Category Archives: Life Science

Variation in Human DNA

Variation on the order of thousands to hundreds of thousands of DNA’s smallest pieces – large swaths varying in length or location or even showing up in reverse order – appeared 4,205 times in a comparison of DNA from just four people.

Those structural differences popped into clear view through computer analysis of more than 500 linear feet of DNA molecules analyzed by the powerful genome mapping system developed over nearly two decades by David C. Schwartz, professor of chemistry and genetics at UW-Madison.

“We probably have the most comprehensive view of the human genome ever,” Schwartz says. “And the variation we’re seeing in the human genome is something we’ve known was there and important for many years, but we haven’t been able to fully study it.”

To get a better picture of those structural variations, Schwartz and his team developed the Optical Mapping System, a wholly new type of genome analysis that directly examines millions of individual DNA molecules.

“Our newer genome analysis systems, if commercialized, promise genome analysis in one hour, at under $1,000,” Schwartz says. “And we require that high speed and low cost to power the new field of personal genomics.”

Read full press release

Essentials of Genetics Website Reference

Scitable is a science library and personal learning tool on genetics developed by Nature. I must admit I am against the closed science stance Nature normally supports. But this is a good effort on their part at actually talking advantage of the internet to openly promote science. I imagine Nature will eventually more and more move toward supporting open science.

The website has a library of over 200 faculty-written, peer-reviewed articles on core concepts in genetics, plus a video-based online primer called Essentials of Genetics, glossaries, spotlights on key issues, and lots more high quality faculty and student resources.

Scitable is a great place to research and learn more about genetics topics such as diseases, evolution, genetics and society.

Trying to Find Pest Solutions While Hoping Evolution Doesn’t Exist Doesn’t Work

How To Make A Superweed

Melander wondered why some populations of scales were becoming able to resist pesticides. Could the sulfur-lime spray trigger a change in their biology, the way manual labor triggers the growth of callouses on our hands? Melander doubted it. After all, ten generations of scales lived and died between sprayings. The resistance must be hereditary, he reasoned. He sometimes would find families of scales still alive amidst a crowd of dead insects.

This was a radical idea at the time. Biologists had only recently rediscovered Mendel’s laws of heredity. They talked about genes being passed down from one generation to the next, yet they didn’t know what genes were made of yet. But they did recognize that genes could spontaneously change–mutate–and in so doing alter traits permanently.
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In the short term, Melander suggested that farmers switch to fuel oil to fight scales, but he warned that they would eventually become resistant to fuel oil as well. In fact, the best way to keep the scales from becoming entirely resistant to pesticides was, paradoxically, to do a bad job of applying those herbicides. By allowing some susceptible scales to survive, farmers would keep their susceptible genes in the scale population. “Thus we may make the strange assertion that the more faulty the spraying this year the easier it will be to control the scale the next year,” Melander predicted.
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What’s striking is how many different ways weeds have found to overcome the chemical. Scientists had thought that Roundup was invincible in part because the enzyme it attacks is pretty much the same in all plants. That uniformity suggests that plants can’t tolerate mutations to it; mutations must change its shape so that it doesn’t work and the plant dies. But it turns out that many populations of ryegrass and goosegrass have independently stumbled across one mutation that can change a single amino acid in the enzyme. The plant can still survive with this altered enzyme. And Roundup has a hard time attacking it thanks to its different shape.
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Another way weeds fight off Roundup is through sheer numbers. Earlier this year an international team of scientists reported their discovery of how Palmer amaranth resists glyphosate. The plants make the ordinary, vulnerable form of the enzyme. But the scientists discovered that they have many extra copies of the gene for the enzyme–up to 160 extra copies, in fact.
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What makes the evolution of Roundup resistance all the more dangerous is how it doesn’t respect species barriers. Scientists have found evidence that once one species evolves resistance, it can pass on those resistance genes to other species. They just interbreed, producing hybrids that can then breed with the vulnerable parent species.

Another great article from Carl Zimmer.

