does not act causally on brain at all, rather it acausally decohers to classicity (for all practical purposes), hence has consequences for brain and body as matter. Epiphenomenalism is averted. A quantum mind, because it is acausal on Copenhagen including Born, yields a free will, but a merely random free will, not a responsible free will. Second, the most radical part of this article proposes that the quantum classical interface is not always describable by a law: specifically in a special relativity setting, no function, F, maps the present state of the system mind-brain into its future. In its place is a nonrandom yet lawless process. I seek in this non-random yet lawless process a source for a responsible free will. Finally, if the quantum-classical boundary can be non-random yet lawless, then no algorithmic simulation of the world or ourselves can calculate the real world, hence the evolutionary selective advantages for evolving consciousness to know it may be great. I make no progress on problem 6, the hard problem of qualia.

Full article: Physics and Five Problems in the Philosophy of Mind…
More from physics arXiv blog…
The Problem of Consciousness video by Roger Penrose…
Image credit: Ian Spreadbury

At Duke University, scientists used a single basal cell to grow hollow spheres of differentiated ciliary and secretory lung cells. This type of research should help investigators to learn more about lung health and to develop new treatments using a standalone test platform that resembles real lungs.

The scientists isolated basal cells, set each separately in a gel suspension, and observed the cells growing into a hollow sphere as they divided. Analysis shows that the basal cells remain on the outside of the sphere, while inside the hollow was lined in an equal arrangement of cilial and secretory cells, as in nature.
“This basal cell is making daughters, which are polarized and retain their orientation so that they will form a structure with luminal (airway lining) cells on the inside,” Hogan [Brigid Hogan, chair of the Duke Department of Cell Biology] said.
“Only about 5 percent of the basal cells we isolated and put into gel formed these spheres; perhaps these are the ones that are normally ready to leap into action when they are challenged.”
After painstakingly sorting individual green fluorescent mouse basal cells from the other lung tissue cells, the scientists studied the genes expressed in these mouse cells using microarray technology. They found more than 600 genes preferentially expressed in the basal cells compared with the other cells.
“We found that many of these genes are similar to genes expressed in stem cells in other tissues,” Hogan said. “We think these genes are helping these cells to stay ‘quiet’ and keep them from dividing until they get the right signal.”
The researchers also found that one gene expressed in the basal cells encodes a surface receptor, also found on human lung basal cells.
“This meant we were able to use a labeled antibody against this receptor to efficiently extract human lung basal cells to create the human bronchospheres for study,” Hogan said.

Press release: Duke Scientists Create Model to Study Lung Diseases…
Image: Ciliary and secretory cells (green) form inside the basal stem cell (red)
Abstract in PNAS: Basal cells as stem cells of the mouse trachea and human airway epithelium

Everyone knows that time has a tendency to flow differently depending on different circumstances. Here’s how Albert Einstein remarked about the similarity between the relativity of physical and psychological time:

“When a man sits with a pretty girl for an hour, it seems like a minute. But let him sit on a hot stove for a minute — and it’s longer than any hour. That’s relativity.”

What we also know, is that elite sportspeople report being able to go into “the zone,” a state in which time starts to slow down, so the play, for example a tennis match, becomes more manageable as the ball glides with less relative speed across the court. Is it a real quantum phenomenon or just a psychological interpretation or voodoo? No one really knows.
What we know is that the biology of how we perceive time lacks a definitive scientific explanation. Now scientists from Medical University of South Carolina and Duke University have thrown a new twist into a theory of time perception, by showing that there seem to be multiple clocks with different temporal contexts operating in the brain. By being able to note the difference between clocks, the scientists claim we make temporal judgments of the world around us.
Abstract from the article in PLoS ONE:

Background
Current theories of interval timing assume that humans and other animals time as if using a single, absolute stopwatch that can be stopped or reset on command. Here we evaluate the alternative view that psychological time is represented by multiple clocks, and that these clocks create separate temporal contexts by which duration is judged in a relative manner. Two predictions of the multiple-clock hypothesis were tested. First, that the multiple clocks can be manipulated (stopped and/or reset) independently. Second, that an event of a given physical duration would be perceived as having different durations in different temporal contexts, i.e., would be judged differently by each clock.
Methodology/Principal Findings
Rats were trained to time three durations (e.g., 10, 30, and 90 s). When timing was interrupted by an unexpected gap in the signal, rats reset the clock used to time the “short” duration, stopped the “medium” duration clock, and continued to run the “long” duration clock. When the duration of the gap was manipulated, the rats reset these clocks in a hierarchical order, first the “short”, then the “medium”, and finally the “long” clock. Quantitative modeling assuming re-allocation of cognitive resources in proportion to the relative duration of the gap to the multiple, simultaneously timed event durations was used to account for the results.
Conclusions/Significance
These results indicate that the three event durations were effectively timed by separate clocks operated independently, and that the same gap duration was judged relative to these three temporal contexts. Results suggest that the brain processes the duration of an event in a manner similar to Einstein’s special relativity theory: A given time interval is registered differently by independent clocks dependent upon the context.

Article in PLoS ONE: Relativity Theory and Time Perception: Single or Multiple Clocks?
Here’s an interesting paper on the topic, recently published on a website of the Foundational Questions Institute: Neurophysiology of Time
Quantum biology flashbacks: Birds Exhibit Longest Suspected Quantum Entanglement; Photosynthesis Thought to Exhibit Quantum Entanglement Phenomenon; Eyes As Photon Detectors for Quantum Experiments; Discover Mag Looks at Quantum Biology
Image credit: Ian Spreadbury