Category Archives: Life Science

Origins of the Domestic Cat

The study suggests the progenitors of today’s cats split from their wild counterparts more than 100,000 years ago – much earlier than once thought. At least five female ancestors from the region gave rise to all the domestic cats alive today, scientists believe. DNA evidence suggests that, apart from accidental cross-breeding, European wildcats are not part of the domestic moggy’s family tree. Neither are the Central Asian wildcat, the Southern African wildcat, or the Chinese desert cat.
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The earliest archaeological evidence of cat domestication dates back 9,500 years, when cats were thought to have lived alongside humans in settlement sites in Cyprus. However, the new results show the house cat lineage is far older. Ancestors of domestic cats are now thought to have broken away from their wild relatives and started living with humans as early as 130,000 years ago. The researchers focused on DNA in the mitochondria, the power plants of cells which supply energy and have their own genetic material.

Evo-Devo

Sean B. Carroll discusses the science of evolution and the field of evo-devo in this New York Times Video. Learn more in this extensive article – From a Few Genes, Life’s Myriad Shapes:

evo-devo is the combined study of evolution and development, the process by which a nubbin of a fertilized egg transforms into a full-fledged adult. And what these scientists are finding is that development, a process that has for more than half a century been largely ignored in the study of evolution, appears to have been one of the major forces shaping the history of life on earth.

For starters, evo-devo researchers are finding that the evolution of complex new forms, rather than requiring many new mutations or many new genes as had long been thought, can instead be accomplished by a much simpler process requiring no more than tweaks to already existing genes and developmental plans. Stranger still, researchers are finding that the genes that can be tweaked to create new shapes and body parts are surprisingly few. The same DNA sequences are turning out to be the spark inciting one evolutionary flowering after another. “Do these discoveries blow people’s minds? Yes,” said Dr. Sean B. Carroll, biologist at the Howard Hughes Medical Institute at the University of Wisconsin, Madison.

via: Justin Hunter (Justin and me in Madison) 🙂 Related: Opossum Genome Shows ‘Junk’ DNA is Not Junk – science webcast directory – Learning About the Human Genome – Curious Cat Science and Engineering Search

Tracking the Ecosystem Within Us

Gut Check: Tracking the Ecosystem Within Us

For more than 100 years, scientists have known that humans carry a rich ecosystem within their intestines. An astonishing number and variety of microbes, including as many as 400 species of bacteria, help humans digest food, mitigate disease, regulate fat storage, and even promote the formation of blood vessels. By applying sophisticated genetic analysis to samples of a year’s worth baby poop, Howard Hughes Medical Institute researchers have now developed a detailed picture of how these bacteria come and go in the intestinal tract during a child’s first year of life.
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Before birth, the human intestinal tract is sterile, but babies immediately begin to acquire the microbial denizens of the gut from their environment — the birth canal, mothers’ breast, and even the touch of a sibling or parent. Within days, a thriving microbial community is established and by adulthood, the human body typically has as many as ten times more microbial cells than human cells.
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The results, said Palmer, were striking: the group found that the intestinal microbial communities varied widely from baby to baby – both in terms of which microbes were present and in how that composition changed over time. That finding, she said, is important because it helps broaden the definition of healthy microbial colonization in a baby.

Another intriguing observation, Palmer noted, was a tendency for sudden shifts in the composition of the infants’ intestinal microbial communities over time as different species of bacteria ebbed and flowed.

I find this area and this study fascinating. I’m not exactly sure why this study and the incredibly significant positive bacteria for human life news doesn’t get more notice. Oh well I guess there are not cool pictures of robots or scary stories of potential threats to those reading which makes the news less interesting to some. Still I find this stuff amazing: Energy Efficiency of Digestion – Beneficial Bacteria – Skin Bacteria – Hacking Your Body’s Bacteria for Better Health – Where Bacteria Get Their Genes

Using Bacteria to Carry Nanoparticles Into Cells

Bacteria ferry nanoparticles into cells for early diagnosis, treatment

Researchers at Purdue University have shown that common bacteria can deliver a valuable cargo of “smart nanoparticles” into a cell to precisely position sensors, drugs or DNA for the early diagnosis and treatment of various diseases. The approach represents a potential way to overcome hurdles in delivering cargo to the interiors of cells, where they could be used as an alterative technology for gene therapy, said Rashid Bashir, a researcher at Purdue’s Birck Nanotechnology Center.

