Archive for the ‘Biology’ Category

The Gulf of Mexico is home to approximately 1,700 sperm whales. Many of them feed just off the continental shelf, particularly around the Mississippi River delta, an area filled with ample food for these huge marine mammals. The whales reside in family groups, and rarely mingle with other sperm whale groups from the open Atlantic Ocean. They live as long as us, but reproduce at most only every five years. The Gulf of Mexico is their full-time home.

Since the Deepwater Horizon oil rig exploded and sank over sixty days ago, scientists have been concerned with the fate of Gulf of Mexico sperm whales. Sperm whales have been sighted in the fouled waters themselves, and no one knows what effect oil droplets will have on whale physiology and behavior. In addition, BP and the U.S. Coast Guard have been using unprecedented levels of chemical dispersants to scatter oil in the water, and no research has been done on the effect of even small amounts of these dispersants on cetaceans.

Given these uncertainties, the National Oceanic and Atmospheric Administration’s discovery this week of a dead sperm whale near the spill zone is a particularly troubling find. On Tuesday, the NOAA ship Pisces cited the decayed corpse of a young, 25 foot long sperm whale adrift nearly 80 miles from the site of the (former) Deepwater Horizon oil rig. Based on the decay of the body and the degree of scavenging by sharks, scientists estimate the whale perished several days ago, but don’t yet know the cause of death. They have taken tissue samples to help determine how the whale may have died, and hopefully analysis of the whale’s genome will determine its sex, and whether or not it was definitely from the endangered Gulf of Mexico population (which, given its location, it probably was). Skin samples taken may determine whether the whale was exposed to large amounts of oil before it died. However, since the whale’s body was adrift for days, scientists will have to infer where it died based on current patterns in the area where the body was found, weather conditions over the past week, and forensic clues of the time of the whale’s death.

All in all, a dead sperm whale is a rare find in the Gulf of Mexico, and this discovery so close to the site of the oil spill may be a harbinger of the spill’s lasting effects on the Gulf’s ecosystem. However, more won’t be known until scientists announce the whale’s cause, time, and location of death. In the meantime, the NOAA vessel Gordon Gunter put to sea on Wednesday to survey Gulf of Mexico cetaceans and catalog some of the oil spill’s effects on their ecology, physiology, and behavior. The ship’s mission also includes orders to observe the Gulf’s endangered sperm whales, all 1,699 of them.

Image of a sperm whale diving near a deep water rig in the Gulf of Mexico provided courtesy of Christoph Richter, the Sperm Whale Seismic Study, the U.S. Office of Naval Research, the Minerals Management Service of the U.S. Department of the Interior, Oregon State University, and Texas A & M University.

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The western honeybee, Apis mellifera.

Scientists from the United States Department of Agriculture announced at a recent meeting that they have identified the primary pathogens associated with honeybee Colony Collapse Disorder (CCD). American beekeepers first reported CCD in 2007, and the implications are dire. Honeybees (Apis mellifera) are major crop pollinators. In California alone, their commercial crop value easily exceeds $1.5 billion annually. Though CCD has only been recognized for a few years, the potential loss of honeybees as crop pollinators sent scientists scrambling to determine the cause of this odd and devastating syndrome.

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The orca, Orcinus orca, is the “official marine mammal of the State of Washington.” It’s status is even preserved in the Revised Code of Washington. Orcas obtained this rare honor as a symbol of the State of Washington in 2005, when a group of second grade students from Oak Harbor, Washington successfully lobbied the Washington Legislature.

When I was a little kid in the American south and midwest, everyone called them “killer whales.” In the Pacific Northwest, the name orca is preferred in the zeitgeist. However, these marine mammals are not just known in my current home. They swim in every ocean, from the tropics to the polar seas.

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Scientists from the Maryland and California-based J. Craig Venter Institute announced today that they successfully created a partially synthetic lifeform. <a href="Their efforts appear in the journal Science, and include a detailed description of the steps they took to create life.

The lifeform in question is a single-celled bacterium called Mycoplasma mycoides. A bacterial cell, like all living organisms, stores “instructions” or “blueprints” for making and maintaining itself in the form of DNA (deoxyribonucleic acid). DNA is the genome of an organism — it is a long strand of chemicals stored within living cells. In single-celled organisms like bacteria, each cell is an individual, and each cell contains a copy of the genome. The instructions for making and maintaining the cell are “read” from the genome by the cell. Thus, the complex chemicals and molecules that cells make to do work, maintain integrity, survive, and reproduce are all made using these DNA-based “instructions.” When a cell divides, DNA is copied, so that each daughter cell has a complete copy of the genome.

A colony of Mycoplasma mycoides cells.

I harp so much on DNA because much of the work done by the J. Craig Venter Institute centers on the Mycoplasma mycoides genome. Scientists had already “read” the full chemical sequence of the DNA strand (also known as the complete genome sequence) from Mycoplasma mycoides. Researchers at the Venter Institute set out to use that known Mycoplasma mycoides genome sequence to create their own Mycoplasma mycoides cell from scratch.

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Scientists from the University of Utah and Qinghai University Medical School in China’s Qinghai Province have discovered some of the genetic changes that have allowed ethnic Tibetans to survive in the high altitudes of their homeland.

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NASA has scheduled only three more space shuttle missions before the fleet is retired later this year. One mission each for the three remaining orbiters: Atlantis, Discovery, and Endeavour. Tomorrow, Atlantis will launch from Kennedy Space Center on its last mission: STS-132.

The six astronauts on board Atlantis are delivering supplies and parts to the International Space Station (ISS). In addition, the ISS is getting a new Russian-built laboratory module, christened Rassvet (“dawn”). Astronauts will also be delivering components for new experiments on the ISS, and conducting a few of their own on the shuttle.

