HOME | ABOUT | RESUME | ESSENTIAL BOOKS | CONTACT ME


How biological patterns emerge?

July 2nd, 2008

butterfly patterns

This article was really interesting to me since it was a butterfly that made me realize that god existed as a child. I remember thinking there is no way something this pretty and delicate could evolve and survive on it’s own. Good luck trying to explain it scientifically lol . And yes I know it’s a little gay to say what I just did.

ScienceDaily (June 20, 2008) — A zebra’s stripes, a seashell’s spirals, a butterfly’s wings: these are all examples of patterns in nature. The formation of patterns is a puzzle for mathematicians and biologists alike. How does the delicate design of a butterfly’s wings come from a single fertilized egg? How does pattern emerge out of no pattern?

Using computer models and live cells, researchers at Johns Hopkins have discovered a specific pattern that can direct cell movement and may help us understand how metastatic cancer cells move.

“Pattern formation is a classic problem in embryology,” says Denise Montell, Ph.D., a professor of biological chemistry at Hopkins. “At some point, cells in an embryo must separate into those that will become heart cells, liver cells, blood cells and so on. Although this has been studied for years, there is still a lot we don’t understand.”

As an example of pattern formation, the researchers studied the process of how about six cells in the fruit fly distinguish themselves from neighboring cells and move from one location in the ovary to another during egg development. “In order for this cell migration to happen, you have to have cells that go and cells that stay,” says Montell. “There must be a clear distinction — a separation between different types of cells, which on the surface look the same.”

Previous work identified a specific signal necessary for getting these fly egg cells to move; the problem is that this signal is “graded.” Like drops of ink spreading out on wet paper, this signal travels in between surrounding cells, gradually fading away as it moves outwards. But clear lines are required for pattern formation — there is no grey area between a zebra’s black and white stripes, between heart and liver cells and, in this case, between migrating cells and those that stay put.

How are graded signals converted to a clear move or stay signal? By examining flies containing mutations in different genes, the researchers discovered that one gene in particular, called apontic, is important for converting a graded signal. “When apontic is mutated, the distinction between migrating and nonmigrating cells is fuzzy,” says Michelle Starz-Gaiano, Ph.D., a postdoctoral fellow in biological chemistry. “In these mutants, we see a lot of cases where migrating cells do not properly detach from their neighbors but instead drag them along as they move away.” This showed that the graded signal alone was not sufficient to kick-start the proper number of cells, but instead needed help from apontic.

Once the team discovered that apontic is important for getting these cells to move, they set out to figure out how apontic works. Collaborating with mathematician Hans Meinhardt, Ph.D., a professor emeritus at the Max Planck Institute in Germany, they designed a computer model that could simulate how graded signals are converted to commands that tell cells to move or to stay.

By making certain assumptions about each gene and assigning functions to each protein, the team built a simple circuit that can predict a cell’s behavior using the graded signal, apontic, and another previously discovered protein called slbo (pronounced “slow-bo”). The computer model shows that in a cell, the graded signal turns on both apontic and slbo. But apontic and slbo work against and battle each other: when one gains a slight advantage, the other weakens, which in turn causes the first to gain an even bigger advantage. This continues until one dominates in each cell. If slbo wins, the cell moves but if apontic wins, the cell stays put; thus a clear separation between move or stay is achieved.

“Not only is this a new solution to the problem of how to create a pattern out of no pattern, but we have also discovered that apontic is a new regulator of cell migration,” says Montell.

Cell migration likely underlies the spreading of cancer cells beyond an original tumor to other areas of the body. Understanding and therefore being able to manipulate the cell migration pathway could potentially prevent the development of these new tumors. At this stage, Montell says, “it’s more about just understanding what the positive and negative regulators of cell migration are.”

The research was funded by the American Cancer Society and the National Institutes of Health.

This study was published in the May 13 issue of Developmental Cell. Authors on the paper are Starz-Gaiano, Mariana Melani, Xiaobo Wang, and Montell, all of Hopkins; and Hans Meinhardt of the Max-Planck-Institut, Tübingen, Germany.

The answers to space might be in the microscopic fibers of atoms

July 1st, 2008

micro science

Suppose we were time travellers, and could transmit one key item of modern knowledge to a great intellect of the ancient world - Aristotle, for instance. What would we choose to tell them, a single sentence that would most transform their view of the world? We could tell them the scale of the universe - that the stars are other suns, and that there are billions of them. Or that all species emerged, over billions of years, via natural selection.

But I think what would enlighten them most of all would be the knowledge that all the stuff in the world is made of atoms - not of earth, air, fire and water, as the ancients believed. But what are the atoms themselves made of? Are they like an onion-skin with layer upon layer of structure, or will we soon reach bedrock, in the sense that the stuff of the universe will be fully understood?

It might seem paradoxical that the biggest scientific instruments of all are needed in order to probe the very smallest things in nature. The micro-world is inherently “fuzzy” - the sharper the detail we wish to study, the higher the energy that is required and the bigger the accelerator that is needed.

The Cern laboratory in Geneva was set up in 1955, to bring together European scientists who wished to pursue research into the nuclear and sub-nuclear world. Physicists then had greater clout than other scientists because the memory of their role in the second world war was fresh in people’s minds. Through a succession of projects - each too expensive for any single European country to fund - Cern has been at the forefront of endeavour to build ever more powerful accelerators probing ever smaller scales. This culminates in the Large Hadron Collider (LHC). Within its circular tunnel, 27km in circumference, protons hurtle around at 99.99% of the speed of light. The amazing technology combines huge civil engineering with microscopic precision.

