Category Archives: Life Science

Viruses Eating Bacteria

“Believe it or not, nobody had looked before,” says Suttle. “On average, there are 50 million viruses per milliliter in seawater. The question is, What the heck they’re doing there?” Microbiologists then documented similar, and even higher, concentrations of phages in soil samples. This led to estimates of 10³¹ bacteriophages worldwide, a staggeringly large number that many scientists initially dismissed. “We can’t wrap our brains around it,” says Pedulla. “If phages were the size of a beetle, they would cover the Earth and be many miles deep.”
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According to estimates put forth by Suttle, phages destroy up to 40 percent of the bacteria in Earth’s oceans each day.
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The students collected soil from barnyards, gardens, and even the monkey pit at the Bronx Zoo. The scientists then taught the students how to isolate a bacteriophage from the soil by growing the viruses in Mycobacterium smegmatis, a harmless bacterial relative of the microbe that causes tuberculosis. “We guarantee them that the bacteriophage they find will never have been discovered before. We know that because the diversity is so high, and we’ve never isolated the same bacteriophage twice,” says Hatfull.

In the April 18 Cell, Hatfull and his professional and teenage collaborators describe the genomes of 10 soil-dwelling bacteriophages that they had isolated. Of the more than 1,600 genes that the team identified, about half are novel, that is, they don’t match any previously described genes in any other organism.

Science is full of amazing new frontiers. Some other amazing stuff: Thinking Slime Moulds – Tracking the Ecosystem Within Us – Retroviruses – Energy Efficiency of Digestion – One Species’ DNA Discovered Inside Another’s

Sudden Oak Death

Sudden Oak Death pathogen is evolving, says new study that reconstructs the epidemic

The pathogen responsible for Sudden Oak Death first got its grip in California’s forests outside a nursery in Santa Cruz and at Mt. Tamalpais in Marin County before spreading out to eventually kill millions of oaks and tanoaks along the Pacific Coast, according to a new study led by researchers at the University of California, Berkeley. It provides, for the first time, evidence of how the epidemic unfolded in this state.
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The study, scheduled to appear later this month in the online early edition of the journal Molecular Ecology, also shows that the pathogen is currently evolving in California, with mutant genotypes appearing as new areas are infested.
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The most likely scenario, said Garbelotto, is that the pathogen arrived in California through the nursery trade, and that it then spread from the nursery in Santa Cruz to trees bordering the facility. While the site at Mt. Tamalpais is not adjacent to a nursery, there is anecdotal evidence of frequent use of ornamental plants from nurseries in landscaping projects in the area, said Garbelotto.

Amazing Designs of Life

The More We Know About Genes, the Less We Understand by Carl Zimmer

All living things, ourselves included, turn genes on and off in a similar way, by making switch-like proteins called transcription factors. And as scientists have identified more of these, they’ve discovered something remarkable: They form a chain of command. The job of some transcription factors is to switch others on and off, and they in turn are controlled by other transcription factors. Even a seemingly simple microbe like E. coli has an impressive hierarchy. Just nine genes rule over about half of the 4,000-odd genes in E. coli.

E. coli’s network allows it to respond quickly to the challenges it meets, from starvation to heat to the loss of oxygen. It can rapidly reorganize itself, switching on hundreds of genes and switching off hundreds of others. What makes this network all the more impressive are the feedback loops that keep it from spinning out of control. When one gene switches on, for example, it may make a protein that shuts down the gene that switched it on in the first place.

Yet even as scientists uncover this network, they discover yet another mystery. In the latest issue of Nature, scientists reported an experiment in which they wreaked havoc with E. coli’s network. They randomly added new links between the transcription factors at the top of the microbe’s hierarchy. Now a transcription factor could turn on another one that it never had before. The scientists randomly rewired the network in 598 different ways and then stepped back to see what happened to the bacteria.

You might expect that they all died. After all, if you were to pop open the back of an iPod and start linking its components together in random ways, you’d expect it to crash. But that’s not what happened.

About 95 percent of the rewired bacteria did just fine with their new networks. They went on with their lives, feeding, growing and dividing. Some even performed better than microbes with the original wiring, under some conditions.

Turtle Camps in Malaysia

Drawing of sea turtles

Pelf Nyok has posted drawing of turtle camps students that she taught in Malaysia. On the image shown on the left:

The third poster shows the threats that our turtles are facing — a turtle is trapped in a fisherman’s net, a turtle is consuming a plastic bag, which it mistakes as a jellyfish, and there are rubbish on the sea floor.

Pelf is on her way to the USA for turtle conservation training on the Asian Scholarship Program for in-situ Chelonian Conservation:

a 4-month scholarship, and involves professional training in the conservation of turtles (including sea turtles, freshwater turtles and tortoises, I presume). The flow of the program has yet to be finalized but according to the Director of the Program, we (the Laotian student and I) would be spending one month visiting turtle scientists and turtle research centers in New Jersey, Tennessee, Florida and maybe California.

And the remaining 3 months would be spent at the Wetlands Institute at Stone Harbor, New Jersey. The training will be conducted at the Wetlands Institute, together with other local participants.

Continue reading →

Bikini Atoll 50 Years Later

Nuked coral reef bounces back

Three islands of Bikini Atoll were vapourised by the Bravo hydrogen bomb in 1954, which shook islands 200 kilometres away. Instead of finding a bare underwater moonscape, ecologists who have dived it have given the 2-kilometre-wide crater a clean bill of health.

“It was fascinating – I’ve never seen corals growing like trees outside of the Marshall Islands,” says Zoe Richards of the ARC Centre of Excellence for Coral Reef Studies in Australia. Richards and colleagues report a thriving ecosystem of 183 species of coral, some of which were 8 metres high. They estimate that the diversity of species represents about 65% of what was present before the atomic tests. The ecologists think the nearby Rongelap Atoll is seeding the Bikini Atoll, and the lack of human disturbance is helping its recovery.
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“When I put the Geiger counter near a coconut, which accumulates radioactive material from the soil, it went berserk,” says Beger.