Food Rules: An Eater’s Manual

Good advice from author Michael Pollan on eating from his new book, Food Rules: An Eater’s Manual. Essentially he suggests eating food. Stuff you can picture in the original form (apples, cashews, celery, trout, tomatoes, grapes, steak, strawberries, milk, figs, peppers, peaches, almonds, chicken) not chemical additions (yes I know real food is made up of chemical – this is additional chemicals). One quote: “the biggest gains in human health can be made from changes in food policy.”

Human health is a complex topic but if we care about our health it is a tough issue we have to try to understand. He makes a good point in his talk about the value of exercise. I do believe exercise is an important component to how to be healthy (as is food – I don’t think it is easy to be healthy without both).

Bee Colonies Continue to Collapse

The activity to find the causes of Colony Collapse Disorder provides a view into the scientific inquiry process of complex living systems. Finding answers is not easy.

Fears for crops as shock figures from America show scale of bee catastrophe

Disturbing evidence that honeybees are in terminal decline has emerged from the United States where, for the fourth year in a row, more than a third of colonies have failed to survive the winter.

The decline of the country’s estimated 2.4 million beehives began in 2006, when a phenomenon dubbed colony collapse disorder (CCD) led to the disappearance of hundreds of thousands of colonies. Since then more than three million colonies in the US and billions of honeybees worldwide have died and scientists are no nearer to knowing what is causing the catastrophic fall in numbers.
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It is estimated that a third of everything we eat depends upon honeybee pollination.
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Potential causes range from parasites, such as the bloodsucking varroa mite, to viral and bacterial infections, pesticides and poor nutrition stemming from intensive farming methods.
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“We believe that some subtle interactions between nutrition, pesticide exposure and other stressors are converging to kill colonies,” said Jeffery Pettis, of the ARS’s bee research laboratory.
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“It’s getting worse,” he said. “The AIA survey doesn’t give you the full picture because it is only measuring losses through the winter. In the summer the bees are exposed to lots of pesticides. Farmers mix them together and no one has any idea what the effects might be.” Pettis agreed that losses in some commercial operations are running at 50% or greater.

High Levels of Miticides and Agrochemicals in North American Apiaries: Implications for Honey Bee Health (open access paper on the topic, March 2010)

The 98 pesticides and metabolites detected in mixtures up to 214 ppm in bee pollen alone represents a remarkably high level for toxicants in the brood and adult food of this primary pollinator. This represents over half of the maximum individual pesticide incidences ever reported for apiaries. While exposure to many of these neurotoxicants elicits acute and sublethal reductions in honey bee fitness, the effects of these materials in combinations and their direct association with CCD or declining bee health remains to be determined.

Antibiotics, Farming and Superbugs

Antibiotics and farming – how superbugs happen

Provocative new research from Boston University’s medical school and department of biomedical engineering now suggests, though, that multi-drug resistance can be acquired in one pass, through a different mutational process triggered by sublethal doses of antibiotics – the same sort of doses that are given to animals on farms.

In earlier work, the authors found that antibiotics attack bacteria not only in the ways they are designed to (the beta-lactams such as methicillin, for instance, interfere with staph’s ability to make new cell walls as the bug reproduces, causing the daughter cells to burst and die), but also in an unexpected way. They stimulate the production of free radicals, oxygen molecules with an extra electron, that bind to and damage the bacteria’s DNA.

That research used lethal doses of antibiotics, and ascertained that the free-radical production killed the bacteria. In the new research, the team uses sublethal doses, and here’s what they find: The same free-radical production doesn’t kill the bacteria, but it acts as a dramatic stimulus to mutation, triggering production of a wide variety of mutations

A single Liter of Seawater Can Hold More Than One Billion Microorganisms

Mat of microbes the size of Greece discovered on seafloor

mighty microbes, which constitute 50 to 90 percent of the oceans’ total biomass, according to newly released data.

These tiny creatures can join together to create some of the largest masses of life on the planet, and researchers working on the decade-long Census of Marine Life project found one such seafloor mat off the Pacific coast of South America that is roughly the size of Greece.