The researchers attached nanoparticles to the outside of bacteria and linked DNA to the nanoparticles. Then the nanoparticle-laden bacteria transported the DNA to the nuclei of cells, causing the cells to produce a fluorescent protein that glowed green. The same method could be used to deliver drugs, genes or other cargo into cells.

“The released cargo is designed to be transported to different locations in the cells to carry out disease detection and treatment simultaneously,” said Bashir, a professor in the Weldon School of Biomedical Engineering and the School of Electrical and Computer Engineering. “Because the bacteria and nanoparticle material can be selected from many choices, this is a delivery system that can be tailored to the characteristics of the receiving cells. It can deliver diagnostic or therapeutic cargo effectively for a wide range of needs.”

Harmless strains of bacteria could be used as vehicles, harnessing bacteria’s natural ability to penetrate cells and their nuclei, Bashir said. “For gene therapy, a big obstacle has been finding ways to transport the therapeutic DNA molecule through the nuclear membrane and into the nucleus,” he said. “Only when it is in the nucleus can the DNA produce proteins that perform specific functions and correct genetic disease conditions.”
Continue reading →

River Blindness Worm Develops Resistance to Drugs

River blindness resistance fears

Resistance could lead to breakouts of the infection in communities where it has been brought under control, a Canadian study in the Lancet reports. Ivermectin, used since the late 1980s, is the only drug available for the mass treatment of river blindness. Experts warned the findings highlighted the urgent need for new treatments. River blindness (onchocerciasis) is caused by a nematode worm which is transmitted by a black fly.
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He added that isolated resistance could be controlled by using insecticides or an antibiotic called doxycycline, which is effective but needs to be given every day for a long time.
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Professor Taylor’s team have recently received a large grant from the Bill and Melinda Gates Foundation to search for new drugs or combinations that can have the same effect as a course of doxycycline but delivered in shorter time frame.

The Bill and Melinda Gates Foundation is funding a tremendous amount of important work.

Life-patents

New Life, New Patent by Carl Zimmer:

ETC is right in suggesting Venter might become “Microbesoft”–controlling operating system for anyone who wants to build an organism from scratch. Other researchers, such as Keasling, are promoting a different way of doing synthetic biology–what they call open source biology. Scientists and their students are amassing an open inventory of parts that anyone can use to design organisms of their own. And it’s open source biology, these researchers argue, that will provide the best protection against any evil uses of synthetic biology. Instead of being hidden behind patents, the information about these parts would be available to everyone, and collectively solutions could be found. As this debate starts to unfold, I think open source biology will keep it from becoming nothing but deja vu.

I support keeping science open. Patents are a tax on society that the government grants inventors for their efforts, in order to benefit society, by encouraging the inventors to innovate. The end is benefiting society. The means is granting a right of the patent holder (a right they do not have without patent law) that will encourage them to make the effort to innovate. I support the proper use of patents, but we have perverted the patent process into something that harms society. The system needs to be fixed. And the whole area of patents on life I find very questionable.

Antibacterial Products May Do More Harm Than Good

photo of a dandelion

Strange but True: Antibacterial Products May Do More Harm Than Good by Coco Ballantyne:

Unlike these traditional cleaners, antibacterial products leave surface residues, creating conditions that may foster the development of resistant bacteria, Levy notes. For example, after spraying and wiping an antibacterial cleaner over a kitchen counter, active chemicals linger behind and continue to kill bacteria, but not necessarily all of them.

When a bacterial population is placed under a stressor—such as an antibacterial chemical—a small subpopulation armed with special defense mechanisms can develop. These lineages survive and reproduce as their weaker relatives perish. “What doesn’t kill you makes you stronger” is the governing maxim here, as antibacterial chemicals select for bacteria that endure their presence.