One particular experiment, in partnership with scientists at the Rensselaer Polytechnic Institute, will study the growth of microbes in different microgravity habitats. Microscopic bacteria are all around us, and have been the most prevalent form of life on Earth for billions of years. In certain growth conditions, bacteria can form large, complex, three-dimensional communities called biofilms. Scientists are concerned that bacteria in microgravity environments could also form biofilms, and may impact the health of astronauts on long-term missions. Thus, biologists from Rensselaer Polytechnic Institute are sending up sealed vials of bacteria. During Atlantis‘ mission, astronauts will manipulate the growth conditions of some vials. Following the shuttle’s return to Earth, scientists will retrieve the vials and see how those different growth conditions affected the formation of biofilms in low gravity. Hopefully, the results of these experiments will help biologists minimize the potential threat of biofilms to astronaut health during longer missions in outer space.

These modest experiments are just at taste of what 30 years of space shuttle missions have delivered: countless scientific endeavors to help us venture further and further into outer space. As the space shuttle missions come to an end, we can only hope that the federal government will fund a future for manned space flight that makes the most of what we’ve learned so far, and will fuel progress for decades to come.

Atlantis launches tomorrow at 2:20PM EDT from Cape Canaveral. Watch it live! You’ll only have two more chances after tomorrow.

STS-132 mission patch provided courtesy of NASA.

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New research published in the journal Nature Genetics is shedding more light on adaptations that allowed woolly mammoths to thrive in frigid latitudes during our planet’s recent ice ages. Woolly mammoths (Mammuthus primigenius) inhabited extreme northern latitudes starting about 150,000 years ago, and died out approximately 10,000 years ago. To study the cold adaptations of this mammal, scientists had to do something remarkable: they rebuilt a blood protein from this extinct species.

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On the left is the African Clawed Frog (Xenopus laevis), while its cousin (the Western Clawed Frog, Xenopus tropicalis), sits on the right. Image provided courtesy of Robert Grainger.

Platannas are 18 species of clawed frogs native to sub-Saharan Africa. Their genus name, Xenopus, means “strange foot,” in reference to the curved claws present on each hind foot. Two members of this genus, Xenopus laevis (the African Clawed Frog) and Xenopus tropicalis (the Western Clawed Frog), are also model organisms studied by biologists to understand the basics of vertebrate development and vertebrate genetics. Yesterday, scientists announced that one of these species, the Western Clawed Frog, became the first amphibian to have its genome sequenced.

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The threespine stickleback made a brief appearance in yesterday’s New York Times. I pay attention to such things (albeit one day late) because I study threespine sticklebacks and their close relatives for my thesis research on the evolution of sex chromosomes.

However, the stickleback’s appearance yesterday had nothing to do with my research. But, a team from the University of Bonn, led by Marion Mehlis, looked at the threespine stickleback to address a very specific question: cannibalism. Many animals, for one reason or another, eat their young. Sticklebacks are no exception. Male sticklebacks guard nests of fertilized eggs during the breeding season (female sticklebacks play no part in parenting). But, sometimes, a male will eat some or all of the eggs in his nest. Why? What triggers this behavior?

It certainly seems counterproductive. Male sticklebacks do all the work in the breeding season: defending a territory, building a nest, courting female after female, chasing a female away once she lays her eggs in the nest, fertilizing the nest, and caring for the eggs until they hatch. Why would any male in his right mind go to all the effort of building a nest a courting a female when he’s just going to devour his kids before they hatch? Well, as it turns out, he might do that when those aren’t his kids in the nest.

In the stickleback field (as in other fields), there is another group of males — the sneaker males. These males don’t typically build nests and defend territories. They lurk near a courting couple, waiting until a female has laid her eggs in another male’s nest. Then, the sneaker male enters the nest (usually while the hard-working male is busy chasing away the female) and fertilizes the eggs. Sneaker male (now sneaker dad) swims away, leaving the hapless hard-working male to tend his offspring.

Mehlis and colleagues wondered: do stickleback males eat the eggs in their nest when those eggs were fertilized by another male? They conducted trials to test this, switching batches of eggs (we call them “clutches”) in a nest tended by one male with eggs that were fertilized by another male. As it turns out, a male stickleback is much more likely to consume eggs if those eggs weren’t fertilized by him — if he wasn’t the dad. Mehlis and colleagues aren’t exactly sure what kind of signal the male is sensing that indicates paternity, but it’s likely some sort of olfactory (“smell”) cue.

The study sheds some light on the puzzle of male stickleback cannibalism. As for the type of signal at work in these fish, stay tuned!

Image of female (upper) and male (lower) threespine sticklebacks provided courtesy of Dr. Joseph Ross.

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One of the fascinating puzzles of evolutionary biology is how old structures change over time to acquire new functions or features. We can ask the “how” on multiple levels:

  • What genetic changes occurred?
  • What physiological changes occurred?
  • Did ecological factors contribute?
  • How quickly did the new function or feature arise?

The list of questions can go on and on.  However, scientists don’t always have tools at their disposal to answer everything.  For extinct organisms, we have only the fossil record.  Molecular biologists like me don’t get DNA to play with in those cases (usually). Physiologists don’t get muscle and bone samples. Thus, we can’t fully answer how whale fins developed from an ancestor who walked on solid ground. Though we have whales here today, all those walking ancestors died millions of years ago.

But, even with these limitations, we can still learn something about how older structures can change to acquire new functions. Recently, two biologists published an account of a “new” feature derived from an “old” structure: the cobra’s hood. In cobras and several other groups of snakes, the ribs, muscles, and skin near the head and neck (as much as snakes have a neck) can spread out away from the body’s core, forming an elaborate display hood when the animal is startled or threatened.

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