Wednesday, August 26, 2009

Genomic Study Yields Plausible Cause Of Colony Collapse Disorder

SITE SUMMARY: ScienceDaily (2009-08-25) -- Researchers have found a surprising but reliable marker of colony collapse disorder, a baffling malady that in 2007-2008 killed off more than a third of commercial honey bees in the US. Their study is the first to identify a single, objective molecular marker of the disorder, and to propose a data-driven hypothesis to explain the mysterious disappearance of American honey bees.

Click HERE to view article


COMMENTS: CCD is a major concern for society.  In addition to the honey that many love & that is an integral ingredient, the real value of bees to humans is that we rely on bees extensively for crop pollination.

Thursday, August 6, 2009

Why we're all so different

A new study finds that LINE elements play a larger role in brain cells than anyone had thought. Because genes can jump around, the capacity of brain cells to be different from each other in form and function is virtually infinite.

'Jumping Genes' Create Diversity In Human Brain Cells, Offering Clues To Evolutionary And Neurological Disease

ScienceDaily (Aug. 6, 2009) — Rather than sticking to a single DNA script, human brain cells harbor astonishing genomic variability, according to scientists at the Salk Institute for Biological Studies. The findings, to be published in the Aug. 5, 2009, advance online edition of Nature, could help explain brain development and individuality, as well as lead to a better understanding of neurological disease.

The team, led by Fred Gage, Ph.D., a professor in the Salk's Laboratory of Genetics and holder of the Vi and John Adler Chair for Research on Age-Related Neurodegenerative Diseases, found that human brain cells contain an unexpected number of so-called mobile elements—extraordinary pieces of DNA that insert extra copies of themselves throughout the genome using a "copy and paste" mechanism.

Tuesday, August 4, 2009

What is this?

In addition to rants and musings about all things Bio, I have decided to also make this blog a collection of interesting/

Thursday, July 16, 2009

Top Ten Ways Biology is Changing Your Life


Much in the way classic physicists, astronomers, or chemists were looked at with skepticism and fear in ancient society, today the new science to fear is Biology. Specific aspects of biology are fascinating and terrifying to people, the same as it was when the Galileo dared to show that the Earth revolved around the Sun.

Despite the pet issues that are in the forefront of American minds when thinking of biological research (abortion, GMO or stem cells anyone?), your world and your life are quietly being altered more drastically by Biology in ways you may not expect. For instance:

10.) Circadian rhythm- The genetic basis for circadian rhythm is the fact that different genes turn "on" or "off" at different times of the day, week, month, or year, so that your body is always able to locate itself in time. You've probably observed this in very common phenomena such as jet lag, the fact that you can approximate what time of day & year it is even in a room with no windows, or (for the ladies) the regularity of the menstrual cycle. But were you aware that the very yeast that ferments your beer is also being used to model these circadian rhythm cycles? Just ask Dr. Benjamin Tu or Dr. Steve McKnight about it- two of the leaders in this rapidly-expanding field. While humans are very complex & scientists can't genetically modify people to see the effects on their circadian rhythm, yeast are single-celled and have much fewer genes- and those genes are easy to mutate so they can see how the rhythm is affected. These techniques lead to breakthroughs in the McKnight lab came when they found that specific genes were turned on and off in yeast in regular patterns throughout the day. These patterns correlate with other factors such as metabolism, growth, reproduction, and activity levels, just as in humans. When the yeast are mutated, everything can go haywire- from metabolizing the wrong proteins at the wrong time to being unable to grow large enough to reproduce to being unable to excrete wastes. The next step for this information? Isolating how these circadian rhythms work can lead to new therapies that allow for the rhythms to be "re-programmed" when they have gone awry, such as with long-term jet-lag in frequent travelers, menstrual cycle irregularity, or mental defects. In the future, travelers across six time-zones could potentially take a pill to help adjust within only a few hours. Fatigue during the night-shift can be alleviated by re-adjusting the sleep cycle. Wannabe moms might get "rhythm therapy" to help their cycles become more regular and adjusted. All this potential from mutating a little eukarytic cell: Yeast. It's not just for beer anymore.

9.) Proteomics. So you've heard of Genomics: the cataloging entire set of genes encoded in the DNA of an organism. By 2003, the Human Genome Project had more or less listed every base pair found in human DNA. (More or less, since every person's DNA is a bit different.) What is coded in that DNA, though? Well, the new challenge is to find out, and that has lead to a related field called Proteomics. This field is focused on cataloging the entire set of proteins that the DNA codes for- and there are far far more proteins than there are genes. But the interesting part about proteomics is that there are a lot more similarities of protein structure & function between different species than there are similarities in the DNA- giving a whole new outlook on evolutionary & phylogenetic studies. Proteomics also attempts to look at what these genes encoded in the genome actually do- because 95% of it is unknown. Poorly-defined diseases or disorders, such as Guillan-Barre syndrome, may become more treatable if a defective protein can be associated with a genetic defect or if it is found to be altered by certain substance. Plus, proteins make great targets for pharmaceuticals. Proteomics and Genomics work together, however: Not all DNA codes for proteins, proteins can be modified by other proteins, proteins can interact with DNA or with parts of the cell, and genes can do seemingly nothing. Putting all of these interactions together in a complete catalog is yet another related and burgeoning field: Bioinformatics.