Eating Breakfast Keeps Teenagers Leaner

Breakfast ‘keeps teenagers lean’

In a five year study of more than 2,000 youngsters, those who skipped breakfast weighed on average 5lbs (2.3kg) more than those who ate first thing. This was despite the fact that the breakfast-eaters consumed more calories in the course of the day. But the study in Pediatrics found they were likely to be much more active.

The University of Minnesota research adds weight to a growing body of evidence that those who eat breakfast – whether young or old – are leaner than those who do not.
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“The real problem is the profusion of messages about obesity. We need to make clear that eating regular meals is vital – and that a proper breakfast is very important. “If you eat well first thing, you’ll feel brighter, you’ll have more get up and go – and that will mean you’ll expend more energy.”

Teenagers are not the only ones who may benefit from sitting down to a proper breakfast. In a study of nearly 7,000 middle-aged people in Norfolk, a team from Cambridge University found that those who ate the most in the morning put on the least amount of weight.

Mutualism – Inter-species Cooperation

Shrimp with Goby Fish

A Mutual Affair by Olivia Judson

I’d like to introduce you to one of my favorite animals: the shrimp goby. These pretty little fish lead lives of enviable indolence. As their name suggests, they live with shrimp (often, a pair). The shrimp build and maintain a burrow, which the goby and shrimp live in together. Each shrimp works hard, shoveling sand out of the front entrance like a miniature bulldozer. As soon as it’s delivered the rubble to a suitable distance, it shoots back into the burrow.

The front entrance of the burrow is often reinforced with bits of shell and coral — all of which is done by the shrimp. The goby just sits in the entrance of the burrow, keeping guard and warning the shrimp, which is nearly blind, of danger. At any sign of danger — a diver coming too close, a passing predator — the goby darts into the burrow. If the goby zooms in, the shrimp hastily retreats deep inside. And before the shrimp emerges from the burrow, it touches the goby’s tail with its long antennae. To show it’s safe to come out, the goby gently wiggles its tail. When the shrimp is out of the burrow, it keeps one antenna touching the goby. If the goby suddenly retreats, so does the shrimp.
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These animals are dependent on each other. Remove the fish, and the shrimp stops burrowing; the shrimp forage while burrowing, so without a fish, they grow more slowly, too. The shrimp need their guard goby. And the guard goby needs its shrimp: deny the goby shelter in a burrow, and it will promptly be killed by predators (yes, someone did the experiment). The shrimp keep the goby clean, too: they groom it.

photo by Boogies with Fish

Self-assembling Nanofibers Heal Spinal Cords in Mice

Self-assembling Nanofibers Heal Spinal Cords by Prachi Patel-Predd

An engineered material that can be injected into damaged spinal cords could help prevent scars and encourage damaged nerve fibers to grow. The liquid material, developed by Northwestern University materials science professor Samuel Stupp, contains molecules that self-assemble into nanofibers, which act as a scaffold on which nerve fibers grow.

Stupp and his colleagues described in a recent paper in the Journal of Neuroscience that treatment with the material restores function to the hind legs of paralyzed mice.
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The new work is the first test for the material to heal spinal cord injuries in animals. And Kessler says that it worked better than the researchers expected. The researchers stimulated a spinal cord injury in mice and injected the material 24 hours later. They found that the material reduced the size of scars and stimulated the growth of the nerve fibers through the scars. It promoted the growth of both types of nerve fibers that make up the spinal cord: motor fibers that carry signals from the brain to the limbs, and sensory fibers that carry sense signals to the brain. What is more, the material encouraged the nerve stem cells to mature into cells that create myelin–an insulating layer around nerve fibers that helps them to conduct signals more effectively.

Clay Versus MRSA Superbug

“Healing clays” hold promise in fight against MRSA superbug infections and disease

Scientists from Arizona State University report that minerals from clay promise could provide inexpensive, highly-effective antimicrobials to fight methicillin-resistant Staphylococcus aureus (MRSA) infections that are moving out of health care settings and into the community.
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Unlike conventional antibiotics routinely administered by injection or pills, the so-called “healing clays” could be applied as rub-on creams or ointments to keep MRSA infections from spreading
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In their latest study, funded by the National Institutes of Health, Williams, Haydel and their colleagues collected more than 20 different clay samples from around the world to investigate their antibacterial activities… The researchers identified at least two clays from the United States that kill or significantly reduce the growth of these bacteria

Also listen to a podcast with the researchers, Lynda Williams and Shelly Haydel, that provides much more detail. The Science Studio podcasts from Arizona State University provides great science podcasts.

First Lungless Frog Found

The first recorded species of frog that breathes without lungs has been found in a clear, cold-water stream on the island of Borneo in Indonesia. The frog, named Barbourula kalimantanensis, gets all its oxygen through its skin.
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Previously the only four-limbed creatures known to lack lungs were salamanders. A species of earthwormlike, limbless amphibian called a caecilian is also lungless. Tetrapods, or four-limbed creatures, that develop without lungs are rare evolutionary events, Bickford and colleagues write.

The trait in amphibians is likely an adaptation to life between water and land and their ability to respire through the skin. The researchers suggest lunglessness in B. kalimantanensis may be an adaptation to the higher oxygen content in fast-flowing, cold water.
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Wake added that for most amphibians, the majority of gas exchange happens through the skin. A low but significant amount of respiration occurs via simple, sac-like lungs. Most species, he noted, have mating calls that require lungs. So biologists are unsure why a few species have entirely gotten rid of the organs, Wake said.