Category Archives: Life Science

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 A few years from now it’ll be routine, and a few years after that it probably won’t be done at all, having been superseded by something more elegant that no one’s come up with yet.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.

Female Sharks Can Reproduce Alone

Female Sharks Can Reproduce Alone, Researchers Find

A team of American and Irish researchers have discovered that some female sharks can reproduce without having sex, the first time that scientists have found the unusual capacity in such an ancient vertebrate species. The[y] report that sharks can reproduce asexually through the process known as parthenogenesis
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Though the three females had been caught before they reached sexual maturity and held in captivity for more than three years, researchers initially thought one had stored sperm from a male shark before fertilizing an egg. But the team — which included scientists at Nova Southeastern University in Florida, Queen’s University Belfast and the zoo — determined that the baby shark’s genetic makeup perfectly matched one of the females in the tank, with no sign of a male parent.

Mahmood Shivji — Nova Southeastern’s Guy Harvey Research Institute director and one of the paper’s authors — said that he and his colleagues determined that a byproduct formed when sharks produce eggs, known as a sister polar body, had fused with an unfertilized egg to produce the baby shark, whose DNA had only half as much genetic variability as the mother.

Water Buffaloes, Lions and Crocodiles Oh My

Pretty amazing video. A look at real wild life with lots of excitement, a bit violence and some surprising turns. On my trip to Kenya I saw an interaction between lions and one water buffalo but it was without much of this action. Basically there was a standoff for like half an hour with half charges and the like. Even that was very interesting.

Deep-Sea Alien Abode Discovered

Deep-Sea Alien Abode Discovered by Jeanna Bryner:

Recent expeditions have uncloaked this polar region, finding nearly 600 organisms never described before and challenging some assumptions that deep-sea biodiversity is depressed. The findings also suggest that all of Earth’s marine life originated in Antarctic waters.

Scientists had assumed that the deep sea of the South Pole would follow similar trends in biodiversity documented for the Arctic. “There are less species in the Arctic than around the equator,” said one of the study scientists, Brigitte Ebbe, a taxonomist at the German Center for Marine Biodiversity Research. “People assumed that it would be the same if you went from the equator south, but it didn’t prove to be true at all.”

Very interesting stuff. Related: Altered Oceans, the Crisis at Sea – Ocean Life – Antarctic Robo-sub

Bird Species Plummeted After West Nile

Bird Species Plummeted After West Nile:

Several common species of North American birds have suffered drastic population declines since the arrival of the West Nile virus eight years ago, leaving rural and suburban areas quieter than they used to be and imposing ecological stresses on a variety of other animals and plants, a new study has found.

In Maryland, for example, 2005 chickadee populations were 68 percent lower than would have been expected had West Nile not arrived, and in Virginia chickadee populations were 50 percent below that prediction.
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It shows that the post-1998 declines were greatest at times and places in which the virus was especially prevalent — as indicated by the number of human infections diagnosed. As expected, American crows were among the worst hit, suffering declines of as much as 45 percent in some regions and wipeouts of 100 percent in some smaller areas. Other species that suffered included the blue jay, the tufted titmouse, the American robin, the house wren, the chickadee and — unexpectedly — the American bluebird.

Bacterium Living with High Level Radiation

Organism found at SRS amazes scientific world by Rob Pavey

In addition to thriving in the face of normally-lethal radiation, the organism also demonstrates remarkable survival characteristics in terms of its DNA. Humans and most organisms can tolerate few breaks in DNA molecules, he said, but kineococcus radiotolerans has the ability to reassemble itself.

“With this organism, we can take an intact DNA molecule, blast it into little pieces, and in five to six hours the organism is restored and growing normally again,” Dr. Bagwell said. Dr. Bagwell and others who have studied the organism hope further research will yield clues that could aid in medical research, cancer studies and other areas.

“There’s a lot of excitement about this organism because of its ability to withstand tremendous abuse,” he said. “What we don’t know is how it does these things – and what more it can do. That’s the direction we’re going now.”

Related: What is an Extremophile? – more info on Kineococcus radiotolerans

Microorganisms on Spaceships

Space Mold photo

Preventing “Sick” Spaceships, NASA:

Moreover, the mass of water was only one of several hiding behind different panels. Scientists later concluded that the water had condensed from humidity that accumulated over time as water droplets coalesced in microgravity. The pattern of air currents in Mir carried air moisture preferentially behind the panel, where it could not readily escape or evaporate.

Nor was the water clean: two samples were brownish and a third was cloudy white. Behind the panels the temperature was toasty warm—82ÂºF (28ÂºC)—just right for growing all kinds of microbeasties. Indeed, samples extracted from the globules by syringes and returned to Earth for analysis contained several dozen species of bacteria and fungi, plus some protozoa, dust mites, and possibly spirochetes.

But wait, there’s more. Aboard Mir, colonies of organisms were also found growing on “the rubber gaskets around windows, on the components of space suits, cable insulations and tubing, on the insulation of copper wires, and on communications devices,”

Photo: Dust mite was found floating in a globule of water onboard Mir. Other microorganisms collected include protozoa and amoeba. [Read more – Microbial Characterization of Free Floating Condensate
aboard the Mir Space Station – pdf]

Diversity Efforts for the Life Science Work Force

Focus on Diversity: INCUBATING INNOVATION – Diversity Efforts Rejuvenate the Life Science Work Force by Alethea Hannemann:

Support for undergraduate and graduate programs that encourage African-American scientists also comes from industry leaders. Merck, in a partnership with the United Negro College Fund, awards at least 37 scholarships a year to African-American researchers at the undergraduate, graduate, and postdoctoral levels; to date, the program has trained more than 370 scientists.
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In the end, building a robust, diverse science work force will take vigorous effort from many camps. The good news is that a host of programs in government, academia, and industry are dedicated to increasing the numbers of African-Americans in science. With continued efforts, education and recruiting programs should soon bear fruit, bringing new power to the life sciences.

Opossum Genome Shows ‘Junk’ DNA is Not Junk

Opossum Genome Shows ‘Junk’ DNA Source Of Genetic Innovation

Scientists previously thought that evolution slowly changed the genes that create specific proteins. As the proteins changed, so did the creatures that owned them. The current research shows that opossum and human protein-coding genes have changed little since their ancestors parted ways, 180 million years ago. It has been the regulation of their genes – when they turn on and off – that has changed dramatically.

“Evolution is tinkering much more with the controls than it is with the genes themselves,” said Broad Institute director Eric Lander. “Almost all of the new innovation … is in the regulatory controls. In fact, marsupial mammals and placental mammals have largely the same set of protein-coding genes. But by contrast, 20 percent of the regulatory instructions in the human genome were invented after we parted ways with the marsupial.”
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It had been initially thought that most of a creature’s DNA was made up of protein-coding genes and that a relatively small part of the DNA was made up of regulatory portions that tell the rest when to turn on and off. As studies of mammalian genomes advanced, however, it became apparent that that view was incorrect. The regulatory part of the genome was two to three times larger than the portion that actually held the instructions for individual proteins.

Very interesting. The more recent articles I read on DNA discoveries the more interesting it seems to get. Related: Learning About the Human Genome – New Understanding of Human DNA – DNA Transcription Webcast