Cern is a triumph of European collaboration, but it now has a global ascendancy, and is the premier laboratory in the world for particle physics. When it switches on this summer, the LHC will generate, in a microscopic region where beams of particles collide, a concentration of energy that has never been achieved before - a concentration that mimics, in microcosm, the conditions that prevailed in the universe during the first trillionth of a second after the big bang.

The impacts may generate particles of a novel kind never before detected in a laboratory (and which may even never have existed on the earth before). This possibility is especially interesting, because one of the most perplexing features of our universe is that there is a lot of material which isn’t made up of ordinary atoms. It’s possible that this “dark matter” consists of particles that are left over from the fiery beginning of the universe. The LHC may allow scientists to create and study these particles.

There are strengthening links between the sciences of the very large and the very small. It’s even possible that the LHC might tell us about the nature of space itself. In everyday life we regard space as dull vacuum. But this dismissive attitude is as misleading as it would be for us to believe that invisible clear air is less substantial that the clouds floating in it. Most theorists suspect that space has an intricate structure - that it is “grainy” - but that this structure is on a much finer scale than any known subatomic particle. The structure could be of an exotic kind: extra dimensions, over and above the three that we are used to (up and down, backward and forward, left and right).

A polished surface may seem smooth, but when viewed under a microscope it has bumps and dips in it: likewise our space, viewed on an ultra-fine scale, may have extra dimensions. The favoured view is that these extra dimensions only manifest themselves on scales a trillion trillion times smaller than atoms, and one of the most fascinating outcomes from the LHC could be the first evidence for them.

Whatever comes out of the LHC, the results will be a stimulus to next-generation Einsteins who will achieve the next steps in a quest, which started in ancient times, to understand the building blocks of the natural world.


Scientists nearer to synthetic spider silk

May 2nd, 2008

spider goat milkspider goat milk

The promise of super strong medical sutures, bullet proof vests and biodegradable fishing lines made of spider silk may at last be realised.

  • ‘Nanoyarn’ protein linked to Alzheimer’s could be super-fibre
  • Meet the real Spider-Man
  • For decades, scientists have been trying to crack the secret of spider silk, which has a tensile strength that is far greater than steel’s per unit weight, is five times more elastic than Kevlar and is easily recyclable.

    Years ago they found the genes for spider silk protein and even genetically altered goats to make the protein in their milk. But the results were disappointing because spider silk is spun in a particularly ingenious way, and from more than one protein.

    Now Prof Andreas Bausch, Prof. Thomas Scheibel and Dr Sebastian Rammensee and colleagues at the Technical University Munich report in the Proceedings of the National Academy of Sciences how they have built a device that mimics the early stages in the assembly of spider silk, which may aid in the eventual synthesis of the strong, lightweight material.

    Spider dragline silk consists of two proteins, ADF3 and ADF4, which coil into fibres in an irreversible process. After using bacteria to make the proteins, using standard genetic engineering methods, the researchers made an artificial spinneret, the organ used by the spider, to explore the ratio of proteins in various conditions.

    “The major breakthrough is that this is the first time one has produced fully synthetic silk threads and understood why,” says Prof Bausch.

    They suggest that three stages appear essential for fibre formation: that the proteins condense into spherical particles; that the acidity rises sharply; and that the particles be forced to slide past each other in a thin chamber.

    The artificial fibres are grainy compared to natural spider silk fibres, but the researchers believe will be like the real thing when they copy the drying and drawing stages employed by spiders. In this way, says Prof Bausch, large scale spider silk production will become a reality “in the near future.”

    Another article on it

    Dairy farmers don’t have to worry about suffering poisonous bites from the cows they milk.

    Greta Binford, however, has slightly less cooperative subjects. Binford collects venom from the world’s most dangerous spiders.

    Binford jokes she has “the dream job of most 8-year-old boys. I sit and watch spiders catch bugs.”

    She specializes in the brown recluse spider and its 100 relatives. Currently, her lab at Lewis & Clark College houses 600 spiders collected in the U.S., Africa, Peru and elsewhere.

    DNA analysis shows the spiders found in South America hold similarities to spiders found in Africa. By mapping patterns in DNA in spider venom, she hopes to learn more about why certain antidotes work against bites from some spiders but not others. “We’re trying to find out why that toxin is so different,” says Binford.

    One current antidote that works for almost all spiders found in North America does not work on one particular brown spider from Peru, which happens to be found in basements in Los Angeles.

    Binford is quick to point out that spider bites are rarely fatal. Particularly poisonous spiders leave behind hard to heal skin wounds.

    To analyze venom, she must collect the poison.

    That’s the tricky part.

    She places a spider in a small chamber filled with carbon dioxide. Within a few minutes the spider falls asleep. That’s when she places the spider under a microscope on its back and proceeds to wash its fangs with individual drops of water, sucked away with a tiny, needle-sized vacuum.

    That vacuum will come in handy in another way in a moment.

    Then with a small electrical current she shocks the spider. It’s mild and does no damage. But at the moment of the shock, all of the spider’s muscles contract causing venom to come out its fangs, and, unfortunately, vomit out of its mouth.

    “I have to work very hard to prevent the vomit from contaminating the venom,” Binford says, as she vacuums spider vomit with one tube and collects venom with another, all while peering through her microscope.

    After a few seconds she’s done.

    After another few minutes, the spider awakes and seems none the worse for wear.

    She sees no lasting side effects on her spiders which she milks regularly over five or six years. “It doesn’t seem to shorten their life,” she says. “They go ahead, they eat. They mate, have babies.”

    Binford and her colleagues hope to figure out “what cocktail of anti-venoms will work for bites from spiders from all of the Americas and maybe the world.”