8.) Agriculture. Before there were GMO's, there was simple crop breeding, just as there is livestock breeding. Advances were accomplished in crop breeding and animal breeding even before the modern principles of genetics were elucidated- far before. Today the methods used are more powerful and much more specific, and most of it does not make use of potentially uncomfortable modifications such as flounder genes in a strawberry. Instead, they are taking the approach to maximize yield in specific areas: Wheat is now being cultivated so that farmers can have a better-yielding crop in drier areas, rice patties are becoming hardy enough to withstand a minor drought, stains of cotton are being grown that have better natural resistance to weevils. Surprisingly to some, these new strains are not made by the insertion of artificial genes, but rather, by crossing strains that already have the desirable properties in them. Plant and crop scientists will comb the world to find a stalk of corn that has resisted a 3-day frost, then take painstaking care to breed those genes in with another crop that is faster growing and has larger ears. The 'super strains' of crops are so great, however, that they are very rare, and most come from recessive genes, so most large farms recieve clones, since the seeds would not yield a new generation that would be as good or as homogenous as the last. New sustainability strategies are looking at the effects of heterogenous plots and the effects of local climate on the natural selection of plant traits. The nature of the work is also making it more of a research-based, rather than patent-based, field, and this means that crops will be cheaper to purchase and of better quality to the farmer. New scientific goals are aiming to bring local and specifically tailored crops as a food supply to different regions, and empower farmers in all areas of the world by having successful crops. And this says nothing of the advances in animal livestock that are being made!

7.) Integrated science. Previous generations of scientists and mathematicians chose a path- be it biology, chemistry, physics, geology, psychology, mathematics, astronomy, or physiology- and stayed neatly in that path without crossing over. Modern scientists, however, tend to have a little of everything at their disposal: Biochemistry, biophysics, biostatistics, theoretical calculus, quantum astronomy, astrogeology, neuroanatomy, neurobiology, pharmacology, chemical engineering, etc etc. What is happening is that scientists and mathematicians started talking to each other, and realizing that they could come together using this machinery and that chemical and that equation and come out with something completely novel. The growing field of pharmacology is based solely on finding how the pathways in the body work (using Bioinformatics) and using that information to chemically design effective drugs. The newest field, Neuroscience, uses painstaking characterizations of brain anatomy & physiology combined with chemical pathways to solve problems related to behaviour, development, cancer, and diseases such Alzheimer's. Even naturalists, the original biologists, are turning to statistics and geology to make more precise and accurate findings, and turning to archaeology to correlate new findings with events in the past. For your own life, this should give you far more confidence in science now than ever before: The more ways of approaching a problem, and the more tools in the scientific toolbox for solving it, the more accurate and precise the outcome. This is becoming the standad, and not the exception, too. Next time they are building an artificial habitat in your city, a new drug is recommended by your doctor, or a quick laser diagnosis is available, feel assured that these things are being looked at by scientists that are analyzing the Bigger Picture from many angles.

6.) Biosensors.
RIGHT: An X-Ray Crystallography image from: Barends et al (2009). Structure and mechanism of a bacterial light-regulated cyclic nucleotide phosphodiesterase. Nature 459, 1015-1018.

X-Ray Crystallography allowed the first "imaging" of the double helix of DNA. Today, these images can be created and interpreted by computers and crystallographers to give a very true-to-life replica of what a protein or a helix of DNA actually looks like. This can be done for small proteins that bind to DNA or for large proteins that capture oxygen (such as hemoglobin). These methods have given biologists and biochemists today some insights about protein functions and action that past generations could only speculate. The structures themselves are like molecular Legos (or building blocks, if you will): You can see which other blocks are going to fit in with which other blocks, how a Lego with a small shape mutation can no longer bind to other Legos to make the Lego Castle, how you could use the building blocks to build other structures, and even how you might create another block to change the way a certain block can stack with the others. Now, if you replace "block" or "Lego" in the above sentence with "protein", you can see the uses of visualizing a protein structure: How it will fit in with other molecules or proteins, how mutations in a protein (caused by genetic mutation or by disease) can make it no longer able to interact with the same proteins that it could if it were not mutated, how the protein might be of use in other protein interactions, or even how to design a drug to specifically interact with that protein. Plus... to be honest, this is just really cool.

5.) Vaccination & Prevention.

4.) The Biology of Aging.

3.) Alzheimer's.

2.) AIDS.

1.) Designer cancer therapy.