A single liter of seawater, once thought to contain about 100,000 microbes, can actually hold more than one billion microorganisms, the census scientists reported. But these small creatures don’t just live in the water column or on the seafloor. Large communities of microscopic animals have even been discovered more than one thousand meters beneath the seafloor. Some of these deep burrowers, such as loriciferans, are only a quarter of a millimeter long.

“Far from being a lifeless desert, the deep sea rivals such highly diverse ecosystems as tropical rainforests and coral reefs,”
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Microbes help to turn atmospheric carbon dioxide into usable carbon, completing about 95 percent of all respiration in the Earth’s oceans…

Non-infectious Prion Protein Linked to Alzheimer’s Disease

‘Harmless’ prion protein linked to Alzheimer’s disease

Non-infectious prion proteins found in the brain may contribute to Alzheimer’s disease, researchers have found.
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normal prion proteins produced naturally in the brain interact with the amyloid-Î² peptides that are hallmarks of Alzheimer’s disease. Blocking this interaction in preparations made from mouse brains halted some neurological defects caused by the accumulation of amyloid-Î² peptide. It was previously thought that only infectious prion proteins, rather than their normal, non-infectious counterparts, played a role in brain degeneration.
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Alzheimer’s disease has long been linked to the build-up of amyloid-Î² peptides, first into relatively short chains known as oligomers, and then eventually into the long, sticky fibrils that form plaques in the brain. The oligomeric form of the peptide is thought to be toxic, but exactly how it acts in the brain is unknown.

Critter Cam: Sea Lion versus Octopus

Octopus vs. Sea Lion – First Ever Video

Sea lions fitted with GPS trackers and a National Geographic Crittercam are taking scientists on amazing journeys to previously unknown marine ‘hot spots.’ These areas are important not only for providing the sea lions’ food, but also for maintaining fish populations.

The Crittercams were deployed at Dangerous Reef in Spencer Gulf, a rocky island the size of a football field, and home to the biggest Australian sea lion colony.
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Dr. Page says, “One important discovery is that the sea lions always feed on the sea floor” and they don’t eat open ocean fish, known as pelagic. “This is critical information because the marine parks are being set up to protect sea floor habitats,” a move that the scientists can now confirm will protect critical sea lion resources.

In one of the more spectacular pieces of Crittercam video so far, we can see this female working hard to handle a challenging prey item – a large octopus. Too big to swallow in one gulp, she drags it to the surface where she can breathe while she works at breaking it down into bite-size pieces.

Poor Results on Evolution and Big Bang Questions Omitted From NSF Report

Evolution, Big Bang Polls Omitted From NSF Report by Yudhijit Bhattacharjee

The section, which was part of the unedited chapter on public attitudes toward science and technology, notes that 45% of Americans in 2008 answered true to the statement, “Human beings, as we know them today, developed from earlier species of animals.” The figure is similar to previous years and much lower than in Japan (78%), Europe (70%), China (69%), and South Korea (64%). The same gap exists for the response to a second statement, “The universe began with a big explosion,” with which only 33% of Americans agreed.

The USA continues to lag far behind the rest of the world in this basic science understanding. Similar to how we lag in other science and mathematical education. Nearly Half of Adults in the USA Don’t Know How Long it Takes the Earth to Circle the Sun.

Jon Miller, a science literacy researcher at Michigan State University in East Lansing who authored the survey 3 decades ago and conducted it for NSF until 2001. “Evolution and the big bang are not a matter of opinion. If a person says that the earth really is at the center of the universe, even if scientists think it is not, how in the world would you call that person scientifically literate? Part of being literate is to both understand and accept scientific constructs.”

I completely agree. People have the right to their opinions. But those opinions which are related to scientific knowledge (whether it is about evolution, the origin of the universe, cancer, the speed of light, polio vaccinations, multi-factorial designed experiments, magnetic fields, chemical catalysts, the effectiveness of antibiotics against viral infections, electricity, optics, bioaccumulation, etc.) are part of their scientific literacy. You can certainly believe antibiotics are affective against viral infections but that is an indication you are scientifically illiterate on that topic.

2006 NSF chapter that included the results
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