Pretty basic understanding of evolution makes the breeding of very resilient bacteria a fairly obvious result. One thing that might not be as obvious until it is mentioned is that by killing off the “weaker” bacteria you also provide a niche for the more resilient bacteria to multiply and fill the gap left by the bacteria that were not a problem that were killed off. Imagine if, instead of digging out the 3 dandelions you wanted to remove from your yard, you removed all plants from your yard (including those 3 dandelions). I would bet most often that would result in more dandelions not fewer as the dandelions were able to fill in the void of plants in the yard.

In general, however, good, long-term hygiene means using regular soaps rather than new, antibacterial ones, experts say. “The main way to keep from getting sick,” Gustafson says, “is to wash your hands three times a day and don’t touch mucous membranes.”

Inner Life of a Cell: Full Version

This is an extremely cool 8 minute movie on the inner workings of a Cell. The earlier version we posted about back in September of last year has been one of our most popular posts – see our most popular posts. They have added the scientific explanation that I mentioned I would love to see in the last post.

update: Unfortunately Harvard seems to want to prevent people from seeing this educational webcast. Why they don’t want to promote science education is beyond me. I guess they have better uses for their $35 billion endowment than promoting science. I sure wish they would hurry up and realize this isn’t the 18th century. They say their mission is “The advancement of all good literature, arts, and sciences; the advancement and education of youth in all manner of good literature, arts, and sciences; and all other necessary provisions that may conduce to the education of the … youth of this country…” (Jun 2008). You don’t have to just educate a few privileged soles in ivy covered buildings. You can do that any provide great education material for others around the globe.

Animation created for Harvard’s Molecular and Cellular Biology program:

Harvard University selected XVIVO, LLC, a Connecticut based scientific animation company, to customize and develop an animation that would propel Harvard’s Molecular and Cellular Biology program to the next level of undergraduate education. XVIVO’s recently completed animation, titled “The Inner Life of the Cell”, has already won awards. The eight minute animation transports Harvard Biology students into a three-dimensional journey through the microscopic world of a cell.

DNA Repair Army

Analysis Reveals Extent of DNA Repair Army

Elledge’s group studied human cells in culture and mapped their response to ionizing radiation and ultraviolet light. Specifically, the group looked to see which proteins in the cell were chemically altered by the enzymes ATM and ATR, finding 900 sites on 700 proteins that changed in response to DNA damage. The discovery that so many proteins are involved in the process, Elledge said, was a big surprise.

Also see: Cell Cycle Regulation and Mechanisms of DNA Repair:

Despite the abuse our DNA endures, our individual genomes usually stay basically intact because DNA has a remarkable capacity for repair. Our cells have built-in, highly efficient machinery that finds and fixes “genetic typos.”
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Researchers have learned much about the complex genetic machinery that cells deploy to fix broken, cut, mutated, and misplaced genetic materials. Out of that evolving understanding has emerged a deeper awareness that DNA is truly dynamic and that responses to genetic damage are nearly as fundamental to life—and health—as is the genetic code itself.

Evolution In Action

the way they watched the process was to sequence the whole genome of each bacterial isolate. What they found were a total of 35 mutations, which developed sequentially as the treatment continued (and the levels of resistance rose). Here’s natural selection, operating in real time, under the strongest magnifying glass available. And it’s in the service of a potentially serious problem, since resistant bacteria are no joke. (Reading between the lines of the PNAS abstract, for example, it appears that the patient involved in this study may well not have survived).

The technology involved here is worth thinking about. Even now, this was a rather costly experiment as these things go, and it’s worth a paper in a good journal. But a few years ago, needless to say, it would have been a borderline-insane idea, and a few years before that it would have been flatly impossible. A few years from now it’ll be routine, and a few years after that it probably won’t be done at all, having been superseded by something more elegant that no one’s come up with yet. But for now, we’re entering the age where wildly sequence-intensive experiments, many of which no one even bothered to think about before, will start to run.

Very interesting. He is exactly right that the technology advances continuing at an amazing pace allow for experiments we (at least I) can’t even imagine today to become common in just a few years. And the insights from those experiments will allow us to think of new experiments… Wonderful.